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Sample records for survey responses reveal

  1. A Survey of Electronic Serials Managers Reveals Diversity in Practice

    Directory of Open Access Journals (Sweden)

    Laura Costello

    2014-09-01

    Full Text Available A Review of: Branscome, B. A. (2013. Management of electronic serials in academic libraries: The results of an online survey. Serials Review, 39(4, 216-226. http://dx.doi.org/10.1016/j.serrev.2013.10.004 Abstract Objective – To examine industry standards for the management of electronic serials and measure the adoption of electronic serials over print. Design – Survey questionnaire. Setting – Email lists aimed at academic librarians working in serials management. Subjects – 195 self-selected subscribers to serials email lists. Methods – The author created a 20 question survey that consisted primarily of closed-ended questions pertaining to the collection demographics, staff, budget, and tools of serials management groups in academic libraries. The survey was conducted via Survey Monkey and examined using the analytical features of the tool. Participants remained anonymous and the survey questions did not ask them to reveal identifiable information about their libraries. Main Results – Collection demographics questions revealed that 78% of surveyed librarians estimated that print-only collections represented 40% or fewer of their serials holdings. The author observed diversity in the factors that influence print to digital transitions in academic libraries. However 71.5% of participants indicated that publisher technology support like IP authentication was required before adopting digital subscriptions. A lack of standardization also marked serials workflows, department responsibilities, and department titles. The author did not find a correlation between serials budget and the enrollment size of the institution. Participants reported that they used tools from popular serials management vendors like Serials Solutions, Innovative Interfaces, EBSCO, and Ex Libris, but most indicated that they used more than one tool for serials management. Participants specified 52 unique serials management products used in their libraries. Conclusion

  2. A survey of resistance to Tomato bushy stunt virus in the genus Nicotiana reveals that the hypersensitive response is triggered by one of three different viral proteins.

    Science.gov (United States)

    Angel, Carlos A; Schoelz, James E

    2013-02-01

    In this study, we screened 22 Nicotiana spp. for resistance to the tombusviruses Tomato bushy stunt virus (TBSV), Cucumber necrosis virus, and Cymbidium ringspot virus. Eighteen species were resistant, and resistance was manifested in at least two different categories. In all, 13 species responded with a hypersensitive response (HR)-type resistance, whereas another five were resistant but either had no visible response or responded with chlorotic lesions rather than necrotic lesions. Three different TBSV proteins were found to trigger HR in Nicotiana spp. in an agroinfiltration assay. The most common avirulence (avr) determinant was the TBSV coat protein P41, a protein that had not been previously recognized as an avr determinant. A mutational analysis confirmed that the coat protein rather than the viral RNA sequence was responsible for triggering HR, and it triggered HR in six species in the Alatae section. The TBSV P22 movement protein triggered HR in two species in section Undulatae (Nicotiana glutinosa and N. edwardsonii) and one species in section Alatae (N. forgetiana). The TBSV P19 RNA silencing suppressor protein triggered HR in sections Sylvestres (N. sylvestris), Nicotiana (N. tabacum), and Alatae (N. bonariensis). In general, Nicotiana spp. were capable of recognizing only one tombusvirus avirulence determinant, with the exceptions of N. bonariensis and N. forgetiana, which were each able to recognize P41, as well as P19 and P22, respectively. Agroinfiltration failed to detect the TBSV avr determinants responsible for triggering HR in N. arentsii, N. undulata, and N. rustica. This study illustrates the breadth and variety of resistance responses to tombusviruses that exists in the Nicotiana genus.

  3. Initial nonresponse and survey response mode biases in survey research.

    Science.gov (United States)

    Chi, Donald L; Chen, Chao Ying

    2015-01-01

    We evaluated survey response factors (particularly initial nonresponse and survey mode) that may be associated with bias in survey research. We examined prevention-related beliefs and outcomes for initial mail survey responders (n=209), follow-up mail survey responders (n=78), and follow-up telephone survey responders (n=74). The Pearson chi-square test and analysis of variance identified beliefs and behavioral outcomes associated with survey response mode. Follow-up options to the initial mail survey improved response rates (22.0-38.0 percent). Initial mail survey responders more strongly believed topical fluoride protects teeth from cavities than others (P=0.04). A significantly larger proportion of parents completing a follow-up telephone survey (30.8 percent) refused topical fluoride for their child than those completing mail surveys (10.3-10.4 percent) (Psurveys with follow-up improve response rates. Initial nonresponse and survey response mode may be associated with biases in survey research. © 2015 American Association of Public Health Dentistry.

  4. Effect of survey mode on response patterns

    DEFF Research Database (Denmark)

    Christensen, Anne Illemann; Ekholm, Ola; Glümer, Charlotte

    2014-01-01

    BACKGROUND: While face-to-face interviews are considered the gold standard of survey modes, self-administered questionnaires are often preferred for cost and convenience. This article examines response patterns in two general population health surveys carried out by face-to-face interview and self......-administered questionnaire, respectively. METHOD: Data derives from a health interview survey in the Region of Southern Denmark (face-to-face interview) and The Danish Health and Morbidity Survey 2010 (self-administered questionnaire). Identical questions were used in both surveys. Data on all individuals were obtained from...... administrative registers and linked to survey data at individual level. Multiple logistic regression analyses were used to examine the effect of survey mode on response patterns. RESULTS: The non-response rate was higher in the self-administered survey (37.9%) than in the face-to-face interview survey (23...

  5. Improving Survey Response Rates in Online Panels

    DEFF Research Database (Denmark)

    Pedersen, Mogens Jin; Nielsen, Christian Videbæk

    2016-01-01

    experiment among 6,162 members of an online survey panel, this article shows how low-cost incentives and cost-free text appeal interventions may impact the survey response rate in online panels. The experimental treatments comprise (a) a cash prize lottery incentive, (b) two donation incentives equating......Identifying ways to efficiently maximize the response rate to surveys is important to survey-based research. However, evidence on the response rate effect of donation incentives and especially altruistic and egotistic-type text appeal interventions is sparse and ambiguous. By a randomized survey...... survey response with a monetary donation to a good cause, (c) an egotistic-type text appeal, and (d) an altruistic-type text appeal. Relative to a control group, we find higher response rates among the recipients of the egotistic-type text appeal and the lottery incentive. Donation incentives yield lower...

  6. Survey of Munitions Response Technologies

    Science.gov (United States)

    2006-06-01

    distributed between two operators and tied with an umbilical cord. Man-portable platforms are also being developed using wireless technology to reduce the...munitions response (Lim 2004, Bucaro 2006, Lavely 2006, Carroll 2006). Models are being validated using data measured in tanks and ponds and in offshore

  7. Maximising response rates in household telephone surveys

    Directory of Open Access Journals (Sweden)

    Sinclair Martha

    2008-11-01

    Full Text Available Abstract Background Epidemiological and other studies that require participants to respond by completing a questionnaire face the growing threat of non-response. Response rates to household telephone surveys are diminishing because of changes in telecommunications, marketing and culture. Accordingly, updated information is required about the rate of telephone listing in directories and optimal strategies to maximise survey participation. Methods A total of 3426 households in Sydney, Australia were approached to participate in a computer assisted telephone interview (CATI regarding their domestic (recycled and/or drinking water usage. Only randomly selected households in the suburb and postcode of interest with a telephone number listed in the Electronic White Pages (EWP that matched Australian electoral records were approached. Results The CATI response rate for eligible households contacted by telephone was 39%. The rate of matching of electoral and EWP records, a measure of telephone directory coverage, was 55%. Conclusion The use of a combination of approaches, such as an advance letter, interviewer training, establishment of researcher credentials, increasing call attempts and targeted call times, remains a good strategy to maximise telephone response rates. However, by way of preparation for future technological changes, reduced telephone number listings and people's increasing resistance to unwanted phone calls, alternatives to telephone surveys, such as internet-based approaches, should be investigated.

  8. Maximising response rates in household telephone surveys.

    Science.gov (United States)

    O'Toole, Joanne; Sinclair, Martha; Leder, Karin

    2008-11-03

    Epidemiological and other studies that require participants to respond by completing a questionnaire face the growing threat of non-response. Response rates to household telephone surveys are diminishing because of changes in telecommunications, marketing and culture. Accordingly, updated information is required about the rate of telephone listing in directories and optimal strategies to maximise survey participation. A total of 3426 households in Sydney, Australia were approached to participate in a computer assisted telephone interview (CATI) regarding their domestic (recycled and/or drinking) water usage. Only randomly selected households in the suburb and postcode of interest with a telephone number listed in the Electronic White Pages (EWP) that matched Australian electoral records were approached. The CATI response rate for eligible households contacted by telephone was 39%. The rate of matching of electoral and EWP records, a measure of telephone directory coverage, was 55%. The use of a combination of approaches, such as an advance letter, interviewer training, establishment of researcher credentials, increasing call attempts and targeted call times, remains a good strategy to maximise telephone response rates. However, by way of preparation for future technological changes, reduced telephone number listings and people's increasing resistance to unwanted phone calls, alternatives to telephone surveys, such as internet-based approaches, should be investigated.

  9. Handling Protest Responses in Contingent Valuation Surveys.

    Science.gov (United States)

    Pennington, Mark; Gomes, Manuel; Donaldson, Cam

    2017-08-01

    Protest responses, whereby respondents refuse to state the value they place on the health gain, are commonly encountered in contingent valuation (CV) studies, and they tend to be excluded from analyses. Such an approach will be biased if protesters differ from non-protesters on characteristics that predict their responses. The Heckman selection model has been commonly used to adjust for protesters, but its underlying assumptions may be implausible in this context. We present a multiple imputation (MI) approach to appropriately address protest responses in CV studies, and compare it with the Heckman selection model. This study exploits data from the multinational EuroVaQ study, which surveyed respondents' willingness-to-pay (WTP) for a Quality Adjusted Life Year (QALY). Here, our simulation study assesses the relative performance of MI and Heckman selection models across different realistic settings grounded in the EuroVaQ study, including scenarios with different proportions of missing data and non-response mechanisms. We then illustrate the methods in the EuroVaQ study for estimating mean WTP for a QALY gain. We find that MI provides lower bias and mean squared error compared with the Heckman approach across all considered scenarios. The simulations suggest that the Heckman approach can lead to considerable underestimation or overestimation of mean WTP due to violations in the normality assumption, even after log-transforming the WTP responses. The case study illustrates that protesters are associated with a lower mean WTP for a QALY gain compared with non-protesters, but that the results differ according to method for handling protesters. MI is an appropriate method for addressing protest responses in CV studies.

  10. Survey reveals the situation of Chinese caterpillar fungus resources

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Following its investigation of aweto (or Chinese caterpillar fungus) resources carried out from May to July 2007 on the Tibetan(or Qinghai-Tibet) Plateau,the central producing area of this precious ingredient for traditional Chinese medicine (TCM),the Xishuangbanna Tropical Botanical Garden (XTBG)under CAS conducted a further survey from May to July 2008 in the marginal habitats of this fungus.

  11. Survey Response Rates and Survey Administration in Counseling and Clinical Psychology: A Meta-Analysis

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    Van Horn, Pamela S.; Green, Kathy E.; Martinussen, Monica

    2009-01-01

    This article reports results of a meta-analysis of survey response rates in published research in counseling and clinical psychology over a 20-year span and describes reported survey administration procedures in those fields. Results of 308 survey administrations showed a weighted average response rate of 49.6%. Among possible moderators, response…

  12. Survey Response Rates and Survey Administration in Counseling and Clinical Psychology: A Meta-Analysis

    Science.gov (United States)

    Van Horn, Pamela S.; Green, Kathy E.; Martinussen, Monica

    2009-01-01

    This article reports results of a meta-analysis of survey response rates in published research in counseling and clinical psychology over a 20-year span and describes reported survey administration procedures in those fields. Results of 308 survey administrations showed a weighted average response rate of 49.6%. Among possible moderators, response…

  13. Survey Reveals Farmers’Perceptions of Modern Life

    Institute of Scientific and Technical Information of China (English)

    赵德余; 方志权

    2008-01-01

    Through a statistical analysis of the results of a field survey conducted in a moderately remote suburb of Shanghai,this article investigates the common problems and concerns that farmers are facing during the process of marketization. In evaluating the level of rural development,farmers pay more attention to social security and their living conditions than an increase in income. Whilst playing a prominent role in the development of the rural economy and environmental governance, the government has failed to adequately cultivate community culture and public spiritual life. The government policies on building a new socialist countryside focus on those issues of most concern to farmers: income,employment,education,social security and rural environmental governance,whilst neglecting the cultural life of farmers.

  14. Accuracy of responses from postal surveys about continuing medical education and information behavior: experiences from a survey among German diabetologists

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    Trelle Sven

    2002-08-01

    Full Text Available Abstract Background Postal surveys are a popular instrument for studies about continuing medical education habits. But little is known about the accuracy of responses in such surveys. The objective of this study was to quantify the magnitude of inaccurate responses in a postal survey among physicians. Methods A sub-analysis of a questionnaire about continuing medical education habits and information management was performed. The five variables used for the quantitative analysis are based on a question about the knowledge of a fictitious technical term and on inconsistencies in contingency tables of answers to logically connected questions. Results Response rate was 52%. Non-response bias is possible but seems not very likely since an association between demographic variables and inconsistent responses could not be found. About 10% of responses were inaccurate according to the definition. Conclusion It was shown that a sub-analysis of a questionnaire makes a quantification of inaccurate responses in postal surveys possible. This sub-analysis revealed that a notable portion of responses in a postal survey about continuing medical education habits and information management was inaccurate.

  15. Increasing Response Rates to Web-Based Surveys

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    Monroe, Martha C.; Adams, Damian C.

    2012-01-01

    We review a popular method for collecing data--Web-based surveys. Although Web surveys are popular, one major concern is their typically low response rates. Using the Dillman et al. (2009) approach, we designed, pre-tested, and implemented a survey on climate change with Extension professionals in the Southeast. The Dillman approach worked well,…

  16. Diabetic acido-ketosis revealing thiamine-responsive megaloblastic anemia.

    Science.gov (United States)

    Bouyahia, O; Ouderni, M; Ben Mansour, F; Matoussi, N; Khaldi, F

    2009-12-01

    Thiamine-responsive megaloblastic anemia (TRMA) is a rare autosomal recessive disorder characterized by megaloblastic anemia, diabetes mellitus and progressive sensorineural deafness. We report the cases of two infants, aged 4 and 5 months, hospitalized for diabetic ketoacidosis requiring insulin therapy. Laboratory tests revealed megaloblasic anemia, thrombocytopenia and normal thiamine level. Neurosensorial investigations showed bilateral deafness and ophthalmic involvement. Treatment with oral thiamine normalized hematological disorders and controlled diabetes; however, thiamine therapy had no impact on neurosensorial disorders.

  17. Planarian Phototactic Assay Reveals Differential Behavioral Responses Based on Wavelength.

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    Taylor R Paskin

    Full Text Available Planarians are free-living aquatic flatworms that possess a well-documented photophobic response to light. With a true central nervous system and simple cerebral eyes (ocelli, planarians are an emerging model for regenerative eye research. However, comparatively little is known about the physiology of their photoreception or how their behavior is affected by various wavelengths. Most phototactic studies have examined planarian behavior using white light. Here, we describe a novel planarian behavioral assay to test responses to small ranges of visible wavelengths (red, blue, green, as well as ultraviolet (UV and infrared (IR which have not previously been examined. Our data show that planarians display behavioral responses across a range of wavelengths. These responses occur in a hierarchy, with the shortest wavelengths (UV causing the most intense photophobic responses while longer wavelengths produce no effect (red or an apparent attraction (IR. In addition, our data reveals that planarian photophobia is comprised of both a general photophobic response (that drives planarians to escape the light source regardless of wavelength and wavelength-specific responses that encompass specific behavioral reactions to individual wavelengths. Our results serve to improve the understanding of planarian phototaxis and suggest that behavioral studies performed with white light mask a complex behavioral interaction with the environment.

  18. Predicting survey responses: how and why semantics shape survey statistics on organizational behaviour.

    Science.gov (United States)

    Arnulf, Jan Ketil; Larsen, Kai Rune; Martinsen, Øyvind Lund; Bong, Chih How

    2014-01-01

    Some disciplines in the social sciences rely heavily on collecting survey responses to detect empirical relationships among variables. We explored whether these relationships were a priori predictable from the semantic properties of the survey items, using language processing algorithms which are now available as new research methods. Language processing algorithms were used to calculate the semantic similarity among all items in state-of-the-art surveys from Organisational Behaviour research. These surveys covered areas such as transformational leadership, work motivation and work outcomes. This information was used to explain and predict the response patterns from real subjects. Semantic algorithms explained 60-86% of the variance in the response patterns and allowed remarkably precise prediction of survey responses from humans, except in a personality test. Even the relationships between independent and their purported dependent variables were accurately predicted. This raises concern about the empirical nature of data collected through some surveys if results are already given a priori through the way subjects are being asked. Survey response patterns seem heavily determined by semantics. Language algorithms may suggest these prior to administering a survey. This study suggests that semantic algorithms are becoming new tools for the social sciences, opening perspectives on survey responses that prevalent psychometric theory cannot explain.

  19. Predicting survey responses: how and why semantics shape survey statistics on organizational behaviour.

    Directory of Open Access Journals (Sweden)

    Jan Ketil Arnulf

    Full Text Available Some disciplines in the social sciences rely heavily on collecting survey responses to detect empirical relationships among variables. We explored whether these relationships were a priori predictable from the semantic properties of the survey items, using language processing algorithms which are now available as new research methods. Language processing algorithms were used to calculate the semantic similarity among all items in state-of-the-art surveys from Organisational Behaviour research. These surveys covered areas such as transformational leadership, work motivation and work outcomes. This information was used to explain and predict the response patterns from real subjects. Semantic algorithms explained 60-86% of the variance in the response patterns and allowed remarkably precise prediction of survey responses from humans, except in a personality test. Even the relationships between independent and their purported dependent variables were accurately predicted. This raises concern about the empirical nature of data collected through some surveys if results are already given a priori through the way subjects are being asked. Survey response patterns seem heavily determined by semantics. Language algorithms may suggest these prior to administering a survey. This study suggests that semantic algorithms are becoming new tools for the social sciences, opening perspectives on survey responses that prevalent psychometric theory cannot explain.

  20. Monkey steering responses reveal rapid visual-motor feedback.

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    Seth W Egger

    Full Text Available The neural mechanisms underlying primate locomotion are largely unknown. While behavioral and theoretical work has provided a number of ideas of how navigation is controlled, progress will require direct physiolgical tests of the underlying mechanisms. In turn, this will require development of appropriate animal models. We trained three monkeys to track a moving visual target in a simple virtual environment, using a joystick to control their direction. The monkeys learned to quickly and accurately turn to the target, and their steering behavior was quite stereotyped and reliable. Monkeys typically responded to abrupt steps of target direction with a biphasic steering movement, exhibiting modest but transient overshoot. Response latencies averaged approximately 300 ms, and monkeys were typically back on target after about 1 s. We also exploited the variability of responses about the mean to explore the time-course of correlation between target direction and steering response. This analysis revealed a broad peak of correlation spanning approximately 400 ms in the recent past, during which steering errors provoke a compensatory response. This suggests a continuous, visual-motor loop controls steering behavior, even during the epoch surrounding transient inputs. Many results from the human literature also suggest that steering is controlled by such a closed loop. The similarity of our results to those in humans suggests the monkey is a very good animal model for human visually guided steering.

  1. Disfluencies and gaze aversion in unreliable responses to survey questions

    NARCIS (Netherlands)

    Schober, Michael F.; Conrad, Frederick G.; Dijkstra, Wil; Ongena, Yfke P.

    2012-01-01

    When survey respondents answer survey questions, they can also produce "paradata" (Couper 2000, 2008): behavioral evidence about their response process. The study reported here demonstrates that two kinds of respondent paradata - fluency of speech and gaze direction during answers - identify answers

  2. Living with Smartphones: Does Completion Device Affect Survey Responses?

    Science.gov (United States)

    Lambert, Amber D.; Miller, Angie L.

    2015-01-01

    With the growing reliance on tablets and smartphones for internet access, understanding the effects of completion device on online survey responses becomes increasing important. This study uses data from the Strategic National Arts Alumni Project, a multi-institution online alumni survey designed to obtain knowledge of arts education, to explore…

  3. Living with Smartphones: Does Completion Device Affect Survey Responses?

    Science.gov (United States)

    Lambert, Amber D.; Miller, Angie L.

    2015-01-01

    With the growing reliance on tablets and smartphones for internet access, understanding the effects of completion device on online survey responses becomes increasing important. This study uses data from the Strategic National Arts Alumni Project, a multi-institution online alumni survey designed to obtain knowledge of arts education, to explore…

  4. A Comparison of Web-Based and Paper-Based Survey Methods: Testing Assumptions of Survey Mode and Response Cost

    Science.gov (United States)

    Greenlaw, Corey; Brown-Welty, Sharon

    2009-01-01

    Web-based surveys have become more prevalent in areas such as evaluation, research, and marketing research to name a few. The proliferation of these online surveys raises the question, how do response rates compare with traditional surveys and at what cost? This research explored response rates and costs for Web-based surveys, paper surveys, and…

  5. A Comparison of Web-Based and Paper-Based Survey Methods: Testing Assumptions of Survey Mode and Response Cost

    Science.gov (United States)

    Greenlaw, Corey; Brown-Welty, Sharon

    2009-01-01

    Web-based surveys have become more prevalent in areas such as evaluation, research, and marketing research to name a few. The proliferation of these online surveys raises the question, how do response rates compare with traditional surveys and at what cost? This research explored response rates and costs for Web-based surveys, paper surveys, and…

  6. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota

    Science.gov (United States)

    Rawls, John F.; Samuel, Buck S.; Gordon, Jeffrey I.

    2004-01-01

    Animals have developed the means for supporting complex and dynamic consortia of microorganisms during their life cycle. A transcendent view of vertebrate biology therefore requires an understanding of the contributions of these indigenous microbial communities to host development and adult physiology. These contributions are most obvious in the gut, where studies of gnotobiotic mice have disclosed that the microbiota affects a wide range of biological processes, including nutrient processing and absorption, development of the mucosal immune system, angiogenesis, and epithelial renewal. The zebrafish (Danio rerio) provides an opportunity to investigate the molecular mechanisms underlying these interactions through genetic and chemical screens that take advantage of its transparency during larval and juvenile stages. Therefore, we developed methods for producing and rearing germ-free zebrafish through late juvenile stages. DNA microarray comparisons of gene expression in the digestive tracts of 6 days post fertilization germ-free, conventionalized, and conventionally raised zebrafish revealed 212 genes regulated by the microbiota, and 59 responses that are conserved in the mouse intestine, including those involved in stimulation of epithelial proliferation, promotion of nutrient metabolism, and innate immune responses. The microbial ecology of the digestive tracts of conventionally raised and conventionalized zebrafish was characterized by sequencing libraries of bacterial 16S rDNA amplicons. Colonization of germ-free zebrafish with individual members of its microbiota revealed the bacterial species specificity of selected host responses. Together, these studies establish gnotobiotic zebrafish as a useful model for dissecting the molecular foundations of host-microbial interactions in the vertebrate digestive tract. PMID:15070763

  7. Metabolomics reveals insect metabolic responses associated with fungal infection.

    Science.gov (United States)

    Xu, Yong-Jiang; Luo, Feifei; Gao, Qiang; Shang, Yanfang; Wang, Chengshu

    2015-06-01

    The interactions between insects and pathogenic fungi are complex. We employed metabolomic techniques to profile insect metabolic dynamics upon infection by the pathogenic fungus Beauveria bassiana. Silkworm larvae were infected with fungal spores and microscopic observations demonstrated that the exhaustion of insect hemocytes was coupled with fungal propagation in the insect body cavity. Metabolomic analyses revealed that fungal infection could significantly alter insect energy and nutrient metabolisms as well as the immune defense responses, including the upregulation of carbohydrates, amino acids, fatty acids, and lipids, but the downregulation of eicosanoids and amines. The insect antifeedant effect of the fungal infection was evident with the reduced level of maclurin (a component of mulberry leaves) in infected insects but elevated accumulations in control insects. Insecticidal and cytotoxic mycotoxins like oosporein and beauveriolides were also detected in insects at the later stages of infection. Taken together, the metabolomics data suggest that insect immune responses are energy-cost reactions and the strategies of nutrient deprivation, inhibition of host immune responses, and toxin production would be jointly employed by the fungus to kill insects. The data obtained in this study will facilitate future functional studies of genes and pathways associated with insect-fungus interactions.

  8. Measuring the Accuracy of Survey Responses using Administrative Register Data

    DEFF Research Database (Denmark)

    Kreiner, Claus Thustrup; Lassen, David Dreyer; Leth-Petersen, Søren

    2015-01-01

    This paper shows how Danish administrative register data can be combined with survey data at the person level and be used to validate information collected in the survey. Register data are collected by automatic third party reporting and the potential errors associated with the two data sources...... are therefore plausibly orthogonal. Two examples are given to illustrate the potential of combining survey and register data. In the first example expenditure survey records with information about total expenditure are merged with income tax records holding information about income and wealth. Income and wealth...... data are used to impute total expenditure which is then compared to the survey measure. Results suggest that the two measures match each other well on average. In the second example we compare responses to a one-shot recall question about total gross personal income ¿collected in another survey...

  9. Response rate, response time, and economic costs of survey research: A randomized trial of practicing pharmacists.

    Science.gov (United States)

    Hardigan, Patrick C; Popovici, Ioana; Carvajal, Manuel J

    2016-01-01

    There is a gap between increasing demands from pharmacy journals, publishers, and reviewers for high survey response rates and the actual responses often obtained in the field by survey researchers. Presumably demands have been set high because response rates, times, and costs affect the validity and reliability of survey results. Explore the extent to which survey response rates, average response times, and economic costs are affected by conditions under which pharmacist workforce surveys are administered. A random sample of 7200 U.S. practicing pharmacists was selected. The sample was stratified by delivery method, questionnaire length, item placement, and gender of respondent for a total of 300 observations within each subgroup. A job satisfaction survey was administered during March-April 2012. Delivery method was the only classification showing significant differences in response rates and average response times. The postal mail procedure accounted for the highest response rates of completed surveys, but the email method exhibited the quickest turnaround. A hybrid approach, consisting of a combination of postal and electronic means, showed the least favorable results. Postal mail was 2.9 times more cost effective than the email approach and 4.6 times more cost effective than the hybrid approach. Researchers seeking to increase practicing pharmacists' survey participation and reduce response time and related costs can benefit from the analytical procedures tested here. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. In Search of Motivation for the Business Survey Response Task

    NARCIS (Netherlands)

    Torres van Grinsven, Vanessa; Bolko, Irena; Bavdaz, Mojca

    2014-01-01

    Increasing reluctance of businesses to participate in surveys often leads to declining or low response rates, poor data quality and burden complaints, and suggests that a driving force, that is, the motivation for participation and accurate and timely response, is insufficient or lacking. Inspiratio

  11. In Search of Motivation for the Business Survey Response Task

    NARCIS (Netherlands)

    Torres van Grinsven, Vanessa; Bolko, Irena; Bavdaz, Mojca

    2014-01-01

    Increasing reluctance of businesses to participate in surveys often leads to declining or low response rates, poor data quality and burden complaints, and suggests that a driving force, that is, the motivation for participation and accurate and timely response, is insufficient or lacking.

  12. Responses to catastrophic AGI risk: a survey

    Science.gov (United States)

    Sotala, Kaj; Yampolskiy, Roman V.

    2015-01-01

    Many researchers have argued that humanity will create artificial general intelligence (AGI) within the next twenty to one hundred years. It has been suggested that AGI may inflict serious damage to human well-being on a global scale (‘catastrophic risk’). After summarizing the arguments for why AGI may pose such a risk, we review the field's proposed responses to AGI risk. We consider societal proposals, proposals for external constraints on AGI behaviors and proposals for creating AGIs that are safe due to their internal design.

  13. Non-response in a survey among immigrants in Denmark

    DEFF Research Database (Denmark)

    Deding, Mette; Fridberg, Torben; Jakobsen, Vibeke

    The purpose of this paper is to study how various characteristics of respondents and interviewers affect non-response among immigrants. We use a survey conducted among immigrants in Denmark and ethnic Danes. First, we analyse the determinants of overall non-response. Second, we analyse how...... the determinants of contact and of response given contact differ. We find that characteristics of the respondents are important for the response rate – especially they are important for the probability of getting in contact with the respondent. The lower probability of response among immigrants compared to ethnic...

  14. Response bias in job satisfaction surveys: English general practitioners

    OpenAIRE

    Gravelle, H.; AR Hole, I Hussein

    2008-01-01

    Job satisfaction may affect the propensity to respond to job satisfaction surveys, so that estimates of average satisfaction and the effects of determinants of satisfaction may be biased. We examine response bias using data from a postal job satisfaction survey of family doctors. We link all the sampled doctors to an administrative database and so have information on the characteristics of responders and non-responders. Allowing for selection increases the estimate of mean job satisfaction in...

  15. In Search of Motivation for the Business Survey Response Task

    Directory of Open Access Journals (Sweden)

    Torres van Grinsven Vanessa

    2014-12-01

    Full Text Available Increasing reluctance of businesses to participate in surveys often leads to declining or low response rates, poor data quality and burden complaints, and suggests that a driving force, that is, the motivation for participation and accurate and timely response, is insufficient or lacking. Inspiration for ways to remedy this situation has already been sought in the psychological theory of self-determination; previous research has favored enhancement of intrinsic motivation compared to extrinsic motivation. Traditionally however, enhancing extrinsic motivation has been pervasive in business surveys. We therefore review this theory in the context of business surveys using empirical data from the Netherlands and Slovenia, and suggest that extrinsic motivation calls for at least as much attention as intrinsic motivation, that other sources of motivation may be relevant besides those stemming from the three fundamental psychological needs (competence, autonomy and relatedness, and that other approaches may have the potential to better explain some aspects of motivation in business surveys (e.g., implicit motives. We conclude with suggestions that survey organizations can consider when attempting to improve business survey response behavior.

  16. Corporate Social Responsibility in Engineering Education. A French Survey

    Science.gov (United States)

    Didier, C.; Huet, R.

    2008-01-01

    In this paper, we present and discuss the results of a survey of how corporate social responsibility (CSR) is being discussed and taught in engineering education in France. We shall first describe how those questions have been recently tackled in various programmes of higher education in France. We shall also analyse what faculty members have to…

  17. Response to ERIS 2014 States' Research Needs Survey

    Science.gov (United States)

    This document is ORD’s response to the states’ needs and priorities, as identified in the 2014 survey. ORD identified existing methods, models, tools and databases on these topics, as well as near-term research and development efforts, that could assist states in thei...

  18. The Department Head: A Survey of Duties and Responsibilities.

    Science.gov (United States)

    Papalia, Anthony

    This study surveys 107 foreign language departments in secondary schools in western New York and identifies duties and practices of those responsible for the departmental leadership. The report also determines the amount of released time granted to perform departmental duties. The educational preparation and work experience of supervisory staff…

  19. Corporate Social Responsibility in Engineering Education. A French Survey

    Science.gov (United States)

    Didier, C.; Huet, R.

    2008-01-01

    In this paper, we present and discuss the results of a survey of how corporate social responsibility (CSR) is being discussed and taught in engineering education in France. We shall first describe how those questions have been recently tackled in various programmes of higher education in France. We shall also analyse what faculty members have to…

  20. Crustal structure of the western Yamato Basin, Japan Sea, revealed from seismic survey

    Science.gov (United States)

    No, T.; Sato, T.; Kodaira, S.; Miura, S.; Ishiyama, T.; Sato, H.

    2015-12-01

    The Yamato Basin is the second largest basin of the Japan Sea. This basin is important to clarify its formation process. Some studies of crustal structure had been carried out in the Yamato Basin (e.g. Ludwig et al., 1975; Katao, 1988; Hirata et al., 1989; Sato et al., 2006). However, the relationship between formation process and crustal structure is not very clear, because the amount of seismic exploration data is very limited. In addition, since there is ODP Leg 127 site 797 (Tamaki et al., 1990) directly beneath our seismic survey line, we contributed to the study on the formation of the Yamato Basin by examining the relation between the ODP results and our results. During July-August 2014, we conducted a multi-channel seismic (MCS) survey and ocean bottom seismometer (OBS) survey to study the crustal structure of the western Yamato Basin. We present an outline of the data acquisition and results of the data processing and preliminary interpretations from this study. As a result of our study, the crust, which is about 12 km thick, is thicker than standard oceanic crust (e.g., Spudich and Orcutt, 1980; White et al., 1992) revealed from P-wave velocity structure by OBS survey. A clear reflector estimated to be the Moho can be identified by MCS profiles. The characteristics of the sedimentary layer are common within the survey area. For example, a strong coherent reflector that is estimated to be an opal-A/opal-CT BSR (bottom simulating reflector) (Kuramoto et al., 1992) was confirmed in the sediment of all survey lines. On the other hand, a coherent reflector in the crust was confirmed in some lines. It is identified as this reflector corresponding with the deformation structure in the sediment and basement.

  1. Non-Response in Student Surveys: The Role of Demographics, Engagement and Personality

    Science.gov (United States)

    Porter, Stephen R.; Whitcomb, Michael E.

    2005-01-01

    What causes a student to participate in a survey? This paper looks at participation across multiple surveys to understand survey non-response; by using multiple surveys we minimize the impact of survey salience. Students at a selective liberal arts college were administered four different surveys throughout the 2002-2003 academic year, and we use…

  2. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

    KAUST Repository

    Kuo, Dwight

    2010-07-23

    Background: Fungal infections are an emerging health risk, especially those involving yeast that are resistant to antifungal agents. To understand the range of mechanisms by which yeasts can respond to anti-fungals, we compared gene expression patterns across three evolutionarily distant species - Saccharomyces cerevisiae, Candida glabrata and Kluyveromyces lactis - over time following fluconazole exposure. Results: Conserved and diverged expression patterns were identified using a novel soft clustering algorithm that concurrently clusters data from all species while incorporating sequence orthology. The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity. In support of this hypothesis we find that only Saccharomyces becomes more azole resistant in ergosterol-supplemented media; that this depends on sterol importers Aus1 and Pdr11; and that transgenic expression of sterol importers in Kluyveromyces alleviates its drug sensitivity. Conclusions: We have compared the dynamic transcriptional responses of three diverse yeast species to fluconazole treatment using a novel clustering algorithm. This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity. In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways.

  3. The Mass Distribution of the Great Attractor as Revealed by a Deep NIR Survey

    CERN Document Server

    Kraan-Korteweg, R C; Woudt, P A; Nagayama, T; Wakamatsu, K

    2011-01-01

    This paper presents the analysis of a deep near-infrared J,H,Ks-imaging survey (37.5 sq deg) aimed at tracing the galaxy distribution of the Great Attractor (GA) in the Zone of Avoidance along the so-called Norma Wall. The resulting galaxy catalog is complete to extinction-corrected magnitudes Ks^o = 14.8 mag for extinctions less than A_K = 1.0 mag and star densities below log N(Ks<14.0) < 4.72. Of the 4360 cataloged galaxies, 99.2% lie in the hereby constrained 89.5% of the survey area. Although the analyzed galaxy distribution reveals no new major galaxy clusters at the GA distance (albeit some more distant ones), the overall number counts and luminosity density indicate a clear and surprisingly smooth overdensity at the GA distance that extends over the whole surveyed region. A mass estimate of the Norma Wall overdensity derived from (a) galaxy number counts and (b) photometric redshift distribution gives a lower value compared to the original prediction by Lynden-Bell et al. 1988 (~14%), but is cons...

  4. Electrocorticography Reveals Enhanced Visual Cortex Responses to Visual Speech.

    Science.gov (United States)

    Schepers, Inga M; Yoshor, Daniel; Beauchamp, Michael S

    2015-11-01

    Human speech contains both auditory and visual components, processed by their respective sensory cortices. We test a simple model in which task-relevant speech information is enhanced during cortical processing. Visual speech is most important when the auditory component is uninformative. Therefore, the model predicts that visual cortex responses should be enhanced to visual-only (V) speech compared with audiovisual (AV) speech. We recorded neuronal activity as patients perceived auditory-only (A), V, and AV speech. Visual cortex showed strong increases in high-gamma band power and strong decreases in alpha-band power to V and AV speech. Consistent with the model prediction, gamma-band increases and alpha-band decreases were stronger for V speech. The model predicts that the uninformative nature of the auditory component (not simply its absence) is the critical factor, a prediction we tested in a second experiment in which visual speech was paired with auditory white noise. As predicted, visual speech with auditory noise showed enhanced visual cortex responses relative to AV speech. An examination of the anatomical locus of the effects showed that all visual areas, including primary visual cortex, showed enhanced responses. Visual cortex responses to speech are enhanced under circumstances when visual information is most important for comprehension.

  5. Transcriptional analysis of the endothelial response to diabetes reveals a role for galectin-3.

    Science.gov (United States)

    Darrow, April L; Shohet, Ralph V; Maresh, J Gregory

    2011-10-20

    To characterize the endothelial dysfunction associated with Type II diabetes, we surveyed transcriptional responses in the vascular endothelia of mice receiving a diabetogenic, high-fat diet. Tie2-GFP mice were fed a diet containing 60% fat calories (HFD); controls were littermates fed normal chow. Following 4, 6, and 8 wk, aortic and leg muscle tissues were enzymatically dispersed, and endothelial cells were obtained by fluorescence-activated cell sorting. Relative mRNA abundance in HFD vs. control endothelia was measured with long-oligo microarrays; highly dysregulated genes were confirmed by real-time PCR and protein quantification. HFD mice were hyperglycemic by 2 wk and displayed vascular insulin resistance and decreased glucose tolerance by 5 and 6 wk, respectively. Endothelial transcripts upregulated by HFD included galectin-3 (Lgals3), 5-lipoxygenase-activating protein, and chemokine ligands 8 and 9. Increased LGALS3 protein was detected in muscle endothelium by immunohistology accompanied by elevated LGALS3 in the serum of HFD mice. Our comprehensive analysis of the endothelial transcriptional response in a model of Type II diabetes reveals novel regulation of transcripts with roles in inflammation, insulin sensitivity, oxidative stress, and atherosclerosis. Increased endothelial expression and elevated humoral levels of LGALS3 supports a role for this molecule in the vascular response to diabetes, and its potential as a direct biomarker for the inflammatory state in diabetes.

  6. Mediated amperometry reveals different modes of yeast responses to sugars.

    Science.gov (United States)

    Garjonyte, Rasa; Melvydas, Vytautas; Malinauskas, Albertas

    2016-02-01

    Menadione-mediated amperometry at carbon paste electrodes modified with various yeasts (Saccharomyces cerevisiae, Candida pulcherrima, Pichia guilliermondii and Debaryomyces hansenii) was employed to monitor redox activity inside the yeast cells induced by glucose, fructose, sucrose, maltose or galactose. Continuous measurements revealed distinct modes (transient or gradually increasing) of the current development during the first 2 to 3 min after subjection to glucose, fructose and sucrose at electrodes containing S. cerevisiae and non-Saccharomyces strains. Different modes (increasing or decreasing) of the current development after yeast subjection to galactose at electrodes with S. cerevisiae or D. hansenii and at electrodes with C. pulcherrima and P. guilliermondii suggested different mechanisms of galactose assimilation.

  7. What boxing-related stimuli reveal about response behaviour.

    Science.gov (United States)

    Ottoboni, Giovanni; Russo, Gabriele; Tessari, Alessia

    2015-01-01

    When two athletes meet inside the ropes of the boxing ring to fight, their cognitive systems have to respond as quickly as possible to a manifold of stimuli to assure victory. In the present work, we studied the pre-attentive mechanisms, which form the basis of an athlete's ability in reacting to an opponent's punches. Expert boxers, beginner boxers and people with no experience of boxing performed a Simon-like task where they judged the colour of the boxing gloves worn by athletes in attack postures by pressing two lateralised keys. Although participants were not instructed to pay attention to the direction of the punches, beginner boxers' responses resembled a defence-related pattern, expert boxers' resembled counterattacks, whereas non-athletes' responses were not influenced by the unrelated task information. Results are discussed in the light of an expertise-related action simulation account.

  8. Planarian Phototactic Assay Reveals Differential Behavioral Responses Based on Wavelength

    OpenAIRE

    Paskin, Taylor R.; John Jellies; Jessica Bacher; Wendy S Beane

    2014-01-01

    Planarians are free-living aquatic flatworms that possess a well-documented photophobic response to light. With a true central nervous system and simple cerebral eyes (ocelli), planarians are an emerging model for regenerative eye research. However, comparatively little is known about the physiology of their photoreception or how their behavior is affected by various wavelengths. Most phototactic studies have examined planarian behavior using white light. Here, we describe a novel planarian b...

  9. Bmp indicator mice reveal dynamic regulation of transcriptional response.

    Directory of Open Access Journals (Sweden)

    Anna L Javier

    Full Text Available Cellular responses to Bmp ligands are regulated at multiple levels, both extracellularly and intracellularly. Therefore, the presence of these growth factors is not an accurate indicator of Bmp signaling activity. While a common approach to detect Bmp signaling activity is to determine the presence of phosphorylated forms of Smad1, 5 and 8 by immunostaining, this approach is time consuming and not quantitative. In order to provide a simpler readout system to examine the presence of Bmp signaling in developing animals, we developed BRE-gal mouse embryonic stem cells and a transgenic mouse line that specifically respond to Bmp ligand stimulation. Our reporter identifies specific transcriptional responses that are mediated by Smad1 and Smad4 with the Schnurri transcription factor complex binding to a conserved Bmp-Responsive Element (BRE, originally identified among Drosophila, Xenopus and human Bmp targets. Our BRE-gal mES cells specifically respond to Bmp ligands at concentrations as low as 5 ng/ml; and BRE-gal reporter mice, derived from the BRE-gal mES cells, show dynamic activity in many cellular sites, including extraembryonic structures and mammary glands, thereby making this a useful scientific tool.

  10. Prenotification, Incentives, and Survey Modality: An Experimental Test of Methods to Increase Survey Response Rates of School Principals

    Science.gov (United States)

    Jacob, Robin Tepper; Jacob, Brian

    2012-01-01

    Teacher and principal surveys are among the most common data collection techniques employed in education research. Yet there is remarkably little research on survey methods in education, or about the most cost-effective way to raise response rates among teachers and principals. In an effort to explore various methods for increasing survey response…

  11. Prenotification, Incentives, and Survey Modality: An Experimental Test of Methods to Increase Survey Response Rates of School Principals

    Science.gov (United States)

    Jacob, Robin Tepper; Jacob, Brian

    2012-01-01

    Teacher and principal surveys are among the most common data collection techniques employed in education research. Yet there is remarkably little research on survey methods in education, or about the most cost-effective way to raise response rates among teachers and principals. In an effort to explore various methods for increasing survey response…

  12. Factors associated with survey response in hand surgery research.

    Science.gov (United States)

    Bot, Arjan G J; Anderson, Jade A; Neuhaus, Valentin; Ring, David

    2013-10-01

    A low response rate is believed to decrease the validity of survey studies. Factors associated with nonresponse to surveys are poorly characterized in orthopaedic research. This study addressed whether (1) psychologic factors; (2) demographics; (3) illness-related factors; and (4) pain are predictors of a lower likelihood of a patient returning a mailed survey. One hundred four adult, new or return patients completed questionnaires including the Pain Catastrophizing Scale, Patient Health Questionnaire-9 depression scale, Short Health Anxiety Index, demographics, and a pain scale (0-10) during a routine visit to a hand and upper extremity surgeon. Of these patients, 38% had undergone surgery and the remainder was seen for various other conditions. Six months after their visit, patients were mailed the DASH questionnaire and a scale to rate their satisfaction with the visit (0-10). Bivariate analysis and logistic regression were used to determine risk factors for being a nonresponder to the followup of this study. The cohort consisted of 57 women and 47 men with a mean age of 51 years with various diagnoses. Thirty-five patients (34%) returned the questionnaire. Responders were satisfied with their visit (mean satisfaction, 8.7) and had a DASH score of 9.6. Compared with patients who returned the questionnaires, nonresponders had higher pain catastrophizing scores, were younger, more frequently male, and had more pain at enrollment. In logistic regression, male sex (odds ratio [OR], 2.6), pain (OR, 1.3), and younger age (OR, 1.03) were associated with not returning the questionnaire. Survey studies should be interpreted in light of the fact that patients who do not return questionnaires in a hand surgery practice differ from patients who do return them. Hand surgery studies that rely on questionnaire evaluation remote from study enrollment should include tactics to improve the response of younger, male patients with more pain. Level II, prognostic study. See

  13. Pharmacometabolomics reveals racial differences in response to atenolol treatment.

    Directory of Open Access Journals (Sweden)

    William R Wikoff

    Full Text Available Antihypertensive drugs are among the most commonly prescribed drugs for chronic disease worldwide. The response to antihypertensive drugs varies substantially between individuals and important factors such as race that contribute to this heterogeneity are poorly understood. In this study we use metabolomics, a global biochemical approach to investigate biochemical changes induced by the beta-adrenergic receptor blocker atenolol in Caucasians and African Americans. Plasma from individuals treated with atenolol was collected at baseline (untreated and after a 9 week treatment period and analyzed using a GC-TOF metabolomics platform. The metabolomic signature of atenolol exposure included saturated (palmitic, monounsaturated (oleic, palmitoleic and polyunsaturated (arachidonic, linoleic free fatty acids, which decreased in Caucasians after treatment but were not different in African Americans (p<0.0005, q<0.03. Similarly, the ketone body 3-hydroxybutyrate was significantly decreased in Caucasians by 33% (p<0.0001, q<0.0001 but was unchanged in African Americans. The contribution of genetic variation in genes that encode lipases to the racial differences in atenolol-induced changes in fatty acids was examined. SNP rs9652472 in LIPC was found to be associated with the change in oleic acid in Caucasians (p<0.0005 but not African Americans, whereas the PLA2G4C SNP rs7250148 associated with oleic acid change in African Americans (p<0.0001 but not Caucasians. Together, these data indicate that atenolol-induced changes in the metabolome are dependent on race and genotype. This study represents a first step of a pharmacometabolomic approach to phenotype patients with hypertension and gain mechanistic insights into racial variability in changes that occur with atenolol treatment, which may influence response to the drug.

  14. 77 FR 20887 - Proposed Information Collection (National Acquisition Center Customer Response Survey) Activity...

    Science.gov (United States)

    2012-04-06

    ... solicits comments on the information needed to measure customer satisfaction with delivered products and... AFFAIRS Proposed Information Collection (National Acquisition Center Customer Response Survey) Activity...: Department of Veterans Affairs (VA) National Acquisition Center Customer Response Survey, VA Form 0863....

  15. Survey of spectral response measurements for photovoltaic devices

    Energy Technology Data Exchange (ETDEWEB)

    Hartman, J.S.; Lind, M.A.

    1981-11-01

    A survey of the photovoltaic community was conducted to ascertain the present state-of-the-art for PV spectral response measurements. Specific topics explored included measurement system designs, good and bad features of the systems, and problems encountered in the evaluation of specific cell structures and materials. The survey showed that most spectral response data are used in diagnostic analysis for the optimization of developmental solar cells. Measurement systems commonly utilize a chopped narrowband source in conjunction with a constant bias illumination which simulates the ambient end use environment. Researchers emphasized the importance of bias illumination for all types of cells in order to minimize the effects of nonlinearities in cell response. Not surprisingly single crystal silicon cells present the fewest measurement problems to the researcher and have been studied more thoroughly than any other type of solar cell. But, the accurate characterization of silicon cells is still difficult and laboratory intercomparison studies have yielded data scatter ranging from +-5% to +-15%. The measurement experience with other types of cells is less extensive. The development of reliable data bases for some solar cells is complicated by problems of cell nonuniformity, environmental instability, nonlinearity, etc. Cascade cells present new problems associated with their structue (multiple cells in series) which are just beginning to be understood. In addition, the importance of many measurement parameters (spectral content of bias light, bias light intensity, bias voltage, chopping frequency, etc.) are not fully understood for most types of solar cells.

  16. Phosphoproteomic dynamics of chickpea (Cicer arietinum L.) reveals shared and distinct components of dehydration response.

    Science.gov (United States)

    Subba, Pratigya; Barua, Pragya; Kumar, Rajiv; Datta, Asis; Soni, Kamlesh Kumar; Chakraborty, Subhra; Chakraborty, Niranjan

    2013-11-01

    Reversible protein phosphorylation is a ubiquitous regulatory mechanism that plays critical roles in transducing stress signals to bring about coordinated intracellular responses. To gain better understanding of dehydration response in plants, we have developed a differential phosphoproteome in a food legume, chickpea (Cicer arietinum L.). Three-week-old chickpea seedlings were subjected to progressive dehydration by withdrawing water, and the changes in the phosphorylation status of a large repertoire of proteins were monitored. The proteins were resolved by 2-DE and stained with phosphospecific fluorescent Pro-Q Diamond dye. Mass spectrometric analysis led to the identification of 91 putative phosphoproteins, presumably involved in a variety of functions including cell defense and rescue, photosynthesis and photorespiration, molecular chaperones, and ion transport, among others. Multiple sites of phosphorylation were predicted on several key elements, which include both the regulatory as well as the functional proteins. A critical survey of the phosphorylome revealed a DREPP (developmentally regulated plasma membrane protein) plasma membrane polypeptide family protein, henceforth designated CaDREPP1. The transcripts of CaDREPP1 were found to be differentially regulated under dehydration stress, further corroborating the proteomic results. This work provides new insights into the possible phosphorylation events triggered by the conditions of progressive water-deficit in plants.

  17. Village energy survey reveals missing rural raw coal in northern China: Significance in science and policy.

    Science.gov (United States)

    Zhi, Guorui; Zhang, Yayun; Sun, Jianzhong; Cheng, Miaomiao; Dang, Hongyan; Liu, Shijie; Yang, Junchao; Zhang, Yuzhe; Xue, Zhigang; Li, Shuyuan; Meng, Fan

    2017-04-01

    Burning coal for winter heating has been considered a major contributor to northern China's winter haze, with the district heating boilers holding the balance. However a decade of intensive efforts on district heating boilers brought few improvements to northern China's winter air quality, arousing a speculation that the household heating stoves mainly in rural area rather than the district heating boilers mainly in urban area dominate coal emissions in winter. This implies an extreme underestimation of rural household coal consumption by the China Energy Statistical Yearbooks (CESYs), although direct evidence supporting this speculation is lacking. A village energy survey campaign was launched to gather the firsthand information on household coal consumption in the rural areas of two cities, Baoding (in Hebei province) and Beijing (the capital of China). The survey data show that the rural raw coal consumption in Baoding (5.04 × 10(3) kt) was approximately 6.5 times the value listed in the official CESY 2013 and exceeded the rural total of whole Hebei Province (4668 kt), revealing a huge amount of raw coal missing from the current statistical system. More importantly, rural emissions of particulate matter (PM) and SO2 from raw coal, which had never been included in widely distributing environmental statistical reports, were found higher than those from industrial and urban household sectors in the two cities in 2013, which highlights the importance of rural coal burning in creating northern China's heavy haze and helps to explain why a number of modeling predictions on ambient pollutant concentrations based on normal emission inventories were more bias-prone in winter season than in other seasons. We therefore recommend placing greater emphasis on the "missing" rural raw coal to help China in its long-term ambition to achieve clean air in the context of rapid economic development.

  18. Connected magma plumbing system between Cerro Negro and El Hoyo Complex, Nicaragua revealed by gravity survey

    Science.gov (United States)

    MacQueen, Patricia; Zurek, Jeffrey; Williams-Jones, Glyn

    2016-11-01

    Cerro Negro, near León, Nicaragua is a young, relatively small basaltic cinder cone volcano that has been unusually active during its short lifespan. Multiple explosive eruptions have deposited significant amounts of ash on León and the surrounding rural communities. While a number of studies investigate the geochemistry and stress regime of the volcano, subsurface structures have only been studied by diffuse soil gas surveys. These studies have raised several questions as to the proper classification of Cerro Negro and its relation to neighboring volcanic features. To address these questions, we collected 119 gravity measurements around Cerro Negro volcano in an attempt to delineate deep structures at the volcano. The resulting complete Bouguer anomaly map revealed local positive gravity anomalies (wavelength 0.5 to 2 km, magnitude +4 mGal) and regional positive (10 km wavelength, magnitudes +10 and +8 mGal) and negative (12 and 6 km wavelength, magnitudes -18 and -13 mGal) Bouguer anomalies. Further analysis of these gravity data through inversion has revealed both local and regional density anomalies that we interpret as intrusive complexes at Cerro Negro and in the Nicaraguan Volcanic Arc. The local density anomalies at Cerro Negro have a density of 2700 kg m-3 (basalt) and are located between -250 and -2000 m above sea level. The distribution of recovered density anomalies suggests that eruptions at Cerro Negro may be tapping an interconnected magma plumbing system beneath El Hoyo, Cerro La Mula, and Cerro Negro, and more than seven other proximal volcanic features, implying that Cerro Negro should be considered the newest cone of a Cerro Negro-El Hoyo volcanic complex.

  19. A randomised trial and economic evaluation of the effect of response mode on response rate, response bias, and item non-response in a survey of doctors.

    Science.gov (United States)

    Scott, Anthony; Jeon, Sung-Hee; Joyce, Catherine M; Humphreys, John S; Kalb, Guyonne; Witt, Julia; Leahy, Anne

    2011-09-05

    Surveys of doctors are an important data collection method in health services research. Ways to improve response rates, minimise survey response bias and item non-response, within a given budget, have not previously been addressed in the same study. The aim of this paper is to compare the effects and costs of three different modes of survey administration in a national survey of doctors. A stratified random sample of 4.9% (2,702/54,160) of doctors undertaking clinical practice was drawn from a national directory of all doctors in Australia. Stratification was by four doctor types: general practitioners, specialists, specialists-in-training, and hospital non-specialists, and by six rural/remote categories. A three-arm parallel trial design with equal randomisation across arms was used. Doctors were randomly allocated to: online questionnaire (902); simultaneous mixed mode (a paper questionnaire and login details sent together) (900); or, sequential mixed mode (online followed by a paper questionnaire with the reminder) (900). Analysis was by intention to treat, as within each primary mode, doctors could choose either paper or online. Primary outcome measures were response rate, survey response bias, item non-response, and cost. The online mode had a response rate 12.95%, followed by the simultaneous mixed mode with 19.7%, and the sequential mixed mode with 20.7%. After adjusting for observed differences between the groups, the online mode had a 7 percentage point lower response rate compared to the simultaneous mixed mode, and a 7.7 percentage point lower response rate compared to sequential mixed mode. The difference in response rate between the sequential and simultaneous modes was not statistically significant. Both mixed modes showed evidence of response bias, whilst the characteristics of online respondents were similar to the population. However, the online mode had a higher rate of item non-response compared to both mixed modes. The total cost of the online

  20. Baseline reef health surveys at Bangka Island (North Sulawesi, Indonesia reveal new threats

    Directory of Open Access Journals (Sweden)

    Massimo Ponti

    2016-10-01

    Full Text Available Worldwide coral reef decline appears to be accompanied by an increase in the spread of hard coral diseases. However, whether this is the result of increased direct and indirect human disturbances and/or an increase in natural stresses remains poorly understood. The provision of baseline surveys for monitoring coral health status lays the foundations to assess the effects of any such anthropogenic and/or natural effects on reefs. Therefore, the objectives of this present study were to provide a coral health baseline in a poorly studied area, and to investigate possible correlations between coral health and the level of anthropogenic and natural disturbances. During the survey period, we recorded 20 different types of coral diseases and other compromised health statuses. The most abundant were cases of coral bleaching, followed by skeletal deformations caused by pyrgomatid barnacles, damage caused by fish bites, general pigmentation response and galls caused by cryptochirid crabs. Instances of colonies affected by skeletal eroding bands, and sedimentation damage increased in correlation to the level of bio-chemical disturbance and/or proximity to villages. Moreover, galls caused by cryptochirid crabs appeared more abundant at sites affected by blast fishing and close to a newly opened metal mine. Interestingly, in the investigated area the percentage of corals showing signs of ‘common’ diseases such as black band disease, brown band disease, white syndrome and skeletal eroding band disease were relatively low. Nevertheless, the relatively high occurrence of less common signs of compromised coral-related reef health, including the aggressive overgrowth by sponges, deserves further investigation. Although diseases appear relatively low at the current time, this area may be at the tipping point and an increase in activities such as mining may irredeemably compromise reef health.

  1. Stigma in Canada: Results From a Rapid Response Survey

    Science.gov (United States)

    Stuart, Heather; Patten, Scott B; Koller, Michelle; Modgill, Geeta; Liinamaa, Tiina

    2014-01-01

    Objective: Our paper presents findings from the first population survey of stigma in Canada using a new measure of stigma. Empirical objectives are to provide a descriptive profile of Canadian’s expectations that people will devalue and discriminate against someone with depression, and to explore the relation between experiences of being stigmatized in the year prior to the survey among people having been treated for a mental illness with a selected number of sociodemographic and mental health–related variables. Method: Data were collected by Statistics Canada using a rapid response format on a representative sample of Canadians (n = 10 389) during May and June of 2010. Public expectations of stigma and personal experiences of stigma in the subgroup receiving treatment for a mental illness were measured. Results: Over one-half of the sample endorsed 1 or more of the devaluation discrimination items, indicating that they believed Canadians would stigmatize someone with depression. The item most frequently endorsed concerned employers not considering an application from someone who has had depression. Over one-third of people who had received treatment in the year prior to the survey reported discrimination in 1 or more life domains. Experiences of discrimination were strongly associated with perceptions that Canadians would devalue someone with depression, younger age (12 to 15 years), and self-reported poor general mental health. Conclusions: The Mental Health Experiences Module reflects an important partnership between 2 national organizations that will help Canada fulfill its monitoring obligations under the United Nations Convention on the Rights of Persons with Disabilities and provide a legacy to researchers and policy-makers who are interested in monitoring changes in stigma over time. PMID:25565699

  2. Bees for development: Brazilian survey reveals how to optimize stingless beekeeping.

    Directory of Open Access Journals (Sweden)

    Rodolfo Jaffé

    Full Text Available Stingless bees are an important asset to assure plant biodiversity in many natural ecosystems, and fulfill the growing agricultural demand for pollination. However, across developing countries stingless beekeeping remains an essentially informal activity, technical knowledge is scarce, and management practices lack standardization. Here we profited from the large diversity of stingless beekeepers found in Brazil to assess the impact of particular management practices on productivity and economic revenues from the commercialization of stingless bee products. Our study represents the first large-scale effort aiming at optimizing stingless beekeeping for honey/colony production based on quantitative data. Survey data from 251 beekeepers scattered across 20 Brazilian States revealed the influence of specific management practices and other confounding factors over productivity and income indicators. Specifically, our results highlight the importance of teaching beekeepers how to inspect and feed their colonies, how to multiply them and keep track of genetic lineages, how to harvest and preserve the honey, how to use vinegar traps to control infestation by parasitic flies, and how to add value by labeling honey containers. Furthermore, beekeeping experience and the network of known beekeepers were found to be key factors influencing productivity and income. Our work provides clear guidelines to optimize stingless beekeeping and help transform the activity into a powerful tool for sustainable development.

  3. Bees for development: Brazilian survey reveals how to optimize stingless beekeeping.

    Science.gov (United States)

    Jaffé, Rodolfo; Pope, Nathaniel; Torres Carvalho, Airton; Madureira Maia, Ulysses; Blochtein, Betina; de Carvalho, Carlos Alfredo Lopes; Carvalho-Zilse, Gislene Almeida; Freitas, Breno Magalhães; Menezes, Cristiano; Ribeiro, Márcia de Fátima; Venturieri, Giorgio Cristino; Imperatriz-Fonseca, Vera Lucia

    2015-01-01

    Stingless bees are an important asset to assure plant biodiversity in many natural ecosystems, and fulfill the growing agricultural demand for pollination. However, across developing countries stingless beekeeping remains an essentially informal activity, technical knowledge is scarce, and management practices lack standardization. Here we profited from the large diversity of stingless beekeepers found in Brazil to assess the impact of particular management practices on productivity and economic revenues from the commercialization of stingless bee products. Our study represents the first large-scale effort aiming at optimizing stingless beekeeping for honey/colony production based on quantitative data. Survey data from 251 beekeepers scattered across 20 Brazilian States revealed the influence of specific management practices and other confounding factors over productivity and income indicators. Specifically, our results highlight the importance of teaching beekeepers how to inspect and feed their colonies, how to multiply them and keep track of genetic lineages, how to harvest and preserve the honey, how to use vinegar traps to control infestation by parasitic flies, and how to add value by labeling honey containers. Furthermore, beekeeping experience and the network of known beekeepers were found to be key factors influencing productivity and income. Our work provides clear guidelines to optimize stingless beekeeping and help transform the activity into a powerful tool for sustainable development.

  4. The VLT-FLAMES Tarantula Survey II: R139 revealed as a massive binary system

    CERN Document Server

    Taylor, W D; Sana, H; Walborn, N R; de Mink, S E; Stroud, V E; Alvarez-Candal, A; Barbá, R H; Bestenlehner, J M; Bonanos, A Z; Brott, I; Crowther, P A; de Koter, A; Friedrich, K; Gräfener, G; Hénault-Brunet, V; Herrero, A; Kaper, L; Langer, N; Lennon, D J; Apellániz, J Maíz; Markova, N; Morrell, N; Monaco, L; Vink, J S

    2011-01-01

    We report the discovery that R139 in 30 Doradus is a massive spectroscopic binary system. Multi-epoch optical spectroscopy of R139 was obtained as part of the VLT-FLAMES Tarantula Survey, revealing a double-lined system. The two components are of similar spectral types; the primary exhibits strong C III 4650 emission and is classified as an O6.5 Iafc supergiant, while the secondary is an O6 Iaf supergiant. The radial-velocity variations indicate a highly eccentric orbit with a period of 153.9 days. Photometry obtained with the Faulkes Telescope South shows no evidence for significant variability within an 18 month period. The orbital solution yields lower mass limits for the components of M1sin^3 i = 78 \\pm 8 Msun and M2sin^3 i = 66 \\pm 7 Msun. As R139 appears to be the most massive binary system known to contain two evolved Of supergiants, it will provide an excellent test for atmospheric and evolutionary models.

  5. A five-year survey of dematiaceous fungi in a tropical hospital reveals potential opportunistic species.

    Directory of Open Access Journals (Sweden)

    Su Mei Yew

    Full Text Available Dematiaceous fungi (black fungi are a heterogeneous group of fungi present in diverse environments worldwide. Many species in this group are known to cause allergic reactions and potentially fatal diseases in humans and animals, especially in tropical and subtropical climates. This study represents the first survey of dematiaceous fungi in Malaysia and provides observations on their diversity as well as in vitro response to antifungal drugs. Seventy-five strains isolated from various clinical specimens were identified by morphology as well as an internal transcribed spacer (ITS-based phylogenetic analysis. The combined molecular and conventional approach enabled the identification of three classes of the Ascomycota phylum and 16 genera, the most common being Cladosporium, Cochliobolus and Neoscytalidium. Several of the species identified have not been associated before with human infections. Among 8 antifungal agents tested, the azoles posaconazole (96%, voriconazole (90.7%, ketoconazole (86.7% and itraconazole (85.3% showed in vitro activity (MIC ≤ 1 µg/mL to the largest number of strains, followed by anidulafungin (89.3%, caspofungin (74.7% and amphotericin B (70.7%. Fluconazole appeared to be the least effective with only 10.7% of isolates showing in vitro susceptibility. Overall, almost half (45.3% of the isolates showed reduced susceptibility (MIC >1 µg/mL to at least one antifungal agent, and three strains (one Pyrenochaeta unguis-hominis and two Nigrospora oryzae showed potential multidrug resistance.

  6. Responses to GM food content in context with food integrity issues: results from Australian population surveys.

    Science.gov (United States)

    Mohr, Philip; Golley, Sinéad

    2016-01-25

    This study examined community responses to use of genetically modified (GM) content in food in the context of responses to familiar food additives by testing an empirically and theoretically derived model of the predictors of responses to both GM content and food integrity issues generally. A nationwide sample of 849 adults, selected at random from the Australian Electoral Roll, responded to a postal Food and Health Survey. Structural equation modelling analyses confirmed that ratings of general concern about food integrity (related to the presence of preservatives and other additives) strongly predicted negativity towards GM content. Concern about food integrity was, in turn, predicted by environmental concern and health engagement. In addition, both concern about food integrity generally and responses to GM content specifically were weakly predicted by attitudes to benefits of science and an intuitive (i.e., emotionally-based) reasoning style. Data from a follow-up survey conducted under the same conditions (N=1184) revealed that ratings of concern were significantly lower for use of genetic engineering in food than for four other common food integrity issues examined. Whereas the question of community responses to GM is often treated as a special issue, these findings support the conclusion that responses to the concept of GM content in food in Australia are substantially a specific instance of a general sensitivity towards the integrity of the food supply. They indicate that the origins of responses to GM content may be largely indistinguishable from those of general responses to preservatives and other common food additives. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. An Extensive Survey of Tyrosine Phosphorylation Revealing New Sites in Human Mammary Epithelial Cells

    Energy Technology Data Exchange (ETDEWEB)

    Heibeck, Tyler H.; Ding, Shi-Jian; Opresko, Lee K.; Zhao, Rui; Schepmoes, Athena A.; Yang, Feng; Tolmachev, Aleksey V.; Monroe, Matthew E.; Camp, David G.; Smith, Richard D.; Wiley, H. S.; Qian, Weijun

    2009-08-01

    Protein tyrosine phosphorylation is a central regulatory mechanism in cell signaling. To extensively characterize the site-specific tyrosine phosphorylation in human cells, we present here a global survey of tyrosine phosphorylation sites in a normal-derived human mammary epithelial cell (HMEC) line by applying anti-phosphotyrosine (pTyr) peptide immunoaffinity purification (IP) coupled with high sensitivity LC-MS/MS. A total of 481 tyrosine phosphorylation sites (covered by 716 unique peptides) from 285 proteins were confidently identified in HMEC following the analysis of both the basal condition and an acute stimulated condition with epidermal growth factor (EGF). The estimated false discovery rate is 1.0% as measured by comparison against a scrambled database search. Comparison of these data to the literature showed significant agreement in site matches. Additionally 281 sites were not previously observed in HMEC culture were found. Twenty-nine of these sites have not been reported in any human cell or tissue system. The global profiling also allowed us to examine the phosphorylation stoichiometry differences based on spectral count information. Comparison of the data to a previous global proteome profiling study illustrates that most of the highly phoshorylated proteins are of relatively low-abundance. Large differences in phosphorylation stoichiometry for sites within the same protein were also observed for many of the identified proteins, suggesting potentially more important functional roles for those highly phosphorylated pTyr sites within a given protein. By mapping to major signaling networks such as EGF receptor and insulin growth factor-1 receptor signaling pathways, many known proteins involved in these pathways were revealed to be tyrosine phosphorylated, which should allow us to select interesting targeted involved in a given pathway for more directed studies. This extensive HMEC tyrosine phosphorylation dataset represents an important database

  8. How Important Are High Response Rates for College Surveys?

    Science.gov (United States)

    Fosnacht, Kevin; Sarraf, Shimon; Howe, Elijah; Peck, Leah K.

    2017-01-01

    Surveys play an important role in understanding the higher education landscape. About 60 percent of the published research in major higher education journals utilized survey data (Pike, 2007). Institutions also commonly use surveys to assess student outcomes and evaluate programs, instructors, and even cafeteria food. However, declining survey…

  9. How Important Are High Response Rates for College Surveys?

    Science.gov (United States)

    Fosnacht, Kevin; Sarraf, Shimon; Howe, Elijah; Peck, Leah K.

    2017-01-01

    Surveys play an important role in understanding the higher education landscape. About 60 percent of the published research in major higher education journals utilized survey data (Pike, 2007). Institutions also commonly use surveys to assess student outcomes and evaluate programs, instructors, and even cafeteria food. However, declining survey…

  10. The LBT/WISSH quasar survey: revealing powerful winds in the most luminous AGN

    Science.gov (United States)

    Vietri, Giustina

    2017-01-01

    The systematic, multi-frequency investigation of hyper-luminous quasars shining at the golden epoch of AGN activity offers the unique opportunity of studying the power and the effect of AGN feedback at its extreme.The WISE/SDSS selected hyper-luminous (WISSH) quasar survey is an extensive multi-band observing program (from millimeter wavelengths to hard X rays) designed to accurately probe the role of nuclear activity in SMBH-galaxy self-regulated growth via extended outflows.Our on-going project aims at constraining both AGN and host galaxy ISM and star-formation properties in a large sample of ~ 90 broad-line quasars at the brightest end of the AGN luminosity function (L_bol > 1e14 L_sun), and at the peak of their number density (z ~ 2.5 - 3.5).I will review the most important results of the near-IR spectroscopic follow-up of WISSH quasars (available for ~40% of the total sample) performed with the LUCI at LBT. These observations were carried out to obtain a reliable Hbeta-based estimate of the SMBH masses and a census of the ionized outflows in these hyper-luminous quasars.We found that WISSH AGN are typically powered by highly accreting (0.3-3 Ledd), ten billion solar masses SMBHs, demonstrating that WISSH provides a simple and valuable tool to complete the census of the extreme SMBH population in the universe.We also succeeded in discovering [OIII] emission lines with a broad, skewed profile and exceptional luminosities (> 6e44 erg/s), tracing very powerful ionized outflows (up to ~4% of L_bol) in ~30% of the sample.Remarkably, the remaining 70% of quasars lacks [OIII] emission but shows strong winds traced by 3,000-8,000 km/s blueshifts of the high-ionization (CIV) with respect to low-ionization (Hbeta) broad emission lines, revealing strong radiatively driven winds that dominate the BLR kinematics.I will discuss the possible origins of this intriguing dichotomy which involves fundamental parameters such as bolometric luminosity, SMBH mass, Eddington ratio

  11. AUV Surveys Reveal Seafloor Linear Cracks Along a Fault Zone Offshore Southwest Taiwan

    Science.gov (United States)

    Chen, T.; Paull, C. K.; Liu, C.; Anderson, K.; Liu, S.; Thomas, H. J.; Mu, L.; Chen, C.; Caress, D. W.; Gwiazda, R.; Conlin, D.; Sumner, E.

    2013-12-01

    On a recent cruise offshore southwest Taiwan a series of seafloor linear cracks along a west-vergent fault zone on the west side of the Good Weather Ridge were explored utilizing the mapping Autonomous Underwater Vehicle of the Monterey Bay Aquarium Research Institute (MBARI) and the Remotely Operated Vehicle (ROV) of the Taiwan Ocean Research Institute (TORI). The unprecedented high-resolution multibeam bathymetry (1 m lateral resolution) and chirp sub-bottom profiles (11 cm vertical resolution) reveal north-south tending cracks occur within a 4.5 km long and 1.5 km wide zone in between 975 and 1450 m water depths. Individual cracks are seen as 5-10 m wide troughs that are 1-4 m deeper than the surrounding seafloor. The average length of these cracks is about 1.6 km, but some are over 3.2 km long. The interval between cracks varies from several tens of meters to over 100 m. Reflectors resolved within the chirp profiles show layered sediments extend uninterrupted between cracks, but no coherent reflections were resolved underneath them . Two dives with TORI's ROV were conducted in the zone of these seafloor cracks. ROV observations show that the sidewalls of the troughs slope at 30° to 60° downward to a distinct flat floor. Scraping with the ROV's arms shows that the sidewalls are composed of cohesive sediment while the floor of the trough is filled with soft fluffy sediment along with a considerable amount of anthropogenic debris, suggesting they are relatively young geomorphic features. The age of these cracks is also constrained by carbon-14 dating of a nearby core (MD178-3274) that shows Holocene sediment accumulation rate of 1.8 mm/yr. Together, these observations suggest that these troughs and cracks have developed within the last few hundred years. Seismic reflection profiles running across the fault zone show that these cracks are developed on top of a small young sediment wedge at the toe of the hanging wall above the west-vergent fault. The sediment of

  12. Can Lottery Incentives Boost Web Survey Response Rates? Findings from Four Experiments

    Science.gov (United States)

    Laguilles, Jerold S.; Williams, Elizabeth A.; Saunders, Daniel B.

    2011-01-01

    Institutions of higher education rely on student surveys for a number of purposes, including planning, assessment, and research. Web surveys are especially prevalent given their ease of use and low-cost; yet, obtaining a high response rate is a challenge. Although researchers have investigated the use of incentives in traditional mail surveys,…

  13. College Student Responses to Web and Paper Surveys: Does Mode Matter?

    Science.gov (United States)

    Carini, Robert M.; Hayek, John C.; Kuh, George D.; Kennedy, John M.; Ouimet, Judith A.

    2003-01-01

    Examined the responses of 58,288 college students to 8 scales involving 53 items from the National Survey of Student Engagement to gauge whether individuals respond differently to surveys administered via the Web and paper. Found that mode effects were generally small; however, students who completed the Web-based survey responded more favorably…

  14. Evaluating Reasons for Low Response from Mail Surveys. AIR 1995 Annual Forum Paper.

    Science.gov (United States)

    Westcott, S. Wickes, III; And Others

    A study was undertaken to solicit opinions from alumni on methods that might improve responses from graduate surveys. Two telephone surveys were conducted, one in 1991 which targeted the graduating classes of 1984 and 1989, and the second in 1994 among alumni of the classes of 1991 and 1993. In the 1994 survey information was gathered regarding…

  15. Surveys of Health Professions Trainees: Prevalence, Response Rates, and Predictive Factors to Guide Researchers.

    Science.gov (United States)

    Phillips, Andrew W; Friedman, Benjamin T; Utrankar, Amol; Ta, Andrew Q; Reddy, Shalini T; Durning, Steven J

    2017-02-01

    To establish a baseline overall response rate for surveys of health professions trainees, determine strategies associated with improved response rates, and evaluate for the presence of nonresponse bias. The authors performed a comprehensive analysis of all articles published in Academic Medicine, Medical Education, and Advances in Health Sciences Education in 2013, recording response rates. Additionally, they reviewed nonresponse bias analyses and factors suggested in other fields to affect response rate including survey delivery method, prenotification, and incentives. The search yielded 732 total articles; of these, 356 were research articles, and of these, 185 (52.0%) used at least one survey. Of these, 66 articles (35.6%) met inclusion criteria and yielded 73 unique surveys. Of the 73 surveys used, investigators reported a response rate for 63.0% of them; response rates ranged from 26.6% to 100%, mean (standard deviation) 71.3% (19.5%). Investigators reported using incentives for only 16.4% of the 73 surveys. The only survey methodology factor significantly associated with response rate was single- vs. multi-institutional surveys (respectively, 74.6% [21.2%] vs. 62.0% [12.8%], P = .022). Notably, statistical power for all analyses was limited. No articles evaluated for nonresponse bias. Approximately half of the articles evaluated used a survey as part of their methods. Limited data are available to establish a baseline response rate among health professions trainees and inform researchers which strategies are associated with higher response rates. Journals publishing survey-based health professions education research should improve reporting of response rate, nonresponse bias, and other survey factors.

  16. Employers' and employees' views on responsibilities for career management in nursing: a cross-sectional survey.

    Science.gov (United States)

    Philippou, Julia

    2015-01-01

    To examine nurse employees' and employers' views about responsibilities for managing nurses' careers. Career management policies are associated with cost savings, in terms of workforce recruitment and retention and an increase in job and career satisfaction. In nursing, responsibility for career management remains relatively unexplored. A multicenter, cross-sectional questionnaire survey. Data were collected from 871 nurse employees and employers in the British National Health Service. The study was conducted in 2008, a period when policy reforms aimed at modernizing the healthcare workforce in England. In the current discussions in Europe and the USA about the future of nursing, these data reveal insights not previously reported. Exploratory analyses were undertaken using descriptive and inferential statistics. The analysis indicated a temporal dimension to career management responsibilities. Short-term responsibilities for securing funding and time for development lay more with employers. Medium-term responsibilities for assessing nurses' strengths and weakness, determining job-related knowledge and skills and identifying education and training needs appeared to be shared. Long-term responsibilities for developing individual careers and future development plans lay primarily with employees. New ways of managing nurses' career development that lead to greater independence for employees and greater flexibility for employers, while retaining a high-calibre and competent workforce, are needed. Ultimately, career management responsibilities should not tilt to either side but rather be shared to benefit both parties. Clarifying employers' and employees' responsibilities for career management may help both parties to develop a common understanding of each other's role and to meet their obligations in a constructive dialogue. © 2014 John Wiley & Sons Ltd.

  17. Click Here to Donate: A New Survey Reveals the State of Online Educational Fundraising in 2009

    Science.gov (United States)

    Thompson, Chris; Weiner, Robert L.

    2009-01-01

    A survey of online fundraising by the "Chronicle of Philanthropy" found that 192 nonprofit organizations raised $1.1 billion online in 2007 and $1.4 billion in 2008. Given this trend, to what extent are educational institutions using and succeeding with online fundraising? Council for Advancement and Support of Education (CASE) explored this…

  18. The Impact of Lottery Incentives on Student Survey Response Rates.

    Science.gov (United States)

    Porter, Stephen R.; Whitcomb, Michael E.

    2003-01-01

    A controlled experiment tested the effects of lottery incentives using a prospective college applicant Web survey, with emails sent to more than 9,000 high school students. Found minimal effect of postpaid incentives for increasing levels of incentive. (EV)

  19. Motivation in Business Survey Response Behavior : Influencing motivation to improve survey outcome

    NARCIS (Netherlands)

    Torres van Grinsven, V.

    2015-01-01

    In this dissertation we show theoretical and empirical insights into the concept of motivation in the context of the business and organizational survey task. The research has led to a number of recommendations on how to improve organizational survey and communication design to enhance motivation and

  20. Motivation in Business Survey Response Behavior : Influencing motivation to improve survey outcome

    NARCIS (Netherlands)

    Torres van Grinsven, V.|info:eu-repo/dai/nl/355608510

    2015-01-01

    In this dissertation we show theoretical and empirical insights into the concept of motivation in the context of the business and organizational survey task. The research has led to a number of recommendations on how to improve organizational survey and communication design to enhance motivation and

  1. Ultralight aircraft surveys reveal marine turtle population increases along the west coast of Reunion Island

    OpenAIRE

    Jean, Claire; Ciccione, Stephane; Ballorain, Katia; Georges, Jean-Yves; Bourjea, Jerome

    2010-01-01

    Reunion Island in the south-west Indian Ocean once had significant nesting populations of marine turtles but they declined rapidly after human colonization. In 1996, after regular sightings of turtles offshore, an aerial survey programme was initiated to monitor the occurrence of marine turtles and their distribution along the west coast of the island Between 1998 and 2008, along a 30-km coastline transect between Saint Leu and Saint Paul, a total of 1,845 marine turtle sightings were recorde...

  2. Revealing the Physics and Evolution of Galaxies and Galaxy Clusters with SKA Continuum Surveys

    CERN Document Server

    Prandoni, I

    2014-01-01

    In this chapter we provide an overview of the science enabled by radio continuum surveys in the SKA era, focusing on galaxy/galaxy cluster physics and evolution studies, and other relevant continuum science in the >2020 scientific framework. We outline a number of 'reference' radio-continuum surveys for SKA1 that can address such topics, and comprehensively discuss the most critical science requirements that we have identified. We highlight what should be achieved by SKA1, to guarantee a major leap forwards with respect to the pre-SKA era, considering the science advances expected in the coming years with existing and upcoming telescopes (JVLA, LOFAR, eMERLIN, and the three SKA precursors: MWA, ASKAP and MeerKAT). In this exercise we take in due account also the other waveband facilities coming online at the same time (e.g. Euclid, LSST, etc.), which tackle overlapping scientific goals, but in a different manner. In this respect particular attention has been payed to ensure that the proposed reference surveys...

  3. Reexamining traditional issues in survey research: Just how evil is the anathema of low response rate?

    Energy Technology Data Exchange (ETDEWEB)

    Clark, S.B. [Oak Ridge Institute for Science and Education, TN (United States). Science/Engineering Education Division; Boser, J.A. [Univ. of Tennessee, Knoxville, TN (United States)

    1995-08-01

    Survey researchers have long been exhorted to strive for high response rates in order to maximize the likelihood that the respondents are representative of the population being surveyed. It is not surprising then, that much survey research has been directed towards examining the effects of various manipulatable factors on response rate. It is clear that attempts to reach the goal of minimizing the likelihood of nonresponse bias through testing various methods of increasing survey response rates have consumed much research and debate. The results obtained in this research have been inconsistent. Some studies have found significant differences, others have found none. The present study was designed to determine the extent to which the results of an employment survey of former graduates of a teacher preparation program would have been affected by changes in response rate.

  4. 16S rRNA survey revealed complex bacterial communities and evidence of bacterial interference on human adenoids.

    Science.gov (United States)

    Ren, Tiantian; Glatt, Dominique Ulrike; Nguyen, Tam Nhu; Allen, Emma Kaitlynn; Early, Stephen V; Sale, Michele; Winther, Birgit; Wu, Martin

    2013-02-01

    Adenoid microbiota plays an important role in the development of various infectious and non-infectious diseases of the upper airways, such as otitis media, adenotonsillitis, rhinosinusitis and adenoid hypertrophy. Studies have suggested that adenoids could act as a potential reservoir of opportunistic pathogens. However, previous bacterial surveys of adenoids were mainly culture based and therefore might only provide an incomplete and potentially biased assessment of the microbial diversity. To develop an in-depth and comprehensive understanding of the adenoid microbial communities and test the 'pathogen reservoir hypothesis', we carried out a 16S rRNA based, culture-independent survey of bacterial communities on 67 human adenoids removed by surgery. Our survey revealed highly diverse adenoid bacterial communities distinct from those of other body habitats. Despite large interpersonal variations, adenoid microbiota shared a core set of taxa and can be classified into at least five major types based on its bacterial species composition. Our results support the 'pathogen reservoir hypothesis' as we found common pathogens of otitis media to be both prevalent and abundant. Co-occurrence analyses revealed evidence consistent with the bacterial interference theory in that multiple common pathogens showed 'non-coexistence' relationships with non-pathogenic members of the commensal microflora.

  5. Continent-wide survey reveals massive decline in African savannah elephants

    Directory of Open Access Journals (Sweden)

    Michael J. Chase

    2016-08-01

    Full Text Available African elephants (Loxodonta africana are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC, the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants’ downward trajectory by preventing poaching and protecting habitat.

  6. Annual surveys of larval Ambystoma cingulatum reveal large differences in dates of pond residency

    Energy Technology Data Exchange (ETDEWEB)

    Bevelhimer, Mark S [ORNL; Giffen, Neil R [ORNL; Stevenson, Dirk [Ft Stewart Fish and Wildlife Branch

    2008-05-01

    Effective sampling of pond-dwelling larval stages of the federally listed Ambystoma cingulatum (Flatwoods Salamander) requires sufficient knowledge of when larvae are present and how best to sample them. Through systematic sampling with active and passive sampling techniques, we found dipnetting to be significantly more effective than three types of passive traps. During surveys for Flatwoods Salamander larvae at Fort Stewart Military Installation, GA in 2005 and 2006, we found that pond residency varied by at least 1.5 months between the 2 years due to the timing of pond filling. In addition, our latest capture on 23 May 2005 was about 2 weeks later than previously recorded at any site range-wide. A simple growth model was used to evaluate likely hatching dates based on significant rain events, observed sizes at capture, and likely growth rates. This analysis suggested that the primary dates of hatching occurred in late February 2005 and early January 2006, a difference that corresponds to that seen in the residency of the latest larval stages. A review of the survey records for Fort Stewart for the past 13 years shows a steep decline in the number of occupied ponds from near 20 to a single pond for the past two years (the only documented breeding success in a natural pond since 1999).

  7. Continent-wide survey reveals massive decline in African savannah elephants

    Science.gov (United States)

    Schlossberg, Scott; Griffin, Curtice R.; Bouché, Philippe J.C.; Djene, Sintayehu W.; Elkan, Paul W.; Ferreira, Sam; Grossman, Falk; Kohi, Edward Mtarima; Landen, Kelly; Omondi, Patrick; Peltier, Alexis; Selier, S.A. Jeanetta; Sutcliffe, Robert

    2016-01-01

    African elephants (Loxodonta africana) are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC), the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants’ downward trajectory by preventing poaching and protecting habitat. PMID:27635327

  8. Continent-wide survey reveals massive decline in African savannah elephants.

    Science.gov (United States)

    Chase, Michael J; Schlossberg, Scott; Griffin, Curtice R; Bouché, Philippe J C; Djene, Sintayehu W; Elkan, Paul W; Ferreira, Sam; Grossman, Falk; Kohi, Edward Mtarima; Landen, Kelly; Omondi, Patrick; Peltier, Alexis; Selier, S A Jeanetta; Sutcliffe, Robert

    2016-01-01

    African elephants (Loxodonta africana) are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC), the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants' downward trajectory by preventing poaching and protecting habitat.

  9. The effect of multiple reminders on response patterns in a Danish health survey

    DEFF Research Database (Denmark)

    Christensen, Anne I; Ekholm, Ola; Kristensen, Peter L;

    2015-01-01

    BACKGROUND: Reminders are routinely applied in surveys to increase response rates and reduce the possibility of bias. This study examines the effect of multiple reminders on the response rate, non-response bias, prevalence estimates and exposure-outcome relations in a national self......-administered health survey. METHODS: Data derive from the Danish National Health Survey 2010, in which 298 550 individuals (16 years of age or older) were invited to participate in a cross-sectional survey using a mixed-mode approach (paper and web questionnaires). At least two reminders were sent to non-respondents......, and 177 639 individuals completed the questionnaire (59.5%). Response patterns were compared between four groups of individuals (first mailing respondents, second mailing respondents, third mailing respondents and non-respondents). RESULTS: Multiple reminders led to an increase in response rate from 36...

  10. [Response rates in three opinion surveys performed through online questionnaires in the health setting].

    Science.gov (United States)

    Aerny Perreten, Nicole; Domínguez-Berjón, Ma Felicitas; Astray Mochales, Jenaro; Esteban-Vasallo, María D; Blanco Ancos, Luis Miguel; Lópaz Pérez, Ma Ángeles

    2012-01-01

    The main advantages of online questionnaires are the speed of data collection and cost savings, but response rates are usually low. This study analyzed response rates and associated factors among health professionals in three opinion surveys in the autonomous region of Madrid. The participants, length of the questionnaire and topic differed among the three surveys. The surveys were conducted by using paid Internet software. The institutional e-mail addresses of distinct groups of health professionals were used. Response rates were highest in hospitals (up to 63%) and administrative services and were lowest in primary care (less than 33%). The differences in response rates were analyzed in primary care professionals according to age, sex and professional category and only the association with age was statistically significant. None of the surveys achieved a response rate of 60%. Differences were observed according to workplace, patterns of Internet usage, and interest in the subject. Copyright © 2011 SESPAS. Published by Elsevier Espana. All rights reserved.

  11. Dissecting a role for melanopsin in behavioural light aversion reveals a response independent of conventional photoreception.

    Directory of Open Access Journals (Sweden)

    Ma'ayan Semo

    Full Text Available Melanopsin photoreception plays a vital role in irradiance detection for non-image forming responses to light. However, little is known about the involvement of melanopsin in emotional processing of luminance. When confronted with a gradient in light, organisms exhibit spatial movements relative to this stimulus. In rodents, behavioural light aversion (BLA is a well-documented but poorly understood phenomenon during which animals attribute salience to light and remove themselves from it. Here, using genetically modified mice and an open field behavioural paradigm, we investigate the role of melanopsin in BLA. While wildtype (WT, melanopsin knockout (Opn4(-/- and rd/rd cl (melanopsin only (MO mice all exhibit BLA, our novel methodology reveals that isolated melanopsin photoreception produces a slow, potentiating response to light. In order to control for the involvement of pupillary constriction in BLA we eliminated this variable with topical atropine application. This manipulation enhanced BLA in WT and MO mice, but most remarkably, revealed light aversion in triple knockout (TKO mice, lacking three elements deemed essential for conventional photoreception (Opn4(-/- Gnat1(-/- Cnga3(-/-. Using a number of complementary strategies, we determined this response to be generated at the level of the retina. Our findings have significant implications for the understanding of how melanopsin signalling may modulate aversive responses to light in mice and humans. In addition, we also reveal a clear potential for light perception in TKO mice.

  12. IMF - metallicity: a tight local relation revealed by the CALIFA survey

    CERN Document Server

    Martín-Navarro, Ignacio; La Barbera, Francesco; Falcón-Barroso, Jesús; Lyubenova, Mariya; van de Ven, Glenn; Ferreras, Ignacio; Sánchez, S F; Trager, S C; García-Benito, R; Mast, D; Mendoza, M A; Sánchez-Blázquez, P; Delgado, R González; Walcher, C J

    2015-01-01

    Variations in the stellar initial mass function (IMF) have been invoked to explain the spectroscopic and dynamical properties of early-type galaxies. However, no observations have yet been able to disentangle the physical driver. We analyse here a sample of 24 early-type galaxies drawn from the CALIFA survey, deriving in a homogeneous way their stellar population and kinematic properties. We find that the local IMF is tightly related to the local metallicity, becoming more bottom-heavy towards metal-rich populations. Our result, combined with the galaxy mass-metallicity relation, naturally explains previous claims of a galaxy mass-IMF relation, derived from non-IFU spectra. If we assume that - within the star formation environment of early-type galaxies - metallicity is the main driver of IMF variations, a significant revision of the interpretation of galaxy evolution observables is necessary.

  13. IMF–METALLICITY: A TIGHT LOCAL RELATION REVEALED BY THE CALIFA SURVEY

    Energy Technology Data Exchange (ETDEWEB)

    Martín-Navarro, Ignacio; Vazdekis, Alexandre; Falcón-Barroso, Jesús [Instituto de Astrofísica de Canarias, c/Vía Láctea s/n, E-38205—La Laguna, Tenerife (Spain); La Barbera, Francesco [INAF—Osservatorio Astronomico di Capodimonte, Napoli (Italy); Lyubenova, Mariya; Trager, S. C. [Kapteyn Astronomical Institute, University of Groningen, Postbus 800, 9700 AV Groningen (Netherlands); Ven, Glenn van de [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany); Ferreras, Ignacio [Mullard Space Science Laboratory, University College London, Holmbury St Mary, Dorking, Surrey RH5 6NT (United Kingdom); Sánchez, S. F. [Instituto de Astronomía, Universidad Nacional Autonóma de México, A.P. 70-264, 04510 México, D.F., México (Mexico); García-Benito, R.; Mendoza, M. A. [Instituto de Astrofísica de Andalucía (CSIC), Glorieta de la Astronomía s/n, Aptdo. 3004, E-18080 Granada (Spain); Mast, D. [Instituto de Cosmologia, Relatividade e Astrofísica—ICRA, Centro Brasileiro de Pesquisas Físicas, Rua Dr.Xavier Sigaud 150, CEP 22290-180, Rio de Janeiro, RJ (Brazil); Sánchez-Blázquez, P., E-mail: imartin@iac.es [Departamento de Física Teórica, Universidad Autónoma de Madrid, Cantoblanco, E-28049 Spain (Spain); Collaboration: CALIFA Team; and others

    2015-06-20

    Variations in the stellar initial mass function (IMF) have been invoked to explain the spectroscopic and dynamical properties of early-type galaxies (ETGs). However, no observations have yet been able to disentangle the physical driver. We analyze here a sample of 24 ETGs drawn from the CALIFA survey, deriving in a homogeneous way their stellar population and kinematic properties. We find that the local IMF is tightly related to the local metallicity, becoming more bottom-heavy toward metal-rich populations. Our result, combined with the galaxy mass–metallicity relation, naturally explains previous claims of a galaxy mass–IMF relation, derived from non-IFU spectra. If we assume that—within the star formation environment of ETGs—metallicity is the main driver of IMF variations, a significant revision of the interpretation of galaxy evolution observables is necessary.

  14. Understanding Low Survey Response Rates Among Young U.S. Military Personnel

    Science.gov (United States)

    2015-01-01

    two years of the RAND survey. We were unable to include some surveys, such as the 2010 Navy Pregnancy and Parenthood Survey, because response rates...stratified random sampling approach, oversampling women (including sampling all women in the Marine Corps) and oversampling men in the Marine Corps (DMDC...during the first week of basic military training, every Air Force recruit completed a behavioral risk questionnaire on such topics as smoking , alcohol use

  15. 2012 Survey of Active Duty Spouses: Tabulations of Responses

    Science.gov (United States)

    2013-09-30

    unit ................. 88 2012 Survey of Active Duty Spouses DMDC v k. My work unit produces high quality products and services... telework preference. 3. Permanent Change of Station (PCS) Moves—Number of spouse moves, length of time since most recent PCS move, length of time...you agree or disagree with the following statements about your workplace? k. My work unit produces high quality products and services. 1. Strongly

  16. THE VVV SURVEY REVEALS CLASSICAL CEPHEIDS TRACING A YOUNG AND THIN STELLAR DISK ACROSS THE GALAXY’S BULGE

    Energy Technology Data Exchange (ETDEWEB)

    Dékány, I. [Instituto Milenio de Astrofísica, Santiago (Chile); Minniti, D. [Departamento de Física, Facultad de Ciencias Exactas, Universidad Andres Bello, República 220, Santiago (Chile); Majaess, D. [Saint Mary’s University, Halifax, Nova Scotia (Canada); Zoccali, M.; Hajdu, G.; Catelan, M. [Instituto de Astrofísica, Facultad de Física, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago (Chile); Alonso-García, J. [Unidad de Astronomía, Fac. Cs. Básicas, Universidad de Antofagasta, Avda. U. de Antofagasta 02800, Antofagasta (Chile); Gieren, W. [Departamento de Astronomía, Universidad de Concepción, Casilla 160-C, Concepción (Chile); Borissova, J., E-mail: idekany@astro.puc.cl [Instituto de Física y Astronomía, Universidad de Valparaíso, Av. Gran Bretaña 1111, Valparaso (Chile)

    2015-10-20

    Solid insight into the physics of the inner Milky Way is key to understanding our Galaxy’s evolution, but extreme dust obscuration has historically hindered efforts to map the area along the Galactic mid-plane. New comprehensive near-infrared time-series photometry from the VVV Survey has revealed 35 classical Cepheids, tracing a previously unobserved component of the inner Galaxy, namely a ubiquitous inner thin disk of young stars along the Galactic mid-plane, traversing across the bulge. The discovered period (age) spread of these classical Cepheids implies a continuous supply of newly formed stars in the central region of the Galaxy over the last 100 million years.

  17. Early events in plant hypersensitive response leaves revealed by IR thermography

    Science.gov (United States)

    Boccara, Martine; Boue, Christine; De Paepe, Rosine; Boccara, Albert C.

    2001-10-01

    Infrared thermography is used to reveal the establishment of Erwinia amylovora harpin-induced hypersensitive response (HR) in Nicotiana sylvestris leaves. We observed a decrease in temperature (1-2 degree(s)C) in the harpin infiltrated zone, correlated with an increase in stomatal opening, strongly suggesting that the temperature decrease is due to higher transpiration rate. IRT experiments were conducted in a laboratory environment and could be widely applied for genotype screening and monitoring drug effects.

  18. Shortening a survey and using alternative forms of prenotification: Impact on response rate and quality

    Directory of Open Access Journals (Sweden)

    Jenkins Sarah

    2010-06-01

    Full Text Available Abstract Background Evidence suggests that survey response rates are decreasing and that the level of survey response can be influenced by questionnaire length and the use of pre-notification. The goal of the present investigation was determine the effect of questionnaire length and pre-notification type (letter vs. postcard on measures of survey quality, including response rates, response times (days to return the survey, and item nonresponse. Methods In July 2008, the authors randomized 900 residents of Olmsted County, Minnesota aged 25-65 years to one of two versions of the Talley Bowel Disease Questionnaire, a survey designed to assess the prevalence of functional gastrointestinal disorders (FGID. One version was two pages long and the other 4 pages. Using a 2 × 2 factorial design, respondents were randomized to survey length and one of two pre-notification types, letter or postcard; 780 residents ultimately received a survey, after excluding those who had moved outside the county or passed away. Results Overall, the response rates (RR did not vary by length of survey (RR = 44.6% for the 2-page survey and 48.4% for the 4-page or pre-notification type (RR = 46.3% for the letter and 46.8% for the postcard. Differences in response rates by questionnaire length were seen among younger adults who were more likely to respond to the 4-page than the 2-page questionnaire (RR = 39.0% compared to 21.8% for individuals in their 20s and RR = 49.0% compared to 32.3% for those in their 30s. There were no differences across conditions with respect to item non-response or time (days after mailing to survey response. Conclusion This study suggests that the shortest survey does not necessarily provide the best option for increased response rates and survey quality. Pre-notification type (letter or postcard did not impact response rate suggesting that postcards may be more beneficial due to the lower associated costs of this method of contact.

  19. Arabidopsis thaliana model system reveals a continuum of responses to root endophyte colonization.

    Science.gov (United States)

    Mandyam, Keerthi G; Roe, Judith; Jumpponen, Ari

    2013-04-01

    We surveyed the non-mycorrhizal model plant Arabidopsis thaliana microscopically for its ability to form dark septate endophyte (DSE) symbioses in field, greenhouse, and laboratory studies. The laboratory studies were also used to estimate host growth responses to 34 Periconia macrospinosa and four Microdochium sp. isolates. Consistent with broad host range observed in previous experiments, field-, greenhouse-, and laboratory-grown A. thaliana were colonized by melanized inter- and intracellular hyphae and microsclerotia or chlamydospores indicative of DSE symbiosis. Host responses to colonization were variable and depended on the host ecotype. On average, two A. thaliana accessions (Col-0 and Cvi-0) responded negatively, whereas one (Kin-1) was unresponsive, a conclusion consistent with our previous analyses with forbs native to the field site where the fungi originate. Despite the average negative responses, examples of positive responses were also observed, a conclusion also congruent with earlier studies. Our results suggest that A. thaliana has potential as a model for more detailed dissection of the DSE symbiosis. Furthermore, our data suggest that host responses are controlled by variability in the host and endophyte genotypes.

  20. A molecular survey of acute febrile illnesses reveals Plasmodium vivax infections in Kedougou, southeastern Senegal.

    Science.gov (United States)

    Niang, Makhtar; Thiam, Laty Gaye; Sow, Abdourahmane; Loucoubar, Cheikh; Bob, Ndeye Sakha; Diop, Fode; Diouf, Babacar; Niass, Oumy; Mansourou, Annick; Varela, Marie Louise; Perraut, Ronald; Sall, Amadou A; Toure-Balde, Aissatou

    2015-07-19

    Control efforts towards malaria due to Plasmodium falciparum significantly decreased the incidence of the disease in many endemic countries including Senegal. Surprisingly, in Kedougou (southeastern Senegal) P. falciparum malaria remains highly prevalent and the relative contribution of other Plasmodium species to the global malaria burden is very poorly documented, partly due to the low sensitivity of routine diagnostic tools. Molecular methods offer better estimate of circulating Plasmodium species in a given area. A molecular survey was carried out to document circulating malaria parasites in Kedougou region. A total of 263 long-term stored sera obtained from patients presenting with acute febrile illness in Kedougou between July 2009 and July 2013 were used for malaria parasite determination. Sera were withdrawn from a collection established as part of a surveillance programme of arboviruses infections in the region. Plasmodium species were characterized by a nested PCR-based approach targeting the 18S small sub-unit ribosomal RNA genes of Plasmodium spp. Of the 263 sera screened in this study, Plasmodium genomic DNA was amplifiable by nested PCR from 62.35% (164/263) of samples. P. falciparum accounted for the majority of infections either as single in 85.97% (141/164) of Plasmodium-positive samples or mixed with Plasmodium ovale (11.58%, 19/164) or Plasmodium vivax (1.21%, 2/164). All 19 (11.58%) P. ovale-infected patients were mixed with P. falciparum, while no Plasmodium malariae was detected in this survey. Four patients (2.43%) were found to be infected by P. vivax, two of whom were mixed with P. falciparum. P. vivax infections originated from Bandafassi and Ninefesha villages and concerned patients aged 4, 9, 10, and 15 years old, respectively. DNA sequences alignment and phylogenetic analysis demonstrated that sequences from Kedougou corresponded to P. vivax, therefore confirming the presence of P. vivax infections in Senegal. The results confirm the

  1. Flood-Induced Riverbed Changes and Sediment Yields Revealed by Twice LiDAR Surveys

    Science.gov (United States)

    Hsieh, Yu-Chung; Chan, Yu-Chang; Hu, Jyr-Ching; Lin, Chao-Chung

    2010-05-01

    Riverbed changes and sediment yields from watersheds greatly influence the conservation of water and soil, the planning of hydraulic engineering, and the river habitat, etc. At present, sediment yield calculation often used empirical or theoretical formula as well as data collected at hydrological stations, and rarely had the actual measured value through high-resolution topography. The Lanyang River is one of main rivers in Taiwan and often suffers the influence of typhoon during summer. Most of sediments generated from slump and soil erosion into river were transported from the upstream watershed and resulted in the riverbed changes during the typhoon season. In 2008, there are four significant typhoon events influencing this area, including the Kalmaegi, Fung-wong, Sinlaku, and Jangmi typhoons. This topographic research funded by the Taiwan Central Geological Survey, surveyed the terrain of the Lanyang River before and after the typhoon season using Airborne LiDAR technique, and computed the terrain variations. The variations of the terrain on the riverbed may be regarded as the sediment yield of the bed load transported during the typhoon season. This research used high-resolution terrain models to compute sediment yield of the bed load, and further discussed volumes of sediment yield in watershed during the typhoon season. In the Lanyang River we discovered that the upstream and midstream channel still had the characteristics of erosion and transportation during the typhoon season. The sediment on the river bed reduced approximately 2.3 million cubic meters; and the erosion rate of the bed load sediments were estimated about 3.4 mm during the 2008 typhoon season. The results imply significant sediment yield and transportation from the upstream watershed of the Lanyang River during only single typhoon season in which cumulated rain falls are high. The leading factors of the riverbed erosion include the riverbed slope, channel curvature, channel width, lithology

  2. Sediment Yields Revealed and Fluid Modelling by Twice LiDAR Surveys in Active Tectonics Area

    Science.gov (United States)

    Hsieh, Y.; Chan, Y.; Hu, J.; Lin, C.

    2010-12-01

    LiDAR technique allows rapid acquisition of high resolution and high precision topographic data. The technique has found considerable use in the earth sciences, for example for fluvial morphology and flood modelling. These developments have offered new opportunities for investigating spatial and temporal patterns of morphological change in gravel-bed river and have contributed to develop in two points: (1)morphometric estimates of sediment transport and sediment yields ;(2)boundary conditions for numerical models, including computational fluid dynamics and modelling. This topographic research funded by the Taiwan Central Geological Survey, surveyed the terrain of the Lanyang River before and after the typhoon season using Airborne LiDAR technique, and computed the terrain variations. The Lanyang River is one of main rivers in Taiwan and often suffers the influence of typhoon during summer. Most of sediments generated from slump and soil erosion into river were transported from the upstream watershed and resulted in the riverbed changes during the typhoon season. In 2008, there are four significant typhoon events influencing this area, including the Kalmaegi, Fung-wong, Sinlaku, and Jangmi typhoons. At present, sediment yield calculation often used empirical or theoretical formula as well as data collected at hydrological stations, and rarely had the actual measured value through high-resolution topography. The variations of the terrain on the riverbed may be regarded as the sediment yield of the bed load transported during the typhoon season. This research used high-resolution terrain models to compute sediment yield of the bed load, and further discussed volumes of sediment yield in watershed during the typhoon season. In the Lanyang River we discovered that the upstream and midstream channel still had the characteristics of erosion and transportation during the typhoon season. The results imply significant sediment yield and transportation from the upstream

  3. RNAseq reveals hypervirulence-specific host responses to M. tuberculosis infection.

    Science.gov (United States)

    Leisching, Gina; Pietersen, Ray-Dean; van Heerden, Carel; van Helden, Paul; Wiid, Ian; Baker, Bienyameen

    2017-08-18

    The distinguishing factors that characterize the host response to infection with virulent Mycobacterium tuberculosis (M.tb) are largely confounding. We present an infection study with 2 genetically closely related M.tb strains that have vastly different pathogenic characteristics. The early host response to infection with these detergent-free cultured strains was analyzed through RNAseq in an attempt to provide information on the subtleties which may ultimately contribute to the virulent phenotype. Murine bone marrow derived macrophages (BMDMs) were infected with either a hyper- (R5527) or hypovirulent (R1507) Beijing M. tuberculosis clinical isolate. RNAseq revealed 69 differentially expressed host genes in BMDMs during comparison of these 2 transcriptomes. Pathway analysis revealed activation of the stress-induced and growth inhibitory Gadd45 signaling pathway in hypervirulent infected BMDMs. Upstream regulators of interferon activation such as and IRF3 and IRF7 were predicted to be upregulated in hypovirulent-infected BMDMs. Additional analysis of the host immune response through ELISA and qPCR included the use of human THP-1 macrophages where a robust proinflammatory response was observed after infection with the hypervirulent strain. RNAseq revealed 2 early-response genes (ier3 and saa3) and 2 host-defense genes (oasl1 and slpi) that were significantly upregulated by the hypervirulent strain. The role of these genes under M.tb infection conditions are largely unknown but here we provide validation of their presence with use of qPCR and Western blot. Further analysis into their biological role during infection with virulent M.tb is required.

  4. Survey of large protein complexes D. vulgaris reveals great structural diversity

    Energy Technology Data Exchange (ETDEWEB)

    Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

    2009-08-15

    An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

  5. Survey of bornaviruses in pet psittacines in Brazil reveals a novel parrot bornavirus.

    Science.gov (United States)

    Philadelpho, Natalia A; Rubbenstroth, Dennis; Guimarães, Marta B; Piantino Ferreira, Antonio J

    2014-12-05

    Avian bornaviruses are the causative agents of proventricular dilatation disease (PDD), a fatal neurological disease considered to be a major threat to psittacine bird populations. We performed a survey of the presence of avian bornaviruses and PDD in pet psittacines in Brazil and also studied PDD's clinical presentation as well as the genomic variability of the viruses. Samples from 112 psittacines with clinical signs compatible with PDD were collected and tested for the presence of bornaviruses. We found 32 birds (28.6%) positive for bornaviruses using reverse transcriptase polymerase chain reaction (RT-PCR). Twenty-one (65.6%) of the 32 bornavirus-positive birds presented neurological signs, seven (21.9%) presented undigested seeds in feces, four (12.5%) showed proventricular dilatation, six (18.8%) regurgitation, three (9.4%) feather plucking and three (9.4%) sudden death. The results confirm that avian bornaviruses are present in pet psittacines in Brazil, and sequence analysis identified a distinct virus, named parrot bornavirus 8 (PaBV-8). Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.

    Science.gov (United States)

    Eloe-Fadrosh, Emiley A; Paez-Espino, David; Jarett, Jessica; Dunfield, Peter F; Hedlund, Brian P; Dekas, Anne E; Grasby, Stephen E; Brady, Allyson L; Dong, Hailiang; Briggs, Brandon R; Li, Wen-Jun; Goudeau, Danielle; Malmstrom, Rex; Pati, Amrita; Pett-Ridge, Jennifer; Rubin, Edward M; Woyke, Tanja; Kyrpides, Nikos C; Ivanova, Natalia N

    2016-01-27

    Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum ('Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.

  7. The HDUV Survey: Six Lyman Continuum Emitter Candidates at z~2 Revealed by HST UV Imaging

    CERN Document Server

    Naidu, R P; Reddy, N; Holden, B; Steidel, C C; Montes, M; Atek, H; Bouwens, R J; Carollo, C M; Cibinel, A; Illingworth, G D; Labbe, I; Magee, D; Morselli, L; Nelson, E J; van Dokkum, P G; Wilkins, S

    2016-01-01

    We present six galaxies at z~2 that show evidence of Lyman continuum (LyC) emission based on the newly acquired UV imaging of the Hubble Deep UV legacy survey (HDUV) conducted with the WFC3/UVIS camera on the Hubble Space Telescope (HST). At the redshift of these sources, the HDUV F275W images partially probe the ionizing continuum. By exploiting the HST multi-wavelength data available in the HDUV/GOODS fields, models of the UV spectral energy distributions, and detailed Monte Carlo simulations of the intergalactic medium absorption, we estimate the absolute ionizing photon escape fractions of these galaxies to be very high -- typically >60% (>13% for all sources at 90% likelihood). Our findings are in broad agreement with previous studies that found only a small fraction of galaxies to show high escape fraction. These six galaxies comprise the largest sample yet of LyC leaking candidates at z~2 whose inferred LyC flux has been cleanly observed at HST resolution. While three of our six candidates show evidenc...

  8. Incomplete categorical data design non-randomized response techniques for sensitive questions in surveys

    CERN Document Server

    Tian, Guo-Liang

    2013-01-01

    Respondents to survey questions involving sensitive information, such as sexual behavior, illegal drug usage, tax evasion, and income, may refuse to answer the questions or provide untruthful answers to protect their privacy. This creates a challenge in drawing valid inferences from potentially inaccurate data. Addressing this difficulty, non-randomized response approaches enable sample survey practitioners and applied statisticians to protect the privacy of respondents and properly analyze the gathered data.Incomplete Categorical Data Design: Non-Randomized Response Techniqu

  9. Temporal trends in mammal responses to fire reveals the complex effects of fire regime attributes.

    Science.gov (United States)

    Lindenmayer, David B; Blanchard, Wade; MacGregor, Christopher; Barton, Philip; Banks, Sam C; Crane, Mason; Michael, Damian; Okada, Sachiko; Berry, Laurence; Florance, Daniel; Gill, Malcolm

    2016-03-01

    Fire is a major ecological process in many ecosystems worldwide. We sought to identify which attributes of fire regimes affect temporal change in the presence and abundance of Australian native mammals. Our detailed study was underpinned by time series data on 11 mammal species at 97 long-term sites in southeastern Australia between 2003 and 2013. We explored how temporal aspects of fire regimes influenced the presence and conditional abundance of species. The key fire regime components examined were: (1) severity of a major fire in 2003, (2) interval between the last major fire (2003) and the fire prior to that, and (3) number of past fires. Our long-term data set enabled quantification of the interactions between survey year and each fire regime variable: an ecological relationship missing from temporally restricted studies. We found no evidence of any appreciable departures from the assumption of independence of the sites. Multiple aspects of fire regimes influenced temporal variation in the presence and abundance of mammals. The best models indicated that six of the 11 species responded to two or more fire regime variables, with two species influenced by all three fire regime attributes. Almost all species responded to time since fire, either as an interaction with survey year or as a main effect. Fire severity or its interaction with survey year was important for most terrestrial rodents. The number of fires at a site was significant for terrestrial rodents and several other species. Our findings contain evidence of the effects on native mammals of heterogeneity in fire regimes. Temporal response patterns of mammal species were influenced by multiple fire regime attributes, often in conjunction with survey year. This underscores the critical importance of long-term studies of biota that are coupled with data sets characterized by carefully documented fire history, severity, and frequency. Long-term studies are essential to predict animal responses to fires and

  10. Transcriptomic profiling of soybean in response to high-intensity UV-B irradiation reveals stress defense signaling

    Directory of Open Access Journals (Sweden)

    Min Young Yoon

    2016-12-01

    Full Text Available The depletion of the ozone layer in the stratosphere has led to a dramatic spike in ultraviolet B (UV-B intensity and increased UV-B light levels. The direct absorption of high-intensity UV-B induces complex abiotic stresses in plants, including excessive light exposure, heat, and dehydration. However, UV-B stress signaling mechanisms in plants including soybean (Glycine max [L.] remain poorly understood. Here, we surveyed the overall transcriptional responses of two soybean genotypes, UV-B-sensitive Cheongja 3 and UV-B-resistant Buseok, to continuous UV-B irradiation for 0 (control, 0.5, and 6 h using RNA-seq analysis. Homology analysis using UV-B-related genes from Arabidopsis thaliana revealed differentially expressed genes (DEGs likely involved in UV-B stress responses. Functional classification of the DEGs showed that the categories of immune response, stress defense signaling, and reactive oxygen species (ROS metabolism were over-represented. UV-B-resistant Buseok utilized phosphatidic acid-dependent signaling pathways (based on subsequent reactions of phospholipase C and diacylglycerol kinase rather than phospholipase D in response to UV-B exposure at high fluence rates, and genes involved in its downstream pathways, such as ABA signaling, mitogen-activated protein kinase cascades, and ROS overproduction, were upregulated in this genotype. In addition, the DEGs for TIR-NBS-LRR and heat shock proteins are positively activated. These results suggest that defense mechanisms against UV-B stress at high fluence rates are separate from the photomorphogenic responses utilized by plants to adapt to low-level UV light. Our study provides valuable information for deep understanding of UV-B stress defense mechanisms and for the development of resistant soybean genotypes that survive under high-intensity UV-B stress.

  11. Multimodal stimulation of Colorado potato beetle reveals modulation of pheromone response by yellow light.

    Directory of Open Access Journals (Sweden)

    Fernando Otálora-Luna

    Full Text Available Orientation of insects to host plants and conspecifics is the result of detection and integration of chemical and physical cues present in the environment. Sensory organs have evolved to be sensitive to important signals, providing neural input for higher order multimodal processing and behavioral output. Here we report experiments to determine decisions made by Colorado potato beetle (CPB, Leptinotarsa decemlineata, in response to isolated stimuli and multimodal combinations of signals on a locomotion compensator. Our results show that in complete darkness and in the absence of other stimuli, pheromonal stimulation increases attraction behavior of CPB as measured in oriented displacement and walking speed. However, orientation to the pheromone is abolished when presented with the alternative stimulation of a low intensity yellow light in a dark environment. The ability of the pheromone to stimulate these diurnal beetles in the dark in the absence of other stimuli is an unexpected but interesting observation. The predominance of the phototactic response over that to pheromone when low intensity lights were offered as choices seems to confirm the diurnal nature of the insect. The biological significance of the response to pheromone in the dark is unclear. The phototactic response will play a key role in elucidating multimodal stimulation in the host-finding process of CPB, and perhaps other insects. Such information might be exploited in the design of applications to attract and trap CPB for survey or control purposes and other insect pests using similar orientation mechanisms.

  12. Shallow magma accumulation at Kilauea Volcano, Hawai'i, revealed by microgravity surveys

    Science.gov (United States)

    Johnson, David J.; Eggers, Albert A.; Bagnardi, Marco; Battaglia, Maurizio; Poland, Michael P.; Miklius, Asta

    2010-01-01

    Using microgravity data collected at Kilauea Volcano, Hawai'i (United States), between November 1975 and January 2008, we document significant mass increase beneath the east margin of Halema'uma'u Crater, within Kilauea's summit caldera. Surprisingly, there was no sustained uplift accompanying the mass accumulation. We propose that the positive gravity residual in the absence of significant uplift is indicative of magma accumulation in void space (probably a network of interconnected cracks), which may have been created when magma withdrew from the summit in response to the 29 November 1975 M = 7.2 south flank earthquake. Subsequent refilling documented by gravity represents a gradual recovery from that earthquake. A new eruptive vent opened at the summit of Kilauea in 2008 within a few hundred meters of the positive gravity residual maximum, probably tapping the reservoir that had been accumulating magma since the 1975 earthquake.

  13. Shallow magma accumulation at Kīlauea Volcano, Hawai‘i, revealed by microgravity surveys

    Science.gov (United States)

    Johnson, Daniel J.; Eggers, Albert A.; Bagnardi, Marco; Battaglia, Maurizio; Poland, Michael P.; Miklius, Asta

    2010-01-01

    Using microgravity data collected at Kīlauea Volcano, Hawai‘i (United States), between November 1975 and January 2008, we document significant mass increase beneath the east margin of Halema‘uma‘u Crater, within Kīlauea's summit caldera. Surprisingly, there was no sustained uplift accompanying the mass accumulation. We propose that the positive gravity residual in the absence of significant uplift is indicative of magma accumulation in void space (probably a network of interconnected cracks), which may have been created when magma withdrew from the summit in response to the 29 November 1975 M = 7.2 south flank earthquake. Subsequent refilling documented by gravity represents a gradual recovery from that earthquake. A new eruptive vent opened at the summit of Kīlauea in 2008 within a few hundred meters of the positive gravity residual maximum, probably tapping the reservoir that had been accumulating magma since the 1975 earthquake.

  14. Survey of stakeholders and responsibilities in the electricity market

    DEFF Research Database (Denmark)

    Enevoldsen, Peter; Tambo, Torben

    2014-01-01

    The purpose of this research was to reveal important stakeholders for the Power-2-Electrolysers (P2E) –project, by determining the stakeholders in the Danish electricity industry with an impact on the hydrogen industry. The research has been conducted using a self-constructed model...... for determination of relevant stakeholders, based on their technological – and commercial influence on the project. The approach of determining stakeholders by using the self-constructed model has been based on a literature review performed on the Hydrogen industry and its cooperation with the Electricity industry...... and on qualitative interviews performed with members of the P2E-project. The research revealed which stakeholders that were affected and could affect the P2E-project both as complementor and competitors from a technological - and commercial point-of-view. However, the stakeholders that made the largest impact...

  15. Conserved S-Layer-Associated Proteins Revealed by Exoproteomic Survey of S-Layer-Forming Lactobacilli.

    Science.gov (United States)

    Johnson, Brant R; Hymes, Jeffrey; Sanozky-Dawes, Rosemary; Henriksen, Emily DeCrescenzo; Barrangou, Rodolphe; Klaenhammer, Todd R

    2015-10-16

    The Lactobacillus acidophilus homology group comprises Gram-positive species that include L. acidophilus, L. helveticus, L. crispatus, L. amylovorus, L. gallinarum, L. delbrueckii subsp. bulgaricus, L. gasseri, and L. johnsonii. While these bacteria are closely related, they have varied ecological lifestyles as dairy and food fermenters, allochthonous probiotics, or autochthonous commensals of the host gastrointestinal tract. Bacterial cell surface components play a critical role in the molecular dialogue between bacteria and interaction signaling with the intestinal mucosa. Notably, the L. acidophilus complex is distinguished in two clades by the presence or absence of S-layers, which are semiporous crystalline arrays of self-assembling proteinaceous subunits found as the outermost layer of the bacterial cell wall. In this study, S-layer-associated proteins (SLAPs) in the exoproteomes of various S-layer-forming Lactobacillus species were proteomically identified, genomically compared, and transcriptionally analyzed. Four gene regions encoding six putative SLAPs were conserved in the S-layer-forming Lactobacillus species but not identified in the extracts of the closely related progenitor, L. delbrueckii subsp. bulgaricus, which does not produce an S-layer. Therefore, the presence or absence of an S-layer has a clear impact on the exoproteomic composition of Lactobacillus species. This proteomic complexity and differences in the cell surface properties between S-layer- and non-S-layer-forming lactobacilli reveal the potential for SLAPs to mediate intimate probiotic interactions and signaling with the host intestinal mucosa.

  16. A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.

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    Alexander Wait Zaranek

    2010-05-01

    Full Text Available While it is widely held that an organism's genomic information should remain constant, several protein families are known to modify it. Members of the AID/APOBEC protein family can deaminate DNA. Similarly, members of the ADAR family can deaminate RNA. Characterizing the scope of these events is challenging. Here we use large genomic data sets, such as the two billion sequences in the NCBI Trace Archive, to look for clusters of mismatches of the same type, which are a hallmark of editing events caused by APOBEC3 and ADAR. We align 603,249,815 traces from the NCBI trace archive to their reference genomes. In clusters of mismatches of increasing size, at least one systematic sequencing error dominates the results (G-to-A. It is still present in mismatches with 99% accuracy and only vanishes in mismatches at 99.99% accuracy or higher. The error appears to have entered into about 1% of the HapMap, possibly affecting other users that rely on this resource. Further investigation, using stringent quality thresholds, uncovers thousands of mismatch clusters with no apparent defects in their chromatograms. These traces provide the first reported candidates of endogenous DNA editing in human, further elucidating RNA editing in human and mouse and also revealing, for the first time, extensive RNA editing in Xenopus tropicalis. We show that the NCBI Trace Archive provides a valuable resource for the investigation of the phenomena of DNA and RNA editing, as well as setting the stage for a comprehensive mapping of editing events in large-scale genomic datasets.

  17. A Validation Study of the Culturally Responsive Teaching Survey

    Science.gov (United States)

    Rhodes, Christy M.

    2017-01-01

    Amidst the ethnic and linguistic diversity in adult English language classes, there is heightened importance to using culturally responsive teaching practices. However, there are limited quantitative examinations of this approach in adult learning environments. The purpose of this investigation was to describe patterns of culturally responsive…

  18. Time-lapse electromagnetic induction surveys under olive tree canopies reveal soil moisture dynamics and controls

    Science.gov (United States)

    Martínez, Gonzalo; Giraldez Cervera, Juan Vicente; Vanderlinden, Karl

    2015-04-01

    Soil moisture (θ) is a critical variable that exerts an important control on plant status and development. Soil sampling, neutron attenuation and electromagnetic methods such as TDR or FDR have been used widely to measure θ and provide point data at a possible range of temporal resolutions. However, these methods require either destructive sampling or permanently installed devices with often limiting measurement depths, or are extremely time-consuming. Moreover, the small support of such measurements compromises its value in heterogeneous soils. To overcome such limitations electromagnetic induction (EMI) can be tested to monitor θ at different spatial and temporal scales. This work investigates the potential of EMI to characterize the spatio-temporal variability of soil moisture from apparent electrical conductivity (ECa) under the canopy of individual olive trees. During one year we measured θ with a frequency of 5 min and ECa on an approximately weekly basis along transects from the tree trunk towards the inter-row area. CS-616 soil moisture sensors where horizontally installed in the walls of a trench at depths of 0.1, 0.2, 0.4, 0.6 and 0.8 m at five locations along the transect, with a separation of 0.8 m. The Dualem-21S sensor was used to measure weekly the ECa at 0.2 m increments, from the tree trunk to a distance of 4.4 m. The results showed similar drying and wetting patterns for θ and ECa. Both variables showed a decreasing pattern from the tree trunk towards the drip line, followed by a sharp increment and constant values towards the center of the inter-row space. This pattern reflects clearly the influence of root-zone water uptake under the tree canopy and higher θ values in the inter-row area where root-water uptake is smaller. Time-lapse ECa data responded to evaporation and infiltration fluxes with the highest sensitivity for the 1 and 1.5 m ECa signals, as compared to the 0.5 and 3.0 m signals. Overall these preliminary results revealed the

  19. Overdeepened glacigenic landforms in Lake Thun (Switzerland) revealed by a multichannel reflection seismic survey

    Science.gov (United States)

    Fabbri, Stefano; Herwegh, Marco; Schlunegger, Fritz; Hübscher, Christian; Weiss, Benedikt J.; Schmelzbach, Cédric; Horstmeyer, Heinrich; Buechi, Marius W.; Anselmetti, Flavio S.

    2016-04-01

    Recently acquired high-resolution multibeam bathymetry, in combination with a 2D multichannel reflection seismic campaign on perialpine Lake Thun (Switzerland) reveals new insights into the diverse geometry of the lake basin and a so far unknown subaquatic moraine crest with unprecedented clarity. These new data will improve our comprehension concerning the retreat phases of the Aare glacier, the morphology of its proximal deposits and the facies architecture of the subglacial units. The overdeepened basin of Lake Thun was formed by a combination of tectonically predefined weak zones and glacial erosion during the last glacial periods. The new data indicate that below the outermost edge of a morphologically distinct platform in the south eastern part of the lake basin, a ridge structure marked by strong reflection amplitudes occurs. This structure is interpreted as a subaquatic terminal moraine crest, most likely created by a slightly advancing or stagnant grounded Aare glacier during its major retreating phase. The terminal moraine smoothly transforms downstream into well distinguishable foresets with internally recognisable layering, which dip steeply towards the deepest part of the basin, eventually transforming into bottomsets. This depositional sequence formed by the fore- and bottomsets represents ˜50% of the overall sediment volume that fills the basin and was deposited while the glacier was stagnant, interpreted to represent a rather short period of time of a few hundreds of years. This sequence is overlain by lacustrine deposits formed by late-glacial and Holocene laminated muds comprising intercalated turbidites (Wirth et al. 2011). Little is known about the exact timing and behaviour of retreating glaciers between their recessional phase from the Alpine foreland to the deglaciation of the inner-Alpine ice cap, mostly due to the lack of well-developed moraines that indicate glacial stabilization or slight readvance. Findings from pollen analyses by

  20. A survey of flowering genes reveals the role of gibberellins in floral control in rose.

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    Remay, Arnaud; Lalanne, David; Thouroude, Tatiana; Le Couviour, Fabien; Hibrand-Saint Oyant, Laurence; Foucher, Fabrice

    2009-09-01

    Exhaustive studies on flowering control in annual plants have provided a framework for exploring this process in other plant species, especially in perennials for which little molecular data are currently available. Rose is a woody perennial plant with a particular flowering strategy--recurrent blooming, which is controlled by a recessive locus (RB). Gibberellins (GA) inhibit flowering only in non-recurrent roses. Moreover, the GA content varies during the flowering process and between recurrent and non-recurrent rose. Only a few rose genes potentially involved in flowering have been described, i.e. homologues of ABC model genes and floral genes from EST screening. In this study, we gained new information on the molecular basis of rose flowering: date of flowering and recurrent blooming. Based on a candidate gene strategy, we isolated genes that have similarities with genes known to be involved in floral control in Arabidopsis (GA pathway, floral repressors and integrators). Candidate genes were mapped on a segregating population, gene expression was studied in different organs and transcript abundance was monitored in growing shoot apices. Twenty-five genes were studied. RoFT, RoAP1 and RoLFY are proposed to be good floral markers. RoSPY and RB co-localized in our segregating population. GA metabolism genes were found to be regulated during floral transition. Furthermore, GA signalling genes were differentially regulated between a non-recurrent rose and its recurrent mutant. We propose that flowering gene networks are conserved between Arabidopsis and rose. The GA pathway appears to be a key regulator of flowering in rose. We postulate that GA metabolism is involved in floral initiation and GA signalling might be responsible for the recurrent flowering character.

  1. Sediment dynamics in paired High Arctic lakes revealed from high-resolution swath bathymetry and acoustic stratigraphy surveys

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    Normandeau, A.; Lamoureux, S. F.; Lajeunesse, P.; Francus, P.

    2016-09-01

    High Arctic lakes are commonly used for paleoclimatic reconstructions because they are particularly sensitive to climate variability. However, the processes leading to sediment deposition and distribution in these lakes are often poorly understood. Here for the first time in the Canadian High Arctic, we present original data resulting from swath bathymetry and subbottom surveys carried out on two lakes at Cape Bounty, Melville Island. The results reveal the dynamic nature of the lakes, in which mass movement deposits and bedforms on the deltas reflect frequent slope instabilities and hyperpycnal flow activity. The analysis of the mass movement deposits reveals that small blocky debris flows/avalanches, debris flows, and a slide occurred during the Holocene. These mass movements are believed to have been triggered by earthquakes and potentially by permafrost thawing along the shoreline. Altogether, these mass movement deposits cover more than 30% of the lake floors. Additionally, the river deltas on both lakes were mapped and reveal the presence of several gullies and bedforms. The presence of gullies along the delta front indicates that hyperpycnal flows generated at the river mouth can transport sediment in different trajectories downslope, resulting in a different sediment accumulation pattern and record. The dynamic nature of these two lakes suggests that further analysis on sediment transport and distribution within Arctic lakes is required in order to improve paleoclimatic reconstructions.

  2. Improving Survey Response Rates of School Counselors: Comparing the Use of Incentives

    Science.gov (United States)

    Bauman, Sheri

    2007-01-01

    This article examines the effectiveness of incentives in improving survey response rates of school counselors and compares the findings with those of previously researched populations. A $1 cash incentive increased response rates for a one-wave mailing of a questionnaire, while a raffle opportunity did not. The number and length of optional…

  3. Research on Mail Surveys: Response Rates and Methods in Relation to Population Group and Time.

    Science.gov (United States)

    Boser, Judith A.; Green, Kathy

    The purpose of this review was to look for trends across time in response rates and variables studied for published mail surveys and to compare response rates and variables studied for different target populations. Studies were identified in databases in four fields: education, psychology, business and marketing, and sociology. A total of 225…

  4. Network analysis of oyster transcriptome revealed a cascade of cellular responses during recovery after heat shock.

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    Lingling Zhang

    Full Text Available Oysters, as a major group of marine bivalves, can tolerate a wide range of natural and anthropogenic stressors including heat stress. Recent studies have shown that oysters pretreated with heat shock can result in induced heat tolerance. A systematic study of cellular recovery from heat shock may provide insights into the mechanism of acquired thermal tolerance. In this study, we performed the first network analysis of oyster transcriptome by reanalyzing microarray data from a previous study. Network analysis revealed a cascade of cellular responses during oyster recovery after heat shock and identified responsive gene modules and key genes. Our study demonstrates the power of network analysis in a non-model organism with poor gene annotations, which can lead to new discoveries that go beyond the focus on individual genes.

  5. The effects of tracking responses and the day of mailing on physician survey response rate: three randomized trials.

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    Elie A Akl

    Full Text Available BACKGROUND: The response rates to physician postal surveys remain modest. The primary objective of this study was to assess the effect of tracking responses on physician survey response rate (i.e., determining whether each potential participant has responded or not. A secondary objective was to assess the effects of day of mailing (Monday vs. Friday on physician survey response rate. METHODS: We conducted 3 randomized controlled trials. The first 2 trials had a 2 x 2 factorial design and tested the effect of day of mailing (Monday vs. Friday and of tracking vs. no tracking responses. The third trial tested the effect of day of mailing (Monday vs. Friday. We meta-analyzed these 3 trials using a random effects model. RESULTS: The total number of participants in the 3 trials was 1339. The response rate with tracked mailing was not statistically different from that with non-tracked mailing by the time of the first reminder (RR = 1.01 95% CI 0.84, 1.22; I²  =  0%. There was a trend towards lower response rate with tracked mailing by the time of the second reminder (RR = 0.91; 95% CI 0.78, 1.06; I²  =  0%. The response rate with mailing on Mondays was not statistically different from that with Friday mailing by the time of first reminder (RR = 1.01; 95% CI 0.87, 1.17; I²  =  0%, and by the time of the 2(nd reminder (RR = 1.08; 95% CI 0.84, 1.39; I²  =  77%. CONCLUSIONS: Tracking response may negatively affect physicians' response rate. The day of mailing does not appear to affect physicians' response rate.

  6. Designing questionnaires: healthcare survey to compare two different response scales

    Science.gov (United States)

    2014-01-01

    Background A widely discussed design issue in patient satisfaction questionnaires is the optimal length and labelling of the answering scale. The aim of the present study was to compare intra-individually the answers on two response scales to five general questions evaluating patients’ perception of hospital care. Methods Between November 2011 and January 2012, all in-hospital patients at a Swiss University Hospital received a patient satisfaction questionnaire on an adjectival scale with three to four labelled categories (LS) and five redundant questions displayed on an 11-point end-anchored numeric scale (NS). The scales were compared concerning ceiling effect, internal consistency (Cronbach’s alpha), individual item answers (Spearman’s rank correlation), and concerning overall satisfaction by calculating an overall percentage score (sum of all answers related to the maximum possible sum). Results The response rate was 41% (2957/7158), of which 2400 (81%) completely filled out all questions. Baseline characteristics of the responders and non-responders were similar. Floor and ceiling effect were high on both response scales, but more pronounced on the LS than on the NS. Cronbach’s alpha was higher on the NS than on the LS. There was a strong individual item correlation between both answering scales in questions regarding the intent to return, quality of treatment and the judgement whether the patient was treated with respect and dignity, but a lower correlation concerning satisfactory information transfer by physicians or nurses, where only three categories were available in the LS. The overall percentage score showed a comparable distribution, but with a wider spread of lower satisfaction in the NS. Conclusions Since the longer scale did not substantially reduce the ceiling effect, the type of questions rather than the type of answering scale could be addressed with a focus on specific questions about concrete situations instead of general questions

  7. Qualitative response models: A survey of methodology and illustrative applications

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    Nojković Aleksandra

    2007-01-01

    Full Text Available This paper introduces econometric modeling with discrete (categorical dependent variables. Such models, commonly referred to as qualitative response (QR models, have become a standard tool of microeconometric analysis. Microeconometric research represents empirical analysis of microdata, i.e. economic information about individuals, households and firms. Microeconometrics has been most widely adopted in various fields, such as labour economics, consumer behavior, or economy of transport. The latest research shows that this methodology can also be successfully transferred to macroeconomic context and applied to time series and panel data analysis in a wider scope. .

  8. Interpatient Variability in Dexmedetomidine Response: A Survey of the Literature

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    Samantha F. Holliday

    2014-01-01

    Full Text Available Fifty-five thousand patients are cared for in the intensive care unit (ICU daily with sedation utilized to reduce anxiety and agitation while optimizing comfort. The Society of Critical Care Medicine (SCCM released updated guidelines for management of pain, agitation, and delirium in the ICU and recommended nonbenzodiazepines, such as dexmedetomidine and propofol, as first line sedation agents. Dexmedetomidine, an alpha-2 agonist, offers many benefits yet its use is mired by the inability to consistently achieve sedation goals. Three hypotheses including patient traits/characteristics, pharmacokinetics in critically ill patients, and clinically relevant genetic polymorphisms that could affect dexmedetomidine response are presented. Studies in patient traits have yielded conflicting results regarding the role of race yet suggest that dexmedetomidine may produce more consistent results in less critically ill patients and with home antidepressant use. Pharmacokinetics of critically ill patients are reported as similar to healthy individuals yet wide, unexplained interpatient variability in dexmedetomidine serum levels exist. Genetic polymorphisms in both metabolism and receptor response have been evaluated in few studies, and the results remain inconclusive. To fully understand the role of dexmedetomidine, it is vital to further evaluate what prompts such marked interpatient variability in critically ill patients.

  9. Global analysis of neutrophil responses to Neisseria gonorrhoeae reveals a self-propagating inflammatory program.

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    Anna Sintsova

    2014-09-01

    Full Text Available An overwhelming neutrophil-driven response causes both acute symptoms and the lasting sequelae that result from infection with Neisseria gonorrhoeae. Neutrophils undergo an aggressive opsonin-independent response to N. gonorrhoeae, driven by the innate decoy receptor CEACAM3. CEACAM3 is exclusively expressed by human neutrophils, and drives a potent binding, phagocytic engulfment and oxidative killing of Opa-expressing bacteria. In this study, we sought to explore the contribution of neutrophils to the pathogenic inflammatory process that typifies gonorrhea. Genome-wide microarray and biochemical profiling of gonococcal-infected neutrophils revealed that CEACAM3 engagement triggers a Syk-, PKCδ- and Tak1-dependent signaling cascade that results in the activation of an NF-κB-dependent transcriptional response, with consequent production of pro-inflammatory cytokines. Using an in vivo model of N. gonorrhoeae infection, we show that human CEACAM-expressing neutrophils have heightened migration toward the site of the infection where they may be further activated upon Opa-dependent binding. Together, this study establishes that the role of CEACAM3 is not restricted to the direct opsonin-independent killing by neutrophils, since it also drives the vigorous inflammatory response that typifies gonorrhea. By carrying the potential to mobilize increasing numbers of neutrophils, CEACAM3 thereby represents the tipping point between protective and pathogenic outcomes of N. gonorrhoeae infection.

  10. Rangeland monitoring reveals long-term plant responses to precipitation and grazing at the landscape scale

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    Munson, Seth M.; Duniway, Michael C.; Johanson, Jamin K.

    2015-01-01

    Managers of rangeland ecosystems require methods to track the condition of natural resources over large areas and long periods of time as they confront climate change and land use intensification. We demonstrate how rangeland monitoring results can be synthesized using ecological site concepts to understand how climate, site factors, and management actions affect long-term vegetation dynamics at the landscape-scale. Forty-six years of rangeland monitoring conducted by the Bureau of Land Management (BLM) on the Colorado Plateau reveals variable responses of plant species cover to cool-season precipitation, land type (ecological site groups), and grazing intensity. Dominant C3 perennial grasses (Achnatherum hymenoides, Hesperostipa comata), which are essential to support wildlife and livestock on the Colorado Plateau, had responses to cool-season precipitation that were at least twice as large as the dominant C4 perennial grass (Pleuraphis jamesii) and woody vegetation. However, these C3 perennial grass responses to precipitation were reduced by nearly one-third on grassland ecological sites with fine- rather than coarse-textured soils, and there were no detectable C3 perennial grass responses to precipitation on ecological sites dominated by a dense-growing shrub, Coleogyne ramosissima. Heavy grazing intensity further reduced the responses of C3 perennial grasses to cool-season precipitation on ecological sites with coarse-textured soils and surprisingly reduced the responses of shrubs as well. By using ecological site groups to assess rangeland condition, we were able to improve our understanding of the long-term relationships between vegetation change and climate, land use, and site characteristics, which has important implications for developing landscape-scale monitoring strategies.

  11. Predicting invasive species impacts: a community module functional response approach reveals context dependencies.

    Science.gov (United States)

    Paterson, Rachel A; Dick, Jaimie T A; Pritchard, Daniel W; Ennis, Marilyn; Hatcher, Melanie J; Dunn, Alison M

    2015-03-01

    Predatory functional responses play integral roles in predator-prey dynamics, and their assessment promises greater understanding and prediction of the predatory impacts of invasive species. Other interspecific interactions, however, such as parasitism and higher-order predation, have the potential to modify predator-prey interactions and thus the predictive capability of the comparative functional response approach. We used a four-species community module (higher-order predator; focal native or invasive predators; parasites of focal predators; native prey) to compare the predatory functional responses of native Gammarus duebeni celticus and invasive Gammarus pulex amphipods towards three invertebrate prey species (Asellus aquaticus, Simulium spp., Baetis rhodani), thus, quantifying the context dependencies of parasitism and a higher-order fish predator on these functional responses. Our functional response experiments demonstrated that the invasive amphipod had a higher predatory impact (lower handling time) on two of three prey species, which reflects patterns of impact observed in the field. The community module also revealed that parasitism had context-dependent influences, for one prey species, with the potential to further reduce the predatory impact of the invasive amphipod or increase the predatory impact of the native amphipod in the presence of a higher-order fish predator. Partial consumption of prey was similar for both predators and occurred increasingly in the order A. aquaticus, Simulium spp. and B. rhodani. This was associated with increasing prey densities, but showed no context dependencies with parasitism or higher-order fish predator. This study supports the applicability of comparative functional responses as a tool to predict and assess invasive species impacts incorporating multiple context dependencies. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

  12. Analysis of gene expression during parabolic flights reveals distinct early gravity responses in Arabidopsis roots.

    Science.gov (United States)

    Aubry-Hivet, D; Nziengui, H; Rapp, K; Oliveira, O; Paponov, I A; Li, Y; Hauslage, J; Vagt, N; Braun, M; Ditengou, F A; Dovzhenko, A; Palme, K

    2014-01-01

    Plant roots are among most intensively studied biological systems in gravity research. Altered gravity induces asymmetric cell growth leading to root bending. Differential distribution of the phytohormone auxin underlies root responses to gravity, being coordinated by auxin efflux transporters from the PIN family. The objective of this study was to compare early transcriptomic changes in roots of Arabidopsis thaliana wild type, and pin2 and pin3 mutants under parabolic flight conditions and to correlate these changes to auxin distribution. Parabolic flights allow comparison of transient 1-g, hypergravity and microgravity effects in living organisms in parallel. We found common and mutation-related genes differentially expressed in response to transient microgravity phases. Gene ontology analysis of common genes revealed lipid metabolism, response to stress factors and light categories as primarily involved in response to transient microgravity phases, suggesting that fundamental reorganisation of metabolic pathways functions upstream of a further signal mediating hormonal network. Gene expression changes in roots lacking the columella-located PIN3 were stronger than in those deprived of the epidermis and cortex cell-specific PIN2. Moreover, repetitive exposure to microgravity/hypergravity and gravity/hypergravity flight phases induced an up-regulation of auxin responsive genes in wild type and pin2 roots, but not in pin3 roots, suggesting a critical function of PIN3 in mediating auxin fluxes in response to transient microgravity phases. Our study provides important insights towards understanding signal transduction processes in transient microgravity conditions by combining for the first time the parabolic flight platform with the transcriptome analysis of different genetic mutants in the model plant, Arabidopsis. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

  13. Soil DNA pyrosequencing and fruitbody surveys reveal contrasting diversity for various fungal ecological guilds in chestnut orchards.

    Science.gov (United States)

    Baptista, Paula; Reis, Francisca; Pereira, Eric; Tavares, Rui M; Santos, Pedro M; Richard, Franck; Selosse, Marc-André; Lino-Neto, Teresa

    2015-12-01

    Fungal diversity in Mediterranean forest soils is poorly documented, particularly when considering saprobic and pathogenic organisms. Next-generation sequencing (NGS) methods applied to soil fungi provide the opportunity to unveil the most inconspicuous functional guilds (e.g. saprobes) and life forms (e.g. Corticiaceae) of this tremendous diversity. We used fruitbody surveys over 2 years and soil 454 metabarcoding in Castanea sativa orchards to evaluate respectively the reproductive (fruitbodies) and vegetative (mycelia) parts of fungal communities in three 100-year-old stands. Analysis of 839 fruitbodies and 210 291 ITS1 reads revealed high fungal diversity, mainly shown by belowground analysis, with high (dominant) abundance of mycorrhizal fruitbodies and reads. Both methods displayed contrasted composition and structure of fungal communities, with Basidio- and Ascomycetes dominating above- and belowground, respectively. For the two dominant fungal guilds (i.e. ectomycorrhizal and saprobic), diversity above- and belowground overlapped weakly. This study is the first assessment of the complementarity of fruitbody surveys and NGS for analysing fungal diversity in Mediterranean ecosystems and shows that belowground methods still need to be completed by fruiting diversity to provide a comprehensive overview of the different fungal guilds. The results shed light on chestnut soil biodiversity and question the spatial distribution and synergies among fungal guilds.

  14. Choice of rating scale labels: implication for minimizing patient satisfaction response ceiling effect in telemedicine surveys.

    Science.gov (United States)

    Masino, Caterina; Lam, Tony C M

    2014-12-01

    Lack of response variability is problematic in surveys because of its detrimental effects on sensitivity and consequently reliability of the responses. In satisfaction surveys, this problem is caused by the ceiling effect resulting from high satisfaction ratings. A potential solution strategy is to manipulate the labels of the rating scale to create greater discrimination of responses on the high end of the response continuum. This study examined the effects of a positive-centered scale on the distribution and reliability of telemedicine satisfaction responses in a highly positive respondent population. In total, 216 telemedicine participants were randomly assigned to one of three experimental conditions as defined by the form of Likert scale: (1) 5-point Balanced Equal-Interval, (2) 5-point Positive-Packed, and (3) 5-point Positive-Centered Equal-Interval. Although the study findings were not statistically significant, partially because of sample size, the distribution and internal consistency reliability of responses occurred in the direction hypothesized. Loading the rating scale with more positive labels appears to be a useful strategy for reducing the ceiling effect and increases the discrimination ability of survey responses. The current research provides a survey design strategy to minimize ceiling effects. Although the findings provide some evidence suggesting the benefit of using rating scales loaded with positive labels, more research is needed to confirm this, as well as extend it to examine other types of rating scales and the interaction between rating scale formats and respondent characteristics.

  15. Transcriptomic analysis of human retinal detachment reveals both inflammatory response and photoreceptor death.

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    Marie-Noëlle Delyfer

    Full Text Available BACKGROUND: Retinal detachment often leads to a severe and permanent loss of vision and its therapeutic management remains to this day exclusively surgical. We have used surgical specimens to perform a differential analysis of the transcriptome of human retinal tissues following detachment in order to identify new potential pharmacological targets that could be used in combination with surgery to further improve final outcome. METHODOLOGY/PRINCIPAL FINDINGS: Statistical analysis reveals major involvement of the immune response in the disease. Interestingly, using a novel approach relying on coordinated expression, the interindividual variation was monitored to unravel a second crucial aspect of the pathological process: the death of photoreceptor cells. Within the genes identified, the expression of the major histocompatibility complex I gene HLA-C enables diagnosis of the disease, while PKD2L1 and SLCO4A1 -which are both down-regulated- act synergistically to provide an estimate of the duration of the retinal detachment process. Our analysis thus reveals the two complementary cellular and molecular aspects linked to retinal detachment: an immune response and the degeneration of photoreceptor cells. We also reveal that the human specimens have a higher clinical value as compared to artificial models that point to IL6 and oxidative stress, not implicated in the surgical specimens studied here. CONCLUSIONS/SIGNIFICANCE: This systematic analysis confirmed the occurrence of both neurodegeneration and inflammation during retinal detachment, and further identifies precisely the modification of expression of the different genes implicated in these two phenomena. Our data henceforth give a new insight into the disease process and provide a rationale for therapeutic strategies aimed at limiting inflammation and photoreceptor damage associated with retinal detachment and, in turn, improving visual prognosis after retinal surgery.

  16. Getting physicians to open the survey: little evidence that an envelope teaser increases response rates

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    Ziegenfuss Jeanette Y

    2012-03-01

    Full Text Available Abstract Background Physician surveys are an important tool to assess attitudes, beliefs and self-reported behaviors of this policy relevant group. In order for a physician to respond to a mailed survey, they must first open the envelope. While there is some evidence that package elements can impact physician response rates, the impact of an envelope teaser is unknown. Here we assess this by testing the impact of adding a brightly colored "$25 incentive" sticker to the outside of an envelope on response rates and nonresponse bias in a survey of physicians. Methods In the second mailing of a survey assessing physicians' moral beliefs and views on controversial health care topics, initial nonrespondents were randomly assigned to receive a survey in an envelope with a colored "$25 incentive" sticker (teaser group or an envelope without a sticker (control group. Response rates were compared between the teaser and control groups overall and by age, gender, region of the United States, specialty and years in practice. Nonresponse bias was assessed by comparing the demographic composition of the respondents to the nonrespondents in the experimental and control condition. Results No significant differences in response rates were observed between the experimental and control conditions overall (p = 0.38 or after stratifying by age, gender, region, or practice type. Within the teaser condition, there was some variation in response rate by years since graduation. There was no independent effect of the teaser on response when simultaneously controlling for demographic characteristics (OR = 0.875, p = 0.4112. Conclusions Neither response rates nor nonresponse bias were impacted by the use of an envelope teaser in a survey of physicians in the United States.

  17. Comparative tissue transcriptomics reveal prompt inter-organ communication in response to local bacterial kidney infection

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    Rhen Mikael

    2011-02-01

    Full Text Available Abstract Background Mucosal infections elicit inflammatory responses via regulated signaling pathways. Infection outcome depends strongly on early events occurring immediately when bacteria start interacting with cells in the mucosal membrane. Hitherto reported transcription profiles on host-pathogen interactions are strongly biased towards in vitro studies. To detail the local in vivo genetic response to infection, we here profiled host gene expression in a recent experimental model that assures high spatial and temporal control of uropathogenic Escherichia coli (UPEC infection within the kidney of a live rat. Results Transcriptional profiling of tissue biopsies from UPEC-infected kidney tissue revealed 59 differentially expressed genes 8 h post-infection. Their relevance for the infection process was supported by a Gene Ontology (GO analysis. Early differential expression at 3 h and 5 h post-infection was of low statistical significance, which correlated to the low degree of infection. Comparative transcriptomics analysis of the 8 h data set and online available studies of early local infection and inflammation defined a core of 80 genes constituting a "General tissue response to early local bacterial infections". Among these, 25% were annotated as interferon-γ (IFN-γ regulated. Subsequent experimental analyses confirmed a systemic increase of IFN-γ in rats with an ongoing local kidney infection, correlating to splenic, rather than renal Ifng induction and suggested this inter-organ communication to be mediated by interleukin (IL-23. The use of comparative transcriptomics allowed expansion of the statistical data handling, whereby relevant data could also be extracted from the 5 h data set. Out of the 31 differentially expressed core genes, some represented specific 5 h responses, illustrating the value of comparative transcriptomics when studying the dynamic nature of gene regulation in response to infections. Conclusion Our hypothesis

  18. Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to UV-B light.

    Science.gov (United States)

    Kusano, Miyako; Tohge, Takayuki; Fukushima, Atsushi; Kobayashi, Makoto; Hayashi, Naomi; Otsuki, Hitomi; Kondou, Youichi; Goto, Hiroto; Kawashima, Mika; Matsuda, Fumio; Niida, Rie; Matsui, Minami; Saito, Kazuki; Fernie, Alisdair R

    2011-07-01

    Because of ever-increasing environmental deterioration it is likely that the influx of UV-B radiation (280-320 nm) will increase as a result of the depletion of stratospheric ozone. Given this fact it is essential that we better understand both the rapid and the adaptive responses of plants to UV-B stress. Here, we compare the metabolic responses of wild-type Arabidopsis with that of mutants impaired in flavonoid (transparent testa 4, tt4; transparent testa 5, tt5) or sinapoyl-malate (sinapoylglucose accumulator 1, sng1) biosynthesis, exposed to a short 24-h or a longer 96-h exposure to this photo-oxidative stress. In control experiments we subjected the genotypes to long-day conditions as well as to 24- and 96-h treatments of continuous light. Following these treatments we evaluated the dynamic response of metabolites including flavonoids, sinapoyl-malate precursors and ascorbate, which are well known to play a role in cellular protection from UV-B stress, as well as a broader range of primary metabolites, in an attempt to more fully comprehend the metabolic shift following the cellular perception of this stress. Our data reveals that short-term responses occur only at the level of primary metabolites, suggesting that these effectively prime the cell to facilitate the later production of UV-B-absorbing secondary metabolites. The combined results of these studies together with transcript profiles using samples irradiated by 24-h UV-B light are discussed in the context of current models concerning the metabolic response of plants to the stress imposed by excessive UV-B irradiation.

  19. Expression of secreted Wnt pathway components reveals unexpected complexity of the planarian amputation response.

    Science.gov (United States)

    Gurley, Kyle A; Elliott, Sarah A; Simakov, Oleg; Schmidt, Heiko A; Holstein, Thomas W; Sánchez Alvarado, Alejandro

    2010-11-01

    Regeneration is widespread throughout the animal kingdom, but our molecular understanding of this process in adult animals remains poorly understood. Wnt/β-catenin signaling plays crucial roles throughout animal life from early development to adulthood. In intact and regenerating planarians, the regulation of Wnt/β-catenin signaling functions to maintain and specify anterior/posterior (A/P) identity. Here, we explore the expression kinetics and RNAi phenotypes for secreted members of the Wnt signaling pathway in the planarian Schmidtea mediterranea. Smed-wnt and sFRP expression during regeneration is surprisingly dynamic and reveals fundamental aspects of planarian biology that have been previously unappreciated. We show that after amputation, a wounding response precedes rapid re-organization of the A/P axis. Furthermore, cells throughout the body plan can mount this response and reassess their new A/P location in the complete absence of stem cells. While initial stages of the amputation response are stem cell independent, tissue remodeling and the integration of a new A/P address with anatomy are stem cell dependent. We also show that WNT5 functions in a reciprocal manner with SLIT to pattern the planarian mediolateral axis, while WNT11-2 patterns the posterior midline. Moreover, we perform an extensive phylogenetic analysis on the Smed-wnt genes using a method that combines and integrates both sequence and structural alignments, enabling us to place all nine genes into Wnt subfamilies for the first time.

  20. Learning theories reveal loss of pancreatic electrical connectivity in diabetes as an adaptive response.

    Directory of Open Access Journals (Sweden)

    Pranay Goel

    Full Text Available Cells of almost all solid tissues are connected with gap junctions which permit the direct transfer of ions and small molecules, integral to regulating coordinated function in the tissue. The pancreatic islets of Langerhans are responsible for secreting the hormone insulin in response to glucose stimulation. Gap junctions are the only electrical contacts between the beta-cells in the tissue of these excitable islets. It is generally believed that they are responsible for synchrony of the membrane voltage oscillations among beta-cells, and thereby pulsatility of insulin secretion. Most attempts to understand connectivity in islets are often interpreted, bottom-up, in terms of measurements of gap junctional conductance. This does not, however, explain systematic changes, such as a diminished junctional conductance in type 2 diabetes. We attempt to address this deficit via the model presented here, which is a learning theory of gap junctional adaptation derived with analogy to neural systems. Here, gap junctions are modelled as bonds in a beta-cell network, that are altered according to homeostatic rules of plasticity. Our analysis reveals that it is nearly impossible to view gap junctions as homogeneous across a tissue. A modified view that accommodates heterogeneity of junction strengths in the islet can explain why, for example, a loss of gap junction conductance in diabetes is necessary for an increase in plasma insulin levels following hyperglycemia.

  1. Transcriptome profile reveals heat response mechanism at molecular and metabolic levels in rice flag leaf.

    Science.gov (United States)

    Zhang, Xianwen; Rerksiri, Wirat; Liu, Ailing; Zhou, Xiaoyun; Xiong, Hairong; Xiang, Jianhua; Chen, Xinbo; Xiong, Xingyao

    2013-11-10

    Flag leaf is one of the key photosynthesis organs during rice reproductive stage. A time course microarray analysis of rice flag leaf was done after 40°C treatment for 0 min, 20 min, 60 min, 2h, 4h, and 8h. The identified significant heat responsive genes were mainly involved in transcriptional regulation, transport, protein binding, antioxidant, and stress response. KMC analysis discovered the time-dependent gene expression pattern under heat. MapMan analysis demonstrated that, under heat treatment, Hsp genes and genes involved in glycolysis and ubiquitin-proteasome were enhanced, and genes involved in TCA, carotenoid, dihydroflavonol and anthocyanin metabolisms and light-reaction in the photosynthesis were widely repressed. Meanwhile, some rate-limiting enzyme genes in shikimate, lignin, and mevalonic acid metabolisms were up-regulated, revealing the importance of maintaining specific secondary metabolites under heat stress. The present study increased our understanding of heat response in rice flag leaf and provided good candidate genes for crop improvement.

  2. Transcriptome analysis of a wild bird reveals physiological responses to the urban environment

    Science.gov (United States)

    Watson, Hannah; Videvall, Elin; Andersson, Martin N.; Isaksson, Caroline

    2017-01-01

    Identifying the molecular basis of environmentally induced phenotypic variation presents exciting opportunities for furthering our understanding of how ecological processes and the environment can shape the phenotype. Urban and rural environments present free-living organisms with different challenges and opportunities, which have marked consequences for the phenotype, yet little is known about responses at the molecular level. We characterised transcriptomes from an urban and a rural population of great tits Parus major, demonstrating striking differences in gene expression profiles in both blood and liver tissues. Differentially expressed genes had functions related to immune and inflammatory responses, detoxification, protection against oxidative stress, lipid metabolism, and regulation of gene expression. Many genes linked to stress responses were expressed at higher levels in the urban birds, in accordance with our prediction that urban animals are exposed to greater environmental stress. This is one of the first studies to reveal transcriptional differences between urban- and rural-dwelling animals and suggests an important role for epigenetics in mediating environmentally induced physiological variation. The study provides valuable resources for developing further in-depth studies of the mechanisms driving phenotypic variation in the urban context at larger spatial and temporal scales. PMID:28290496

  3. Transcriptional profiling of Petunia seedlings reveals candidate regulators of the cold stress response

    Directory of Open Access Journals (Sweden)

    Bei eLi

    2015-03-01

    Full Text Available Petunias are important ornamentals with the capacity for cold acclimation. So far, there is limited information concerning gene regulation and signaling pathways related to the cold stress response in petunias. A custom-designed petunia microarray representing 24816 genes was used to perform transcriptome profiling in petunia seedlings subjected to cold at 2°C for 0.5 h, 2 h, 24 h and 5 d. A total of 2071 transcripts displayed differential expression patterns under cold stress, of which 1149 were up-regulated and 922 were down-regulated. Gene ontology enrichment analysis demarcated related biological processes, suggesting a possible link between flavonoid metabolism and plant adaptation to low temperatures. Many novel stress-responsive regulators were revealed, suggesting that diverse regulatory pathways may exist in petunias in addition to the well-characterized CBF pathway. The expression changes of selected genes under cold and other abiotic stress conditions were confirmed by real-time RT-PCR. Furthermore, weighted gene co-expression network analysis divided the petunia genes on the array into 65 modules that showed high co-expression and identified stress-specific hub genes with high connectivity. Our identification of these transcriptional responses and groups of differentially expressed regulators will facilitate the functional dissection of the molecular mechanism in petunias responding to environment stresses and extend our ability to improve cold tolerance in plants.

  4. The strange case of online surveys: response issues and respondent characteristics

    DEFF Research Database (Denmark)

    Adamsen, Jannie Mia; Rundle-Thiele, Sharyn; Mehnert, Christina

    2011-01-01

    This research contributes to existing knowledge about collecting data online by analysing multiple data sets on key criteria including overall representativeness of the samples, response and break-off rates, timeliness of response and reminder effects. Across eight online surveys that initially...... in responses on the preference measures for Leaders, Early or Late Majority or Laggards and secondly, we have only considered the demographic characteristics of responders. The information can be utilised by researchers in the planning and management process of online surveys, especially since the results...... a reminder 48-72 hours after the initial invitation and closing the survey one to two days later; based on our results this time-wise approach still captures 90% of respondents. This study must be viewed in light of some key limitations. Firstly, we have not considered whether there are differences...

  5. Promoting quality of care in disaster response: A survey of core surgical competencies.

    Science.gov (United States)

    Wong, Evan G; Razek, Tarek; Elsharkawi, Hossam; Wren, Sherry M; Kushner, Adam L; Giannou, Christos; Khwaja, Kosar A; Beckett, Andrew; Deckelbaum, Dan L

    2015-07-01

    Recent humanitarian crises have led to a call for professionalization of the humanitarian field, but core competencies for the delivery of surgical care have yet to be established. The objective of this study was to survey surgeons with experience in disaster response to identify surgical competencies required to be effective in these settings. An online survey elucidating demographic information, scope of practice, and previous experience in global health and disaster response was transmitted to surgeons from a variety of surgical societies and nongovernmental organizations. Participants were provided with a list of 111 operative procedures and were asked to identify those deemed essential to the toolset of a frontline surgeon in disaster response via a Likert scale. Responses from personnel with experience in disaster response were contrasted with those from nonexperienced participants. A total of 147 surgeons completed the survey. Participants held citizenship in 22 countries, were licensed in 30 countries, and practiced in >20 countries. Most respondents (56%) had previous experience in humanitarian response. The majority agreed or strongly agreed that formal training (54%), past humanitarian response (94%), and past global health experiences (80%) provided adequate preparation. The most commonly deemed important procedures included control of intraabdominal hemorrhage (99%), abdominal packing for trauma (99%), and wound debridement (99%). Procedures deemed important by experienced personnel spanned multiple specialties. This study addressed specifically surgical competencies in disaster response. We provide a list of operative procedures that should set the stage for further structured education programs. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Differential effects of pre and post-payment on neurologists' response rates to a postal survey

    Directory of Open Access Journals (Sweden)

    Wessely Simon C

    2010-10-01

    Full Text Available Abstract Background Monetary incentives are an effective way of increasing response rates to surveys, though they are generally less effective in physicians, and are more effective when the incentive is paid up-front rather than when made conditional on completion. Methods In this study we examine the effectiveness of pre- and post-completion incentives on the response rates of all the neurologists in the UK to a survey about conversion disorder, using a cluster randomised controlled design. A postal survey was sent to all practicing consultant neurologists, in two rounds, including either a book token, the promise of a book token, or nothing at all. Results Three hundred and fifty-one of 591 eligible neurologists completed the survey, for a response rate of 59%. While the post-completion incentive exerted no discernible influence on response rates, a pre-completion incentive did, with an odds-ratio of 2.1 (95% confidence interval 1.5 - 3.0. Conclusions We conclude that neurologists, in the UK at least, may be influenced to respond to a postal survey by a pre-payment incentive but are unaffected by a promised reward.

  7. Factors affecting study efficiency and item non-response in health surveys in developing countries: the Jamaica national healthy lifestyle survey

    Directory of Open Access Journals (Sweden)

    Bennett Franklyn

    2007-02-01

    Full Text Available Abstract Background Health surveys provide important information on the burden and secular trends of risk factors and disease. Several factors including survey and item non-response can affect data quality. There are few reports on efficiency, validity and the impact of item non-response, from developing countries. This report examines factors associated with item non-response and study efficiency in a national health survey in a developing Caribbean island. Methods A national sample of participants aged 15–74 years was selected in a multi-stage sampling design accounting for 4 health regions and 14 parishes using enumeration districts as primary sampling units. Means and proportions of the variables of interest were compared between various categories. Non-response was defined as failure to provide an analyzable response. Linear and logistic regression models accounting for sample design and post-stratification weighting were used to identify independent correlates of recruitment efficiency and item non-response. Results We recruited 2012 15–74 year-olds (66.2% females at a response rate of 87.6% with significant variation between regions (80.9% to 97.6%; p Conclusion Informative health surveys are possible in developing countries. While survey response rates may be satisfactory, item non-response was high in respect of income and sexual practice. In contrast to developed countries, non-response to questions on income is higher and has different correlates. These findings can inform future surveys.

  8. Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas.

    Science.gov (United States)

    Timmins-Schiffman, Emma; Coffey, William D; Hua, Wilber; Nunn, Brook L; Dickinson, Gary H; Roberts, Steven B

    2014-11-03

    Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end-of-century open ocean pH reductions. In order to assess the impact of ocean acidification on marine invertebrates, Pacific oysters (Crassostrea gigas) were exposed to one of four different p CO2 levels for four weeks: 400 μatm (pH 8.0), 800 μatm (pH 7.7), 1000 μatm (pH 7.6), or 2800 μatm (pH 7.3). At the end of the four week exposure period, oysters in all four p CO2 environments deposited new shell, but growth rate was not different among the treatments. However, micromechanical properties of the new shell were compromised by elevated p CO2. Elevated p CO2 affected neither whole body fatty acid composition, nor glycogen content, nor mortality rate associated with acute heat shock. Shotgun proteomics revealed that several physiological pathways were significantly affected by ocean acidification, including antioxidant response, carbohydrate metabolism, and transcription and translation. Additionally, the proteomic response to a second stress differed with p CO2, with numerous processes significantly affected by mechanical stimulation at high versus low p CO2 (all proteomics data are available in the ProteomeXchange under the identifier PXD000835). Oyster physiology is significantly altered by exposure to elevated p CO2, indicating changes in energy resource use. This is especially apparent in the assessment of the effects of p CO2 on the proteomic response to a second stress. The altered stress response illustrates that ocean acidification may impact how oysters respond to other changes in their environment. These data contribute to an integrative view of the effects of ocean acidification on oysters as well as physiological trade-offs during environmental stress.

  9. Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability.

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    Catarina Barbosa

    Full Text Available Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23, under low (67 mg/L and high nitrogen (670 mg/L regimes, at three time points during fermentation (12 h, 24 h and 96 h. Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12 h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this

  10. A microfluidic platform reveals differential response of regulatory T cells to micropatterned costimulation arrays.

    Science.gov (United States)

    Lee, Joung-Hyun; Dustin, Michael L; Kam, Lance C

    2015-11-01

    T cells are key mediators of adaptive immunity. However, the overall immune response is often directed by minor subpopulations of this heterogeneous family of cells, owing to specificity of activation and amplification of functional response. Knowledge of differences in signaling and function between T cell subtypes is far from complete, but is clearly needed for understanding and ultimately leveraging this branch of the adaptive immune response. This report investigates differences in cell response to micropatterned surfaces by conventional and regulatory T cells. Specifically, the ability of cells to respond to the microscale geometry of TCR/CD3 and CD28 engagement is made possible using a magnetic-microfluidic device that overcomes limitations in imaging efficiency associated with conventional microscopy equipment. This device can be readily assembled onto micropatterned surfaces while maintaining the activity of proteins and other biomolecules necessary for such studies. In operation, a target population of cells is tagged using paramagnetic beads, and then trapped in a divergent magnetic field within the chamber. Following washing, the target cells are released to interact with a designated surface. Characterization of this system with mouse CD4(+) T cells demonstrated a 50-fold increase in target-to-background cell purity, with an 80% collection efficiency. Applying this approach to CD4(+)CD25(+) regulatory T cells, it is then demonstrated that these rare cells respond less selectively to micro-scale features of anti-CD3 antibodies than CD4(+)CD25(-) conventional T cells, revealing a difference in balance between TCR/CD3 and LFA-1-based adhesion. PKC-θ localized to the distal pole of regulatory T cells, away from the cell-substrate interface, suggests a mechanism for differential regulation of TCR/LFA-1-based adhesion. Moreover, specificity of cell adhesion to anti-CD3 features was dependent on the relative position of anti-CD28 signaling within the cell

  11. Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the integrated stress response

    Science.gov (United States)

    Gao, Xing-Huang; Krokowski, Dawid; Guan, Bo-Jhih; Bederman, Ilya; Majumder, Mithu; Parisien, Marc; Diatchenko, Luda; Kabil, Omer; Willard, Belinda; Banerjee, Ruma; Wang, Benlian; Bebek, Gurkan; Evans, Charles R.; Fox, Paul L.; Gerson, Stanton L.; Hoppel, Charles L.; Liu, Ming; Arvan, Peter; Hatzoglou, Maria

    2015-01-01

    The sulfhydration of cysteine residues in proteins is an important mechanism involved in diverse biological processes. We have developed a proteomics approach to quantitatively profile the changes of sulfhydrated cysteines in biological systems. Bioinformatics analysis revealed that sulfhydrated cysteines are part of a wide range of biological functions. In pancreatic β cells exposed to endoplasmic reticulum (ER) stress, elevated H2S promotes the sulfhydration of enzymes in energy metabolism and stimulates glycolytic flux. We propose that transcriptional and translational reprogramming by the integrated stress response (ISR) in pancreatic β cells is coupled to metabolic alternations triggered by sulfhydration of key enzymes in intermediary metabolism. DOI: http://dx.doi.org/10.7554/eLife.10067.001 PMID:26595448

  12. Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes

    Directory of Open Access Journals (Sweden)

    Deyholos Michael K

    2006-10-01

    Full Text Available Abstract Background Roots are an attractive system for genomic and post-genomic studies of NaCl responses, due to their primary importance to agriculture, and because of their relative structural and biochemical simplicity. Excellent genomic resources have been established for the study of Arabidopsis roots, however, a comprehensive microarray analysis of the root transcriptome following NaCl exposure is required to further understand plant responses to abiotic stress and facilitate future, systems-based analyses of the underlying regulatory networks. Results We used microarrays of 70-mer oligonucleotide probes representing 23,686 Arabidopsis genes to identify root transcripts that changed in relative abundance following 6 h, 24 h, or 48 h of hydroponic exposure to 150 mM NaCl. Enrichment analysis identified groups of structurally or functionally related genes whose members were statistically over-represented among up- or down-regulated transcripts. Our results are consistent with generally observed stress response themes, and highlight potentially important roles for underappreciated gene families, including: several groups of transporters (e.g. MATE, LeOPT1-like; signalling molecules (e.g. PERK kinases, MLO-like receptors, carbohydrate active enzymes (e.g. XTH18, transcription factors (e.g. members of ZIM, WRKY, NAC, and other proteins (e.g. 4CL-like, COMT-like, LOB-Class 1. We verified the NaCl-inducible expression of selected transcription factors and other genes by qRT-PCR. Conclusion Micorarray profiling of NaCl-treated Arabidopsis roots revealed dynamic changes in transcript abundance for at least 20% of the genome, including hundreds of transcription factors, kinases/phosphatases, hormone-related genes, and effectors of homeostasis, all of which highlight the complexity of this stress response. Our identification of these transcriptional responses, and groups of evolutionarily related genes with either similar or divergent

  13. Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution.

    Science.gov (United States)

    Coelho, Francisco J R C; Cleary, Daniel F R; Costa, Rodrigo; Ferreira, Marina; Polónia, Ana R M; Silva, Artur M S; Simões, Mário M Q; Oliveira, Vanessa; Gomes, Newton C M

    2016-09-01

    There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)-based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate-reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH-oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH-oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH-oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH-oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k-/r-strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events.

  14. Excess fertilizer responsive miRNAs revealed in Linum usitatissimum L.

    Science.gov (United States)

    Melnikova, Nataliya V; Dmitriev, Alexey A; Belenikin, Maxim S; Speranskaya, Anna S; Krinitsina, Anastasia A; Rachinskaia, Olga A; Lakunina, Valentina A; Krasnov, George S; Snezhkina, Anastasiya V; Sadritdinova, Asiya F; Uroshlev, Leonid A; Koroban, Nadezda V; Samatadze, Tatiana E; Amosova, Alexandra V; Zelenin, Alexander V; Muravenko, Olga V; Bolsheva, Nadezhda L; Kudryavtseva, Anna V

    2015-02-01

    Effective fertilizer application is necessary to increase crop yields and reduce risk of plant overdosing. It is known that expression level of microRNAs (miRNAs) alters in plants under different nutrient concentrations in soil. The aim of our study was to identify and characterize miRNAs with expression alterations under excessive fertilizer in agriculturally important crop - flax (Linum usitatissimum L.). We have sequenced small RNAs in flax grown under normal and excessive fertilizer using Illumina GAIIx. Over 14 million raw reads was obtained for two small RNA libraries. 84 conserved miRNAs from 20 families were identified. Differential expression was revealed for several flax miRNAs under excessive fertilizer according to high-throughput sequencing data. For 6 miRNA families (miR395, miR169, miR408, miR399, miR398 and miR168) expression level alterations were evaluated on the extended sampling using qPCR. Statistically significant up-regulation was revealed for miR395 under excessive fertilizer. It is known that target genes of miR395 are involved in sulfate uptake and assimilation. However, according to our data alterations of the expression level of miR395 could be associated not only with excess sulfur application, but also with redundancy of other macro- and micronutrients. Furthermore expression level was evaluated for miRNAs and their predicted targets. The negative correlation between miR399 expression and expression of its predicted target ubiquitin-conjugating enzyme E2 gene was shown in flax for the first time. So we suggested miR399 involvement in phosphate regulation in L. usitatissimum. Revealed in our study expression alterations contribute to miRNA role in flax response to excessive fertilizer.

  15. Postcaldera volcanism and hydrothermal activity revealed by autonomous underwater vehicle surveys in Myojin Knoll caldera, Izu-Ogasawara arc

    Science.gov (United States)

    Honsho, Chie; Ura, Tamaki; Kim, Kangsoo; Asada, Akira

    2016-06-01

    Myojin Knoll caldera, one of the submarine silicic calderas lying on the volcanic front of the northern Izu-Ogasawara arc, has attracted increasing attention since the discovery of a large hydrothermal field called the Sunrise deposit. Although numerous submersible surveys have been conducted in Myojin Knoll caldera, they have not sufficiently explored areas to produce a complete picture of the caldera and understand the origin of the Sunrise deposit. We conducted comprehensive deep-sea surveys using an autonomous underwater vehicle and obtained high-resolution bathymetric and magnetic data and sonar images from ~70% of the caldera. The detailed bathymetric map revealed that faulting and magma eruptions, possibly associated with an inflation-deflation cycle of the magma reservoir during postcaldera volcanism, had generally occurred in the caldera wall. The main dome of the central cone was covered with lava flows and exhibits exogenous growth, which is unusual for rhyolitic domes. The magnetization distribution in the central cone indicates preferential magma intrusion along a NW-SE direction. It is presumed that magma migrated along this direction and formed a rhyolite dome at the foot of the southeastern caldera wall, where the Sunrise deposit occurs. The Sunrise deposit is composed mainly of three ridges extending in slope directions and covers ~400 × ~400 m. Magnetization reduction in the deposit area is small, indicating that the alteration zone beneath the Sunrise deposit is slanting rather than vertical. It is presumed that several slanting and near-vertical volcanic vents serve as pathways of hydrothermal fluid in Myojin Knoll caldera.

  16. A primary survey on bryophyte species reveals two novel classes of nucleotide-binding site (NBS genes.

    Directory of Open Access Journals (Sweden)

    Jia-Yu Xue

    Full Text Available Due to their potential roles in pathogen defense, genes encoding nucleotide-binding site (NBS domain have been particularly surveyed in many angiosperm genomes. Two typical classes were found: one is the TIR-NBS-LRR (TNL class and the other is the CC-NBS-LRR (CNL class. It is seldom known, however, what kind of NBS-encoding genes are mainly present in other plant groups, especially the most ancient groups of land plants, that is, bryophytes. To fill this gap of knowledge, in this study, we mainly focused on two bryophyte species: the moss Physcomitrella patens and the liverwort Marchantia polymorpha, to survey their NBS-encoding genes. Surprisingly, two novel classes of NBS-encoding genes were discovered. The first novel class is identified from the P. patens genome and a typical member of this class has a protein kinase (PK domain at the N-terminus and a LRR domain at the C-terminus, forming a complete structure of PK-NBS-LRR (PNL, reminiscent of TNL and CNL classes in angiosperms. The second class is found from the liverwort genome and a typical member of this class possesses an α/β-hydrolase domain at the N-terminus and also a LRR domain at the C-terminus (Hydrolase-NBS-LRR, HNL. Analysis on intron positions and phases also confirmed the novelty of HNL and PNL classes, as reflected by their specific intron locations or phase characteristics. Phylogenetic analysis covering all four classes of NBS-encoding genes revealed a closer relationship among the HNL, PNL and TNL classes, suggesting the CNL class having a more divergent status from the others. The presence of specific introns highlights the chimerical structures of HNL, PNL and TNL genes, and implies their possible origin via exon-shuffling during the quick lineage separation processes of early land plants.

  17. Dynamic Feedbacks Between Flow, Erosion and Evolving River Bank Roughness Revealed Through Repeat High-Resolution Topographic Surveys

    Science.gov (United States)

    Leyland, J.; Darby, S. E.; Rinaldi, M.; Teruggi, L. B.; Ostuni, D.

    2012-12-01

    Bank erosion is a key process in fluvial dynamics, with significant fractions of the total sediment load being sourced from river banks. Studies have shown that hydraulic erosion of the bank toe is a driving factor of long term rates of bank retreat. Fluvial bank erosion rates are often quantified using an excess shear stress model where the erosion rate is a function of the boundary shear stress applied by the flow above a critical threshold. Research has shown that the form roughness induced by natural topographic bank features such as slumps, spurs and embayments, is a major component of the spatially-averaged total shear stress. The skin friction component of this shear stress is typically an order of magnitude less than the total, meaning that the form roughness provides an important control on bank erosion rates. However, measuring the relative components of the total shear stress for a natural system is not straightforward. In this research we apply the method of Kean and Smith [2006, J. Geophys. Res., 111(4), F04009, doi:10.1029/2006JF000467] to partition the form and skin drag components of river bank roughness for an eroding bank of the Cecina River in central Italy. This method approximates the form drag component of the roughness along a longitudinal bank profile as a series of user defined Gaussian curves, with the skin friction component estimated through analysis of the deviations of the data from the fitted curves. For our site, a temporal sequence (2003 - 2011) of high-resolution topographic surveys has been collected through a combination of photogrammetry and Terrestrial Laser Scanning. For each survey five vertically equidistant profiles are extracted and analysed alongside DEMs of difference and associated flow data modelled using the distributed hydrological model MOBIDIC. The data are used to explore the dynamic feedbacks that exist between river discharge, bank erosion processes and bank form roughness, revealing insights into the self

  18. Magnitude and extent of land subsidence in central Mexico revealed by regional InSAR ALOS time-series survey

    Science.gov (United States)

    Chaussard, E.; Wdowinski, S.; Amelung, F.; Cabral-Cano, E.

    2013-05-01

    Massive groundwater extraction is very common in Mexico and is well known to result in land subsidence. However, most surveys dedicated to land subsidence focus on one single city, mainly Mexico City, and thus fail to provide a comprehensive picture of the problem. Here we use a space-based radar remote sensing technique, known as Interferometric Synthetic Aperture Radar (InSAR) to detect land subsidence in the entire central Mexico area. We used data from the Japanese satellite ALOS, processed over 600 SAR images acquired between 2007-2011 and produced over 3000 interferograms to cover and area of 200,000 km2 in central Mexico. We identify land subsidence in twenty-one areas, including seventeen cities, namely from east to west, Puebla, Mexico city, Toluca de Lerdo, Queretaro, San Luis de la Paz, south of San Luis de la Paz, Celaya, south of Villa de Reyes, San Luis Potosi, west of Villa de Arista, Morelia, Salamanca, Irapuato, Silao, Leon, Aguascalientes, north of Aguascalientes, Zamora de Hidalgo, Guadalajara, Ahuacatlan, and Tepic. Subsidence rates of 30 cm/yr are observed in Mexico City, while in the other locations typical rates of 5-10 cm/yr are noticed. Regional surveys of this type are necessary for the development of hazard mitigation plans and efficient use of ground-based monitoring. We additionally correlate subsidence with land use, surface geology, and faults distribution and suggest that groundwater extraction for agricultural, urban, and industrial uses are the main causes of land subsidence. We also reveal that the limits of the subsiding areas often correlate with existing faults, motion on these faults being driven by water extraction rather than by tectonic activity. In all the subsiding locations we observe high ground velocity gradients emphasizing the significant risks associated with land subsidence in central Mexico. Averaged 2007-2011 ground velocity map from ALOS InSAR time-series in central Mexico, revealing land subsidence in 21

  19. Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol.

    Science.gov (United States)

    Tian, Xiaoxu; Chen, Lei; Wang, Jiangxin; Qiao, Jianjun; Zhang, Weiwen

    2013-01-14

    Butanol is a promising biofuel, and recent metabolic engineering efforts have demonstrated the use of photosynthetic cyanobacterial hosts for its production. However, cyanobacteria have very low tolerance to butanol, limiting the economic viability of butanol production from these renewable producing systems. The existing knowledge of molecular mechanism involved in butanol tolerance in cyanobacteria is very limited. To build a foundation necessary to engineer robust butanol-producing cyanobacterial hosts, in this study, the responses of Synechocystis PCC 6803 to butanol were investigated using a quantitative proteomics approach with iTRAQ - LC-MS/MS technologies. The resulting high-quality dataset consisted of 25,347 peptides corresponding to 1452 unique proteins, a coverage of approximately 40% of the predicted proteins in Synechocystis. Comparative quantification of protein abundances led to the identification of 303 differentially regulated proteins by butanol. Annotation and GO term enrichment analysis showed that multiple biological processes were regulated, suggesting that Synechocystis probably employed multiple and synergistic resistance mechanisms in dealing with butanol stress. Notably, the analysis revealed the induction of heat-shock protein and transporters, along with modification of cell membrane and envelope were the major protection mechanisms against butanol. A conceptual cellular model of Synechocystis PCC 6803 responses to butanol stress was constructed to illustrate the putative molecular mechanisms employed to defend against butanol stress. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. Comprehensive DNA Adduct Analysis Reveals Pulmonary Inflammatory Response Contributes to Genotoxic Action of Magnetite Nanoparticles

    Directory of Open Access Journals (Sweden)

    Kousuke Ishino

    2015-02-01

    Full Text Available Nanosized-magnetite (MGT is widely utilized in medicinal and industrial fields; however, its toxicological properties are not well documented. In our previous report, MGT showed genotoxicity in both in vitro and in vivo assay systems, and it was suggested that inflammatory responses exist behind the genotoxicity. To further clarify mechanisms underlying the genotoxicity, a comprehensive DNA adduct (DNA adductome analysis was conducted using DNA samples derived from the lungs of mice exposed to MGT. In total, 30 and 42 types of DNA adducts were detected in the vehicle control and MGT-treated groups, respectively. Principal component analysis (PCA against a subset of DNA adducts was applied and several adducts, which are deduced to be formed by inflammation or oxidative stress, as the case of etheno-deoxycytidine (εdC, revealed higher contributions to MGT exposure. By quantitative-LC-MS/MS analysis, εdC levels were significantly higher in MGT-treated mice than those of the vehicle control. Taken together with our previous data, it is suggested that inflammatory responses might be involved in the genotoxicity induced by MGT in the lungs of mice.

  1. Capturing Arabidopsis root architecture dynamics with ROOT-FIT reveals diversity in responses to salinity.

    Science.gov (United States)

    Julkowska, Magdalena M; Hoefsloot, Huub C J; Mol, Selena; Feron, Richard; de Boer, Gert-Jan; Haring, Michel A; Testerink, Christa

    2014-11-01

    The plant root is the first organ to encounter salinity stress, but the effect of salinity on root system architecture (RSA) remains elusive. Both the reduction in main root (MR) elongation and the redistribution of the root mass between MRs and lateral roots (LRs) are likely to play crucial roles in water extraction efficiency and ion exclusion. To establish which RSA parameters are responsive to salt stress, we performed a detailed time course experiment in which Arabidopsis (Arabidopsis thaliana) seedlings were grown on agar plates under different salt stress conditions. We captured RSA dynamics with quadratic growth functions (root-fit) and summarized the salt-induced differences in RSA dynamics in three growth parameters: MR elongation, average LR elongation, and increase in number of LRs. In the ecotype Columbia-0 accession of Arabidopsis, salt stress affected MR elongation more severely than LR elongation and an increase in LRs, leading to a significantly altered RSA. By quantifying RSA dynamics of 31 different Arabidopsis accessions in control and mild salt stress conditions, different strategies for regulation of MR and LR meristems and root branching were revealed. Different RSA strategies partially correlated with natural variation in abscisic acid sensitivity and different Na(+)/K(+) ratios in shoots of seedlings grown under mild salt stress. Applying root-fit to describe the dynamics of RSA allowed us to uncover the natural diversity in root morphology and cluster it into four response types that otherwise would have been overlooked.

  2. Ribosome•RelA structures reveal the mechanism of stringent response activation

    Science.gov (United States)

    Loveland, Anna B; Bah, Eugene; Madireddy, Rohini; Zhang, Ying; Brilot, Axel F; Grigorieff, Nikolaus; Korostelev, Andrei A

    2016-01-01

    Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding. DOI: http://dx.doi.org/10.7554/eLife.17029.001 PMID:27434674

  3. Dynamic Regulation of Auxin Response during Rice Development Revealed by Newly Established Hormone Biosensor Markers

    Science.gov (United States)

    Yang, Jing; Yuan, Zheng; Meng, Qingcai; Huang, Guoqiang; Périn, Christophe; Bureau, Charlotte; Meunier, Anne-Cécile; Ingouff, Mathieu; Bennett, Malcolm J.; Liang, Wanqi; Zhang, Dabing

    2017-01-01

    The hormone auxin is critical for many plant developmental processes. Unlike the model eudicot plant Arabidopsis (Arabidopsis thaliana), auxin distribution and signaling in rice tissues has not been systematically investigated due to the absence of suitable auxin response reporters. In this study we observed the conservation of auxin signaling components between Arabidopsis and model monocot crop rice (Oryza sativa), and generated complementary types of auxin biosensor constructs, one derived from the Aux/IAA-based biosensor DII-VENUS but constitutively driven by maize ubiquitin-1 promoter, and the other termed DR5-VENUS in which a synthetic auxin-responsive promoter (DR5rev) was used to drive expression of the yellow fluorescent protein (YFP). Using the obtained transgenic lines, we observed that during the vegetative development, accumulation of DR5-VENUS signal was at young and mature leaves, tiller buds and stem base. Notably, abundant DR5-VENUS signals were observed in the cytoplasm of cortex cells surrounding lateral root primordia (LRP) in rice. In addition, auxin maxima and dynamic re-localization were seen at the initiation sites of inflorescence and spikelet primordia including branch meristems (BMs), female and male organs. The comparison of these observations among Arabidopsis, rice and maize suggests the unique role of auxin in regulating rice lateral root emergence and reproduction. Moreover, protein localization of auxin transporters PIN1 homologs and GFP tagged OsAUX1 overlapped with DR5-VENUS during spikelet development, helping validate these auxin response reporters are reliable markers in rice. This work firstly reveals the direct correspondence between auxin distribution and rice reproductive and root development at tissue and cellular level, and provides high-resolution auxin tools to probe fundamental developmental processes in rice and to establish links between auxin, development and agronomical traits like yield or root architecture. PMID

  4. Survey Satisficing Inflates Stereotypical Responses in Online Experiment: The Case of Immigration Study

    Directory of Open Access Journals (Sweden)

    Asako Miura

    2016-10-01

    Full Text Available Though survey satisficing, grudging cognitive efforts required to provide optimal answers in the survey response process, poses a serious threat to the validity of online experiments, a detailed explanation of the mechanism has yet to be established. Focusing on attitudes toward immigrants, we examined the mechanism by which survey satisficing distorts treatment effect estimates in online experiments. We hypothesized that satisficers would display more stereotypical responses than non-satisficers would when presented with stereotype-disconfirming information about an immigrant. Results of two experiments largely supported our hypotheses. Satisficers, whom we identified through an instructional manipulation check (IMC, processed information about immigrants’ personality traits congruently with the stereotype activated by information provided about nationality. The significantly shorter vignette reading time of satisficers corroborates their time-efficient impression formation based on stereotyping. However, the shallow information processing of satisficers can be rectified by alerting them to their inattentiveness through use of a repeated IMC.

  5. Survey non-response in the Netherlands : Effects on prevalence estimates and associations

    NARCIS (Netherlands)

    Van Loon, AJM; Tijhuis, M; Picavet, HSJ; Surtees, PG; Ormel, J

    2003-01-01

    PURPOSE: Differences in respondent characteristics may lead to bias in prevalence estimates and bias in associations. Both forms of non-response bias are investigated in a study on psychosocial factors and cancer risk, which is a sub-study of a large-scale monitoring survey in the Netherlands. METHO

  6. Text analysis of open-ended survey responses : a complementary method to preference mapping

    NARCIS (Netherlands)

    ten Kleij, F; Musters, PAD

    2003-01-01

    The present study illustrates the use of computer-aided text analysis to evaluate the content of open-ended survey responses. During an in-hall test, different varieties of mayonnaise were evaluated by 165 respondents on a 10-point liking scale, with the option to freely comment on these assessments

  7. Assessing subaqueous mudslide hazard on the Mississippi River delta front, Part 2: Insights revealed through high-resolution geophysical surveying

    Science.gov (United States)

    Obelcz, J.; Xu, K.; Bentley, S. J.; Georgiou, I. Y.; Maloney, J. M.; Miner, M. D.; Hanegan, K.; Keller, G.

    2014-12-01

    The northern Gulf of Mexico, including the subaqueous Mississippi River delta front (MRDF), has been productive for oil and gas development since the early 1900s. In 1969 cyclic seafloor wave loading associated with the passage of Hurricane Camille triggered subaqueous mudflows across the MRDF, destroying several offshore oil platforms. This incident spurred geophysical and geotechnical studies of the MRDF, which found that the delta front is prone to mass failures on gentle gradients (survey area can be classified into four primary sedimentary facies: mudflow gullies, mudflow lobes, undisturbed prodelta, and undisturbed delta front. Subbottom profiles reveal extensive biogenic gas from 20 to about 80 m water depths on the delta front; sidescan data show a variety of bottleneck slides, mudflow gullies and mudflow noses. Previous studies have attempted to constrain the periodicity and magnitude of subaqueous mudslides on the MRDF. However, large age gaps and varied resolution between datasets result in ambiguity regarding the cause and magnitude of observed bathymetric changes. We present high-temporal resolution MRDF bathymetric variations from 2005 (post Hurricane Katrina), 2009 (relatively quiescent storm period), and 2014 (post 2011 Mississippi River flood). These data yield better magnitude and timing estimates of mass movements. This exercise represents a first step towards (1) assembling a comprehensive geologic dataset upon which future MRDF geohazard assessments can be founded, and (2) understanding the dynamics of a massive passive margin deltaic lobe entering a phase of decline.

  8. Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity.

    Science.gov (United States)

    Everard, Amandine; Lazarevic, Vladimir; Gaïa, Nadia; Johansson, Maria; Ståhlman, Marcus; Backhed, Fredrik; Delzenne, Nathalie M; Schrenzel, Jacques; François, Patrice; Cani, Patrice D

    2014-10-01

    The gut microbiota is involved in metabolic and immune disorders associated with obesity and type 2 diabetes. We previously demonstrated that prebiotic treatment may significantly improve host health by modulating bacterial species related to the improvement of gut endocrine, barrier and immune functions. An analysis of the gut metagenome is needed to determine which bacterial functions and taxa are responsible for beneficial microbiota-host interactions upon nutritional intervention. We subjected mice to prebiotic (Pre) treatment under physiological (control diet: CT) and pathological conditions (high-fat diet: HFD) for 8 weeks and investigated the production of intestinal antimicrobial peptides and the gut microbiome. HFD feeding significantly decreased the expression of regenerating islet-derived 3-gamma (Reg3g) and phospholipase A2 group-II (PLA2g2) in the jejunum. Prebiotic treatment increased Reg3g expression (by ∼50-fold) and improved intestinal homeostasis as suggested by the increase in the expression of intectin, a key protein involved in intestinal epithelial cell turnover. Deep metagenomic sequencing analysis revealed that HFD and prebiotic treatment significantly affected the gut microbiome at different taxonomic levels. Functional analyses based on the occurrence of clusters of orthologous groups (COGs) of proteins also revealed distinct profiles for the HFD, Pre, HFD-Pre and CT groups. Finally, the gut microbiota modulations induced by prebiotics counteracted HFD-induced inflammation and related metabolic disorders. Thus, we identified novel putative taxa and metabolic functions that may contribute to the development of or protection against the metabolic alterations observed during HFD feeding and HFD-Pre feeding.

  9. Metagenomics, metatranscriptomics and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill

    Energy Technology Data Exchange (ETDEWEB)

    Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon; Chain, Patrick S. G.; Dubinsky, Eric A.; Fortney, Julian L.; Han, James; Holman, Hoi-Ying N.; Hultman, Jenni; Lamendella, Regina; Mackelprang, Rachel; Malfatti, Stephanie; Tom, Lauren M.; Tringe, Susannah G.; Woyke, Tanja; Zhou, Jizhong; Rubin, Edward M.; Jansson, Janet K.

    2012-06-12

    The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.

  10. Measuring the mental health care system responsiveness: results of an outpatient survey in Tehran

    Directory of Open Access Journals (Sweden)

    Setareh eForouzan

    2016-01-01

    Full Text Available AbstractAs explained by the World Health Organisation (WHO in 2000, the concept of health system responsiveness is one of the core goals of health systems. Since 2000, further efforts have been made to measure health system responsiveness and the factors affecting responsiveness, yet few studies have applied responsiveness concepts to the evaluation of mental health systems. The present study aims to measure responsiveness and its related domains in the mental health care system of Tehran. Utilising the same method used by the WHO for its responsiveness survey, responsiveness for outpatient mental health care was evaluated using a validated Farsi questionnaire. A sample of 500 public mental health service users in Tehran participated and subsequently completed the questionnaire. On average, 47% of participants reported experiencing poor responsiveness. Among responsiveness domains, confidentiality and dignity were the best performing factors while autonomy, access to care and quality of basic amenities were the worst performing. Respondents who reported their social status as low were more likely to experience poor responsiveness overall. Autonomy, quality of basic amenities and clear communication were responsiveness dimensions that performed poorly but were considered to be important by study participants. In summary, the study suggests that measuring responsiveness could provide guidance for further development of mental health care systems to become more patient orientated and provide patients with more respect.

  11. Electrical brain responses in language-impaired children reveal grammar-specific deficits.

    Directory of Open Access Journals (Sweden)

    Elisabeth Fonteneau

    Full Text Available BACKGROUND: Scientific and public fascination with human language have included intensive scrutiny of language disorders as a new window onto the biological foundations of language and its evolutionary origins. Specific language impairment (SLI, which affects over 7% of children, is one such disorder. SLI has received robust scientific attention, in part because of its recent linkage to a specific gene and loci on chromosomes and in part because of the prevailing question regarding the scope of its language impairment: Does the disorder impact the general ability to segment and process language or a specific ability to compute grammar? Here we provide novel electrophysiological data showing a domain-specific deficit within the grammar of language that has been hitherto undetectable through behavioural data alone. METHODS AND FINDINGS: We presented participants with Grammatical(G-SLI, age-matched controls, and younger child and adult controls, with questions containing syntactic violations and sentences containing semantic violations. Electrophysiological brain responses revealed a selective impairment to only neural circuitry that is specific to grammatical processing in G-SLI. Furthermore, the participants with G-SLI appeared to be partially compensating for their syntactic deficit by using neural circuitry associated with semantic processing and all non-grammar-specific and low-level auditory neural responses were normal. CONCLUSIONS: The findings indicate that grammatical neural circuitry underlying language is a developmentally unique system in the functional architecture of the brain, and this complex higher cognitive system can be selectively impaired. The findings advance fundamental understanding about how cognitive systems develop and all human language is represented and processed in the brain.

  12. Transgenic zebrafish reveal tissue-specific differences in estrogen signaling in response to environmental water samples

    Science.gov (United States)

    Gorelick, Daniel A.; Iwanowicz, Luke R.; Hung, Alice L.; Blazer, Vicki; Halpern, Marnie E.

    2014-01-01

    Background: Environmental endocrine disruptors (EED) are exogenous chemicals that mimic endogenous hormones, such as estrogens. Previous studies using a zebrafish transgenic reporter demonstrated that the EEDs bisphenol A and genistein preferentially activate estrogen receptors (ER) in the larval heart compared to the liver. However, it was not known whether the transgenic zebrafish reporter was sensitive enough to detect estrogens from environmental samples, whether environmental estrogens would exhibit similar tissue-specific effects as BPA and genistein or why some compounds preferentially target receptors in the heart. Methods: We tested surface water samples using a transgenic zebrafish reporter with tandem estrogen response elements driving green fluorescent protein expression (5xERE:GFP). Reporter activation was colocalized with tissue-specific expression of estrogen receptor genes by RNA in situ hybridization. Results: Selective patterns of ER activation were observed in transgenic fish exposed to river water samples from the Mid-Atlantic United States, with several samples preferentially activating receptors in embryonic and larval heart valves. We discovered that tissue-specificity in ER activation is due to differences in the expression of estrogen receptor subtypes. ERα is expressed in developing heart valves but not in the liver, whereas ERβ2 has the opposite profile. Accordingly, subtype-specific ER agonists activate the reporter in either the heart valves or the liver. Conclusion: The use of 5xERE:GFP transgenic zebrafish has revealed an unexpected tissue-specific difference in the response to environmentally relevant estrogenic compounds. Exposure to estrogenic EEDs in utero is associated with adverse health effects, with the potentially unanticipated consequence of targeting developing heart valves.

  13. Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins

    Directory of Open Access Journals (Sweden)

    Davey Jennifer C

    2007-12-01

    Full Text Available Abstract Background Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant. Results Our microarray identified genes reported in the literature to be regulated in response to cadmium exposure, suggested functional attributes for genes that share no sequence similarity to proteins in the public databases, and pointed to genes that are likely members of expanded gene families in the Daphnia genome. Genes identified on the microarray also were associated with cadmium induced phenotypes and population-level outcomes that we experimentally determined. A subset of genes regulated in response to cadmium exposure was independently validated using quantitative-realtime (Q-RT-PCR. These microarray studies led to the discovery of three genes coding for the metal detoxication protein metallothionein (MT. The gene structures and predicted translated sequences of D. pulex MTs clearly place them in this gene family. Yet, they share little homology with previously characterized MTs. Conclusion The genomic information obtained from this study represents an important first step in characterizing microarray patterns that may be diagnostic to specific environmental contaminants and give insights into their toxicological mechanisms, while also providing a practical tool for evolutionary, ecological, and toxicological functional gene discovery studies. Advances in Daphnia genomics will enable the further development of this species as a model organism for

  14. Barcoded pyrosequencing reveals that consumption of galactooligosaccharides results in a highly specific bifidogenic response in humans.

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    Lauren M G Davis

    Full Text Available Prebiotics are selectively fermented ingredients that allow specific changes in the gastrointestinal microbiota that confer health benefits to the host. However, the effects of prebiotics on the human gut microbiota are incomplete as most studies have relied on methods that fail to cover the breadth of the bacterial community. The goal of this research was to use high throughput multiplex community sequencing of 16S rDNA tags to gain a community wide perspective of the impact of prebiotic galactooligosaccharide (GOS on the fecal microbiota of healthy human subjects. Fecal samples from eighteen healthy adults were previously obtained during a feeding trial in which each subject consumed a GOS-containing product for twelve weeks, with four increasing dosages (0, 2.5, 5, and 10 gram of GOS. Multiplex sequencing of the 16S rDNA tags revealed that GOS induced significant compositional alterations in the fecal microbiota, principally by increasing the abundance of organisms within the Actinobacteria. Specifically, several distinct lineages of Bifidobacterium were enriched. Consumption of GOS led to five- to ten-fold increases in bifidobacteria in half of the subjects. Increases in Firmicutes were also observed, however, these changes were detectable in only a few individuals. The enrichment of bifidobacteria was generally at the expense of one group of bacteria, the Bacteroides. The responses to GOS and the magnitude of the response varied between individuals, were reversible, and were in accordance with dosage. The bifidobacteria were the only bacteria that were consistently and significantly enriched by GOS, although this substrate supported the growth of diverse colonic bacteria in mono-culture experiments. These results suggest that GOS can be used to enrich bifidobacteria in the human gastrointestinal tract with remarkable specificity, and that the bifidogenic properties of GOS that occur in vivo are caused by selective fermentation as well as by

  15. Mixed adjuvant formulations reveal a new combination that elicit antibody response comparable to Freund's adjuvants.

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    Rachel P J Lai

    Full Text Available Adjuvant formulations capable of inducing high titer and high affinity antibody responses would provide a major advance in the development of vaccines to viral infections such as HIV-1. Although oil-in-water emulsions, such as Freund's adjuvant (FCA/FIA, are known to be potent, their toxicity and reactogenicity make them unacceptable for human use. Here, we explored different adjuvants and compared their ability to elicit antibody responses to FCA/FIA. Recombinant soluble trimeric HIV-1 gp140 antigen was formulated in different adjuvants, including FCA/FIA, Carbopol-971P, Carbopol-974P and the licensed adjuvant MF59, or combinations of MF59 and Carbopol. The antigen-adjuvant formulation was administered in a prime-boost regimen into rabbits, and elicitation of antigen binding and neutralizing antibodies (nAbs was evaluated. When used individually, only FCA/FIA elicited significantly higher titer of nAbs than the control group (gp140 in PBS (p<0.05. Sequential prime-boost immunizations with different adjuvants did not offer improvements over the use of FCA/FIA or MF59. Remarkably however, the concurrent use of the combination of Carbopol-971P and MF59 induced potent adjuvant activity with significantly higher titer nAbs than FCA/FIA (p<0.05. This combination was not associated with any obvious local or systemic adverse effects. Antibody competition indicated that the majority of the neutralizing activities were directed to the CD4 binding site (CD4bs. Increased antibody titers to the gp41 membrane proximal external region (MPER and gp120 V3 were detected when the more potent adjuvants were used. These data reveal that the combination of Carbopol-971P and MF59 is unusually potent for eliciting nAbs to a variety of HIV-1 nAb epitopes.

  16. Characteristics of non-response in the Danish Health Interview Surveys, 1987-1994

    DEFF Research Database (Denmark)

    Kjøller, Mette; Thoning, Henrik

    2005-01-01

    -response biased the estimated population prevalence of morbidity when solely based on responders. METHODS: The data were for the 23,096 adults sampled for the Danish Health Interview Surveys in 1987, 1991 and 1994. All were followed using the National Patient Registry to obtain such information as hospital...... data collection. CONCLUSIONS: Although admission rates differed between respondents and non-respondents these differences were too small to bias the estimated population prevalence of morbidity when solely based on respondents....... admissions. RESULTS: Non-response increased from 20.0% in 1987 to 22.6% in 1994. Four combinations of background variables characterized the non-response: gender and age; gender and civil status; county of residence and age; survey year and age. Non-respondents and respondents had identical gender- and age...

  17. Fair reckoning: a qualitative investigation of responses to an economic health resource allocation survey.

    Science.gov (United States)

    Giacomini, Mita; Hurley, Jeremiah; DeJean, Deirdre

    2014-04-01

    To investigate how participants in an economic resource allocation survey construct notions of fairness. Qualitative interview study guided by interpretive grounded theory methods. Qualitative interviews were conducted with volunteer university- (n=39) and community-based (n =7) economic survey participants. INTERVENTION OR MAIN VARIABLES STUDIED: We explored how participants constructed meanings to guide or explain fair survey choices, focusing on rationales, imagery and additional desired information not provided in the survey scenarios. Data were transcribed and coded into qualitative categories. Analysis iterated with data collection iterated through three waves of interviews. Participants compared the survey dilemmas to domains outside the health system. Most compared them with other micro-level, inter-personal sharing tasks. Participants raised several fairness-relevant factors beyond need or capacity to benefit. These included age, weight, poverty, access to other options and personal responsibility for illness; illness duration, curability or seriousness; life expectancy; possibilities for sharing; awareness of other's needs; and ability to explain allocations to those affected. They also articulated a fairness principle little considered by equity theories: that everybody must get something and nobody should get nothing. Lay criteria for judging fairness are myriad. Simple scenarios may be used to investigate lay commitments to abstract principles. Although principles are the focus of analysis and inference, participants may solve simplified dilemmas by imputing extraneous features to the problem or applying unanticipated principles. These possibilities should be taken into account in the design of resource allocation surveys eliciting the views of the public. © 2012 John Wiley & Sons Ltd.

  18. Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure.

    Directory of Open Access Journals (Sweden)

    Amira Amrani

    Full Text Available RNA-seq was used to study the response of Desulfovibrio hydrothermalis, isolated from a deep-sea hydrothermal chimney on the East-Pacific Rise at a depth of 2,600 m, to various hydrostatic pressure growth conditions. The transcriptomic datasets obtained after growth at 26, 10 and 0.1 MPa identified only 65 differentially expressed genes that were distributed among four main categories: aromatic amino acid and glutamate metabolisms, energy metabolism, signal transduction, and unknown function. The gene expression patterns suggest that D. hydrothermalis uses at least three different adaptation mechanisms, according to a hydrostatic pressure threshold (HPt that was estimated to be above 10 MPa. Both glutamate and energy metabolism were found to play crucial roles in these mechanisms. Quantitation of the glutamate levels in cells revealed its accumulation at high hydrostatic pressure, suggesting its role as a piezolyte. ATP measurements showed that the energy metabolism of this bacterium is optimized for deep-sea life conditions. This study provides new insights into the molecular mechanisms linked to hydrostatic pressure adaptation in sulfate-reducing bacteria.

  19. Optical tweezers reveal a dynamic mechanical response of cationic peptide-DNA complexes

    Science.gov (United States)

    Lee, Amy; Zheng, Tai; Sucayan, Sarah; Chou, Szu-Ting; Tricoli, Lucas; Hustedt, Jason; Kahn, Jason; Mixson, A. James; Seog, Joonil

    2013-03-01

    Nonviral carriers have been developed to deliver nucleic acids by forming nanoscale complexes; however, there has been limited success in achieving high transfection efficiency. Our hypothesis is that a factor affecting gene delivery efficiency is the mechanical response of the condensed complex. To begin to test this hypothesis, we directly measured the mechanical properties of DNA-carrier complexes using optical tweezers. Histidine-lysine (HK) polymer, Asparagine-lysine (NK) polymer and poly-L-lysine were used to form complexes with a single DNA molecule. As carriers were introduced, a sudden decrease in DNA extension occurrs at a force level which is defined as critical force (Fc). Fc is carrier and concentration dependent. Pulling revealed reduction in DNA extension length for HK-DNA complexes. The characteristics of force profiles vary by agent and can be dynamically manipulated by changes in environmental conditions such as ionic strength of the buffer as well as pH. Heparin can remove cationic reagents which are otherwise irreversibly bound to DNA. The implications for optimizing molecular interactions to enhance transfection efficiency will be discussed.

  20. Delay discounting task in pigs reveals response strategies related to dopamine metabolite.

    Science.gov (United States)

    Melotti, Luca; Thomsen, Liat Romme; Toscano, Michael J; Mendl, Michael; Held, Suzanne

    2013-08-15

    We developed a novel delay discounting task to investigate outcome impulsivity in pigs. As impulsivity can affect aggression, and might also relate to proactive and reactive coping styles, eight proactive (HR) and eight reactive (LR) pigs identified in a manual restraint test ("Backtest", after Bolhuis et al., 2003) were weaned and mixed in four pens of four unfamiliar pigs, so that each pen had two HR and two LR pigs, and aggression was scored in the 9h after mixing. In the delay discounting task, each pig chose between two levers, one always delivering a small immediate reward, the other a large delayed reward with daily increasing delays, impulsive individuals being the ones discounting the value of the large reward quicker. Two novel strategies emerged: some pigs gradually switched their preference towards the small reward ('Switchers') as predicted, but others persistently preferred the large reward until they stopped making choices ('Omitters'). Outcome impulsivity itself was unrelated to these strategies, to urinary serotonin metabolite (5-HIAA) or dopamine metabolite (HVA) levels, aggression at weaning, or coping style. However, HVA was relatively higher in Omitters than Switchers, and positively correlated with behavioural measures of indecisiveness and frustration during choosing. The delay discounting task thus revealed two response strategies that seemed to be related to the activity of the dopamine system and might indicate a difference in execution, rather than outcome, impulsivity.

  1. Retrospective stable isotope analysis reveals ecosystem responses to river regulation over the last century.

    Science.gov (United States)

    Turner, Thomas F; Krabbenhoft, Trevor I; Collyer, Michael L; Krabbenhoft, Corey A; Edwards, Melanie S; Sharp, Zachary D

    2015-12-01

    Disruption of natural flow regimes, nutrient pollution, and other consequences of human population growth and development have impacted most major rivers of the world. Alarming losses of aquatic biodiversity coincide with human-caused river alteration, but effects of biotic homogenization on aquatic ecosystem processes are not as well documented. This is because unaltered systems for comparison are scarce, and some ecosystem-wide effects may take decades to manifest. We evaluated aquatic ecosystem responses to extensive river- floodplain engineering and nutrient addition in the Rio Grande of southwestern North America as revealed by changes in trophic structure of, and resource availability to, the fish community. Stable Isotope Analysis (SIA) was conducted on museum-preserved fishes collected over a 70-year period of intensive river management and exponential human population growth. Trophic complexity and resource heterogeneity for fish consumers (measured as "isotopic niche breadth") decreased following sediment deprivation and channelization, and these effects persist into the present. Increased nutrient inputs led to δ15N enrichment in the entire fish community at all affected sites, and a shift to autochthonous sources of carbon at the most proximal site downstream of wastewater release, probably via bottom-up transfer. Overall, retrospective SIA of apex consumers suggests radical change and functional impairment of a floodplain river ecosystem already marked by significant biodiversity loss.

  2. Genetic structure along an elevational gradient in Hawaiian honeycreepers reveals contrasting evolutionary responses to avian malaria

    Directory of Open Access Journals (Sweden)

    Hart Patrick J

    2008-11-01

    Full Text Available Abstract Background The Hawaiian honeycreepers (Drepanidinae are one of the best-known examples of an adaptive radiation, but their persistence today is threatened by the introduction of exotic pathogens and their vector, the mosquito Culex quinquefasciatus. Historically, species such as the amakihi (Hemignathus virens, the apapane (Himatione sanguinea, and the iiwi (Vestiaria coccinea were found from the coastal lowlands to the high elevation forests, but by the late 1800's they had become extremely rare in habitats below 900 m. Recently, however, populations of amakihi and apapane have been observed in low elevation habitats. We used twelve polymorphic microsatellite loci to investigate patterns of genetic structure, and to infer responses of these species to introduced avian malaria along an elevational gradient on the eastern flanks of Mauna Loa and Kilauea volcanoes on the island of Hawaii. Results Our results indicate that amakihi have genetically distinct, spatially structured populations that correspond with altitude. We detected very few apapane and no iiwi in low-elevation habitats, and genetic results reveal only minimal differentiation between populations at different altitudes in either of these species. Conclusion Our results suggest that amakihi populations in low elevation habitats have not been recolonized by individuals from mid or high elevation refuges. After generations of strong selection for pathogen resistance, these populations have rebounded and amakihi have become common in regions in which they were previously rare or absent.

  3. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.

    Science.gov (United States)

    Mackelprang, Rachel; Waldrop, Mark P; DeAngelis, Kristen M; David, Maude M; Chavarria, Krystle L; Blazewicz, Steven J; Rubin, Edward M; Jansson, Janet K

    2011-11-06

    Permafrost contains an estimated 1672 Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 °C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.

  4. Genetic structure along an elevational gradient in Hawaiian honeycreepers reveals contrasting evolutionary responses to avian malaria

    Science.gov (United States)

    Eggert, L.S.; Terwilliger, L.A.; Woodworth, B.L.; Hart, P.J.; Palmer, D.; Fleischer, R.C.

    2008-01-01

    Background. The Hawaiian honeycreepers (Drepanidinae) are one of the best-known examples of an adaptive radiation, but their persistence today is threatened by the introduction of exotic pathogens and their vector, the mosquito Culex quinquefasciatus. Historically, species such as the amakihi (Hemignathus virens), the apapane (Himatione sanguinea), and the iiwi (Vestiaria coccinea) were found from the coastal lowlands to the high elevation forests, but by the late 1800's they had become extremely rare in habitats below 900 m. Recently, however, populations of amakihi and apapane have been observed in low elevation habitats. We used twelve polymorphic microsatellite loci to investigate patterns of genetic structure, and to infer responses of these species to introduced avian malaria along an elevational gradient on the eastern flanks of Mauna Loa and Kilauea volcanoes on the island of Hawaii. Results. Our results indicate that amakihi have genetically distinct, spatially structured populations that correspond with altitude. We detected very few apapane and no iiwi in low-elevation habitats, and genetic results reveal only minimal differentiation between populations at different altitudes in either of these species. Conclusion. Our results suggest that amakihi populations in low elevation habitats have not been recolonized by individuals from mid or high elevation refuges. After generations of strong selection for pathogen resistance, these populations have rebounded and amakihi have become common in regions in which they were previously rare or absent. ?? 2008 Eggert et al; licensee BioMed Central Ltd.

  5. Extensive hydrothermal activity revealed by multi-tracer survey in the Wallis and Futuna region (SW Pacific)

    Science.gov (United States)

    Konn, C.; Fourré, E.; Jean-Baptiste, P.; Donval, J. P.; Guyader, V.; Birot, D.; Alix, A. S.; Gaillot, A.; Perez, F.; Dapoigny, A.; Pelleter, E.; Resing, J. A.; Charlou, J. L.; Fouquet, Y.

    2016-10-01

    The study area is close to the Wallis and Futuna Islands in the French EEZ. It exists on the western boundary of the fastest tectonic area in the world at the junction of the Lau and North-Fiji basins. At this place, the unstable back-arc accommodates the plate motion in three ways: (i) the north Fiji transform fault, (ii) numerous unstable spreading ridges, and (iii) large areas of recent volcanic activity. This instability creates bountiful opportunity for hydrothermal discharge to occur. Based on geochemical (CH4, TDM, 3He) and geophysical (nephelometry) tracer surveys: (1) no hydrothermal activity could be found on the Futuna Spreading Centre (FSC) which sets the western limit of hydrothermal activity; (2) four distinct hydrothermal active areas were identified: Kulo Lasi Caldera, Amanaki Volcano, Fatu Kapa and Tasi Tulo areas; (3) extensive and diverse hydrothermal manifestations were observed and especially a 2D distribution of the sources. At Kulo Lasi, our data and especially tracer ratios (CH4/3He 50×106 and CH4/TDM 4.5) reveal a transient CH4 input, with elevated levels of CH4 measured in 2010, that had vanished in 2011, most likely caused by an eruptive magmatic event. By contrast at Amanaki, vertical tracer profiles and tracer ratios point to typical seawater/basalt interactions. Fatu Kapa is characterised by a substantial spatial variability of the hydrothermal water column anomalies, most likely due to widespread focused and diffuse hydrothermal discharge in the area. In the Tasi Tulo zone, the hydrothermal signal is characterised by a total lack of turbidity, although other tracer anomalies are in the same range as in nearby Fatu Kapa. The background data set revealed the presence of a Mn and 3He chronic plume due to the extensive and cumulative venting over the entire area. To that respect, we believe that the joined domain composed of our active area and the nearby active area discovered in the East by Lupton et al. (2012) highly contribute to the

  6. Fluid circulation and reservoir conditions of the Los Humeros Geothermal Field (LHGF), Mexico, as revealed by a noble gas survey

    Science.gov (United States)

    Pinti, Daniele L.; Castro, M. Clara; Lopez-Hernandez, Aida; Han, Guolei; Shouakar-Stash, Orfan; Hall, Chris M.; Ramírez-Montes, Miguel

    2017-03-01

    Los Humeros Geothermal Field (LHGF) is one of four geothermal fields currently operating in Mexico, in exploitation since 1990. Located in a caldera complex filled with very low-permeability rhyolitic ignimbrites that are the reservoir cap-rock, recharge of the geothermal field is both limited and localized. Because of this, planning of any future geothermal exploitation must be based on a clear understanding of the fluid circulation. To this end, a first noble gas survey was carried out in which twenty-two production wells were sampled for He, Ne, Ar, Kr, and Xe isotope analysis. Air-corrected 3He/4He ratios (Rc) measured in the fluid, normalized to the helium atmospheric ratio (Ra; 1.384 × 10- 6), are consistently high across the field, with an average value of 7.03 ± 0.40 Ra. This value is close to that of the sub-continental upper mantle, indicating that LHGF mines heat from an active magmatic system. Freshwater recharge does not significantly affect He isotopic ratios, contributing 1-10% of the total fluid amount. The presence of radiogenic 40Ar* in the fluid suggests a fossil fluid component that might have circulated within the metacarbonate basement with radiogenic argon produced from detrital dispersed illite. Solubility-driven elemental fractionation of Ne/Ar, Kr/Ar, and Xe/Ar confirm extreme boiling in the reservoir. However, a combined analysis of these ratios with 40Ar/36Ar reveals mixing with an air component, possibly introduced by re-injected geothermal fluids.

  7. Prospective evaluation of direct approach with a tablet device as a strategy to enhance survey study participant response rate

    Directory of Open Access Journals (Sweden)

    Parker Melissa J

    2012-10-01

    Full Text Available Abstract Background Investigators conduct survey studies for a variety of reasons. Poor participant response rates are common, however, and may limit the generalizability and utility of results. The objective of this study was to determine whether direct approach with a tablet device enhances survey study participant response rate and to assess participants’ experiences with this mode of survey administration. Findings An interventional study nested within a single center survey study was conducted at McMaster Children’s Hospital. The primary outcome was the ability to achieve of a survey study response rate of 70% or greater. Eligible participants received 3 email invitations (Week 0, 2, 4 to complete a web-based (Survey Monkey survey. The study protocol included plans for a two-week follow-up phase (Phase 2 where non-responders were approached by a research assistant and invited to complete an iPad-based version of the survey. The Phase 1 response rate was 48.7% (56/115. Phase 2 effectively recruited reluctant responders, increasing the overall response rate to 72.2% (83/115. On a 7-point Likert scale, reluctant responders highly rated their enjoyment (mean 6.0, sd 0.83 [95% CI: 5.7-6.3] and ease of use (mean 6.7, sd 0.47 [95% CI: 6.5-6.9] completing the survey using the iPad. Reasons endorsed for Phase 2 participation included: direct approach (81%, immediate survey access (62%, and the novelty of completing a tablet-based survey (54%. Most reluctant responders (89% indicated that a tablet-based survey is their preferred method of survey completion. Conclusions Use of a tablet-based version of the survey was effective in recruiting reluctant responders and this group reported positive experiences with this mode of survey administration.

  8. Cultural differences in survey responding: Issues and insights in the study of response biases.

    Science.gov (United States)

    Kemmelmeier, Markus

    2016-12-01

    This paper introduces the special section "Cultural differences in questionnaire responding" and discusses central topics in the research on response biases in cross-cultural survey research. Based on current conceptions of acquiescent, extreme, and socially desirable responding, the author considers current data on the correlated nature of response biases and the conditions under which different response styles they emerge. Based on evidence relating different response styles to the cultural dimension of individualism-collectivism, the paper explores how research presented as part of this special section might help resolves some tensions in this literature. The paper concludes by arguing that response styles should not be treated merely as measurement error, but as cultural behaviors in themselves.

  9. Understanding Spanish-Language Response in a National Health Communication Survey: Implications for Health Communication Research.

    Science.gov (United States)

    Ramírez, A Susana; Willis, Gordon; Rutten, Lila Finney

    2017-05-01

    Spanish-speaking Latinos account for 13% of the U.S. population yet are chronically under-represented in national surveys; additionally, the response quality suffers from low literacy rates and translation challenges. These are the same issues that health communicators face when understanding how best to communicate important health information to Latinos. The Health Information National Trends Survey (HINTS) offers a unique opportunity to understand the health communication landscape and information needs of the U.S. We describe the challenges in recruiting Spanish-speaking HINTS respondents and strategies used to improve rates and quality of responses among Spanish-speaking Latinos. Cognitive interviewing techniques helped to better understand how Spanish-speaking Latinos were interpreting the survey questions, and the extent to which these interpretations matched English-speaking respondents' interpretations. Some Spanish-speaking respondents had difficulty with the questions because of a lack of access to health care. Additionally, Spanish-speaking respondents had a particularly hard time answering questions that were presented in a grid format. We describe the cognitive interview process, and consider the impact of format changes on Spanish-speaking people's responses and response quality. We discuss challenges that remain in understanding health information needs of non-English-speakers.

  10. Hepatitis C virus reveals a novel early control in acute immune response.

    Directory of Open Access Journals (Sweden)

    Noëlla Arnaud

    2011-10-01

    Full Text Available Recognition of viral RNA structures by the intracytosolic RNA helicase RIG-I triggers induction of innate immunity. Efficient induction requires RIG-I ubiquitination by the E3 ligase TRIM25, its interaction with the mitochondria-bound MAVS protein, recruitment of TRAF3, IRF3- and NF-κB-kinases and transcription of Interferon (IFN. In addition, IRF3 alone induces some of the Interferon-Stimulated Genes (ISGs, referred to as early ISGs. Infection of hepatocytes with Hepatitis C virus (HCV results in poor production of IFN despite recognition of the viral RNA by RIG-I but can lead to induction of early ISGs. HCV was shown to inhibit IFN production by cleaving MAVS through its NS3/4A protease and by controlling cellular translation through activation of PKR, an eIF2α-kinase containing dsRNA-binding domains (DRBD. Here, we have identified a third mode of control of IFN induction by HCV. Using HCVcc and the Huh7.25.CD81 cells, we found that HCV controls RIG-I ubiquitination through the di-ubiquitine-like protein ISG15, one of the early ISGs. A transcriptome analysis performed on Huh7.25.CD81 cells silenced or not for PKR and infected with JFH1 revealed that HCV infection leads to induction of 49 PKR-dependent genes, including ISG15 and several early ISGs. Silencing experiments revealed that this novel PKR-dependent pathway involves MAVS, TRAF3 and IRF3 but not RIG-I, and that it does not induce IFN. Use of PKR inhibitors showed that this pathway requires the DRBD but not the kinase activity of PKR. We then demonstrated that PKR interacts with HCV RNA and MAVS prior to RIG-I. In conclusion, HCV recruits PKR early in infection as a sensor to trigger induction of several IRF3-dependent genes. Among those, ISG15 acts to negatively control the RIG-I/MAVS pathway, at the level of RIG-I ubiquitination.These data give novel insights in the machinery involved in the early events of innate immune response.

  11. Development of Survey Scales for Measuring Exposure and Behavioral Responses to Disruptive Intraoperative Behavior.

    Science.gov (United States)

    Villafranca, Alexander; Hamlin, Colin; Rodebaugh, Thomas L; Robinson, Sandra; Jacobsohn, Eric

    2017-09-10

    Disruptive intraoperative behavior has detrimental effects to clinicians, institutions, and patients. How clinicians respond to this behavior can either exacerbate or attenuate its effects. Previous investigations of disruptive behavior have used survey scales with significant limitations. The study objective was to develop appropriate scales to measure exposure and responses to disruptive behavior. We obtained ethics approval. The scales were developed in a sequence of steps. They were pretested using expert reviews, computational linguistic analysis, and cognitive interviews. The scales were then piloted on Canadian operating room clinicians. Factor analysis was applied to half of the data set for question reduction and grouping. Item response analysis and theoretical reviews ensured that important questions were not eliminated. Internal consistency was evaluated using Cronbach α. Model fit was examined on the second half of the data set using confirmatory factor analysis. Content validity of the final scales was re-evaluated. Consistency between observed relationships and theoretical predictions was assessed. Temporal stability was evaluated on a subsample of 38 respondents. A total of 1433 and 746 clinicians completed the exposure and response scales, respectively. Content validity indices were excellent (exposure = 0.96, responses = 1.0). Internal consistency was good (exposure = 0.93, responses = 0.87). Correlations between the exposure scale and secondary measures were consistent with expectations based on theory. Temporal stability was acceptable (exposure = 0.77, responses = 0.73). We have developed scales measuring exposure and responses to disruptive behavior. They generate valid and reliable scores when surveying operating room clinicians, and they overcome the limitations of previous tools. These survey scales are freely available.

  12. SURVEY

    DEFF Research Database (Denmark)

    SURVEY er en udbredt metode og benyttes inden for bl.a. samfundsvidenskab, humaniora, psykologi og sundhedsforskning. Også uden for forskningsverdenen er der mange organisationer som f.eks. konsulentfirmaer og offentlige institutioner samt marketingsafdelinger i private virksomheder, der arbejder...... med surveys. Denne bog gennemgår alle surveyarbejdets faser og giver en praktisk indføring i: • design af undersøgelsen og udvælgelse af stikprøver, • formulering af spørgeskemaer samt indsamling og kodning af data, • metoder til at analysere resultaterne...

  13. Differential molecular responses of rapeseed cotyledons to light and dark reveal metabolic adaptations towards autotrophy establishment

    Directory of Open Access Journals (Sweden)

    Dongli He

    2016-07-01

    Full Text Available Photosynthesis competent autotrophy should be established during the postgerminative stage of plant growth. Among the multiple factors, light plays a decisive role in the switch from heterotrophic to autotrophic growth. Under dark condition, the rapeseed hypocotyl extends quickly with an apical hook, and the cotyledon is yellow and folded, and maintains high level of the isocitrate lyase (ICL. By contrast, in the light, the hypocotyl extends slowly, the cotyledon unfolds and turns green, the ICL content changes in parallel with the cotyledon greening. To reveal metabolic adaptations during the establishment of postgerminative autotrophy in rapeseed, we conducted comparative proteomic and metabolomic analyses of the cotyledons of seedlings grown under light versus dark conditions. Under both conditions, the increase of the protease, fatty acids β-oxidation and glyoxylate-cycle related proteins was accompanied with rapid degradation of the stored proteins and lipids with an accumulation of the amino acids, while light condition partially retarded these conversions. Light significantly induced the expression of chlorophyll-binding and photorespiration related proteins, resulting in an increase of the reducing-sugar. However, the levels of some chlide conversion, Calvin-cycle and photorespiration related proteins also accumulated in dark grown cotyledons, implying that the transition from heterotrophy to autotrophy is programmed in the seed rather than induced by light. Various anti-stress systems, e.g., redox related proteins, salicylic acid, proline and chaperones, were employed to release the oxidative stress, which was mainly derived from lipid oxidation or photorespiration, under both conditions. This study provides a comprehensive understanding of the differential molecular responses of rapeseed cotyledons to light and dark conditions, which will facilitate further study on the complex mechanism underlying the transition from heterotrophy to

  14. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

    Science.gov (United States)

    MacKelprang, R.; Waldrop, M.P.; Deangelis, K.M.; David, M.M.; Chavarria, K.L.; Blazewicz, S.J.; Rubin, E.M.; Jansson, J.K.

    2011-01-01

    Permafrost contains an estimated 1672????????Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 ??C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost. ?? 2011 Macmillan Publishers Limited. All rights reserved.

  15. Dropout Rates and Response Times of an Occupation Search Tree in a Web Survey

    Directory of Open Access Journals (Sweden)

    Tijdens Kea

    2014-03-01

    Full Text Available Occupation is key in socioeconomic research. As in other survey modes, most web surveys use an open-ended question for occupation, though the absence of interviewers elicits unidentifiable or aggregated responses. Unlike other modes, web surveys can use a search tree with an occupation database. They are hardly ever used, but this may change due to technical advancements. This article evaluates a three-step search tree with 1,700 occupational titles, used in the 2010 multilingual WageIndicator web survey for UK, Belgium and Netherlands (22,990 observations. Dropout rates are high; in Step 1 due to unemployed respondents judging the question not to be adequate, and in Step 3 due to search tree item length. Median response times are substantial due to search tree item length, dropout in the next step and invalid occupations ticked. Overall the validity of the occupation data is rather good, 1.7-7.5% of the respondents completing the search tree have ticked an invalid occupation.

  16. 25-year trends and socio-demographic differences in response rates: Finnish adult health behaviour survey.

    Science.gov (United States)

    Tolonen, Hanna; Helakorpi, Satu; Talala, Kirsi; Helasoja, Ville; Martelin, Tuija; Prättälä, Ritva

    2006-01-01

    When estimating population level changes in health indicators, the declining response rate, especially if also the characteristics of non-respondents are changing may bias the outcome. There is evidence that survey response rates are declining in many countries. It is also known that respondents and non-respondents differ in their socio-economic and demographic status as well as in their health and health behaviours. There is no information about the changes in the differences between respondents and non-respondents over time. Our purpose was to investigate the changes over time in the differences between respondents and non-respondents in respect to their sex, age, marital status and educational level. The data from the Finnish Adult Health Behaviour Survey (1978-2002) was used. The response rate declined over the past 25 years for both men and women in all age groups. The decline was faster among men than women, and also faster in younger age groups than older age groups. There is a marked difference in the response rate between married and non-married persons but it did not change over time. Also the response rate between different educational levels differed for both men and women, and this difference increased over the years. The declining response rate and at the same time occurring change in the non-respondent characteristics will decrease the representativeness of the results, limit the comparability of the results with other surveys, increase the bias of the trend estimates and limit the comparability of the results between population groups.

  17. A survey of hospitals to determine the prevalence and characteristics of healthcare coalitions for emergency preparedness and response.

    Science.gov (United States)

    Rambhia, Kunal J; Waldhorn, Richard E; Selck, Frederick; Mehta, Ambereen Kurwa; Franco, Crystal; Toner, Eric S

    2012-09-01

    Previous reports have identified the development of healthcare coalitions as the foundation for disaster response across the United States. This survey of acute care hospitals characterizes the current status of participation by US hospitals in healthcare coalitions for emergency preparedness planning and response. The survey results show the nearly universal nature of a coalition approach to disaster response. The results suggest a need for wide stakeholder involvement but also for flexibility in structure and organization. Based on the survey results, the authors make recommendations to guide the further development of healthcare coalitions and to improve local and national response to disasters.

  18. A literature survey of private sector methods of determining personal financial responsibility

    OpenAIRE

    Bodzin, Martin Bradley

    1988-01-01

    Approved for public release; distribution is unlimited Credit grantors and employers have two clearly established methods-- judgmental and empirically derived--of determining personal financial responsibility that can be used as a basis for accepting or rejecting credit or job applicants. This thesis is a literature survey and analysis of those methods. The foundations of the two methods are examined and models of the empirically derived method are discussed. The pa...

  19. Are Divorce Studies Trustworthy? The Effects of Survey Nonresponse and Response Errors

    OpenAIRE

    Mitchell, Colter

    2010-01-01

    Researchers rely on relationship data to measure the multifaceted nature of families. This article speaks to relationship data quality by examining the ramifications of different types of error on divorce estimates, models predicting divorce behavior, and models employing divorce as a predictor. Comparing matched survey and divorce certificate information from the 1995 Life Events and Satisfaction Study (N = 1,811) showed that nonresponse error is responsible for the majority of the error in ...

  20. Patient and dental student responses to a survey about AIDS in the dental setting.

    Science.gov (United States)

    Thaker, H J; Gobetti, J P; Green, T G

    1993-01-01

    The purpose of the study was to gain information about patients' and dental students' attitudes concerning AIDS and dentistry. Opinions of patients and students at a Midwestern dental school were surveyed. The dental students' responses were not as consistent as the patient responses. Both groups felt there was a risk to patients and dentists of HIV infection. Both groups had confidence in the CDC infection control guidelines. The patient responses to the testing questions were significantly more positive than the student responses. The patients responded positively to the concept that healthcare professionals had the right to ask patients to be tested and to being required to be tested if a healthcare provider is accidentally stuck by a needle used on a patient. The dental students were more cautious with both issues. Patients would use knowledge about a healthcare provider's HIV status and the office treatment of AIDS patients to determine if they should continue treatment at that dental office.

  1. Visual surveys can reveal rather different 'pictures' of fish densities: Comparison of trawl and video camera surveys in the Rockall Bank, NE Atlantic Ocean

    Science.gov (United States)

    McIntyre, F. D.; Neat, F.; Collie, N.; Stewart, M.; Fernandes, P. G.

    2015-01-01

    Visual surveys allow non-invasive sampling of organisms in the marine environment which is of particular importance in deep-sea habitats that are vulnerable to damage caused by destructive sampling devices such as bottom trawls. To enable visual surveying at depths greater than 200 m we used a deep towed video camera system, to survey large areas around the Rockall Bank in the North East Atlantic. The area of seabed sampled was similar to that sampled by a bottom trawl, enabling samples from the towed video camera system to be compared with trawl sampling to quantitatively assess the numerical density of deep-water fish populations. The two survey methods provided different results for certain fish taxa and comparable results for others. Fish that exhibited a detectable avoidance behaviour to the towed video camera system, such as the Chimaeridae, resulted in mean density estimates that were significantly lower (121 fish/km2) than those determined by trawl sampling (839 fish/km2). On the other hand, skates and rays showed no reaction to the lights in the towed body of the camera system, and mean density estimates of these were an order of magnitude higher (64 fish/km2) than the trawl (5 fish/km2). This is probably because these fish can pass under the footrope of the trawl due to their flat body shape lying close to the seabed but are easily detected by the benign towed video camera system. For other species, such as Molva sp, estimates of mean density were comparable between the two survey methods (towed camera, 62 fish/km2; trawl, 73 fish/km2). The towed video camera system presented here can be used as an alternative benign method for providing indices of abundance for species such as ling in areas closed to trawling, or for those fish that are poorly monitored by trawl surveying in any area, such as the skates and rays.

  2. Modifications of some simple One-stage Randomized Response Models to Two-stage in complex surveys

    Directory of Open Access Journals (Sweden)

    Mohammad Rafiq

    2016-06-01

    Full Text Available Warner (1965 introduced a Randomized Response Technique (RRT to minimize bias due to non- response or false response. Thereafter, several researchers have made significant contribution in the development and modification of different Randomized Response Models. We have modified a few one-stage Simple Randomized Response Models to two-stage randomized response models in complex surveys and found that our developed models are more efficient.

  3. Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members.

    Science.gov (United States)

    Ariani, Pietro; Regaiolo, Alice; Lovato, Arianna; Giorgetti, Alejandro; Porceddu, Andrea; Camiolo, Salvatore; Wong, Darren; Castellarin, Simone; Vandelle, Elodie; Polverari, Annalisa

    2016-12-02

    The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes. Most of the grapevine ATL genes lacked introns and were scattered among the 19 chromosomes, with a high level of duplication retention. Expression profiling revealed that some ATL genes are expressed specifically during early or late development and may participate in the juvenile to mature plant transition, whereas others may play a role in pathogen and/or abiotic stress responses, making them key candidates for further functional analysis. Our data offer the first genome-wide overview and annotation of the grapevine ATL family, and provide a basis for investigating the roles of specific family members in grapevine physiology and stress responses, as well as potential biotechnological applications.

  4. Internal Medicine Residents' Perceived Responsibility for Patients at Hospital Discharge: A National Survey.

    Science.gov (United States)

    Young, Eric; Stickrath, Chad; McNulty, Monica C; Calderon, Aaron J; Chapman, Elizabeth; Gonzalo, Jed D; Kuperman, Ethan F; Lopez, Max; Smith, Christopher J; Sweigart, Joseph R; Theobald, Cecelia N; Burke, Robert E

    2016-12-01

    Medical residents are routinely entrusted with transitions of care, yet little is known about the duration or content of their perceived responsibility for patients they discharge from the hospital. To examine the duration and content of internal medicine residents' perceived responsibility for patients they discharge from the hospital. The secondary objective was to determine whether specific individual experiences and characteristics correlate with perceived responsibility. Multi-site, cross-sectional 24-question survey delivered via email or paper-based form. Internal medicine residents (post-graduate years 1-3) at nine university and community-based internal medicine training programs in the United States. Perceived responsibility for patients after discharge as measured by a previously developed single-item tool for duration of responsibility and novel domain-specific questions assessing attitudes towards specific transition of care behaviors. Of 817 residents surveyed, 469 responded (57.4 %). One quarter of residents (26.1 %) indicated that their responsibility for patients ended at discharge, while 19.3 % reported perceived responsibility extending beyond 2 weeks. Perceived duration of responsibility did not correlate with level of training (P = 0.57), program type (P = 0.28), career path (P = 0.12), or presence of burnout (P = 0.59). The majority of residents indicated they were responsible for six of eight transitional care tasks (85.1-99.3 % strongly agree or agree). Approximately half of residents (57 %) indicated that it was their responsibility to directly contact patients' primary care providers at discharge. and 21.6 % indicated that it was their responsibility to ensure that patients attended their follow-up appointments. Internal medicine residents demonstrate variability in perceived duration of responsibility for recently discharged patients. Neither the duration nor the content of residents' perceived responsibility was

  5. Pairing call-response surveys and distance sampling for a mammalian carnivore

    Science.gov (United States)

    Hansen, Sara J. K.; Frair, Jacqueline L.; Underwood, Harold B.; Gibbs, James P.

    2015-01-01

    Density estimates accounting for differential animal detectability are difficult to acquire for wide-ranging and elusive species such as mammalian carnivores. Pairing distance sampling with call-response surveys may provide an efficient means of tracking changes in populations of coyotes (Canis latrans), a species of particular interest in the eastern United States. Blind field trials in rural New York State indicated 119-m linear error for triangulated coyote calls, and a 1.8-km distance threshold for call detectability, which was sufficient to estimate a detection function with precision using distance sampling. We conducted statewide road-based surveys with sampling locations spaced ≥6 km apart from June to August 2010. Each detected call (be it a single or group) counted as a single object, representing 1 territorial pair, because of uncertainty in the number of vocalizing animals. From 524 survey points and 75 detections, we estimated the probability of detecting a calling coyote to be 0.17 ± 0.02 SE, yielding a detection-corrected index of 0.75 pairs/10 km2 (95% CI: 0.52–1.1, 18.5% CV) for a minimum of 8,133 pairs across rural New York State. Importantly, we consider this an index rather than true estimate of abundance given the unknown probability of coyote availability for detection during our surveys. Even so, pairing distance sampling with call-response surveys provided a novel, efficient, and noninvasive means of monitoring populations of wide-ranging and elusive, albeit reliably vocal, mammalian carnivores. Our approach offers an effective new means of tracking species like coyotes, one that is readily extendable to other species and geographic extents, provided key assumptions of distance sampling are met.

  6. Autonomic Nervous System Responses Can Reveal Visual Fatigue Induced by 3D Displays

    Directory of Open Access Journals (Sweden)

    Eui Chul Lee

    2013-09-01

    Full Text Available Previous research has indicated that viewing 3D displays may induce greater visual fatigue than viewing 2D displays. Whether viewing 3D displays can evoke measureable emotional responses, however, is uncertain. In the present study, we examined autonomic nervous system responses in subjects viewing 2D or 3D displays. Autonomic responses were quantified in each subject by heart rate, galvanic skin response, and skin temperature. Viewers of both 2D and 3D displays showed strong positive correlations with heart rate, which indicated little differences between groups. In contrast, galvanic skin response and skin temperature showed weak positive correlations with average difference between viewing 2D and 3D. We suggest that galvanic skin response and skin temperature can be used to measure and compare autonomic nervous responses in subjects viewing 2D and 3D displays.

  7. Effects of Using Visual Design Principles to Group Response Options in Web Surveys

    Directory of Open Access Journals (Sweden)

    Michael J. Stern

    2006-03-01

    Full Text Available In this paper, we show that in Web questionnaires verbal and visual languages can be used to create groups and subgroups of information, which influence how respondents process Web questionnaires. Following Schwarz (1996; and also Schwarz, Grayson, & Knäuper, 1998 we argue that respondents act as cooperative communicators who use formal features of the questionnaire to help guide them through the survey conversation. Using data from three Web surveys of random samples of Washington State University undergraduates, we found that when response options are placed in close graphical proximity to each other and separated from other options, respondents perceive visual subgroups of the categories, increasing the likelihood that they select an answer from each subgroup. We also found that graphical proximity creates subgroups with and without the use of category heading to describe the subgroups and that the addition of a verbal instruction to “please select the best answer” encouraged respondents to select one answer from each subgroup instead of overriding the effects of proximity. In addition, the effects of grouping were consistent when the subgroups were positioned either vertically or horizontally in relation to each other. Lastly, we found that the effects of visual grouping are consistent across both opinion- and behavior/fact-based questions, although the effects appear to be greater on opinion-based questions. Our findings contribute to the increasing evidence that both verbal and visual languages influence how respondents process and respond to surveys. Because respondents interpret the verbal and graphical features of survey questionnaires as relevant to answering the survey, inadvertent or stylistic design changes can influence how respondents process and respond to survey questions.

  8. A genome-wide survey for host response of silkworm, Bombyx mori during pathogen Bacillus bombyseptieus infection.

    Directory of Open Access Journals (Sweden)

    Lulin Huang

    Full Text Available Host-pathogen interactions are complex relationships, and a central challenge is to reveal the interactions between pathogens and their hosts. Bacillus bombysepticus (Bb which can produces spores and parasporal crystals was firstly separated from the corpses of the infected silkworms (Bombyx mori. Bb naturally infects the silkworm can cause an acute fuliginosa septicaemia and kill the silkworm larvae generally within one day in the hot and humid season. Bb pathogen of the silkworm can be used for investigating the host responses after the infection. Gene expression profiling during four time-points of silkworm whole larvae after Bb infection was performed to gain insight into the mechanism of Bb-associated host whole body effect. Genome-wide survey of the host genes demonstrated many genes and pathways modulated after the infection. GO analysis of the induced genes indicated that their functions could be divided into 14 categories. KEGG pathway analysis identified that six types of basal metabolic pathway were regulated, including genetic information processing and transcription, carbohydrate metabolism, amino acid and nitrogen metabolism, nucleotide metabolism, metabolism of cofactors and vitamins, and xenobiotic biodegradation and metabolism. Similar to Bacillus thuringiensis (Bt, Bb can also induce a silkworm poisoning-related response. In this process, genes encoding midgut peritrophic membrane proteins, aminopeptidase N receptors and sodium/calcium exchange protein showed modulation. For the first time, we found that Bb induced a lot of genes involved in juvenile hormone synthesis and metabolism pathway upregulated. Bb also triggered the host immune responses, including cellular immune response and serine protease cascade melanization response. Real time PCR analysis showed that Bb can induce the silkworm systemic immune response, mainly by the Toll pathway. Anti-microorganism peptides (AMPs, including of Attacin, Lebocin, Enbocin, Gloverin

  9. Survey of state and tribal emergency response capabilities for radiological transportation incidents

    Energy Technology Data Exchange (ETDEWEB)

    Vilardo, F J; Mitter, E L; Palmer, J A; Briggs, H C; Fesenmaier, J [Indiana Univ., Bloomington, IN (USA). School of Public and Environmental Affairs

    1990-05-01

    This publication is the final report of a project to survey the fifty states, the District of Columbia, Puerto Rico, and selected Indian Tribal jurisdictions to ascertain their emergency-preparedness planning and capabilities for responding to transportation incidents involving radioactive materials. The survey was conducted to provide the Nuclear Regulatory Commission and other federal agencies with information concerning the current level of emergency-response preparedness of the states and selected tribes and an assessment of the changes that have occurred since 1980. There have been no major changes in the states' emergency-response planning strategies and field tactics. The changes noted included an increased availability of dedicated emergency-response vehicles, wider availability of specialized radiation-detection instruments, and higher proportions of police and fire personnel with training in the handling of suspected radiation threats. Most Indian tribes have no capability to evaluate suspected radiation threats and have no formal relations with emergency-response personnel in adjacent states. For the nation as a whole, the incidence of suspected radiation threats declined substantially from 1980 to 1988. 58 tabs.

  10. The Survey of Hospitals Affiliated with Kerman University of Medical Sciences in Preparedness Response to Disasters

    Directory of Open Access Journals (Sweden)

    Mahmood Nekoei-Moghadam

    2016-12-01

    Full Text Available Background and Objectives : Natural and man-made disasters always threaten human lives and properties. Iran as one of the disastrous countries has experienced both natural and man-made disasters. Preparedness is one of the vital elements in response to disasters. So, this study was arranged and carried out with the aim of measuring preparedness of hospitals affiliated with Kerman University of Medical Sciences in response to disasters. Material and Methods: This cross-sectional descriptive study was performed in four hospitals affiliated with Kerman University of Medical Sciences in 2015. A satisfactorily valid (kappa: 0.8 and reliable checklist was used. Data were analyzed using descriptive statistics in SPSS version 17. Results: The surveyed hospitals with the total score of 67 % were in good condition in response to disasters. The emergency departments (83%, reception (75%, communication (69%, education (70%, supply services (61%, human sources (71% and command (79% also acquired good scores. Discharge units (60%, traffic (55% and security (53% were in moderate condition in preparedness. In necessary fields for response to disasters, the whole research units acquired 67% which showed good condition in this field. Conclusion: The surveyed hospitals were in prepared and suitable condition in the emergency departments, reception, communication, education, human sources and command. In order to improve and enhance the preparedness, a schedule plan should be programmed for some elements such as discharge, transfer, traffic, security and six-crucial elements of the field.

  11. Mental health first aid responses of the public: results from an Australian national survey

    Directory of Open Access Journals (Sweden)

    Kitchener Betty A

    2005-02-01

    Full Text Available Abstract Background The prevalence of mental disorders is so high that members of the public will commonly have contact with someone affected. How they respond to that person (the mental health first aid response may affect outcomes. However, there is no information on what members of the public might do in such circumstances. Methods In a national survey of 3998 Australian adults, respondents were presented with one of four case vignettes and asked what they would do if that person was someone they had known for a long time and cared about. There were four types of vignette: depression, depression with suicidal thoughts, early schizophrenia, and chronic schizophrenia. Verbatim responses to the open-ended question were coded into categories. Results The most common responses to all vignettes were to encourage professional help-seeking and to listen to and support the person. However, a significant minority did not give these responses. Much less common responses were to assess the problem or risk of harm, to give or seek information, to encourage self-help, or to support the family. Few respondents mentioned contacting a professional on the person's behalf or accompanying them to a professional. First aid responses were generally more appropriate in women, those with less stigmatizing attitudes, and those who correctly identified the disorder in the vignette. Conclusions There is room for improving the range of mental health first aid responses in the community. Lack of knowledge of mental disorders and stigmatizing attitudes are important barriers to effective first aid.

  12. Cetacean behavioral responses to noise exposure generated by seismic surveys: how to mitigate better?

    Directory of Open Access Journals (Sweden)

    Clara Monaco

    2016-09-01

    Full Text Available Cetaceans use sound in many contexts, such as in social interactions, as well as to forage and to react in dangerous situations. Little information exists to describe how they respond physically and behaviorally to intense and long-term noise levels. Effects on cetaceans from seismic survey activities need to be understood in order to determine detailed acoustic exposure guidelines and to apply appropriated mitigation measures. This study examines direct behavioral responses of cetaceans in the southern Mediterranean Sea during seismic surveys with large airgun arrays (volume up to 5200 ci used in the TOMO-ETNA active seismic experiment of summer 2014. Wide Angle Seismic and Multi-Channel Seismic surveys had carried out with refraction and reflection seismic methods, producing about 25,800 air-gun shots. Visual monitoring undertaken in the 26 daylights of seismic exploration adopted the protocol of the Joint Nature Conservation Committee. Data recorded were analyzed to examine effects on cetaceans. Sighting rates, distance and orientation from the airguns were compared for different volume categories of the airgun arrays. Results show that cetaceans can be disturbed by seismic survey activities, especially during particularly events. Here we propose many integrated actions to further mitigate this exposure and implications for management.

  13. Harmonizing Measures of Cognitive Performance Across International Surveys of Aging Using Item Response Theory.

    Science.gov (United States)

    Chan, Kitty S; Gross, Alden L; Pezzin, Liliana E; Brandt, Jason; Kasper, Judith D

    2015-12-01

    To harmonize measures of cognitive performance using item response theory (IRT) across two international aging studies. Data for persons ≥65 years from the Health and Retirement Study (HRS, N = 9,471) and the English Longitudinal Study of Aging (ELSA, N = 5,444). Cognitive performance measures varied (HRS fielded 25, ELSA 13); 9 were in common. Measurement precision was examined for IRT scores based on (a) common items, (b) common items adjusted for differential item functioning (DIF), and (c) DIF-adjusted all items. Three common items (day of date, immediate word recall, and delayed word recall) demonstrated DIF by survey. Adding survey-specific items improved precision but mainly for HRS respondents at lower cognitive levels. IRT offers a feasible strategy for harmonizing cognitive performance measures across other surveys and for other multi-item constructs of interest in studies of aging. Practical implications depend on sample distribution and the difficulty mix of in-common and survey-specific items. © The Author(s) 2015.

  14. Human cortical responses to slow and fast binaural beats reveal multiple mechanisms of binaural hearing

    National Research Council Canada - National Science Library

    Ross, Bernhard; Miyazaki, Takahiro; Thompson, Jessica; Jamali, Shahab; Fujioka, Takako

    2014-01-01

    .... To examine the neural representations underlying these different perceptions, we recorded neuromagnetic cortical responses while participants listened to binaural beats at a continuously varying rate...

  15. The '10 Excess' Phenomenon in Responses to Survey Questions on Happiness.

    Science.gov (United States)

    Brulé, Gaël; Veenhoven, Ruut

    2017-01-01

    Happiness in nations is typically measured in surveys using a single question. A common question is: 'all things considered, how satisfied or dissatisfied are you with your life as-a-whole these days on a scale from 0 to 10?'. The responses typically follow a uni-modal distribution with highest frequencies between 5 and 8. Yet in some nations, the percentage of 10 responses stands out and is higher than the percentage of 9 responses. This is particularly present in Latin America and in the Middle East. In this paper we explore the prevalence of the '10-excess' pattern and check some possible explanations. We conclude that the 10-excess phenomenon is partly due to cultural influence.

  16. The pupillary light response reveals the focus of covert visual attention.

    Science.gov (United States)

    Mathôt, Sebastiaan; van der Linden, Lotje; Grainger, Jonathan; Vitu, Françoise

    2013-01-01

    The pupillary light response is often assumed to be a reflex that is not susceptible to cognitive influences. In line with recent converging evidence, we show that this reflexive view is incomplete, and that the pupillary light response is modulated by covert visual attention: Covertly attending to a bright area causes a pupillary constriction, relative to attending to a dark area under identical visual input. This attention-related modulation of the pupillary light response predicts cuing effects in behavior, and can be used as an index of how strongly participants attend to a particular location. Therefore, we suggest that pupil size may offer a new way to continuously track the focus of covert visual attention, without requiring a manual response from the participant. The theoretical implication of this finding is that the pupillary light response is neither fully reflexive, nor under complete voluntary control, but is instead best characterized as a stereotyped response to a voluntarily selected target. In this sense, the pupillary light response is similar to saccadic and smooth pursuit eye movements. Together, eye movements and the pupillary light response maximize visual acuity, stabilize visual input, and selectively filter visual information as it enters the eye.

  17. The pupillary light response reveals the focus of covert visual attention.

    Directory of Open Access Journals (Sweden)

    Sebastiaan Mathôt

    Full Text Available The pupillary light response is often assumed to be a reflex that is not susceptible to cognitive influences. In line with recent converging evidence, we show that this reflexive view is incomplete, and that the pupillary light response is modulated by covert visual attention: Covertly attending to a bright area causes a pupillary constriction, relative to attending to a dark area under identical visual input. This attention-related modulation of the pupillary light response predicts cuing effects in behavior, and can be used as an index of how strongly participants attend to a particular location. Therefore, we suggest that pupil size may offer a new way to continuously track the focus of covert visual attention, without requiring a manual response from the participant. The theoretical implication of this finding is that the pupillary light response is neither fully reflexive, nor under complete voluntary control, but is instead best characterized as a stereotyped response to a voluntarily selected target. In this sense, the pupillary light response is similar to saccadic and smooth pursuit eye movements. Together, eye movements and the pupillary light response maximize visual acuity, stabilize visual input, and selectively filter visual information as it enters the eye.

  18. A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate

    DEFF Research Database (Denmark)

    Bataillon, Thomas; Galtier, Nicolas; Bernard, Aurelien

    2016-01-01

    Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out innatural field conditions. We examined the evolutionary response to ...

  19. Comparison of self-administered survey questionnaire responses collected using mobile apps versus other methods.

    Science.gov (United States)

    Marcano Belisario, José S; Jamsek, Jan; Huckvale, Kit; O'Donoghue, John; Morrison, Cecily P; Car, Josip

    2015-07-27

    Self-administered survey questionnaires are an important data collection tool in clinical practice, public health research and epidemiology. They are ideal for achieving a wide geographic coverage of the target population, dealing with sensitive topics and are less resource-intensive than other data collection methods. These survey questionnaires can be delivered electronically, which can maximise the scalability and speed of data collection while reducing cost. In recent years, the use of apps running on consumer smart devices (i.e., smartphones and tablets) for this purpose has received considerable attention. However, variation in the mode of delivering a survey questionnaire could affect the quality of the responses collected. To assess the impact that smartphone and tablet apps as a delivery mode have on the quality of survey questionnaire responses compared to any other alternative delivery mode: paper, laptop computer, tablet computer (manufactured before 2007), short message service (SMS) and plastic objects. We searched MEDLINE, EMBASE, PsycINFO, IEEEXplore, Web of Science, CABI: CAB Abstracts, Current Contents Connect, ACM Digital, ERIC, Sociological Abstracts, Health Management Information Consortium, the Campbell Library and CENTRAL. We also searched registers of current and ongoing clinical trials such as ClinicalTrials.gov and the World Health Organization (WHO) International Clinical Trials Registry Platform. We also searched the grey literature in OpenGrey, Mobile Active and ProQuest Dissertation & Theses. Lastly, we searched Google Scholar and the reference lists of included studies and relevant systematic reviews. We performed all searches up to 12 and 13 April 2015. We included parallel randomised controlled trials (RCTs), crossover trials and paired repeated measures studies that compared the electronic delivery of self-administered survey questionnaires via a smartphone or tablet app with any other delivery mode. We included data obtained from

  20. DNA sequence and structure properties analysis reveals similarities and differences to promoters of stress responsive genes in Arabidopsis thaliana.

    Science.gov (United States)

    Zhu, Pan; Zhou, Yanhong; Zhang, Libin; Ma, Chuang

    2015-01-01

    Understanding regulatory mechanisms of stress response in plants has important biological and agricultural significances. In this study, we firstly compiled a set of genes responsive to different stresses in Arabidopsis thaliana and then comparatively analysed their promoters at both the DNA sequence and three-dimensional structure levels. Amazingly, the comparison revealed that the profiles of several sequence and structure properties vary distinctly in different regions of promoters. Moreover, the content of nucleotide T and the profile of B-DNA twist are distinct in promoters from different stress groups, suggesting Arabidopsis genes might exploit different regulatory mechanisms in response to various stresses. Finally, we evaluated the performance of two representative promoter predictors including EP3 and PromPred. The evaluation results revealed their strengths and weakness for identifying stress-related promoters, providing valuable guidelines to accelerate the discovery of novel stress-related promoters and genes in plants.

  1. A survey on the Relationship between Social Responsibility and Social Capital

    Directory of Open Access Journals (Sweden)

    Moahmmadtaghi Iman

    2010-04-01

    Full Text Available AbstractThis article aims to explain the relationship between social responsibility and social capital ofthe young with the age range of 18 to 29 in the Shiraz city. Development of social responsibilityand commitment are important subjects which are considered more than cognitive subjects byscholars (Fathi Azar, 1373:180. Social responsibility is a part of socialization process. The mostimportant factors which have major roles in socialization are culture, family and social institutions.Social responsibility is a skill of doing behavior which is evaluated by people. These skills canmake positive and successfully results and lead to personal and group’s satisfaction. Otherwise, thelake of social responsibility results to less confidence and cooperation. In this article theresearchers used survey method and questionnaire to collect the data. Sample size is 386 youngwhich were selected randomly. The result of multiple regression showed the effects of the variablesare as follows: social capital (beta=0.27, self esteem (beta=0. 27, age (beta=0. 21 and gender(beta=0. 22 have significant and positive relations with social responsibility. These variablesexplain 20 percent of the variation of social responsibility (R2=0.20. In path analysis model,maximum direct effect belongs to social capital and maximum indirect effect belongs to mother’seducation.

  2. Social Responsibility of the Hospitals in Isfahan City, Iran: Results from a Cross-Sectional Survey

    Directory of Open Access Journals (Sweden)

    Mahmoud Keyvanara

    2015-08-01

    Full Text Available Background Changes in modern societies develop the perception that the external environment is essential in organization’s practices, especially in the way they deal with aspects such as human rights, community needs, market demands and environmental interests. These issues are usually under the umbrella of the concept of social responsibility. Given the importance of this concept in the context of health care delivery, suggesting a new paradigm in hospital governance, the aim of this study was to measure the social responsibility in hospitals. Methods A cross-sectional survey was employed to collect data from a sample of 946 hospital staff of Isfahan city. Data was obtained by structured and valid self-administrated questionnaire and analyzed by descriptive and analytic statistics using SPSS. Results The mean score of hospitals’ social responsibility was 3.0 compared with the justified range from 1.0 to 5.0. Results showed that there was a significant relationship between social responsibility score and hospitals’ ownership (public or private. Also, there was no significant relationship between social responsibility and type of hospital specialty. Conclusion It is recommended that hospital managers develop and apply appropriate policies and strategies to improve their hospitals’ social responsibility level, especially through concentrating on their staff’s working environment.

  3. Social responsibility of the hospitals in Isfahan city, Iran: Results from a cross-sectional survey.

    Science.gov (United States)

    Keyvanara, Mahmoud; Sajadi, Haniye Sadat

    2015-02-12

    Changes in modern societies develop the perception that the external environment is essential in organization's practices, especially in the way they deal with aspects such as human rights, community needs, market demands and environmental interests. These issues are usually under the umbrella of the concept of social responsibility. Given the importance of this concept in the context of health care delivery, suggesting a new paradigm in hospital governance, the aim of this study was to measure the social responsibility in hospitals. A cross-sectional survey was employed to collect data from a sample of 946 hospital staff of Isfahan city. Data was obtained by structured and valid self-administrated questionnaire and analyzed by descriptive and analytic statistics using SPSS. The mean score of hospitals' social responsibility was 3.0 compared with the justified range from 1.0 to 5.0. Results showed that there was a significant relationship between social responsibility score and hospitals' ownership (public or private). Also, there was no significant relationship between social responsibility and type of hospital specialty. It is recommended that hospital managers develop and apply appropriate policies and strategies to improve their hospitals' social responsibility level, especially through concentrating on their staff's working environment. © 2015 by Kerman University of Medical Sciences.

  4. Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response.

    Directory of Open Access Journals (Sweden)

    Stuart Aitken

    2015-04-01

    Full Text Available The immediate-early response mediates cell fate in response to a variety of extracellular stimuli and is dysregulated in many cancers. However, the specificity of the response across stimuli and cell types, and the roles of non-coding RNAs are not well understood. Using a large collection of densely-sampled time series expression data we have examined the induction of the immediate-early response in unparalleled detail, across cell types and stimuli. We exploit cap analysis of gene expression (CAGE time series datasets to directly measure promoter activities over time. Using a novel analysis method for time series data we identify transcripts with expression patterns that closely resemble the dynamics of known immediate-early genes (IEGs and this enables a comprehensive comparative study of these genes and their chromatin state. Surprisingly, these data suggest that the earliest transcriptional responses often involve promoters generating non-coding RNAs, many of which are produced in advance of canonical protein-coding IEGs. IEGs are known to be capable of induction without de novo protein synthesis. Consistent with this, we find that the response of both protein-coding and non-coding RNA IEGs can be explained by their transcriptionally poised, permissive chromatin state prior to stimulation. We also explore the function of non-coding RNAs in the attenuation of the immediate early response in a small RNA sequencing dataset matched to the CAGE data: We identify a novel set of microRNAs responsible for the attenuation of the IEG response in an estrogen receptor positive cancer cell line. Our computational statistical method is well suited to meta-analyses as there is no requirement for transcripts to pass thresholds for significant differential expression between time points, and it is agnostic to the number of time points per dataset.

  5. Response to an Online Version of a PRAMS-like Survey in South Dakota.

    Science.gov (United States)

    Binkley, Teresa; Beare, Tianna; Minett, Maggie; Koepp, Kriston; Wey, Howard; Specker, Bonny

    2017-02-01

    Objectives Increasing response rates for research surveys is challenging, especially in minority populations. A unique minority group in South Dakota is the American Indian (AI) representing about 9 % of the state's population and 15 % of the births. The purpose of this study was to determine race differences among White, AI, and Other Races (OR) in contact, participation, and response rates in the South Dakota Pregnancy Risk Assessment Monitoring System (SDPRAMS). We determined response rates of an online version and evaluated demographic characteristics associated with online response. Methods The SDPRAMS was sent to 1814 mothers randomly sampled from 2014 birth certificate files. Results The weighted response rate was 71.3 %, and varied significantly among the three races: 79.1 % for White race, 48.6 % for AI race, and 60.6 % for OR (p online than AI and OR (35, 25 and 26 %, respectively; p = 0.001); no difference between AI and OR. Online responders were more likely to be married, educated beyond high school and having annual incomes ≥$25,000 (p ≤ 0.01 for all), but only education (p online respondents used a smartphone to respond (p = 0.01). Conclusions Response rates differed among races. An online version of the PRAMS is a viable method of response to offer participants. Response to the online version via smartphone may increase response from minority populations, emphasizing the importance of mobile friendly formats.

  6. Thermal reactionomes reveal divergent responses to thermal extremes in warm and cool-climate ant species

    DEFF Research Database (Denmark)

    Stanton-Geddes, John; Nguyen, Andrew; Chick, Lacy

    2016-01-01

    (enhanced response), constitutively elevated expression of protective genes (genetic assimilation) or a shift from damage resistance to passive mechanisms of thermal stability (tolerance), we conducted an analysis of the reactionome: the reaction norm for all genes in an organism’s transcriptome measured......The distributions of species and their responses to climate change are in part determined by their thermal tolerances. However, little is known about how thermal tolerance evolves. To test whether evolutionary extension of thermal limits is accomplished through enhanced cellular stress response...

  7. Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response

    DEFF Research Database (Denmark)

    Beli, Petra; Lukashchuk, Natalia; Wagner, Sebastian A

    2012-01-01

    The regulatory networks of the DNA damage response (DDR) encompass many proteins and posttranslational modifications. Here, we use mass spectrometry-based proteomics to analyze the systems-wide response to DNA damage by parallel quantification of the DDR-regulated phosphoproteome, acetylome, and ...... cellular hypersensitivity to DNA-damaging agents. Collectively, these data broaden our knowledge of DNA damage signaling networks and highlight an important link between RNA metabolism and DNA repair....

  8. Human cortical responses to slow and fast binaural beats reveal multiple mechanisms of binaural hearing.

    Science.gov (United States)

    Ross, Bernhard; Miyazaki, Takahiro; Thompson, Jessica; Jamali, Shahab; Fujioka, Takako

    2014-10-15

    When two tones with slightly different frequencies are presented to both ears, they interact in the central auditory system and induce the sensation of a beating sound. At low difference frequencies, we perceive a single sound, which is moving across the head between the left and right ears. The percept changes to loudness fluctuation, roughness, and pitch with increasing beat rate. To examine the neural representations underlying these different perceptions, we recorded neuromagnetic cortical responses while participants listened to binaural beats at a continuously varying rate between 3 Hz and 60 Hz. Binaural beat responses were analyzed as neuromagnetic oscillations following the trajectory of the stimulus rate. Responses were largest in the 40-Hz gamma range and at low frequencies. Binaural beat responses at 3 Hz showed opposite polarity in the left and right auditory cortices. We suggest that this difference in polarity reflects the opponent neural population code for representing sound location. Binaural beats at any rate induced gamma oscillations. However, the responses were largest at 40-Hz stimulation. We propose that the neuromagnetic gamma oscillations reflect postsynaptic modulation that allows for precise timing of cortical neural firing. Systematic phase differences between bilateral responses suggest that separate sound representations of a sound object exist in the left and right auditory cortices. We conclude that binaural processing at the cortical level occurs with the same temporal acuity as monaural processing whereas the identification of sound location requires further interpretation and is limited by the rate of object representations. Copyright © 2014 the American Physiological Society.

  9. Stromal transcriptional profiles reveal hierarchies of anatomical site, serum response and disease and identify disease specific pathways.

    Science.gov (United States)

    Filer, Andrew; Antczak, Philipp; Parsonage, Greg N; Legault, Holly M; O'Toole, Margot; Pearson, Mark J; Thomas, Andrew M; Scheel-Toellner, Dagmar; Raza, Karim; Buckley, Christopher D; Falciani, Francesco

    2015-01-01

    Synovial fibroblasts in persistent inflammatory arthritis have been suggested to have parallels with cancer growth and wound healing, both of which involve a stereotypical serum response programme. We tested the hypothesis that a serum response programme can be used to classify diseased tissues, and investigated the serum response programme in fibroblasts from multiple anatomical sites and two diseases. To test our hypothesis we utilized a bioinformatics approach to explore a publicly available microarray dataset including rheumatoid arthritis (RA), osteoarthritis (OA) and normal synovial tissue, then extended those findings in a new microarray dataset representing matched synovial, bone marrow and skin fibroblasts cultured from RA and OA patients undergoing arthroplasty. The classical fibroblast serum response programme discretely classified RA, OA and normal synovial tissues. Analysis of low and high serum treated fibroblast microarray data revealed a hierarchy of control, with anatomical site the most powerful classifier followed by response to serum and then disease. In contrast to skin and bone marrow fibroblasts, exposure of synovial fibroblasts to serum led to convergence of RA and OA expression profiles. Pathway analysis revealed three inter-linked gene networks characterising OA synovial fibroblasts: Cell remodelling through insulin-like growth factors, differentiation and angiogenesis through _3 integrin, and regulation of apoptosis through CD44. We have demonstrated that Fibroblast serum response signatures define disease at the tissue level, and that an OA specific, serum dependent repression of genes involved in cell adhesion, extracellular matrix remodelling and apoptosis is a critical discriminator between cultured OA and RA synovial fibroblasts.

  10. Understanding the Diffusion of Efficient Consumer Response: an Australian survey study

    Directory of Open Access Journals (Sweden)

    Sherah Kurnia

    2002-05-01

    Full Text Available Efficient Consumer Response (ECR is designed to make the grocery industry more efficient. Although it originated in the US, the concept has been adopted in many regions. To enrich the findings of the existing studies that indicate a slow diffusion rate of ECR, this study examines ECR adoption in Australia by conducting a survey. The findings suggest that in Australia, ECR diffusion has also been slow. Differences in barriers, perceptions, and benefits experienced between manufacturers and retailers discovered in this study suggest that Australian retailers are leading manufacturers in ECR implementation and that they experience more benefits than manufacturers.

  11. RNA-Seq reveals an integrated immune response in nucleated erythrocytes.

    Directory of Open Access Journals (Sweden)

    Davinia Morera

    Full Text Available BACKGROUND: Throughout the primary literature and within textbooks, the erythrocyte has been tacitly accepted to have maintained a unique physiological role; namely gas transport and exchange. In non-mammalian vertebrates, nucleated erythrocytes are present in circulation throughout the life cycle and a fragmented series of observations in mammals support a potential role in non-respiratory biological processes. We hypothesised that nucleated erythrocytes could actively participate via ligand-induced transcriptional re-programming in the immune response. METHODOLOGY/PRINCIPAL FINDINGS: Nucleated erythrocytes from both fish and birds express and regulate specific pattern recognition receptor (PRR mRNAs and, thus, are capable of specific pathogen associated molecular pattern (PAMP detection that is central to the innate immune response. In vitro challenge with diverse PAMPs led to de novo specific mRNA synthesis of both receptors and response factors including interferon-alpha (IFNα that exhibit a stimulus-specific polysomal shift supporting active translation. RNA-Seq analysis of the PAMP (Poly (I:C, polyinosinic:polycytidylic acid-erythrocyte response uncovered diverse cohorts of differentially expressed mRNA transcripts related to multiple physiological systems including the endocrine, reproductive and immune. Moreover, erythrocyte-derived conditioned mediums induced a type-1 interferon response in macrophages thus supporting an integrative role for the erythrocytes in the immune response. CONCLUSIONS/SIGNIFICANCE: We demonstrate that nucleated erythrocytes in non-mammalian vertebrates spanning significant phylogenetic distance participate in the immune response. RNA-Seq studies highlight a mRNA repertoire that suggests a previously unrecognized integrative role for the erythrocytes in other physiological systems.

  12. Colony-specific investigations reveal highly variable responses among individual corals to ocean acidification and warming.

    Science.gov (United States)

    Kavousi, Javid; Reimer, James Davis; Tanaka, Yasuaki; Nakamura, Takashi

    2015-08-01

    As anthropogenic climate change is an ongoing concern, scientific investigations on its impacts on coral reefs are increasing. Although impacts of combined ocean acidification (OA) and temperature stress (T) on reef-building scleractinian corals have been studied at the genus, species and population levels, there are little data available on how individual corals respond to combined OA and anomalous temperatures. In this study, we exposed individual colonies of Acropora digitifera, Montipora digitata and Porites cylindrica to four pCO2-temperature treatments including 400 μatm-28 °C, 400 μatm-31 °C, 1000 μatm-28 °C and 1000 μatm-31 °C for 26 days. Physiological parameters including calcification, protein content, maximum photosynthetic efficiency, Symbiodinium density, and chlorophyll content along with Symbiodinium type of each colony were examined. Along with intercolonial responses, responses of individual colonies versus pooled data to the treatments were investigated. The main results were: 1) responses to either OA or T or their combination were different between individual colonies when considering physiological functions; 2) tolerance to either OA or T was not synonymous with tolerance to the other parameter; 3) tolerance to both OA and T did not necessarily lead to tolerance of OA and T combined (OAT) at the same time; 4) OAT had negative, positive or no impacts on physiological functions of coral colonies; and 5) pooled data were not representative of responses of all individual colonies. Indeed, the pooled data obscured actual responses of individual colonies or presented a response that was not observed in any individual. From the results of this study we recommend improving experimental designs of studies investigating physiological responses of corals to climate change by complementing them with colony-specific examinations. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. The nature of riverbank erosion along the South River, Virginia revealed through terrestrial laser-scanner surveys

    Science.gov (United States)

    O'Neal, M. A.; Pizzuto, J. E.

    2012-12-01

    We surveyed 23 eroding banks along the South River, Virginia between 2006 and 2008 CE using a terrestrial laser scanner. At 6 sites with varying bank vegetation, soil type, and geomorphic settings, a total of 11 repeat surveys were completed to document rates and spatial patterns of contemporary bank erosion. Time intervals between surveys ranged from 89 days to 421 days. Our survey data, averaging 15,000 points per square meter, were manually and mathematically filtered to remove non-bank elements and converted into 0.05 m x 0.05 m gridded models. Comparison of our data-dense, mathematically filtered models indicates that the streamwise spatial extent of significant erosion varied from 0% to about 80% of the surveyed bank area. Annualized maximum rates of localized bank erosion varied from 0 to about 2.4 m/yr, the latter of which greatly exceeds estimated rates from historical aerial photographs. Comparison of our LIDAR-derived erosion rates, with those from field observations, identified the geologic setting (i.e. bank material type) as the most important control on the extent of bank erosion and suggests that large trees can reduce erosion rates. Model comparisons indicate that maximum erosion along the forested banks focused around leaning trees, while elsewhere the extent of bank retreat was negligible. On grassy banks, retreat was controlled by the creation of small overhanging clumps of turf at the top of the bank, their occasional failure, and the ultimate removal of failed debris from the bank toe. Partial autocorrelation analysis of vertically integrated bank retreat at two eroding banks demonstrates that bank profile erosion is virtually uncorrelated at horizontal distances greater than about 1 m, a length scale of approximately half the bank height. This extensive streamwise variability suggests that widely spaced profile data cannot adequately represent bank erosion at these sites. Additional analysis of our comprehensive spatial data also indicates

  14. Repeated diffusion MRI reveals earliest time point for stratification of radiotherapy response in brain metastases

    Science.gov (United States)

    Mahmood, Faisal; Johannesen, Helle H.; Geertsen, Poul; Hansen, Rasmus H.

    2017-04-01

    An imaging biomarker for early prediction of treatment response potentially provides a non-invasive tool for better prognostics and individualized management of the disease. Radiotherapy (RT) response is generally related to changes in gross tumor volume manifesting months later. In this prospective study we investigated the apparent diffusion coefficient (ADC), perfusion fraction and pseudo diffusion coefficient derived from diffusion weighted MRI as potential early biomarkers for radiotherapy response of brain metastases. It was a particular aim to assess the optimal time point for acquiring the DW-MRI scan during the course of treatment, since to our knowledge this important question has not been addressed directly in previous studies. Twenty-nine metastases (N  =  29) from twenty-one patients, treated with whole-brain fractionated external beam RT were analyzed. Patients were scanned with a 1 T MRI system to acquire DW-, T2*W-, T2W- and T1W scans, before start of RT, at each fraction and at follow up two to three months after RT. The DW-MRI parameters were derived using regions of interest based on high b-value images (b  =  800 s mm‑2). Both volumetric and RECIST criteria were applied for response evaluation. It was found that in non-responding metastases the mean ADC decreased and in responding metastases it increased. The volume based response proved to be far more consistently predictable by the ADC change found at fraction number 7 and later, compared to the linear response (RECIST). The perfusion fraction and pseudo diffusion coefficient did not show sufficient prognostic value with either response assessment criteria. In conclusion this study shows that the ADC derived using high b-values may be a reliable biomarker for early assessment of radiotherapy response for brain metastases patients. The earliest response stratification can be achieved using two DW-MRI scans, one pre-treatment and one at treatment day 7–9 (equivalent to 21

  15. Physiological and transcriptomic analyses reveal a response mechanism to cold stress in Santalum album L. leaves

    Science.gov (United States)

    Zhang, Xinhua; Teixeira da Silva, Jaime A.; Niu, Meiyun; Li, Mingzhi; He, Chunmei; Zhao, Jinhui; Zeng, Songjun; Duan, Jun; Ma, Guohua

    2017-01-01

    Santalum album L. (Indian sandalwood) is an economically important plant species because of its ability to produce highly valued perfume oils. Little is known about the mechanisms by which S. album adapts to low temperatures. In this study, we obtained 100,445,724 raw reads by paired-end sequencing from S. album leaves. Physiological and transcriptomic changes in sandalwood seedlings exposed to 4 °C for 0–48 h were characterized. Cold stress induced the accumulation of malondialdehyde, proline and soluble carbohydrates, and increased the levels of antioxidants. A total of 4,424 differentially expressed genes were responsive to cold, including 3,075 cold-induced and 1,349 cold-repressed genes. When cold stress was prolonged, there was an increase in the expression of cold-responsive genes coding for transporters, responses to stimuli and stress, regulation of defense response, as well as genes related to signal transduction of all phytohormones. Candidate genes in the terpenoid biosynthetic pathway were identified, eight of which were significantly involved in the cold stress response. Gene expression analyses using qRT-PCR showed a peak in the accumulation of SaCBF2 to 4, 50-fold more than control leaves and roots following 12 h and 24 h of cold stress, respectively. The CBF-dependent pathway may play a crucial role in increasing cold tolerance. PMID:28169358

  16. [Salmonella typhi vaccination response study reveals defective antibody production selective IgA deficiency patient].

    Science.gov (United States)

    Pleguezuelo, Daniel E; Gianelli, Carla

    2015-01-01

    Selective IgA deficiency (SIgAD) is the most prevalent immunodeficiency worldwide, progressing to common variable immunodeficiency only in few reported cases. We report the case of a Spanish female aged 22 and diagnosed of selective IgA deficiency, a long history of bronchitis, several episodes of pneumonia, bilateral bronchiectasis, normal IgG, IgM, IgG subclasses, and detectable pre-vaccination IgG antibodies against tetanus toxoid and Streptococcus pneumoniae. She was evaluated in our clinic in order to rule out common variable immunodeficiency. We observed good antibody response to tetanus toxoid, absence of circulating switched memory B cells, decreased response to pneumococcal polysaccharide antigens and a lack of response to Salmonella typhi vaccine. Most SIgAD patients presents with upper respiratory tract infections or mild diarrhea. Those with lower tract infections, pneumonia or untreatable diarrhea should follow B-cell subpopulations' study and antibody response to vaccines. Absence of response to Salmonella typhi vaccine allowed us to expose the defective antibody production.

  17. Stem transcriptome reveals mechanisms to reduce the energetic cost of shade-avoidance responses in tomato.

    Science.gov (United States)

    Cagnola, Juan Ignacio; Ploschuk, Edmundo; Benech-Arnold, Tomás; Finlayson, Scott A; Casal, Jorge José

    2012-10-01

    While the most conspicuous response to low red/far-red ratios (R:FR) of shade light perceived by phytochrome is the promotion of stem growth, additional, less obvious effects may be discovered by studying changes in the stem transcriptome. Here, we report rapid and reversible stem transcriptome responses to R:FR in tomato (Solanum lycopersicum). As expected, low R:FR promoted the expression of growth-related genes, including those involved in the metabolism of cell wall carbohydrates and in auxin responses. In addition, genes involved in flavonoid synthesis, isoprenoid metabolism, and photosynthesis (dark reactions) were overrepresented in clusters showing reduced expression in the stem of low R:FR-treated plants. Consistent with these responses, low R:FR decreased the levels of flavonoids (anthocyanin, quercetin, kaempferol) and selected isoprenoid derivatives (chlorophyll, carotenoids) in the stem and severely reduced the photosynthetic capacity of this organ. However, lignin contents were unaffected. Low R:FR reduced the stem levels of jasmonate, which is a known inducer of flavonoid synthesis. The rate of stem respiration was also reduced in low R:FR-treated plants, indicating that by downsizing the stem photosynthetic apparatus and the levels of photoprotective pigments under low R:FR, tomato plants reduce the energetic cost of shade-avoidance responses.

  18. [Heat-responsive mechanisms in plants revealed by proteomic analysis: A review].

    Science.gov (United States)

    Liu, Jun-ming; Zhao, Qi; Yin, Ze-peng; Xu, Chen-xi; Wang, Quan-hua; Dai, Shao-jun

    2015-08-01

    Heat stress is a major abiotic stress that limits plant growth and productivity. In recent years, proteomic investigations provide more information for understanding the sophisticated heat-responsive molecular mechanism in plants at systematic biological level. The heat-responsive proteomic patterns in several plants, i. e., model plants (Arabidopsis thaliana), staple food crops (soybean, rice and wheat), heat-tolerant plants (Agrostis stolonifera, Portulaca oleracea, and Carissa spinarum), grapevine, Populus euphratica, Medicago sativa, and Pinellia ternate, were reported. A total of 838 heat-responsive proteins have been identified in these studies. Among them, 534 proteins were induced and the expression of 304 proteins was reduced in plants under heat stress. In this paper, the diverse protein patterns in plants under various heat stress conditions (30-45 °C for 0-10 d) were analyzed integratively. This provided new evidences and clues for further interpreting the signaling and metabolic pathways, e.g., signaling, stress and defense, carbohydrate and energy metabolism, photosynthesis, transcription, protein synthesis and fate, membrane and transport, in heat-responsive networks, and laid a foundation for a holistic understanding of the molecular regulatory mechanism in plants in response to heat stress.

  19. Wetland survey of selected areas in the K-24 Site Area of responsibility

    Energy Technology Data Exchange (ETDEWEB)

    Rosensteel, B.A.; Awl, D.J. [JAYCOR, Environmental Division, Oak Ridge, TN (United States)

    1995-07-01

    In accordance with DOE Regulations for Compliance with Floodplain/Wetlands Environmental Review Requirements, wetland surveys were conducted in selected areas within the K-25 Area of Responsibility during the summer of 1994. These areas are Mitchell Branch, Poplar Creek, the K-770 OU, Duct Island Peninsula, the Powerhouse area, and the K-25 South Corner. Previously surveyed areas included in this report are the main plant area of the K-25 Site, the K-901 OU, the AVLIS site, and the K-25 South Site. Wetland determinations were based on the USACE methodology. Forty-four separate wetland areas, ranging in size from 0.13 to 4.23 ha, were identified. Wetlands were identified in all of the areas surveyed with the exception of the interior of the Duct Island Peninsula and the main plant area of the K-25 Site. Wetlands perform functions such as floodflow alteration, sediment stabilization, sediment and toxicant retention, nutrient transformation, production export, and support of aquatic species and wildlife diversity and abundance. The forested, scrub-shrub, and emergent wetlands identified in the K-25 area perform some or all of these functions to varying degrees.

  20. A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate

    DEFF Research Database (Denmark)

    Bataillon, Thomas; Galtier, Nicolas; Bernard, Aurelien

    2016-01-01

    Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out innatural field conditions. We examined the evolutionary response...... to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies...... associated to changes in soil temperature and soil moisture. This shows an evolutionaryresponse to realistic climate change happening over short-time scale, and calls for incorporating evolution into modelspredicting future response of species to climate change. It also shows that designed climate change...

  1. Learning theories reveal loss of pancreatic electrical connectivity in diabetes as an adaptive response

    CERN Document Server

    Goel, Pranay

    2013-01-01

    Cells of almost all solid tissues are connected with gap junctions which permit the direct transfer of ions and small molecules, integral to regulating coordinated function in the tissue. The pancreatic islets of Langerhans are responsible for secreting the hormone insulin in response to glucose stimulation. Gap junctions are the only electrical contacts between the beta-cells in the tissue of these excitable islets. It is generally believed that they are responsible for synchrony of the membrane voltage oscillations among beta-cells, and thereby pulsatility of insulin secretion. Most attempts to understand connectivity in islets are often interpreted, bottom-up, in terms of measurements of gap junctional conductance. This does not, however explain systematic changes, such as a diminished junctional conductance in type 2 diabetes. We attempt to address this deficit via the model presented here, which is a learning theory of gap junctional adaptation derived with analogy to neural systems. Here, gap junctions ...

  2. Pupillary responses reveal infants' discrimination of facial emotions independent of conscious perception.

    Science.gov (United States)

    Jessen, Sarah; Altvater-Mackensen, Nicole; Grossmann, Tobias

    2016-05-01

    Sensitive responding to others' emotions is essential during social interactions among humans. There is evidence for the existence of subcortically mediated emotion discrimination processes that occur independent of conscious perception in adults. However, only recently work has begun to examine the development of automatic emotion processing systems during infancy. In particular, it is unclear whether emotional expressions impact infants' autonomic nervous system regardless of conscious perception. We examined this question by measuring pupillary responses while subliminally and supraliminally presenting 7-month-old infants with happy and fearful faces. Our results show greater pupil dilation, indexing enhanced autonomic arousal, in response to happy compared to fearful faces regardless of conscious perception. Our findings suggest that, early in ontogeny, emotion discrimination occurs independent of conscious perception and is associated with differential autonomic responses. This provides evidence for the view that automatic emotion processing systems are an early-developing building block of human social functioning.

  3. Stochastic kinetic model of two component system signalling reveals all-or-none, graded and mixed mode stochastic switching responses.

    Science.gov (United States)

    Kierzek, Andrzej M; Zhou, Lu; Wanner, Barry L

    2010-03-01

    Two-component systems (TCSs) are prevalent signal transduction systems in bacteria that control innumerable adaptive responses to environmental cues and host-pathogen interactions. We constructed a detailed stochastic kinetic model of two component signalling based on published data. Our model has been validated with flow cytometry data and used to examine reporter gene expression in response to extracellular signal strength. The model shows that, depending on the actual kinetic parameters, TCSs exhibit all-or-none, graded or mixed mode responses. In accordance with other studies, positively autoregulated TCSs exhibit all-or-none responses. Unexpectedly, our model revealed that TCSs lacking a positive feedback loop exhibit not only graded but also mixed mode responses, in which variation of the signal strength alters the level of gene expression in induced cells while the regulated gene continues to be expressed at the basal level in a substantial fraction of cells. The graded response of the TCS changes to mixed mode response by an increase of the translation initiation rate of the histidine kinase. Thus, a TCS is an evolvable design pattern capable of implementing deterministic regulation and stochastic switches associated with both graded and threshold responses. This has implications for understanding the emergence of population diversity in pathogenic bacteria and the design of genetic circuits in synthetic biology applications. The model is available in systems biology markup language (SBML) and systems biology graphical notation (SBGN) formats and can be used as a component of large-scale biochemical reaction network models.

  4. Metabolomics reveals amino acids contribute to variation in response to simvastatin treatment.

    Directory of Open Access Journals (Sweden)

    Miles Trupp

    Full Text Available UNLABELLED: Statins are widely prescribed for reducing LDL-cholesterol (C and risk for cardiovascular disease (CVD, but there is considerable variation in therapeutic response. We used a gas chromatography-time-of-flight mass-spectrometry-based metabolomics platform to evaluate global effects of simvastatin on intermediary metabolism. Analyses were conducted in 148 participants in the Cholesterol and Pharmacogenetics study who were profiled pre and six weeks post treatment with 40 mg/day simvastatin: 100 randomly selected from the full range of the LDL-C response distribution and 24 each from the top and bottom 10% of this distribution ("good" and "poor" responders, respectively. The metabolic signature of drug exposure in the full range of responders included essential amino acids, lauric acid (p<0.0055, q<0.055, and alpha-tocopherol (p<0.0003, q<0.017. Using the HumanCyc database and pathway enrichment analysis, we observed that the metabolites of drug exposure were enriched for the pathway class amino acid degradation (p<0.0032. Metabolites whose change correlated with LDL-C lowering response to simvastatin in the full range responders included cystine, urea cycle intermediates, and the dibasic amino acids ornithine, citrulline and lysine. These dibasic amino acids share plasma membrane transporters with arginine, the rate-limiting substrate for nitric oxide synthase (NOS, a critical mediator of cardiovascular health. Baseline metabolic profiles of the good and poor responders were analyzed by orthogonal partial least square discriminant analysis so as to determine the metabolites that best separated the two response groups and could be predictive of LDL-C response. Among these were xanthine, 2-hydroxyvaleric acid, succinic acid, stearic acid, and fructose. Together, the findings from this study indicate that clusters of metabolites involved in multiple pathways not directly connected with cholesterol metabolism may play a role in modulating

  5. Men's responses to HPV test results: development of a theory-based survey.

    Science.gov (United States)

    Daley, Ellen M; Buhi, Eric R; Baldwin, Julie; Lee, Ji-Hyun; Vadaparampil, Susan; Abrahamsen, Martha; Vamos, Cheryl A; Kolar, Stephanie; Chandler, Rasheeta; Anstey, Erica Hesch; Giuliano, Anna

    2009-01-01

    To develop and perform psychometric testing on an instrument designed to assess cognitive/emotional responses among men receiving HPV testing. Men enrolled in an HPV natural history study (N = 139) completed a computer-assisted survey instrument based on Leventhal's parallel processing/common-sense model. Data were analyzed using SPSS and Mplus. Reliability analyses resulted in Cronbach alpha of 0.72 (knowledge), 0.86 (perceived threat), 0.83 (self-efficacy), and 0.55 (response efficacy). A revised measurement model exhibited evidence of construct validity, as indicated by acceptable model fit statistics. To our knowledge, this is the only validated instrument assessing men's reactions to an HPV test result.

  6. A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate

    DEFF Research Database (Denmark)

    Bataillon, Thomas; Galtier, Nicolas; Bernard, Aurelien;

    2016-01-01

    associated to changes in soil temperature and soil moisture. This shows an evolutionaryresponse to realistic climate change happening over short-time scale, and calls for incorporating evolution into modelspredicting future response of species to climate change. It also shows that designed climate change...

  7. RNAseq analysis reveals oxidative stress responses of Aspergillus flavus related to stress tolerance and aflatoxin production

    Science.gov (United States)

    Aflatoxin contamination by Aspergillus flavus is exacerbated by drought stress in the field. Given that reactive oxygen species (ROS) both accumulate in plant tissues during drought and can stimulate aflatoxin production in vitro, we examined the responses of toxigenic isolates of A. flavus to oxida...

  8. Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells

    DEFF Research Database (Denmark)

    Pines, Alex; Kelstrup, Christian D; Vrouwe, Mischa G

    2011-01-01

    (stable isotope labeling by amino acids in cell culture)-labeled murine embryonic stem cells with the anticancer drug cisplatin. Network and pathway analyses indicated that processes related to the DNA damage response and cytoskeleton organization were significantly affected. Although the ATM (ataxia...

  9. Transcriptome Analyses Reveal Candidate Genes Potentially Involved in Al Stress Response in Alfalfa

    Science.gov (United States)

    Liu, Wenxian; Xiong, Conghui; Yan, Longfeng; Zhang, Zhengshe; Ma, Lichao; Wang, Yanrong; Liu, Yajie; Liu, Zhipeng

    2017-01-01

    Alfalfa is the most extensively cultivated forage legume, yet most alfalfa cultivars are not aluminum tolerant, and the molecular mechanisms underlying alfalfa responses to Al stress are largely unknown. In this study, we aimed to understand how alfalfa responds to Al stress by identifying and analyzing Al-stress-responsive genes in alfalfa roots at the whole-genome scale. The transcriptome changes in alfalfa roots under Al stress for 4, 8, or 24 h were analyzed using Illumina high-throughput sequencing platforms. A total of 2464 differentially expressed genes (DEGs) were identified, and most were up-regulated at early (4 h) and/or late (24 h) Al exposure time points rather than at the middle exposure time point (8 h). Metabolic pathway enrichment analysis demonstrated that the DEGs involved in ribosome, protein biosynthesis, and process, the citrate cycle, membrane transport, and hormonal regulation were preferentially enriched and regulated. Biosynthesis inhibition and signal transduction downstream of auxin- and ethylene-mediated signals occur during alfalfa responses to root growth inhibition. The internal Al detoxification mechanisms play important roles in alfalfa roots under Al stress. These findings provide valuable information for identifying and characterizing important components in the Al signaling network in alfalfa and enhance understanding of the molecular mechanisms underlying alfalfa responses to Al stress. PMID:28217130

  10. Shadow response in the blind cavefish Astyanax reveals conservation of a functional pineal eye.

    Science.gov (United States)

    Yoshizawa, Masato; Jeffery, William R

    2008-02-01

    The blind cavefish Astyanax mexicanus undergoes bilateral eye degeneration during embryonic development. Despite the absence of light in the cave environment, cavefish have retained a structurally intact pineal eye. We show here that contrary to visual degeneration in the bilateral eyes, the cavefish pineal eye has conserved the ability to detect light. Larvae of two different Astyanax cavefish populations and the con-specific sighted surface-dwelling form (surface fish) respond similarly to light dimming by shading the pineal eye. As a response to shading, cavefish larvae swim upward vertically. This behavior resembles that of amphibian tadpoles rather than other teleost larvae, which react to shadows by swimming downward. The shadow response is highest at 1.5-days post-fertilization (d.p.f.), gradually diminishes, and is virtually undetectable by 7.5 d.p.f. The shadow response was substantially reduced after surgical removal of the pineal gland from surface fish or cavefish larvae, indicating that it is based on pineal function. In contrast, removal of one or both bilateral eye primordia did not affect the shadow response. Consistent with its light detecting capacity, immunocytochemical studies indicate that surface fish and cavefish pineal eyes express a rhodopsin-like antigen, which is undetectable in the degenerating bilateral eyes of cavefish larvae. We conclude that light detection by the pineal eye has been conserved in cavefish despite a million or more years of evolution in complete darkness.

  11. Starvation stress during larval development reveals predictive adaptive response in adult worker honey bees (Apis mellifera)

    Science.gov (United States)

    A variety of organisms exhibit developmental plasticity that results in differences in adult morphology, physiology or behavior. This variation in the phenotype, called “Predictive Adaptive Response (PAR),” gives a selective advantage in an adult's environment if the adult experiences environments s...

  12. Comparative proteomic analysis of a sea urchin (Heliocidaris erythrogramma) antibacterial response revealed the involvement of apextrin and calreticulin.

    Science.gov (United States)

    Dheilly, Nolwenn M; Haynes, Paul A; Bove, Ulysse; Nair, Sham V; Raftos, David A

    2011-02-01

    Echinoderms evolved early in the deuterostome lineage, and as such constitute model organisms for comparative physiology and immunology. The sea urchin genome sequence (Strongylocentrotus purpuratus) revealed a complex repertoire of genes with similarities to the immune response genes of other species. To complement these genomic data, we investigated the responses of sea urchins to the injection of bacteria using a comparative proteomics approach on a closely related species. In the sea urchin, Heliocidaris erythrogramma, the relative abundance of many proteins was altered in response to the injection of both bacteria and saline, suggesting their involvement in wounding responses, while others were differentially altered in response to bacteria only. The identities of 15 proteins that differed in relative abundance were determined by mass spectrometry. These proteins revealed a significant modification in energy metabolism in coelomocytes towards the consumption of glutamate and the production of NADPH after injection, as well as an increased concentration of cell signalling molecules, such as heterotrimeric guanine nucleotide-binding protein. The injection of bacteria specifically increased the abundance of apextrin and calreticulin, suggesting that these two proteins are involved in the sequestration or inactivation of bacteria.

  13. Coral-zooxanthellae meta-transcriptomics reveals integrated response to pollutant stress.

    Science.gov (United States)

    Gust, Kurt A; Najar, Fares Z; Habib, Tanwir; Lotufo, Guilherme R; Piggot, Alan M; Fouke, Bruce W; Laird, Jennifer G; Wilbanks, Mitchell S; Rawat, Arun; Indest, Karl J; Roe, Bruce A; Perkins, Edward J

    2014-07-12

    Corals represent symbiotic meta-organisms that require harmonization among the coral animal, photosynthetic zooxanthellae and associated microbes to survive environmental stresses. We investigated integrated-responses among coral and zooxanthellae in the scleractinian coral Acropora formosa in response to an emerging marine pollutant, the munitions constituent, 1,3,5-trinitro-1,3,5 triazine (RDX; 5 day exposures to 0 (control), 0.5, 0.9, 1.8, 3.7, and 7.2 mg/L, measured in seawater). RDX accumulated readily in coral soft tissues with bioconcentration factors ranging from 1.1 to 1.5. Next-generation sequencing of a normalized meta-transcriptomic library developed for the eukaryotic components of the A. formosa coral holobiont was leveraged to conduct microarray-based global transcript expression analysis of integrated coral/zooxanthellae responses to the RDX exposure. Total differentially expressed transcripts (DET) increased with increasing RDX exposure concentrations as did the proportion of zooxanthellae DET relative to the coral animal. Transcriptional responses in the coral demonstrated higher sensitivity to RDX compared to zooxanthellae where increased expression of gene transcripts coding xenobiotic detoxification mechanisms (i.e. cytochrome P450 and UDP glucuronosyltransferase 2 family) were initiated at the lowest exposure concentration. Increased expression of these detoxification mechanisms was sustained at higher RDX concentrations as well as production of a physical barrier to exposure through a 40% increase in mucocyte density at the maximum RDX exposure. At and above the 1.8 mg/L exposure concentration, DET coding for genes involved in central energy metabolism, including photosynthesis, glycolysis and electron-transport functions, were decreased in zooxanthellae although preliminary data indicated that zooxanthellae densities were not affected. In contrast, significantly increased transcript expression for genes involved in cellular energy production

  14. Adaptive responses reveal contemporary and future ecotypes in a desert shrub.

    Science.gov (United States)

    Richardson, Bryce A; Kitchen, Stanley G; Pendleton, Rosemary L; Pendleton, Burton K; Germino, Matthew J; Rehfeldt, Gerald E; Meyer, Susan E

    2014-03-01

    Interacting threats to ecosystem function, including climate change, wildfire, and invasive species necessitate native plant restoration in desert ecosystems. However, native plant restoration efforts often remain unguided by ecological genetic information. Given that many ecosystems are in flux from climate change, restoration plans need to account for both contemporary and future climates when choosing seed sources. In this study we analyze vegetative responses, including mortality, growth, and carbon isotope ratios in two blackbrush (Coleogyne ramosissima) common gardens that included 26 populations from a range-wide collection. This shrub occupies ecotones between the warm and cold deserts of Mojave and Colorado Plateau ecoregions in western North America. The variation observed in the vegetative responses of blackbrush populations was principally explained by grouping populations by ecoregions and by regression with site-specific climate variables. Aridity weighted by winter minimum temperatures best explained vegetative responses; Colorado Plateau sites were usually colder and drier than Mojave sites. The relationship between climate and vegetative response was mapped within the boundaries of the species-climate space projected for the contemporary climate and for the decade surrounding 2060. The mapped ecological genetic pattern showed that genetic variation could be classified into cool-adapted and warm-adapted ecotypes, with populations often separated by steep dines. These transitions are predicted to occur in both the Mojave Desert and Colorado Plateau ecoregions. While under contemporary conditions the warm-adapted ecotype occupies the majority of climate space, climate projections predict that the cool-adapted ecotype could prevail as the dominant ecotype as the climate space of blackbrush expands into higher elevations and latitudes. This study provides the framework for delineating climate change-responsive seed transfer guidelines, which are needed

  15. Fine-root responses to fertilization reveal multiple nutrient limitation in a lowland tropical forest.

    Science.gov (United States)

    Wurzburger, Nina; Wright, S Joseph

    2015-08-01

    Questions remain as to which soil nutrients limit primary production in tropical forests. Phosphorus (P) has long been considered the primary limiting element in lowland forests, but recent evidence demonstrates substantial heterogeneity in response to nutrient addition, highlighting a need to understand and diagnose nutrient limitation across diverse forests. Fine-root characteristics including their abundance, functional traits, and mycorrhizal symbionts can be highly responsive to changes in soil nutrients and may help to diagnose nutrient limitation. Here, we document the response of fine roots to long-term nitrogen (N), P, and potassium (K) fertilization in a lowland forest in Panama. Because this experiment has demonstrated that N and K together limit tree growth and P limits fine litter production, we hypothesized that fine roots would also respond to nutrient addition. Specifically we hypothesized that N, P, and K addition would reduce the biomass, diameter, tissue density, and mycorrhizal colonization of fine roots, and increase nutrient concentration in root tissue. Most morphological root traits responded to the single addition of K and the paired addition of N and P, with the greatest response to all three nutrients combined. The addition of N, P, and K together reduced fine-root biomass, length, and tissue density, and increased specific root length, whereas root diameter remained unchanged. Nitrogen addition did not alter root N concentration, but P and K addition increased root P and K concentration, respectively. Mycorrhizal colonization of fine roots declined with N, increased with P, and was unresponsive to K addition. Although plant species composition remains unchanged after 14 years of fertilization, fine-root characteristics responded to N, P, and K addition, providing some of the strongest stand-level responses in this experiment. Multiple soil nutrients regulate fine-root abundance, morphological and chemical traits, and their association

  16. Responsibility for managing musculoskeletal disorders – A cross-sectional postal survey of attitudes

    Directory of Open Access Journals (Sweden)

    Larsson Maria EH

    2008-08-01

    Full Text Available Abstract Background Musculoskeletal disorders are a major burden on individuals, health systems and social care systems and rehabilitation efforts in these disorders are considerable. Self-care is often considered a cost effective treatment alternative owing to limited health care resources. But what are the expectations and attitudes in this question in the general population? The purpose of this study was to describe general attitudes to responsibility for the management of musculoskeletal disorders and to explore associations between attitudes and background variables. Methods A cross-sectional, postal questionnaire survey was carried out with a random sample of a general adult Swedish population of 1770 persons. Sixty-one percent (n = 1082 responded to the questionnaire and was included for the description of general attitudes towards responsibility for the management of musculoskeletal disorders. For the further analyses of associations to background variables 683–693 individuals could be included. Attitudes were measured by the "Attitudes regarding Responsibility for Musculoskeletal disorders" (ARM instrument, where responsibility is attributed on four dimensions; to myself, as being out of my hands, to employers or to (medical professionals. Multiple logistic regression was used to explore associations between attitudes to musculoskeletal disorders and the background variables age, sex, education, physical activity, presence of musculoskeletal disorders, sick leave and whether the person had visited a care provider. Results A majority of participants had internal views, i.e. showed an attitude of taking personal responsibility for musculoskeletal disorders, and did not place responsibility for the management out of their own hands or to employers. However, attributing shared responsibility between self and medical professionals was also found. The main associations found between attitude towards responsibility for musculoskeletal

  17. Analysis of morphine responses in mice reveals a QTL on Chromosome 7 [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Wim E. Crusio

    2016-09-01

    Full Text Available In this study we identified a quantitative trait locus (QTL on mouse Chromosome 7 associated with locomotor activity and rearing post morphine treatment. This QTL was revealed after correcting for the effects of another QTL peak on Chromosome 10 using composite interval mapping. The positional candidate genes are Syt9 and Ppfibp2. Several other genes within the interval are linked to neural processes, locomotor activity, and the defensive response to harmful stimuli.

  18. Analysis of morphine responses in mice reveals a QTL on Chromosome 7 [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Wim E. Crusio

    2016-10-01

    Full Text Available In this study we identified a quantitative trait locus (QTL on mouse Chromosome 7 associated with locomotor activity and rearing post morphine treatment. This QTL was revealed after correcting for the effects of another QTL peak on Chromosome 10 using composite interval mapping. The positional candidate genes are Syt9 and Ppfibp2. Several other genes within the interval are linked to neural processes, locomotor activity, and the defensive response to harmful stimuli.

  19. RNA-Seq reveals complex genetic response to deepwater horizon oil release in Fundulus grandis

    Directory of Open Access Journals (Sweden)

    Garcia Tzintzuni I

    2012-09-01

    Full Text Available Abstract Background The release of oil resulting from the blowout of the Deepwater Horizon (DH drilling platform was one of the largest in history discharging more than 189 million gallons of oil and subject to widespread application of oil dispersants. This event impacted a wide range of ecological habitats with a complex mix of pollutants whose biological impact is still not yet fully understood. To better understand the effects on a vertebrate genome, we studied gene expression in the salt marsh minnow Fundulus grandis, which is local to the northern coast of the Gulf of Mexico and is a sister species of the ecotoxicological model Fundulus heteroclitus. To assess genomic changes, we quantified mRNA expression using high throughput sequencing technologies (RNA-Seq in F. grandis populations in the marshes and estuaries impacted by DH oil release. This application of RNA-Seq to a non-model, wild, and ecologically significant organism is an important evaluation of the technology to quickly assess similar events in the future. Results Our de novo assembly of RNA-Seq data produced a large set of sequences which included many duplicates and fragments. In many cases several of these could be associated with a common reference sequence using blast to query a reference database. This reduced the set of significant genes to 1,070 down-regulated and 1,251 up-regulated genes. These genes indicate a broad and complex genomic response to DH oil exposure including the expected AHR-mediated response and CYP genes. In addition a response to hypoxic conditions and an immune response are also indicated. Several genes in the choriogenin family were down-regulated in the exposed group; a response that is consistent with AH exposure. These analyses are in agreement with oligonucleotide-based microarray analyses, and describe only a subset of significant genes with aberrant regulation in the exposed set. Conclusion RNA-Seq may be successfully applied to feral and

  20. Survey Response Styles, Acculturation, and Culture Among a Sample of Mexican American Adults.

    Science.gov (United States)

    Davis, Rachel E; Resnicow, Ken; Couper, Mick P

    2011-10-01

    A number of studies have investigated use of extreme (ERS) and acquiescent (ARS) response styles across cultural groups. However, due to within-group heterogeneity, it is important to also examine use of response styles, acculturation, and endorsement of cultural variables at the individual level. This study explores relationships between acculturation, six Mexican cultural factors, ERS, and ARS among a sample of 288 Mexican American telephone survey respondents. Three aspects of acculturation were assessed: Spanish use, the importance of preserving Mexican culture, and interaction with Mexican Americans versus Anglos. These variables were hypothesized to positively associate with ERS and ARS. Participants with higher Spanish use did utilize more ERS and ARS; however, value for preserving Mexican culture and interaction with Mexican Americans were not associated with response style use. In analyses of cultural factors, endorsement of familismo and simpatia were related to more frequent ERS and ARS, machismo was associated with lower ERS among men, and la mujer was related to higher ERS among women. Caballerismo was marginally associated with utilization of ERS among men. No association was found between la mujer abnegada and ERS among women. Relationships between male gender roles and ARS were nonsignificant. Relationships between female gender roles and ARS were mixed but trended in the positive direction. Overall, these findings suggest that Mexican American respondents vary in their use of response styles by acculturation and cultural factors. This usage may be specifically influenced by participants' valuing of and engagement with constructs directly associated with social behavior.

  1. An unbiased genetic screen reveals the polygenic nature of the influenza virus anti-interferon response.

    Science.gov (United States)

    Pérez-Cidoncha, Maite; Killip, Marian J; Oliveros, Juan C; Asensio, Víctor J; Fernández, Yolanda; Bengoechea, José A; Randall, Richard E; Ortín, Juan

    2014-05-01

    Influenza A viruses counteract the cellular innate immune response at several steps, including blocking RIG I-dependent activation of interferon (IFN) transcription, interferon (IFN)-dependent upregulation of IFN-stimulated genes (ISGs), and the activity of various ISG products; the multifunctional NS1 protein is responsible for most of these activities. To determine the importance of other viral genes in the interplay between the virus and the host IFN response, we characterized populations and selected mutants of wild-type viruses selected by passage through non-IFN-responsive cells. We reasoned that, by allowing replication to occur in the absence of the selection pressure exerted by IFN, the virus could mutate at positions that would normally be restricted and could thus find new optimal sequence solutions. Deep sequencing of selected virus populations and individual virus mutants indicated that nonsynonymous mutations occurred at many phylogenetically conserved positions in nearly all virus genes. Most individual mutants selected for further characterization induced IFN and ISGs and were unable to counteract the effects of exogenous IFN, yet only one contained a mutation in NS1. The relevance of these mutations for the virus phenotype was verified by reverse genetics. Of note, several virus mutants expressing intact NS1 proteins exhibited alterations in the M1/M2 proteins and accumulated large amounts of deleted genomic RNAs but nonetheless replicated to high titers. This suggests that the overproduction of IFN inducers by these viruses can override NS1-mediated IFN modulation. Altogether, the results suggest that influenza viruses replicating in IFN-competent cells have tuned their complete genomes to evade the cellular innate immune system and that serial replication in non-IFN-responsive cells allows the virus to relax from these constraints and find a new genome consensus within its sequence space. In natural virus infections, the production of interferons

  2. Systematic tracking of altered haematopoiesis during sporozoite-mediated malaria development reveals multiple response points.

    Science.gov (United States)

    Vainieri, Maria L; Blagborough, Andrew M; MacLean, Adam L; Haltalli, Myriam L R; Ruivo, Nicola; Fletcher, Helen A; Stumpf, Michael P H; Sinden, Robert E; Celso, Cristina Lo

    2016-06-01

    Haematopoiesis is the complex developmental process that maintains the turnover of all blood cell lineages. It critically depends on the correct functioning of rare, quiescent haematopoietic stem cells (HSCs) and more numerous, HSC-derived, highly proliferative and differentiating haematopoietic progenitor cells (HPCs). Infection is known to affect HSCs, with severe and chronic inflammatory stimuli leading to stem cell pool depletion, while acute, non-lethal infections exert transient and even potentiating effects. Both whether this paradigm applies to all infections and whether the HSC response is the dominant driver of the changes observed during stressed haematopoiesis remain open questions. We use a mouse model of malaria, based on natural, sporozoite-driven Plasmodium berghei infection, as an experimental platform to gain a global view of haematopoietic perturbations during infection progression. We observe coordinated responses by the most primitive HSCs and multiple HPCs, some starting before blood parasitaemia is detected. We show that, despite highly variable inter-host responses, primitive HSCs become highly proliferative, but mathematical modelling suggests that this alone is not sufficient to significantly impact the whole haematopoietic cascade. We observe that the dramatic expansion of Sca-1(+) progenitors results from combined proliferation of direct HSC progeny and phenotypic changes in downstream populations. We observe that the simultaneous perturbation of HSC/HPC population dynamics is coupled with early signs of anaemia onset. Our data uncover a complex relationship between Plasmodium and its host's haematopoiesis and raise the question whether the variable responses observed may affect the outcome of the infection itself and its long-term consequences on the host.

  3. Transcriptome Analysis of Pepper (Capsicum annuum Revealed a Role of 24-epibrassinolide in Response to Chilling

    Directory of Open Access Journals (Sweden)

    Li Jie

    2016-08-01

    Full Text Available Brassinosteroids (BRs have positive effects on many processes during plant growth, development, and various abiotic stress responses. However, little information is available regarding the global gene expression of BRs in response to chilling stress in pepper. In this study, we used RNA sequencing to determine the molecular roles of 24-epibrassinolide (EBR during a chilling stress response. There were 39,829 transcripts, and, among them, 656 were differently-expressed genes (DEGs following EBR treatment (Chill+EBR compared with the control (Chill only, including 335 up-regulated and 321 down-regulated DEGs. We selected 20 genes out of the 656 DEGs for RT-qPCR analysis to confirm the RNA-Seq. Based on GO enrich and KEGG pathway analysis, we found that photosynthesis was significantly up-enriched in biological processes, accompanied by significant increases in the net photosynthetic rate (Pn, Fv/Fm and chlorophyll content. Furthermore, the results indicate that EBR enhanced endogenous levels of salicylic acid (SA and jasmonic acid (JA while suppressing the ethylene (ETH biosynthesis pathway, suggesting that BRs function via a synergistic cross-talk with SA, JA and ETH signaling pathways in response to chilling stress. In addition, EBR induced cellulose synthase-like protein and UDP-glycosyltransferase, suggesting a contribution to the formation of cell wall and hormone metabolism. EBR also triggered the calcium signaling transduction in cytoplasm, and activated the expression of cellular redox homeostasis related genes, such as GSTX1, PER72, and CAT2. This work, therefor, identified the specific genes showed different expression patterns in EBR-treated pepper and associated with the processes of hormone metabolism, redox, signaling, transcription and defense. Our study provides the first evidence of the potent roles of BRs, at the transcription level, to induce the tolerance to chilling stress in pepper as a function of the combination of the

  4. Proteomics reveals a core molecular response of Pseudomonas putida F1 to acute chromate challenge

    Directory of Open Access Journals (Sweden)

    McCarthy Andrea T

    2010-05-01

    Full Text Available Abstract Background Pseudomonas putida is a model organism for bioremediation because of its remarkable metabolic versatility, extensive biodegradative functions, and ubiquity in contaminated soil environments. To further the understanding of molecular pathways responding to the heavy metal chromium(VI [Cr(VI], the proteome of aerobically grown, Cr(VI-stressed P. putida strain F1 was characterized within the context of two disparate nutritional environments: rich (LB media and minimal (M9L media containing lactate as the sole carbon source. Results Growth studies demonstrated that F1 sensitivity to Cr(VI was impacted substantially by nutrient conditions, with a carbon-source-dependent hierarchy (lactate > glucose >> acetate observed in minimal media. Two-dimensional HPLC-MS/MS was employed to identify differential proteome profiles generated in response to 1 mM chromate under LB and M9L growth conditions. The immediate response to Cr(VI in LB-grown cells was up-regulation of proteins involved in inorganic ion transport, secondary metabolite biosynthesis and catabolism, and amino acid metabolism. By contrast, the chromate-responsive proteome derived under defined minimal growth conditions was characterized predominantly by up-regulated proteins related to cell envelope biogenesis, inorganic ion transport, and motility. TonB-dependent siderophore receptors involved in ferric iron acquisition and amino acid adenylation domains characterized up-regulated systems under LB-Cr(VI conditions, while DNA repair proteins and systems scavenging sulfur from alternative sources (e.g., aliphatic sulfonates tended to predominate the up-regulated proteome profile obtained under M9L-Cr(VI conditions. Conclusions Comparative analysis indicated that the core molecular response to chromate, irrespective of the nutritional conditions tested, comprised seven up-regulated proteins belonging to six different functional categories including transcription, inorganic ion

  5. Metabolomics Reveals Amino Acids Contribute to Variation in Response to Simvastatin Treatment

    OpenAIRE

    Miles Trupp; Hongjie Zhu; Wikoff, William R.; Rebecca A. Baillie; Zhao-Bang Zeng; Karp, Peter D.; Oliver Fiehn; Krauss, Ronald M.; Rima Kaddurah-Daouk

    2012-01-01

    UNLABELLED: Statins are widely prescribed for reducing LDL-cholesterol (C) and risk for cardiovascular disease (CVD), but there is considerable variation in therapeutic response. We used a gas chromatography-time-of-flight mass-spectrometry-based metabolomics platform to evaluate global effects of simvastatin on intermediary metabolism. Analyses were conducted in 148 participants in the Cholesterol and Pharmacogenetics study who were profiled pre and six weeks post treatment with 40 mg/day si...

  6. Transcriptome profiling reveals similarities and differences in plant responses to cadmium and lead.

    Science.gov (United States)

    Kovalchuk, Igor; Titov, Victor; Hohn, Barbara; Kovalchuk, Olga

    2005-03-01

    We analyzed the influence of salts of two heavy metals--lead and cadmium (Pb2+ and Cd2+) on plants, including plant and root size, plant genome stability as well as global genome expression. Measurement of the metal uptake showed that there was a significantly higher incorporation of Cd than of Pb, 0.6 and 0.15 uM per gram of dry weight, respectively. The analysis of the root length and plant size showed a dose dependent decrease in plants exposed to cadmium. In contrast there was little difference in the size of plants exposed to lead, although there was nearly four-fold increase of the root length. Analysis of the genome stability revealed that cadmium led to a dose dependent increase of homologous recombination whereas lead had no effect. Analysis of the global genome expression of plants chronically exposed to 50 uM of Cd and Pb revealed 65 and 338 up- and down-regulated genes by Cd and 19 and 76 by Pb, respectively. Interestingly, half of the genes that changed their expression in Pb-treated plants also changed their expression in Cd-treated ones. The greater number of genes regulated by Cd reflects generally higher genome instability of plants as well as higher uptake as compared to Pb.

  7. Transcriptome profiling reveals similarities and differences in plant responses to cadmium and lead

    Energy Technology Data Exchange (ETDEWEB)

    Kovalchuk, Igor [Department of Biological Sciences, University of Lethbridge, Alta., T1K 3M4 (Canada); Titov, Victor [Department of Biological Sciences, University of Lethbridge, Alta., T1K 3M4 (Canada); Hohn, Barbara [Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH4058 Basel (Switzerland); Kovalchuk, Olga [Department of Biological Sciences, University of Lethbridge, Alta., T1K 3M4 (Canada)]. E-mail: olga.kovalchuk@uleth.ca

    2005-03-01

    We analyzed the influence of salts of two heavy metals--lead and cadmium (Pb{sup 2+} and Cd{sup 2+}) on plants, including plant and root size, plant genome stability as well as global genome expression. Measurement of the metal uptake showed that there was a significantly higher incorporation of Cd than of Pb, 0.6 and 0.15 uM per gram of dry weight, respectively. The analysis of the root length and plant size showed a dose dependent decrease in plants exposed to cadmium. In contrast there was little difference in the size of plants exposed to lead, although there was nearly four-fold increase of the root length. Analysis of the genome stability revealed that cadmium led to a dose dependent increase of homologous recombination whereas lead had no effect. Analysis of the global genome expression of plants chronically exposed to 50 uM of Cd and Pb revealed 65 and 338 up- and down-regulated genes by Cd and 19 and 76 by Pb, respectively. Interestingly, half of the genes that changed their expression in Pb-treated plants also changed their expression in Cd-treated ones. The greater number of genes regulated by Cd reflects generally higher genome instability of plants as well as higher uptake as compared to Pb.

  8. Physiological, biochemical, and proteome profiling reveals key pathways underlying the drought stress responses of Hippophae rhamnoides.

    Science.gov (United States)

    He, Cai Y; Zhang, Guo Y; Zhang, Jian G; Duan, Ai G; Luo, Hong M

    2016-10-01

    The effects of drought on plant growth and development are occurring as a result of climate change and the growing scarcity of water resources. Hippophae rhamnoides has been exploited for soil and water conservation for many years. However, the outstanding drought-resistance mechanisms possessed by this species remain unclear. The protein, physiological, and biochemical responses to medium and severe drought stresses in H. rhamnoides seedlings are analyzed. Linear decreases in photosynthesis rate, transpiration rate, and the content of indole acetic acid in roots, as well as a linear increase in the contents of abscisic acid, superoxide dismutase, glutathione reductase, and zeatin riboside in leaves are observed as water potential decreased. At the same time, cell membrane permeability, malondialdehyde, stomatal conductance, water use efficiency, and contents of zeatin riboside in roots and indole acetic acid in leaves showed nonconsistent changes. DIGE and MS/MS analysis identified 51 differently expressed protein spots in leaves with functions related to epigenetic modification and PTM in addition to normal metabolism, photosynthesis, signal transduction, antioxidative systems, and responses to stimuli. This study provides new insights into the responses and adaptations in this drought-resistant species and may benefit future agricultural production. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Virus and dsRNA-triggered transcriptional responses reveal key components of honey bee antiviral defense.

    Science.gov (United States)

    Brutscher, Laura M; Daughenbaugh, Katie F; Flenniken, Michelle L

    2017-07-25

    Recent high annual losses of honey bee colonies are associated with many factors, including RNA virus infections. Honey bee antiviral responses include RNA interference and immune pathway activation, but their relative roles in antiviral defense are not well understood. To better characterize the mechanism(s) of honey bee antiviral defense, bees were infected with a model virus in the presence or absence of dsRNA, a virus associated molecular pattern. Regardless of sequence specificity, dsRNA reduced virus abundance. We utilized next generation sequencing to examine transcriptional responses triggered by virus and dsRNA at three time-points post-infection. Hundreds of genes exhibited differential expression in response to co-treatment of dsRNA and virus. Virus-infected bees had greater expression of genes involved in RNAi, Toll, Imd, and JAK-STAT pathways, but the majority of differentially expressed genes are not well characterized. To confirm the virus limiting role of two genes, including the well-characterized gene, dicer, and a probable uncharacterized cyclin dependent kinase in honey bees, we utilized RNAi to reduce their expression in vivo and determined that virus abundance increased, supporting their involvement in antiviral defense. Together, these results further our understanding of honey bee antiviral defense, particularly the role of a non-sequence specific dsRNA-mediated antiviral pathway.

  10. Transcriptomic profiling of microglia reveals signatures of cell activation and immune response, during experimental cerebral malaria

    Science.gov (United States)

    Capuccini, Barbara; Lin, Jingwen; Talavera-López, Carlos; Khan, Shahid M.; Sodenkamp, Jan; Spaccapelo, Roberta; Langhorne, Jean

    2016-01-01

    Cerebral malaria is a pathology involving inflammation in the brain. There are many immune cell types activated during this process, but there is little information on the response of microglia, in this severe complication. We examined microglia by genome wide transcriptomic analysis in a model of experimental cerebral malaria (ECM), in which C57BL/6 mice are infected with Plasmodium berghei ANKA. Thousands of transcripts were differentially expressed in microglia at two different time points during infection. Proliferation of microglia was a dominant feature before the onset of ECM, and supporting this, we observed an increase in numbers of these cells in the brain. When cerebral malaria symptoms were manifest, genes involved in immune responses and chemokine production were upregulated, which were possibly driven by Type I Interferon. Consistent with this hypothesis, in vitro culture of a microglial cell line with Interferon-β, but not infected red blood cells, resulted in production of several of the chemokines shown to be upregulated in the gene expression analysis. It appears that these responses are associated with ECM, as microglia from mice infected with a mutant P. berghei parasite (ΔDPAP3), which does not cause ECM, did not show the same level of activation or proliferation. PMID:27991544

  11. Medicago truncatula root nodule proteome analysis reveals differential plant and bacteroid responses to drought stress.

    Science.gov (United States)

    Larrainzar, Estíbaliz; Wienkoop, Stefanie; Weckwerth, Wolfram; Ladrera, Rubén; Arrese-Igor, Cesar; González, Esther M

    2007-07-01

    Drought is one of the environmental factors most affecting crop production. Under drought, symbiotic nitrogen fixation is one of the physiological processes to first show stress responses in nodulated legumes. This inhibition process involves a number of factors whose interactions are not yet understood. This work aims to further understand changes occurring in nodules under drought stress from a proteomic perspective. Drought was imposed on Medicago truncatula 'Jemalong A17' plants grown in symbiosis with Sinorhizobium meliloti strain 2011. Changes at the protein level were analyzed using a nongel approach based on liquid chromatography coupled to tandem mass spectrometry. Due to the complexity of nodule tissue, the separation of plant and bacteroid fractions in M. truncatula root nodules was first checked with the aim of minimizing cross contamination between the fractions. Second, the protein plant fraction of M. truncatula nodules was profiled, leading to the identification of 377 plant proteins, the largest description of the plant nodule proteome so far. Third, both symbiotic partners were independently analyzed for quantitative differences at the protein level during drought stress. Multivariate data mining allowed for the classification of proteins sets that were involved in drought stress responses. The isolation of the nodule plant and bacteroid protein fractions enabled the independent analysis of the response of both counterparts, gaining further understanding of how each symbiotic member is distinctly affected at the protein level under a water-deficit situation.

  12. Digital quantification of gene expression in sequential breast cancer biopsies reveals activation of an immune response.

    Directory of Open Access Journals (Sweden)

    Rinath M Jeselsohn

    Full Text Available Advancements in molecular biology have unveiled multiple breast cancer promoting pathways and potential therapeutic targets. Large randomized clinical trials remain the ultimate means of validating therapeutic efficacy, but they require large cohorts of patients and are lengthy and costly. A useful approach is to conduct a window of opportunity study in which patients are exposed to a drug pre-surgically during the interval between the core needle biopsy and the definitive surgery. These are non-therapeutic studies and the end point is not clinical or pathological response but rather evaluation of molecular changes in the tumor specimens that can predict response. However, since the end points of the non-therapeutic studies are biologic, it is critical to first define the biologic changes that occur in the absence of treatment. In this study, we compared the molecular profiles of breast cancer tumors at the time of the diagnostic biopsy versus the definitive surgery in the absence of any intervention using the Nanostring nCounter platform. We found that while the majority of the transcripts did not vary between the two biopsies, there was evidence of activation of immune related genes in response to the first biopsy and further investigations of the immune changes after a biopsy in early breast cancer seem warranted.

  13. Comparative Transcriptomics Reveals Discrete Survival Responses of S. aureus and S. epidermidis to Sapienic Acid.

    Science.gov (United States)

    Moran, Josephine C; Alorabi, Jamal A; Horsburgh, Malcolm J

    2017-01-01

    Staphylococcal colonization of human skin is ubiquitous, with particular species more frequent at different body sites. Whereas Staphylococcus epidermidis can be isolated from the skin of every individual tested, Staphylococcus aureus is isolated from S. aureus is inhibited to a greater extent than S. epidermidis by the sebaceous lipid sapienic acid, supporting a role for this skin antimicrobial in selection of skin staphylococci. We used RNA-Seq and comparative transcriptomics to identify the sapienic acid survival responses of S. aureus and S. epidermidis. Consistent with the membrane depolarization mode of action of sapienic acid, both species shared a common transcriptional response to counteract disruption of metabolism and transport. The species differed in their regulation of SaeRS and VraRS regulons. While S. aureus upregulated urease operon transcription, S. epidermidis upregulated arginine deiminase, the oxygen-responsive NreABC nitrogen regulation system and the nitrate and nitrite reduction pathways. The role of S. aureus ACME and chromosomal arginine deiminase pathways in sapienic acid resistance was determined through mutational studies. We speculate that ammonia production could contribute to sapienic acid resistance in staphylococci.

  14. Survey of 800+ datasets from human tissue and body fluid reveals XenomiRs are likely artifacts

    DEFF Research Database (Denmark)

    Kang, Wenjing; Bang-Berthelsen, Claus Heiner; Holm, Anja;

    2017-01-01

    -study in the field, surveying the presence and abundances of cross-species miRNAs (xenomiRs) in 824 sequencing datasets from various human tissues and body fluids. We find that xenomiRs are commonly present in tissues (17%) and body fluids (69%), however the abundances are low, comprising 0.001% of host human mi......RNA counts. Further, we do not detect a significant enrichment of xenomiRs in sequencing data originating from tissues and body fluids that are exposed to dietary intake (such as liver). Likewise, there is no significant depletion of xenomiRs in tissues and body fluids that are relatively separated from...

  15. Incentive and Reminder Strategies to Improve Response Rate for Internet-Based Physician Surveys: A Randomized Experiment

    Science.gov (United States)

    Wittich, Christopher M; Daniels, Wendlyn L; West, Colin P; Harris, Ann M; Beebe, Timothy J

    2016-01-01

    Background Most research on how to enhance response rates in physician surveys has been done using paper surveys. Uncertainties remain regarding how to enhance response rates in Internet-based surveys. Objective To evaluate the impact of a low-cost nonmonetary incentive and paper mail reminders (formal letter and postcard) on response rates in Internet-based physician surveys. Methods We executed a factorial-design randomized experiment while conducting a nationally representative Internet-based physician survey. We invited 3966 physicians (randomly selected from a commercial database of all licensed US physicians) via email to complete an Internet-based survey. We used 2 randomly assigned email messages: one message offered a book upon survey completion, whereas the other did not mention the book but was otherwise identical. All nonrespondents received several email reminders. Some physicians were further assigned at random to receive 1 reminder via paper mail (either a postcard or a letter) or no paper reminder. The primary outcome of this study was the survey response rate. Results Of the 3966 physicians who were invited, 451 (11.4%) responded to at least one survey question and 336 (8.5%) completed the entire survey. Of those who were offered a book, 345/2973 (11.6%) responded compared with 106/993 (10.7%) who were not offered a book (odds ratio 1.10, 95% CI 0.87-1.38, P=.42). Regarding the paper mail reminder, 168/1572 (10.7%) letter recipients, 148/1561 (9.5%) postcard recipients, and 69/767 (9.0%) email-only recipients responded (P=.35). The response rate for those receiving letters or postcards was similar (odds ratio 1.14, 95% CI 0.91-1.44, P=.26). Conclusions Offering a modest nonmonetary incentive and sending a paper reminder did not improve survey response rate. Further research on how to enhance response rates in Internet-based physician surveys is needed. PMID:27637296

  16. Correlation of transcriptomic responses and metal bioaccumulation in Mytilus edulis L. reveals early indicators of stress

    Energy Technology Data Exchange (ETDEWEB)

    Poynton, Helen C., E-mail: helen.poynton@umb.edu; Robinson, William E.; Blalock, Bonnie J.; Hannigan, Robyn E.

    2014-10-15

    Highlights: • Gene expression and metal tissue concentrations were compared in Mytilus edulis. • Expression levels of several transcripts correlated with metal concentrations. • Transcripts involved in the unfolded protein response (UPR) were induced. • Integration of transcriptomics and tissue levels provides insight to toxicity. - Abstract: Marine biomonitoring programs in the U.S. and Europe have historically relied on monitoring tissue concentrations of bivalves to monitor contaminant levels and ecosystem health. By integrating ‘omic methods with these tissue residue approaches we can uncover mechanistic insight to link tissue concentrations to potential toxic effects. In an effort to identify novel biomarkers and better understand the molecular toxicology of metal bioaccumulation in bivalves, we exposed the blue mussel, Mytilus edulis L., to sub-lethal concentrations (0.54 μM) of cadmium, lead, and a Cd + Pb mixture. Metal concentrations were measured in gill tissues at 1, 2, and 4 weeks, and increased linearly over the 4 week duration. In addition, there was evidence that Pb interfered with Cd uptake in the mixture treatment. Using a 3025 sequence microarray for M. edulis, we performed transcriptomic analysis, identifying 57 differentially expressed sequences. Hierarchical clustering of these sequences successfully distinguished the different treatment groups demonstrating that the expression profiles were reproducible among the treatments. Enrichment analysis of gene ontology terms identified several biological processes that were perturbed by the treatments, including nucleoside phosphate biosynthetic processes, mRNA metabolic processes, and response to stress. To identify transcripts whose expression level correlated with metal bioaccumulation, we performed Pearson correlation analysis. Several transcripts correlated with gill metal concentrations including mt10, mt20, and contig 48, an unknown transcript containing a wsc domain. In addition

  17. A zebrafish larval model reveals early tissue-specific innate immune responses to Mucor circinelloides

    Directory of Open Access Journals (Sweden)

    Kerstin Voelz

    2015-11-01

    Full Text Available Mucormycosis is an emerging fungal infection that is clinically difficult to manage, with increasing incidence and extremely high mortality rates. Individuals with diabetes, suppressed immunity or traumatic injury are at increased risk of developing disease. These individuals often present with defects in phagocytic effector cell function. Research using mammalian models and phagocytic effector cell lines has attempted to decipher the importance of the innate immune system in host defence against mucormycosis. However, these model systems have not been satisfactory for direct analysis of the interaction between innate immune effector cells and infectious sporangiospores in vivo. Here, we report the first real-time in vivo analysis of the early innate immune response to mucormycete infection using a whole-animal zebrafish larval model system. We identified differential host susceptibility, dependent on the site of infection (hindbrain ventricle and swim bladder, as well as differential functions of the two major phagocyte effector cell types in response to viable and non-viable spores. Larval susceptibility to mucormycete spore infection was increased upon immunosuppressant treatment. We showed for the first time that macrophages and neutrophils were readily recruited in vivo to the site of infection in an intact host and that spore phagocytosis can be observed in real-time in vivo. While exploring innate immune effector recruitment dynamics, we discovered the formation of phagocyte clusters in response to fungal spores that potentially play a role in fungal spore dissemination. Spores failed to activate pro-inflammatory gene expression by 6 h post-infection in both infection models. After 24 h, induction of a pro-inflammatory response was observed only in hindbrain ventricle infections. Only a weak pro-inflammatory response was initiated after spore injection into the swim bladder during the same time frame. In the future, the zebrafish larva

  18. A Dose-Response Strategy Reveals Differences between Normal-Weight and Obese Men in Their Metabolic and Inflammatory Responses to a High-Fat Meal.

    OpenAIRE

    Schwander, Flurina; Kopf-Bolanz, Katrin A.; Buri, Caroline; Portmann, Reto; Egger, Lotti; Chollet, Magali; McTernan, P.G.; Piya, Milan K.; Gijs, Martin A. M.; Vionnet, Nathalie; Pralong, Franc̨ois; Laederach, Kurt; Vergeres, Guy

    2014-01-01

    A dose-response strategy may not only allow investigation of the impact of foods and nutrients on human health but may also reveal differences in the response of individuals to food ingestion based on their metabolic health status. In a randomized crossover study, we challenged 19 normal-weight (BMI: 20-25 kg/m(2)) and 18 obese (BMI: >30 kg/m(2)) men with 500, 1000, and 1500 kcal of a high-fat (HF) meal (60.5% energy from fat). Blood was taken at baseline and up to 6 h postprandially and a...

  19. H I Structure and Topology of the Galaxy Revealed by the I-GALFA H I 21-cm Line Survey

    Science.gov (United States)

    Koo, Bon-Chul; Park, G.; Cho, W.; Gibson, S. J.; Kang, J.; Douglas, K. A.; Peek, J. E. G.; Korpela, E. J.; Heiles, C. E.

    2011-05-01

    The I-GALFA survey mapping all the H I in the inner Galactic disk visible to the Arecibo 305m telescope within 10 degrees of the Galactic plane (longitudes of 32 to 77 degrees at b = 0) completed observations in 2009 September and will soon be made publicly available. The high (3.4 arcmin) resolution and tremendous sensitivity of the survey offer a great opportunity to observe the fine details of H I both in the inner and in the far outer Galaxy. The reduced HI column density maps show that the HI structure is highly filamentary and clumpy, pervaded by shell-like structures, vertical filaments, and small clumps. By inspecting individual maps, we have found 36 shell candidates of angular sizes ranging from 0.4 to 12 degrees, half of which appear to be expanding. In order to characterize the filamentary/clumpy morphology of the HI structure, we have carried out statistical analyses of selected areas representing the spiral arms in the inner and outer Galaxy. Genus statistics that can distinguish the ``meatball'' and ``swiss-cheese'' topologies show that the HI topology is clump-like in most regions. The two-dimensional Fourier analysis further shows the HI structures are filamentary and mainly parallel to the plane in the outer Galaxy. We also examine the level-crossing statistics, the results of which are described in detail in an accompanying poster by Park et al.

  20. Revealing plot scale heterogeneity in soil moisture dynamics under contrasting vegetation assemblages using 3D electrical resistivity tomography (ERT) surveys

    Science.gov (United States)

    Dick, Jonathan; Tetzlaff, Doerthe; Bradford, John; Soulsby, Chris

    2016-04-01

    Soil moisture is a fundamental component of the water cycle that influences many hydrological processes, such as flooding, solute transport, biogeochemical processes, and land-atmosphere interactions. The relationship between vegetation and soil moisture is complex and reciprocal. Soil moisture may affect vegetation distribution due to its function as the primary source of water, in turn the structure of vegetation canopies regulate water partitioning into interception, throughfall and steam flow. Such spatial differences in inputs, together with complex patterns of water uptake from distributed root networks can create marked heterogeneity in soil moisture dynamics at small scales. Traditional methods of monitoring soil moisture have revolved around limited point measurements, but improved geophysical techniques have facilitated a trend towards more spatially distributed measurements to help understand this heterogeneity. Here, we present a study using 3D ERT surveys in a 3.2km upland catchment in the Scottish Highlands where increasing afforestation (for climate change adaptation, biofuels and conservation) has the potential to increase interception losses and reduce soil moisture storage. The study combined 3D surveys, traditional point measurements and laboratory analysis of soil cores to assess the plot scale soil moisture dynamics in podzolic soils under forest stands of 15m high Scots pine (Pinus sylvestris) and adjacent non-forest plots dominated by heather (Calluna vulgaris) shrubs (water content in the soils below. These results are important as the point to potential water stresses with planned increased afforestation which may be compounded by climate change projections of decreasing precipitation during the growing season.

  1. Seasonal and Diel Activity Patterns of Eight Sympatric Mammals in Northern Japan Revealed by an Intensive Camera-Trap Survey

    Science.gov (United States)

    Ikeda, Takashi; Uchida, Kenta; Matsuura, Yukiko; Takahashi, Hiroshi; Yoshida, Tsuyoshi; Kaji, Koichi; Koizumi, Itsuro

    2016-01-01

    The activity patterns of mammals are generally categorized as nocturnal, diurnal, crepuscular (active at twilight), and cathemeral (active throughout the day). These patterns are highly variable across regions and seasons even within the same species. However, quantitative data is still lacking, particularly for sympatric species. We monitored the seasonal and diel activity patterns of terrestrial mammals in Hokkaido, Japan. Through an intensive camera-trap survey a total of 13,279 capture events were recorded from eight mammals over 20,344 camera-trap days, i.e., two years. Diel activity patterns were clearly divided into four categories: diurnal (Eurasian red squirrels), nocturnal (raccoon dogs and raccoons), crepuscular (sika deer and mountain hares), and cathemeral (Japanese martens, red foxes, and brown bears). Some crepuscular and cathemeral mammals shifted activity peaks across seasons. Particularly, sika deer changed peaks from twilight during spring–autumn to day-time in winter, possibly because of thermal constraints. Japanese martens were cathemeral during winter–summer, but nocturnal in autumn. We found no clear indication of predator-prey and competitive interactions, suggesting that animal densities are not very high or temporal niche partitioning is absent among the target species. This long-term camera-trap survey was highly cost-effective and provided one of the most detailed seasonal and diel activity patterns in multiple sympatric mammals under natural conditions. PMID:27732611

  2. The Rates and Spatial Patterns of Annual Riverbank Erosion Revealed Through Terrestrial Laser Scanner Surveys of the South River, Virginia

    Science.gov (United States)

    O'Neal, M. A.; Pizzuto, J. E.

    2011-12-01

    Between 2006 and 2008 A.D., we completed annual surveys of two mercury-contaminated eroding banks, one forested and the other grass covered, along the gravel-bed, bedrock South River in Virginia. Gridded digital terrain models with a resolution of 0.05 m were created from bank topography data collected using a terrestrial laser scanner. The forested bank retreated nearly 1 m around two leaning trees, while elsewhere the extent of bank retreat was negligible. On the grassy bank, retreat was controlled by the creation of small overhanging clumps of turf at the top of the bank, their occasional failure, and the ultimate removal of failed debris from the bank toe. Partial autocorrelation analysis of vertically integrated bank retreat demonstrates that bank profile erosion is virtually uncorrelated at horizontal distances greater than about 1 m on both banks, a length scale of approximately 1/2 the bank height. This extensive streamwise variability suggests that widely spaced profile data cannot adequately represent bank erosion at these sites. Additional analysis of our comprehensive spatial data also indicates that traditional bank profile surveys with any spacing greater than 1 m would result in measurement errors exceeding 10%, an important conclusion for assessing annual rates of mercury loading into the South River from bank erosion. Our results suggest that 3-dimensional gridded bare-earth models of bank topography may be required to accurately measure annual bank retreat in similar river systems.

  3. Vector-Enabled Metagenomic (VEM Surveys Using Whiteflies (Aleyrodidae Reveal Novel Begomovirus Species in the New and OldWorlds

    Directory of Open Access Journals (Sweden)

    Karyna Rosario

    2015-10-01

    Full Text Available Whitefly-transmitted viruses belonging to the genus Begomovirus (family Geminiviridae represent a substantial threat to agricultural food production. The rapid evolutionary potential of these single-stranded DNA viruses combined with the polyphagous feeding behavior of their whitefly vector (Bemisia tabaci can lead to the emergence of damaging viral strains. Therefore, it is crucial to characterize begomoviruses circulating in different regions and crops globally. This study utilized vector-enabled metagenomics (VEM coupled with high-throughput sequencing to survey begomoviruses directly from whiteflies collected in various locations (California (USA, Guatemala, Israel, Puerto Rico, and Spain. Begomoviruses were detected in all locations, with the highest diversity identified in Guatemala where up to seven different species were identified in a single field. Both bipartite and monopartite viruses were detected, including seven new begomovirus species from Guatemala, Puerto Rico, and Spain. This begomovirus survey extends the known diversity of these highly damaging plant viruses. However, the new genomes described here and in the recent literature appear to reflect the outcome of interactions between closely-related species, often resulting from recombination, instead of unique, highly divergent species.

  4. Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) Reveal Novel Begomovirus Species in the New and Old Worlds.

    Science.gov (United States)

    Rosario, Karyna; Seah, Yee Mey; Marr, Christian; Varsani, Arvind; Kraberger, Simona; Stainton, Daisy; Moriones, Enrique; Polston, Jane E; Duffy, Siobain; Breitbart, Mya

    2015-10-26

    Whitefly-transmitted viruses belonging to the genus Begomovirus (family Geminiviridae) represent a substantial threat to agricultural food production. The rapid evolutionary potential of these single-stranded DNA viruses combined with the polyphagous feeding behavior of their whitefly vector (Bemisia tabaci) can lead to the emergence of damaging viral strains. Therefore, it is crucial to characterize begomoviruses circulating in different regions and crops globally. This study utilized vector-enabled metagenomics (VEM) coupled with high-throughput sequencing to survey begomoviruses directly from whiteflies collected in various locations (California (USA), Guatemala, Israel, Puerto Rico, and Spain). Begomoviruses were detected in all locations, with the highest diversity identified in Guatemala where up to seven different species were identified in a single field. Both bipartite and monopartite viruses were detected, including seven new begomovirus species from Guatemala, Puerto Rico, and Spain. This begomovirus survey extends the known diversity of these highly damaging plant viruses. However, the new genomes described here and in the recent literature appear to reflect the outcome of interactions between closely-related species, often resulting from recombination, instead of unique, highly divergent species.

  5. Insights into the metabolic response to traumatic brain injury as revealed by 13C NMR spectroscopy.

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    Brenda eBartnik-Olson

    2013-10-01

    Full Text Available The present review highlights critical issues related to cerebral metabolism following traumatic brain injury (TBI and the use of 13C labeled substrates and nuclear magnetic resonance (NMR spectroscopy to study these changes. First we address some pathophysiologic factors contributing to metabolic dysfunction following TBI. We then examine how 13C NMR spectroscopy strategies have been used to investigate energy metabolism, neurotransmission, the intracellular redox state, and neuroglial compartmentation following injury. 13C NMR spectroscopy studies of brain extracts from animal models of TBI have revealed enhanced glycolytic production of lactate, evidence of pentose phosphate pathway (PPP activation, and alterations in neuronal and astrocyte oxidative metabolism that are dependent on injury severity. Differential incorporation of label into glutamate and glutamine from 13C labeled glucose or acetate also suggest TBI-induced adaptations to the glutamate-glutamine cycle.

  6. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.

    Science.gov (United States)

    Mason, Olivia U; Scott, Nicole M; Gonzalez, Antonio; Robbins-Pianka, Adam; Bælum, Jacob; Kimbrel, Jeffrey; Bouskill, Nicholas J; Prestat, Emmanuel; Borglin, Sharon; Joyner, Dominique C; Fortney, Julian L; Jurelevicius, Diogo; Stringfellow, William T; Alvarez-Cohen, Lisa; Hazen, Terry C; Knight, Rob; Gilbert, Jack A; Jansson, Janet K

    2014-07-01

    The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using (14)C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of (14)C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)'s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem.

  7. Microbial Response to Soil Liming of Damaged Ecosystems Revealed by Pyrosequencing and Phospholipid Fatty Acid Analyses

    Science.gov (United States)

    Narendrula-Kotha, Ramya; Nkongolo, Kabwe K.

    2017-01-01

    Aims To assess the effects of dolomitic limestone applications on soil microbial communities’ dynamics and bacterial and fungal biomass, relative abundance, and diversity in metal reclaimed regions. Methods and Results The study was conducted in reclaimed mining sites and metal uncontaminated areas. The limestone applications were performed over 35 years ago. Total microbial biomass was determined by Phospholipid fatty acids. Bacterial and fungal relative abundance and diversity were assessed using 454 pyrosequencing. There was a significant increase of total microbial biomass in limed sites (342 ng/g) compared to unlimed areas (149 ng/g). Chao1 estimates followed the same trend. But the total number of OTUs (Operational Taxonomic Units) in limed (463 OTUs) and unlimed (473 OTUs) soil samples for bacteria were similar. For fungi, OTUs were 96 and 81 for limed and unlimed soil samples, respectively. Likewise, Simpson and Shannon diversity indices revealed no significant differences between limed and unlimed sites. Bacterial and fungal groups specific to either limed or unlimed sites were identified. Five major bacterial phyla including Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, and Proteobacteria were found. The latter was the most prevalent phylum in all the samples with a relative abundance of 50%. Bradyrhizobiaceae family with 12 genera including the nitrogen fixing Bradirhizobium genus was more abundant in limed sites compared to unlimed areas. For fungi, Ascomycota was the most predominant phylum in unlimed soils (46%) while Basidiomycota phylum represented 86% of all fungi in the limed areas. Conclusion Detailed analysis of the data revealed that although soil liming increases significantly the amount of microbial biomass, the level of species diversity remain statistically unchanged even though the microbial compositions of the damaged and restored sites are different. Significance and Impact of the study Soil liming still have a significant

  8. Disordered semantic representation in schizophrenic temporal cortex revealed by neuromagnetic response patterns

    Directory of Open Access Journals (Sweden)

    Silberman Yaron

    2006-05-01

    Full Text Available Abstract Background Loosening of associations and thought disruption are key features of schizophrenic psychopathology. Alterations in neural networks underlying this basic abnormality have not yet been sufficiently identified. Previously, we demonstrated that spatio-temporal clustering of magnetic brain responses to pictorial stimuli map categorical representations in temporal cortex. This result has opened the possibility to quantify associative strength within and across semantic categories in schizophrenic patients. We hypothesized that in contrast to controls, schizophrenic patients exhibit disordered representations of semantic categories. Methods The spatio-temporal clusters of brain magnetic activities elicited by object pictures related to super-ordinate (flowers, animals, furniture, clothes and base-level (e.g. tulip, rose, orchid, sunflower categories were analysed in the source space for the time epochs 170–210 and 210–450 ms following stimulus onset and were compared between 10 schizophrenic patients and 10 control subjects. Results Spatio-temporal correlations of responses elicited by base-level concepts and the difference of within vs. across super-ordinate categories were distinctly lower in patients than in controls. Additionally, in contrast to the well-defined categorical representation in control subjects, unsupervised clustering indicated poorly defined representation of semantic categories in patients. Within the patient group, distinctiveness of categorical representation in the temporal cortex was positively related to negative symptoms and tended to be inversely related to positive symptoms. Conclusion Schizophrenic patients show a less organized representation of semantic categories in clusters of magnetic brain responses than healthy adults. This atypical neural network architecture may be a correlate of loosening of associations, promoting positive symptoms.

  9. Super-resolution microscopy reveals protein spatial reorganization in early innate immune responses.

    Energy Technology Data Exchange (ETDEWEB)

    Carson, Bryan D.; Aaron, Jesse S.; Timlin, Jerilyn Ann

    2010-10-01

    Over the past decade optical approaches were introduced that effectively break the diffraction barrier. Of particular note were introductions of Stimulated Emission/Depletion (STED) microscopy, Photo-Activated Localization Microscopy (PALM), and the closely related Stochastic Optical Reconstruction Microscopy (STORM). STORM represents an attractive method for researchers, as it does not require highly specialized optical setups, can be implemented using commercially available dyes, and is more easily amenable to multicolor imaging. We implemented a simultaneous dual-color, direct-STORM imaging system through the use of an objective-based TIRF microscope and filter-based image splitter. This system allows for excitation and detection of two fluorophors simultaneously, via projection of each fluorophor's signal onto separate regions of a detector. We imaged the sub-resolution organization of the TLR4 receptor, a key mediator of innate immune response, after challenge with lipopolysaccharide (LPS), a bacteria-specific antigen. While distinct forms of LPS have evolved among various bacteria, only some LPS variations (such as that derived from E. coli) typically result in significant cellular immune response. Others (such as from the plague bacteria Y. pestis) do not, despite affinity to TLR4. We will show that challenge with LPS antigens produces a statistically significant increase in TLR4 receptor clusters on the cell membrane, presumably due to recruitment of receptors to lipid rafts. These changes, however, are only detectable below the diffraction limit and are not evident using conventional imaging methods. Furthermore, we will compare the spatiotemporal behavior of TLR4 receptors in response to different LPS chemotypes in order to elucidate possible routes by which pathogens such as Y. pestis are able to circumvent the innate immune system. Finally, we will exploit the dual-color STORM capabilities to simultaneously image LPS and TLR4 receptors in the

  10. RNA-seq Analysis of Clinical-Grade Osteochondral Allografts Reveals Activation of Early Response Genes

    Science.gov (United States)

    Lin, Yang; Lewallen, Eric A.; Camilleri, Emily T.; Bonin, Carolina A.; Jones, Dakota L.; Dudakovic, Amel; Galeano-Garces, Catalina; Wang, Wei; Karperien, Marcel J.; Larson, Annalise N.; Dahm, Diane L.; Stuart, Michael J.; Levy, Bruce A.; Smith, Jay; Ryssman, Daniel B.; Westendorf, Jennifer J.; Im, Hee-Jeong; van Wijnen, Andre J.; Riester, Scott M.; Krych, Aaron J.

    2016-01-01

    Preservation of osteochondral allografts used for transplantation is critical to ensure favorable outcomes for patients after surgical treatment of cartilage defects. To study the biological effects of protocols currently used for cartilage storage, we investigated differences in gene expression between stored allograft cartilage and fresh cartilage from living donors using high throughput molecular screening strategies. We applied next generation RNA sequencing (RNA-seq) and real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) to assess genome-wide differences in mRNA expression between stored allograft cartilage and fresh cartilage tissue from living donors. Gene ontology analysis was used to characterize biological pathways associated with differentially expressed genes. Our studies establish reduced levels of mRNAs encoding cartilage related extracellular matrix (ECM) proteins (i.e., COL1A1, COL2A1, COL10A1, ACAN, DCN, HAPLN1, TNC, and COMP) in stored cartilage. These changes occur concomitantly with increased expression of “early response genes” that encode transcription factors mediating stress/cytoprotective responses (i.e., EGR1, EGR2, EGR3, MYC, FOS, FOSB, FOSL1, FOSL2, JUN, JUNB, and JUND). The elevated expression of “early response genes” and reduced levels of ECM-related mRNAs in stored cartilage allografts suggests that tissue viability may be maintained by a cytoprotective program that reduces cell metabolic activity. These findings have potential implications for future studies focused on quality assessment and clinical optimization of osteochondral allografts used for cartilage transplantation. PMID:26909883

  11. Suppressive responses by visual food cues in postprandial activities of insular cortex as revealed by magnetoencephalography.

    Science.gov (United States)

    Yoshikawa, Takahiro; Tanaka, Masaaki; Ishii, Akira; Watanabe, Yasuyoshi

    2014-06-01

    'Hara-Hachibu' in Japanese means a subjective sense by which we stop eating just before the motivation to eat is completely lost, a similar concept to caloric restriction (CR). Insular cortex is a critical platform which integrates sensory information into decision-making processes in eating behavior. We compared the responses of insular cortex, as assessed by magnetoencephalography (MEG), immediately after presentation of food images in the Fasting condition with those in the 'Hara-Hachibu' condition. Eleven healthy, right-handed males [age, 27.2±9.6 years; body mass index, 22.6±2.1kg/m(2) (mean±SD)] were enrolled in a randomized, two-crossover experiment (Fasting and 'Hara-Hachibu' conditions). Before the MEG recordings in the 'Hara-Hachibu' condition, the participants consumed rice balls as much as they judged themselves to have consumed shortly before reaching satiety. During the MEG recordings, they viewed food pictures projected on a screen. The intensities of MEG responses to viewing food pictures were significantly lower in the 'Hara-Hachibu' condition than those in the Fasting condition (P<0.05). The intensities of the MEG responses to the visual food stimuli in the 'Hara-Hachibu' condition was positively associated with the factor-3 (food tasted) (r=0.693, P=0.018) and aggregated scores (r=0.659, P=0.027) of the Power of Food Scale, a self-report measure of hedonic hunger. These findings may help to elucidate the neural basis of variability of appetite phenotypes under the condition of CR among individuals, and to develop possible strategies for the maintenance of adequate CR in daily life.

  12. Proteomic and Physiological Analyses Reveal Putrescine Responses in Roots of Cucumber Stressed by NaCl

    Directory of Open Access Journals (Sweden)

    Yinghui Yuan

    2016-07-01

    Full Text Available Soil salinity is a major environmental constraint that threatens agricultural productivity. Different strategies have been developed to improve crop salt tolerance, among which the effects of polyamines have been well reported. To gain a better understanding of the cucumber (Cucumis sativus L. responses to NaCl and unravel the underlying mechanism of exogenous putrescine (Put alleviating salt-induced damage, comparative proteomic analysis was conducted on cucumber roots treated with NaCl and/or Put for 7 days. The results showed that exogenous Put restored the root growth inhibited by NaCl. 62 differentially expressed proteins implicated in various biological processes were successfully identified by MALDI-TOF/TOF MS. The four largest categories included proteins involved in defense response (24.2%, protein metabolism (24.2%, carbohydrate metabolism (19.4% and amino acid metabolism (14.5%. Exogenous Put up-regulated most identified proteins involved in carbohydrate metabolism, implying an enhancement in energy generation. Proteins involved in defense response and protein metabolism were differently regulated by Put, which indicated the roles of Put in stress resistance and proteome rearrangement. Put also increased the abundance of proteins involved in amino acid metabolism. Meanwhile, physiological analysis showed that Put could further up-regulated the levels of free amino acids in salt stressed-roots. In addition, Put also improved endogenous polyamines contents by regulating the transcription levels of key enzymes in polyamine metabolism. Taken together, these results suggest that Put may alleviate NaCl-induced growth inhibition through degradation of misfolded/damaged proteins, activation of stress defense, and the promotion of carbohydrate metabolism to generate more energy.

  13. The Application of Factorial Surveys in General Population Samples: The Effects of Respondent Age and Education on Response Times and Response Consistency

    Directory of Open Access Journals (Sweden)

    Carsten Sauer

    2011-12-01

    Full Text Available Over the last decade, there has been a marked increase in the number of studies on attitude and decision research which use the factorial survey (FS design. The FS integrates experimental set-ups into a survey: respondents react to hypothetical descriptions (vignettes while the values of each attribute (dimension of these descriptions systematically vary in order to estimate their impact on respondent judgments. As the vignettes are based on a number of dimensions and as respondents evaluate several vignettes, FSs are demanding in terms of individual cognitive and information-processing abilities. So far, there is little empirical knowledge of whether and to what extent this complexity is feasible in general population samples with heterogeneous respondents. Using data from a study on the fairness of earnings (with a mixed mode sample consisting a computer assisted personal interview [CAPI], computer assisted self interview [CASI], and paper and pencil [PAPI] mode, the complexity of FSs is analyzed in terms of: 1 design dimensions, such as the number of vignette dimensions (five, eight, or 12 and the number of vignettes for single respondents (10, 20, or 30, which were varied in a 3x3 experimental design; and 2 respondent characteristics that are associated with cognitive abilities (age and education. Two different indicators for cognitive load as well as learning and fatigue effects are analyzed: 1 latency time and 2 response consistency. The results show that raw reaction times but not latency times are longer for older respondents, suggesting that the cognitive effort needed for the evaluation of vignettes is not particularly high. Consistency measures reveal that respondents with a lower educational level show greater inconsistency in their evaluations when the number of vignettes is high. The number of dimensions has an effect on consistency only when respondents have to rate a large number of vignettes. In short, the results demonstrate

  14. Quantised transistor response to ion channels revealed by nonstationary noise analysis

    Science.gov (United States)

    Becker-Freyseng, C.; Fromherz, P.

    2011-11-01

    We report on the quantised response of a field-effect transistor to molecular ion channels in a biomembrane. HEK293-type cells overexpressing the Shaker B potassium channel were cultured on a silicon chip. An enhanced noise of the transistor is observed when the ion channels are activated. The analysis of the fluctuations in terms of binomial statistics identifies voltage quanta of about 1 μV on the gate. They are attributed to the channel currents that affect the gate voltage according to the Green's function of the cell-chip junction.

  15. Comparative Transcriptomics Reveals Discrete Survival Responses of S. aureus and S. epidermidis to Sapienic Acid

    Science.gov (United States)

    Moran, Josephine C.; Alorabi, Jamal A.; Horsburgh, Malcolm J.

    2017-01-01

    Staphylococcal colonization of human skin is ubiquitous, with particular species more frequent at different body sites. Whereas Staphylococcus epidermidis can be isolated from the skin of every individual tested, Staphylococcus aureus is isolated from arginine deiminase, the oxygen-responsive NreABC nitrogen regulation system and the nitrate and nitrite reduction pathways. The role of S. aureus ACME and chromosomal arginine deiminase pathways in sapienic acid resistance was determined through mutational studies. We speculate that ammonia production could contribute to sapienic acid resistance in staphylococci. PMID:28179897

  16. Framework for a U.S. Geological Survey Hydrologic Climate-Response Program in Maine

    Science.gov (United States)

    Hodgkins, Glenn A.; Lent, Robert M.; Dudley, Robert W.; Schalk, Charles W.

    2009-01-01

    This report presents a framework for a U.S. Geological Survey (USGS) hydrologic climate-response program designed to provide early warning of changes in the seasonal water cycle of Maine. Climate-related hydrologic changes on Maine's rivers and lakes in the winter and spring during the last century are well documented, and several river and lake variables have been shown to be sensitive to air-temperature changes. Monitoring of relevant hydrologic data would provide important baseline information against which future climate change can be measured. The framework of the hydrologic climate-response program presented here consists of four major parts: (1) identifying homogeneous climate-response regions; (2) identifying hydrologic components and key variables of those components that would be included in a hydrologic climate-response data network - as an example, streamflow has been identified as a primary component, with a key variable of streamflow being winter-spring streamflow timing; the data network would be created by maintaining existing USGS data-collection stations and establishing new ones to fill data gaps; (3) regularly updating historical trends of hydrologic data network variables; and (4) establishing basins for process-based studies. Components proposed for inclusion in the hydrologic climate-response data network have at least one key variable for which substantial historical data are available. The proposed components are streamflow, lake ice, river ice, snowpack, and groundwater. The proposed key variables of each component have extensive historical data at multiple sites and are expected to be responsive to climate change in the next few decades. These variables are also important for human water use and (or) ecosystem function. Maine would be divided into seven climate-response regions that follow major river-basin boundaries (basins subdivided to hydrologic units with 8-digit codes or larger) and have relatively homogeneous climates. Key

  17. Anisotropic optical response of optically opaque elastomers with conductive fillers as revealed by terahertz polarization spectroscopy

    Science.gov (United States)

    Okano, Makoto; Watanabe, Shinichi

    2016-12-01

    Elastomers are one of the most important materials in modern society because of the inherent viscoelastic properties due to their cross-linked polymer chains. Their vibration-absorbing and adhesive properties are especially useful and thus utilized in various applications, for example, tires in automobiles and bicycles, seismic dampers in buildings, and seals in a space shuttle. Thus, the nondestructive inspection of their internal states such as the internal deformation is essential in safety. Generally, industrial elastomers include various kinds of additives, such as carbon blacks for reinforcing them. The additives make most of them opaque in a wide spectral range from visible to mid-infrared, resulting in that the nondestructive inspection of the internal deformation is quite difficult. Here, we demonstrate transmission terahertz polarization spectroscopy as a powerful technique for investigating the internal optical anisotropy in optically opaque elastomers with conductive additives, which are transparent only in the terahertz frequency region. The internal deformation can be probed through the polarization changes inside the material due to the anisotropic dielectric response of the conductive additives. Our study about the polarization-dependent terahertz response of elastomers with conductive additives provides novel knowledge for in situ, nondestructive evaluation of their internal deformation.

  18. Climate response to the Samalas volcanic eruption in 1257 revealed by proxy records

    Science.gov (United States)

    Guillet, Sébastien; Corona, Christophe; Stoffel, Markus; Khodri, Myriam; Lavigne, Franck; Ortega, Pablo; Eckert, Nicolas; Sielenou, Pascal Dkengne; Daux, Valérie; Churakova (Sidorova), Olga V.; Davi, Nicole; Edouard, Jean-Louis; Zhang, Yong; Luckman, Brian H.; Myglan, Vladimir S.; Guiot, Joël; Beniston, Martin; Masson-Delmotte, Valérie; Oppenheimer, Clive

    2017-01-01

    The eruption of Samalas in Indonesia in 1257 ranks among the largest sulfur-rich eruptions of the Common Era with sulfur deposition in ice cores reaching twice the volume of the Tambora eruption in 1815. Sedimentological analyses of deposits confirm the exceptional size of the event, which had both an eruption magnitude and a volcanic explosivity index of 7. During the Samalas eruption, more than 40 km3 of dense magma was expelled and the eruption column is estimated to have reached altitudes of 43 km. However, the climatic response to the Samalas event is debated since climate model simulations generally predict a stronger and more prolonged surface air cooling of Northern Hemisphere summers than inferred from tree-ring-based temperature reconstructions. Here, we draw on historical archives, ice-core data and tree-ring records to reconstruct the spatial and temporal climate response to the Samalas eruption. We find that 1258 and 1259 experienced some of the coldest Northern Hemisphere summers of the past millennium. However, cooling across the Northern Hemisphere was spatially heterogeneous. Western Europe, Siberia and Japan experienced strong cooling, coinciding with warmer-than-average conditions over Alaska and northern Canada. We suggest that in North America, volcanic radiative forcing was modulated by a positive phase of the El Niño-Southern Oscillation. Contemporary records attest to severe famines in England and Japan, but these began prior to the eruption. We conclude that the Samalas eruption aggravated existing crises, but did not trigger the famines.

  19. Functional characterisation of wheat Pgip genes reveals their involvement in the local response to wounding.

    Science.gov (United States)

    Janni, M; Bozzini, T; Moscetti, I; Volpi, C; D'Ovidio, R

    2013-11-01

    Polygalacturonase-inhibiting proteins (PGIPs) are cell wall leucine-rich repeat (LRR) proteins involved in plant defence. The hexaploid wheat (Triticum aestivum, genome AABBDD) genome contains one Pgip gene per genome. Tapgip1 (B genome) and Tapgip2 (D genome) are expressed in all tissues, whereas Tapgip3 (A genome) is inactive because of a long terminal repeat, Copia retrotransposon insertion within the coding region. To verify whether Tapgip1 and Tapgip2 encode active PGIPs and are involved in the wheat defence response, we expressed them transiently and analysed their expression under stress conditions. Neither TaPGIP1 nor TaPGIP2 showed inhibition activity in vitro against fungal polygalacturonases. Moreover, a wheat genotype (T. turgidum ssp. dicoccoides) lacking active homologues of Tapgip1 or Tapgip2 possesses PGIP activity. At transcript level, Tapgip1 and Tapgip2 were both up-regulated after fungal infection and strongly induced following wounding. This latter result has been confirmed in transgenic wheat plants expressing the β-glucuronidase (GUS) gene under control of the 5'-flanking region of Tdpgip1, a homologue of Tapgip1 with an identical sequence. Strong and transient GUS staining was mainly restricted to the damaged tissues and was not observed in adjacent tissues. Taken together, these results suggest that Tapgips and their homologues are involved in the wheat defence response by acting at the site of the lesion caused by pathogen infection.

  20. Shipwreck rates reveal Caribbean tropical cyclone response to past radiative forcing

    Science.gov (United States)

    Trouet, Valerie; Harley, Grant L.; Domínguez-Delmás, Marta

    2016-03-01

    Assessing the impact of future climate change on North Atlantic tropical cyclone (TC) activity is of crucial societal importance, but the limited quantity and quality of observational records interferes with the skill of future TC projections. In particular, North Atlantic TC response to radiative forcing is poorly understood and creates the dominant source of uncertainty for twenty-first-century projections. Here, we study TC variability in the Caribbean during the Maunder Minimum (MM; 1645-1715 CE), a period defined by the most severe reduction in solar irradiance in documented history (1610-present). For this purpose, we combine a documentary time series of Spanish shipwrecks in the Caribbean (1495-1825 CE) with a tree-growth suppression chronology from the Florida Keys (1707-2009 CE). We find a 75% reduction in decadal-scale Caribbean TC activity during the MM, which suggests modulation of the influence of reduced solar irradiance by the cumulative effect of cool North Atlantic sea surface temperatures, El Niño-like conditions, and a negative phase of the North Atlantic Oscillation. Our results emphasize the need to enhance our understanding of the response of these oceanic and atmospheric circulation patterns to radiative forcing and climate change to improve the skill of future TC projections.

  1. Transcriptomic analysis reveals adaptive responses of an Enterobacteriaceae strain LSJC7 to arsenic exposure

    Directory of Open Access Journals (Sweden)

    Yingjiao eZhang

    2016-05-01

    Full Text Available Arsenic (As resistance determinant ars operon is present in many bacteria and has been demonstrated to enhance As(V resistance of bacteria. However, whole molecular mechanism adaptations of bacteria in response to As(V stress remain largely unknown. In this study, transcriptional profiles of Enterobacteriaceae strain LSJC7 responding to As(V stress were analyzed using RNA-seq and qRT-PCR. As expected, genes involved in As(V uptake were down-regulated, those involved in As(V reduction and As(III efflux were up-regulated, which avoided cellular As accumulation. Reactive oxygen species and nitric oxide (NO were induced, which caused cellular damages including DNA, proteins, and Fe-S clusters damages in LSJC7. The expression of specific genes encoding transcriptional regulators, such as nsrR and soxRS were also induced. NsrR and SoxRS modulated many critical metabolic activities in As(V stressed LSJC7 cells, including reactive species scavenging and repairing the damages of DNA, proteins, and Fe-S clusters. Therefore, besides As uptake, reduction, and efflux, oxidative stress defense and damage repair were the main cellular adaptive responses of LSJC7 to As(V stress.

  2. Transcriptomic Analysis Reveals Adaptive Responses of an Enterobacteriaceae Strain LSJC7 to Arsenic Exposure.

    Science.gov (United States)

    Zhang, Yingjiao; Chen, Songcan; Hao, Xiuli; Su, Jian-Qiang; Xue, Ximei; Yan, Yu; Zhu, Yong-Guan; Ye, Jun

    2016-01-01

    Arsenic (As) resistance determinant ars operon is present in many bacteria and has been demonstrated to enhance As(V) resistance of bacteria. However, whole molecular mechanism adaptations of bacteria in response to As(V) stress remain largely unknown. In this study, transcriptional profiles of Enterobacteriaceae strain LSJC7 responding to As(V) stress were analyzed using RNA-seq and qRT-PCR. As expected, genes involved in As(V) uptake were down-regulated, those involved in As(V) reduction and As(III) efflux were up-regulated, which avoided cellular As accumulation. Reactive oxygen species and nitric oxide (NO) were induced, which caused cellular damages including DNA, protein, and Fe-S cluster damage in LSJC7. The expression of specific genes encoding transcriptional regulators, such as nsrR and soxRS were also induced. NsrR and SoxRS modulated many critical metabolic activities in As(V) stressed LSJC7 cells, including reactive species scavenging and repairing damaged DNA, proteins, and Fe-S clusters. Therefore, besides As uptake, reduction, and efflux; oxidative stress defense and damage repair were the main cellular adaptive responses of LSJC7 to As(V) stress.

  3. Simulated seed predation reveals a variety of germination responses of neotropical rain forest species.

    Science.gov (United States)

    Vallejo-Marín, Mario; Domínguez, César A; Dirzo, Rodolfo

    2006-03-01

    Seed predation, an omnipresent phenomenon in tropical rain forests, is an important determinant of plant recruitment and forest regeneration. Although seed predation destroys large amounts of the seed crop of numerous tropical species, in many cases individual seed damage is only partial. The extent to which partial seed predation affects the recruitment of new individuals in the population depends on the type and magnitude of alteration of the germination behavior of the damaged seeds. We analyzed the germination dynamics of 11 tropical woody species subject to increasing levels of simulated seed predation (0-10% seed mass removal). Germination response to seed damage varied considerably among species but could be grouped into four distinct types: (1) complete inability to germinate under damage ≥1%, (2) no effect on germination dynamics, (3) reduced germination with increasing damage, and (4) reduced final germination but faster germination with increasing damage. We conclude that partial seed predation is often nonlethal and argue that different responses to predation may represent different proximal mechanisms for coping with partial damage, with potential to shape, in the long run, morphological and physiological adaptations in tropical, large-seeded species.

  4. Failure analysis of porcupine quills under axial compression reveals their mechanical response during buckling.

    Science.gov (United States)

    Torres, Fernando G; Troncoso, Omar P; Diaz, John; Arce, Diego

    2014-11-01

    Porcupine quills are natural structures formed by a thin walled conical shell and an inner foam core. Axial compression tests, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and Fourier transform infrared spectroscopy (FT-IR) were all used to compare the characteristics and mechanical properties of porcupine quills with and without core. The failure mechanisms that occur during buckling were analyzed by scanning electron microscopy (SEM), and it was found that delamination buckling is mostly responsible for the decrease in the measured buckling stress of the quills with regard to predicted theoretical values. Our analysis also confirmed that the foam core works as an energy dissipater improving the mechanical response of an empty cylindrical shell, retarding the onset of buckling as well as producing a step wise decrease in force after buckling, instead of an instantaneous decrease in force typical for specimens without core. Cell collapse and cell densification in the inner foam core were identified as the key mechanisms that allow for energy absorption during buckling.

  5. Genome-wide transcriptome analysis revealed organelle specific responses to temperature variations in algae

    Science.gov (United States)

    Shin, HyeonSeok; Hong, Seong-Joo; Yoo, Chan; Han, Mi-Ae; Lee, Hookeun; Choi, Hyung-Kyoon; Cho, Suhyung; Lee, Choul-Gyun; Cho, Byung-Kwan

    2016-01-01

    Temperature is a critical environmental factor that affects microalgal growth. However, microalgal coping mechanisms for temperature variations are unclear. Here, we determined changes in transcriptome, total carbohydrate, total fatty acid methyl ester, and fatty acid composition of Tetraselmis sp. KCTC12432BP, a strain with a broad temperature tolerance range, to elucidate the tolerance mechanisms in response to large temperature variations. Owing to unavailability of genome sequence information, de novo transcriptome assembly coupled with BLAST analysis was performed using strand specific RNA-seq data. This resulted in 26,245 protein-coding transcripts, of which 83.7% could be annotated to putative functions. We identified more than 681 genes differentially expressed, suggesting an organelle-specific response to temperature variation. Among these, the genes related to the photosynthetic electron transfer chain, which are localized in the plastid thylakoid membrane, were upregulated at low temperature. However, the transcripts related to the electron transport chain and biosynthesis of phosphatidylethanolamine localized in mitochondria were upregulated at high temperature. These results show that the low energy uptake by repressed photosynthesis under low and high temperature conditions is compensated by different mechanisms, including photosystem I and mitochondrial oxidative phosphorylation, respectively. This study illustrates that microalgae tolerate different temperature conditions through organelle specific mechanisms. PMID:27883062

  6. RNA-Seq analysis of rice roots reveals the involvement of post-transcriptional regulation in response to cadmium stress

    Directory of Open Access Journals (Sweden)

    Luqing eZheng

    2015-12-01

    Full Text Available Widely-spread cadmium (Cd pollution in the soil threatens both crop production and human health. How plants deal with the excess Cd are largely unknown. To evaluate the molecular mechanism by which plants respond to Cd stress, rice seedlings were treated with two concentrations of Cd and subjected to deep RNA sequencing. Comprehensive RNA-Seq analysis of rice roots under two gradients of Cd treatment revealed 1,169 Cd toxicity-responsive genes. These genes were involved in the reactive oxygen species scavenging system, stress response, cell wall formation, ion transport, and signal transduction. Nine out of 93 predicted long non coding RNAs (lncRNAs were detected as Cd-responsive lncRNAs due to their high correlation with the Cd stress response. In addition, we analyzed alternative splicing (AS events under different Cd concentrations. 476 differential alternatively spliced genes with 542 aberrant splicing events were identified. GO analysis indicated that these genes were highly enriched in oxidation reduction and cellular response to chemical stimulus. Real-time qRT-PCR validation analysis strengthened the reliability of our RNA-Seq results. The results suggest that post-transcriptional AS regulation may also be involved in plant responses to high Cd stress.

  7. Genome Wide Transcriptome Analysis reveals ABA mediated response in Arabidopsis during Gold (AuCl4- treatment

    Directory of Open Access Journals (Sweden)

    Devesh eShukla

    2014-11-01

    Full Text Available The unique physico-chemical properties of gold nanoparticles (AuNPs find manifold applications in diagnostics, medicine and catalysis. Chemical synthesis produces reactive AuNPs and generates hazardous by-products. Alternatively, plants can be utilized to produce AuNPs in an eco-friendly manner. To better control the biosynthesis of AuNPs, we need to first understand the detailed molecular response induced by AuCl4- In this study, we carried out global transcriptome analysis in root tissue of Arabidopsis grown for 12- hours in presence of gold solution (HAuCl4 using the novel unbiased Affymetrix exon array. Transcriptomics analysis revealed differential regulation of a total of 704 genes and 4900 exons. Of these, 492 and 212 genes were up- and downregulated, respectively. The validation of the expressed key genes, such as glutathione-S-transferases, auxin responsive genes, cytochrome P450 82C2, methyl transferases, transducin (G protein beta subunit, ERF transcription factor, ABC, and MATE transporters, was carried out through quantitative RT-PCR. These key genes demonstrated specific induction under AuCl4- treatment relative to other heavy metals, suggesting a unique plant-gold interaction. GO enrichment analysis reveals the upregulation of processes like oxidative stress, glutathione binding, metal binding, transport, and plant hormonal responses. Changes predicted in biochemical pathways indicated major modulation in glutathione mediated detoxification, flavones and derivatives, and plant hormone biosynthesis. Motif search analysis identified a highly significant enriched motif, ACGT, which is an abscisic acid responsive core element (ABRE, suggesting the possibility of ABA- mediated signaling. Identification of abscisic acid response element (ABRE points to the operation of a predominant signaling mechanism in response to AuCl4- exposure. Overall, this study presents a useful picture of plant-gold interaction with an identification of

  8. Stromal transcriptional profiles reveal hierarchies of anatomical site, serum response and disease and identify disease specific pathways.

    Directory of Open Access Journals (Sweden)

    Andrew Filer

    Full Text Available Synovial fibroblasts in persistent inflammatory arthritis have been suggested to have parallels with cancer growth and wound healing, both of which involve a stereotypical serum response programme. We tested the hypothesis that a serum response programme can be used to classify diseased tissues, and investigated the serum response programme in fibroblasts from multiple anatomical sites and two diseases. To test our hypothesis we utilized a bioinformatics approach to explore a publicly available microarray dataset including rheumatoid arthritis (RA, osteoarthritis (OA and normal synovial tissue, then extended those findings in a new microarray dataset representing matched synovial, bone marrow and skin fibroblasts cultured from RA and OA patients undergoing arthroplasty. The classical fibroblast serum response programme discretely classified RA, OA and normal synovial tissues. Analysis of low and high serum treated fibroblast microarray data revealed a hierarchy of control, with anatomical site the most powerful classifier followed by response to serum and then disease. In contrast to skin and bone marrow fibroblasts, exposure of synovial fibroblasts to serum led to convergence of RA and OA expression profiles. Pathway analysis revealed three inter-linked gene networks characterising OA synovial fibroblasts: Cell remodelling through insulin-like growth factors, differentiation and angiogenesis through _3 integrin, and regulation of apoptosis through CD44. We have demonstrated that Fibroblast serum response signatures define disease at the tissue level, and that an OA specific, serum dependent repression of genes involved in cell adhesion, extracellular matrix remodelling and apoptosis is a critical discriminator between cultured OA and RA synovial fibroblasts.

  9. Survey of 800+ datasets from human tissue and body fluid reveals XenomiRs are likely artifacts

    DEFF Research Database (Denmark)

    Kang, Wenjing; Bang-Berthelsen, Claus Heiner; Holm, Anja

    2017-01-01

    -study in the field, surveying the presence and abundances of cross-species miRNAs (xenomiRs) in 824 sequencing datasets from various human tissues and body fluids. We find that xenomiRs are commonly present in tissues (17%) and body fluids (69%), however the abundances are low, comprising 0.001% of host human mi......RNA counts. Further, we do not detect a significant enrichment of xenomiRs in sequencing data originating from tissues and body fluids that are exposed to dietary intake (such as liver). Likewise, there is no significant depletion of xenomiRs in tissues and body fluids that are relatively separated from...... the main bloodstream (such as brain and cerebro-spinal fluids). Interestingly, the majority (81%) of body fluid xenomiRs stem from rodents, which are rare human dietary contributions, but common laboratory animals. Body fluid samples from the same studies tend to group together when clustered by xenomi...

  10. The HDUV Survey: Six Lyman Continuum Emitter Candidates at z ∼ 2 Revealed by HST UV Imaging

    Science.gov (United States)

    Naidu, R. P.; Oesch, P. A.; Reddy, N.; Holden, B.; Steidel, C. C.; Montes, M.; Atek, H.; Bouwens, R. J.; Carollo, C. M.; Cibinel, A.; Illingworth, G. D.; Labbé, I.; Magee, D.; Morselli, L.; Nelson, E. J.; van Dokkum, P. G.; Wilkins, S.

    2017-09-01

    We present six galaxies at z∼ 2 that show evidence of Lyman continuum (LyC) emission based on the newly acquired UV imaging of the Hubble Deep UV legacy survey (HDUV) conducted with the WFC3/UVIS camera on the Hubble Space Telescope (HST). At the redshift of these sources, the HDUV F275W images partially probe the ionizing continuum. By exploiting the HST multiwavelength data available in the HDUV/GOODS fields, models of the UV spectral energy distributions, and detailed Monte Carlo simulations of the intergalactic medium absorption, we estimate the absolute ionizing photon escape fractions of these galaxies to be very high—typically > 60 % (> 13 % for all sources at 90% likelihood). Our findings are in broad agreement with previous studies that found only a small fraction of galaxies with high escape fraction. These six galaxies compose the largest sample yet of LyC leaking candidates at z∼ 2 whose inferred LyC flux has been observed at HST resolution. While three of our six candidates show evidence of hosting an active galactic nucleus, two of these are heavily obscured and their LyC emission appears to originate from star-forming regions rather than the central nucleus. Extensive multiwavelength data in the GOODS fields, especially the near-IR grism spectra from the 3D-HST survey, enable us to study the candidates in detail and tentatively test some recently proposed indirect methods to probe LyC leakage. High-resolution spectroscopic follow-up of our candidates will help constrain such indirect methods, which are our only hope of studying f esc at z∼ 5-9 in the JWST era. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained from the data archive at the Space Telescope Science Institute. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

  11. Predicting Where a Radiation Will Occur: Acoustic and Molecular Surveys Reveal Overlooked Diversity in Indian Ocean Island Crickets (Mogoplistinae: Ornebius).

    Science.gov (United States)

    Warren, Ben H; Baudin, Rémy; Franck, Antoine; Hugel, Sylvain; Strasberg, Dominique

    2016-01-01

    Recent theory suggests that the geographic location of island radiations (local accumulation of species diversity due to cladogenesis) can be predicted based on island area and isolation. Crickets are a suitable group for testing these predictions, as they show both the ability to reach some of the most isolated islands in the world, and to speciate at small spatial scales. Despite substantial song variation between closely related species in many island cricket lineages worldwide, to date this characteristic has not received attention in the western Indian Ocean islands; existing species descriptions are based on morphology alone. Here we use a combination of acoustics and DNA sequencing to survey these islands for Ornebius crickets. We uncover a small but previously unknown radiation in the Mascarenes, constituting a three-fold increase in the Ornebius species diversity of this archipelago (from two to six species). A further new species is detected in the Comoros. Although double archipelago colonisation is the best explanation for species diversity in the Seychelles, in situ cladogenesis is the best explanation for the six species in the Mascarenes and two species of the Comoros. Whether the radiation of Mascarene Ornebius results from intra- or purely inter- island speciation cannot be determined on the basis of the phylogenetic data alone. However, the existence of genetic, song and ecological divergence at the intra-island scale is suggestive of an intra-island speciation scenario in which ecological and mating traits diverge hand-in-hand. Our results suggest that the geographic location of Ornebius radiations is partially but not fully explained by island area and isolation. A notable anomaly is Madagascar, where our surveys are consistent with existing accounts in finding no Ornebius species present. Possible explanations are discussed, invoking ecological differences between species and differences in environmental history between islands.

  12. Predicting Where a Radiation Will Occur: Acoustic and Molecular Surveys Reveal Overlooked Diversity in Indian Ocean Island Crickets (Mogoplistinae: Ornebius.

    Directory of Open Access Journals (Sweden)

    Ben H Warren

    Full Text Available Recent theory suggests that the geographic location of island radiations (local accumulation of species diversity due to cladogenesis can be predicted based on island area and isolation. Crickets are a suitable group for testing these predictions, as they show both the ability to reach some of the most isolated islands in the world, and to speciate at small spatial scales. Despite substantial song variation between closely related species in many island cricket lineages worldwide, to date this characteristic has not received attention in the western Indian Ocean islands; existing species descriptions are based on morphology alone. Here we use a combination of acoustics and DNA sequencing to survey these islands for Ornebius crickets. We uncover a small but previously unknown radiation in the Mascarenes, constituting a three-fold increase in the Ornebius species diversity of this archipelago (from two to six species. A further new species is detected in the Comoros. Although double archipelago colonisation is the best explanation for species diversity in the Seychelles, in situ cladogenesis is the best explanation for the six species in the Mascarenes and two species of the Comoros. Whether the radiation of Mascarene Ornebius results from intra- or purely inter- island speciation cannot be determined on the basis of the phylogenetic data alone. However, the existence of genetic, song and ecological divergence at the intra-island scale is suggestive of an intra-island speciation scenario in which ecological and mating traits diverge hand-in-hand. Our results suggest that the geographic location of Ornebius radiations is partially but not fully explained by island area and isolation. A notable anomaly is Madagascar, where our surveys are consistent with existing accounts in finding no Ornebius species present. Possible explanations are discussed, invoking ecological differences between species and differences in environmental history between

  13. In Vivo Profiling Reveals a Competent Heat Shock Response in Adult Neurons: Implications for Neurodegenerative Disorders.

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    Alisia Carnemolla

    Full Text Available The heat shock response (HSR is the main pathway used by cells to counteract proteotoxicity. The inability of differentiated neurons to induce an HSR has been documented in primary neuronal cultures and has been proposed to play a critical role in ageing and neurodegeneration. However, this accepted dogma has not been demonstrated in vivo. We used BAC transgenic mice generated by the Gene Expression Nervous System Atlas project to investigate the capacity of striatal medium sized spiny neurons to induce an HSR as compared to that of astrocytes and oligodendrocytes. We found that all cell populations were competent to induce an HSR upon HSP90 inhibition. We also show the presence and relative abundance of heat shock-related genes and proteins in these striatal cell populations. The identification of a competent HSR in adult neurons supports the development of therapeutics that target the HSR pathway as treatments for neurodegenerative disorders.

  14. Plant root transcriptome profiling reveals a strain-dependent response during Azospirillum-rice cooperation

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    Benoît eDrogue

    2014-11-01

    Full Text Available Cooperation involving Plant Growth-Promoting Rhizobacteria results in improvements of plant growth and health. While pathogenic and symbiotic interactions are known to induce transcriptional changes for genes related to plant defence and development, little is known about the impact of phytostimulating rhizobacteria on plant gene expression. This study aims at identifying genes significantly regulated in rice roots upon Azospirillum inoculation, considering possible favored interaction between a strain and its original host cultivar. Genome-wide analyses of Oryza sativa japonica cultivars Cigalon and Nipponbare were performed, by using microarrays, seven days post inoculation with A. lipoferum 4B (isolated from Cigalon or Azospirillum sp. B510 (isolated from Nipponbare and compared to the respective non-inoculated condition. A total of 7,384 genes were significantly regulated, which represent about 16 % of total rice genes. A set of 34 genes is regulated by both Azospirillum strains in both cultivars, including a gene orthologous to PR10 of Brachypodium, and these could represent plant markers of Azospirillum-rice interactions. The results highlight a strain-dependent response of rice, with 83 % of the differentially expressed genes being classified as combination-specific. Whatever the combination, most of the differentially expressed genes are involved in primary metabolism, transport, regulation of transcription and protein fate. When considering genes involved in response to stress and plant defence, it appears that strain B510, a strain displaying endophytic properties, leads to the repression of a wider set of genes than strain 4B. Individual genotypic variations could be the most important driving force of rice roots gene expression upon Azospirillum inoculation. Strain-dependent transcriptional changes observed for genes related to auxin and ethylene signalling highlight the complexity of hormone signalling networks in the Azospirillum

  15. Apoplast proteome reveals that extracellular matrix contributes to multistress response in poplar

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    Lawrence Amanda M

    2010-11-01

    Full Text Available Abstract Background Riverine ecosystems, highly sensitive to climate change and human activities, are characterized by rapid environmental change to fluctuating water levels and siltation, causing stress on their biological components. We have little understanding of mechanisms by which riverine plant species have developed adaptive strategies to cope with stress in dynamic environments while maintaining growth and development. Results We report that poplar (Populus spp. has evolved a systems level "stress proteome" in the leaf-stem-root apoplast continuum to counter biotic and abiotic factors. To obtain apoplast proteins from P. deltoides, we developed pressure-chamber and water-displacement methods for leaves and stems, respectively. Analyses of 303 proteins and corresponding transcripts coupled with controlled experiments and bioinformatics demonstrate that poplar depends on constitutive and inducible factors to deal with water, pathogen, and oxidative stress. However, each apoplast possessed a unique set of proteins, indicating that response to stress is partly compartmentalized. Apoplast proteins that are involved in glycolysis, fermentation, and catabolism of sucrose and starch appear to enable poplar to grow normally under water stress. Pathogenesis-related proteins mediating water and pathogen stress in apoplast were particularly abundant and effective in suppressing growth of the most prevalent poplar pathogen Melampsora. Unexpectedly, we found diverse peroxidases that appear to be involved in stress-induced cell wall modification in apoplast, particularly during the growing season. Poplar developed a robust antioxidative system to buffer oxidation in stem apoplast. Conclusion These findings suggest that multistress response in the apoplast constitutes an important adaptive trait for poplar to inhabit dynamic environments and is also a potential mechanism in other riverine plant species.

  16. Seismic survey across the Japan trench using ultra-deep water OBSs to reveal the structural evolution within the incoming plate prior to subduction

    Science.gov (United States)

    Fujie, G.; Takahashi, T.; Kodaira, S.; Obana, K.; Yamada, T.

    2013-12-01

    Dehydration processes and the expulsion of the water from the subducting oceanic plate affect various subduction-zone processes, including arc volcanism and generation of earthquakes and tremor. Since the amount of chemically bound water in the oceanic plate is highest in serpentinized mantle, it is important to reveal the water amount that penetrates into the oceanic mantle prior to subduction. In 2009, we conducted wide-angle seismic surveys in the outer rise regions of the Japan trench and the Kuril trench. We found that the P-wave velocity (Vp) within the oceanic crust and mantle gradually decreases toward the trench axis. In addition, we found the Vp/Vs ratio within the oceanic crust gradually increases toward the trench, suggesting the water infiltration into the oceanic crust. However, we could not observe any changes in Vp/Vs ratio within the oceanic mantle. This was probably because our seismic survey profile did not cover the area where we would expect the largest structural changes, the trench axis, because the trench axis was too deep to operate our conventional Ocean Bottom Seismometers (OBSs). To examine the Vp/Vs ratio at the area where the largest structural changes are expected and to evaluate the amount of the water penetrating into the oceanic mantle prior to subduction, we need a seismic survey across the trench axis. In August 2013, we plan to conduct an extensive seismic survey across the Japan trench using newly developed 10 ultra-deep water OBSs that are capable of operating at the deepest point of the Japan trench. The seismic profile is a trenchward extension of the existing outer rise profile and we are going to analyze the new data by combining with the existing seismic survey data in order to reveal the structural evolution of the incoming Pacific plate from the outer rise to the trench axis. Since all the ultra-deep water OBSs are equipped with 3-component geophones (or 3-component accelerometers), we have a possibility to determine S

  17. Plasma proteome response to severe burn injury revealed by 18O-labeled "universal" reference-based quantitative proteomics.

    Science.gov (United States)

    Qian, Wei-Jun; Petritis, Brianne O; Kaushal, Amit; Finnerty, Celeste C; Jeschke, Marc G; Monroe, Matthew E; Moore, Ronald J; Schepmoes, Athena A; Xiao, Wenzhong; Moldawer, Lyle L; Davis, Ronald W; Tompkins, Ronald G; Herndon, David N; Camp, David G; Smith, Richard D

    2010-09-01

    A burn injury represents one of the most severe forms of human trauma and is responsible for significant mortality worldwide. Here, we present the first quantitative proteomics investigation of the blood plasma proteome response to severe burn injury by comparing the plasma protein concentrations of 10 healthy control subjects with those of 15 severe burn patients at two time-points following the injury. The overall analytical strategy for this work integrated immunoaffinity depletion of the 12 most abundant plasma proteins with cysteinyl-peptide enrichment-based fractionation prior to LC-MS analyses of individual patient samples. Incorporation of an 18O-labeled "universal" reference among the sample sets enabled precise relative quantification across samples. In total, 313 plasma proteins confidently identified with two or more unique peptides were quantified. Following statistical analysis, 110 proteins exhibited significant abundance changes in response to the burn injury. The observed changes in protein concentrations suggest significant inflammatory and hypermetabolic response to the injury, which is supported by the fact that many of the identified proteins are associated with acute phase response signaling, the complement system, and coagulation system pathways. The regulation of approximately 35 proteins observed in this study is in agreement with previous results reported for inflammatory or burn response, but approximately 50 potentially novel proteins previously not known to be associated with burn response or inflammation are also found. Elucidating proteins involved in the response to severe burn injury may reveal novel targets for therapeutic interventions as well as potential predictive biomarkers for patient outcomes such as multiple organ failure.

  18. Socially responsible ethnobotanical surveys in the Cape Floristic Region: ethical principles, methodology and quantification of data

    Directory of Open Access Journals (Sweden)

    Ben-Erik Van Wyk

    2012-03-01

    Full Text Available A broad overview of published and unpublished ethnobotanical surveys in the Cape Floristic Region (the traditional home of the San and Khoi communities shows that the data is incomplete. There is an urgent need to record the rich indigenous knowledge about plants in a systematic and social responsible manner in order to preserve this cultural and scientific heritage for future generations. Improved methods for quantifying data are introduced, with special reference to the simplicity and benefits of the new Matrix Method. This methodology prevents or reduces the number of false negatives, and also ensures the participation of elderly people who might be immobile. It also makes it possible to compare plant uses in different local communities. This method enables the researcher to quantify the knowledge on plant use that was preserved in a community, and to determine the relative importance of a specific plant in a more objective way. Ethical considerations for such ethnobotanical surveys are discussed, through the lens of current ethical codes and international conventions. This is an accessible approach, which can also be used in the life sciences classroom.

  19. Efficient Consumer Response (ECR: a survey of the Australian grocery industry

    Directory of Open Access Journals (Sweden)

    Paula Swatman

    1998-05-01

    Full Text Available Efficient consumer response (ECR is a U.S. supply chain management strategy which attempts to address the inefficiencies which have led to excessive inventory and unnecessary costs at all levels within the grocery industry supply chain. This paper discusses the traditional grocery store format, the supermarket, and the ways in which inefficient business practices developed in the U.S. grocery supply chain; and discusses the major business activities needed for successful implementation of ECR. The paper then presents a brief summary of the results of a survey of ECR knowledge and usage within the Australian grocery industry, which is the initial phase of a long term research project whose main purpose is to evaluate ECR as it applies to that industry.

  20. One-year survey of a single Micronesian reef reveals extraordinarily rich diversity of Symbiodinium types in soritid foraminifera

    Science.gov (United States)

    Pochon, X.; Garcia-Cuetos, L.; Baker, A. C.; Castella, E.; Pawlowski, J.

    2007-12-01

    Recent molecular studies of symbiotic dinoflagellates (genus Symbiodinium) from a wide array of invertebrate hosts have revealed exceptional fine-scale symbiont diversity whose distribution among hosts, regions and environments exhibits significant biogeographic, ecological and evolutionary patterns. Here, similar molecular approaches using the internal transcribed spacer-2 (ITS-2) region were applied to investigate cryptic diversity in Symbiodinium inhabiting soritid foraminifera. Approximately 1,000 soritid specimens were collected and examined during a 12-month period over a 40 m depth gradient from a single reef in Guam, Micronesia. Out of 61 ITS-2 types distinguished, 46 were novel. Most types found are specific for soritid hosts, except for three types (C1, C15 and C19) that are common in metazoan hosts. The distribution of these symbionts was compared with the phylotype of their foraminiferal hosts, based on soritid small subunit ribosomal DNA sequences, and three new phylotypes of soritid hosts were identified based on these sequences. Phylogenetic analyses of 645 host-symbiont pairings revealed that most Symbiodinium types associated specifically with a particular foraminiferal host genus or species, and that the genetic diversity of these symbiont types was positively correlated with the genetic diversity found within each of the three host genera. Compared to previous molecular studies of Symbiodinium from other locations worldwide, the diversity reported here is exceptional and suggests that Micronesian coral reefs are home to a remarkably large Symbiodinium assemblage.

  1. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

    Science.gov (United States)

    Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

    2016-01-01

    The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall. PMID:27680878

  2. Surface Response to Regional Uplift of Madagascar Reveals Short Wavelength Dynamic Topography

    Science.gov (United States)

    Stephenson, S.; White, N.

    2016-12-01

    The physiography of Madagascar is characterized by high elevation but low relief topography with 42% of the landscape at an elevation grgeater than 500 m. Eocene marine limestones crop out at an elevation of 400 m, extensive low relief erosion surfaces capped by laterites occur at elevations of up to 2 km, and longitudinal river profiles are disequilibrated. Together, these observations suggest that Madagascar underwent regional uplift in Neogene times. Inverse modeling of drainage networks suggests that regional uplift is diachronous and has occurred on wavelengths of 1000 km. The existence of deeply incised river channels together with low-temperature thermochronologic measurements (i.e. AFT, AHe) implies that erosion occurred in response to regional Neogene uplift. Admittance analysis of long wavelength free-air gravity and topography shows that admittance, Z = 45 ± 5 mGal/km. The history of Neogene volcanism and a lack of significant tectonic shortening both suggest that uplift is dynamically supported. Here we present a suite of U-Th dates of emergent coral reef deposits from northern Madagascar, whose margins are sometimes considered `stable'. Elevation of these coeval coral reefs decreases from 7.2 m at the northern tip of Madagascar to sea level 100 km to the south. The existence of a spatial gradient suggests that differential vertical motions occurred during Late Quaternary times. These results raise significant questions about the reliability both of emergent coral reefs as global sea-level markers and the length-scale of variations in dynamic topography.

  3. Revealing Real-Time Emotional Responses: a Personalized Assessment based on Heartbeat Dynamics

    Science.gov (United States)

    Valenza, Gaetano; Citi, Luca; Lanatá, Antonio; Scilingo, Enzo Pasquale; Barbieri, Riccardo

    2014-05-01

    Emotion recognition through computational modeling and analysis of physiological signals has been widely investigated in the last decade. Most of the proposed emotion recognition systems require relatively long-time series of multivariate records and do not provide accurate real-time characterizations using short-time series. To overcome these limitations, we propose a novel personalized probabilistic framework able to characterize the emotional state of a subject through the analysis of heartbeat dynamics exclusively. The study includes thirty subjects presented with a set of standardized images gathered from the international affective picture system, alternating levels of arousal and valence. Due to the intrinsic nonlinearity and nonstationarity of the RR interval series, a specific point-process model was devised for instantaneous identification considering autoregressive nonlinearities up to the third-order according to the Wiener-Volterra representation, thus tracking very fast stimulus-response changes. Features from the instantaneous spectrum and bispectrum, as well as the dominant Lyapunov exponent, were extracted and considered as input features to a support vector machine for classification. Results, estimating emotions each 10 seconds, achieve an overall accuracy in recognizing four emotional states based on the circumplex model of affect of 79.29%, with 79.15% on the valence axis, and 83.55% on the arousal axis.

  4. Nanoscale histone localization in live cells reveals reduced chromatin mobility in response to DNA damage.

    Science.gov (United States)

    Liu, Jing; Vidi, Pierre-Alexandre; Lelièvre, Sophie A; Irudayaraj, Joseph M K

    2015-02-01

    Nuclear functions including gene expression, DNA replication and genome maintenance intimately rely on dynamic changes in chromatin organization. The movements of chromatin fibers might play important roles in the regulation of these fundamental processes, yet the mechanisms controlling chromatin mobility are poorly understood owing to methodological limitations for the assessment of chromatin movements. Here, we present a facile and quantitative technique that relies on photoactivation of GFP-tagged histones and paired-particle tracking to measure chromatin mobility in live cells. We validate the method by comparing live cells to ATP-depleted cells and show that chromatin movements in mammalian cells are predominantly energy dependent. We also find that chromatin diffusion decreases in response to DNA breaks induced by a genotoxic drug or by the ISceI meganuclease. Timecourse analysis after cell exposure to ionizing radiation indicates that the decrease in chromatin mobility is transient and precedes subsequent increased mobility. Future applications of the method in the DNA repair field and beyond are discussed.

  5. Parameter identification using stochastic simulations reveals a robustness in CD95 apoptotic response.

    Science.gov (United States)

    Zimmer, Christoph; Schleich, Kolja; Lavrik, Inna

    2016-04-26

    A number of mathematical models of apoptosis generated recently allowed us to understand intrinsic mechanisms of life/death decisions in a cell. Nevertheless, the parameters for the mathematical models are often experimentally difficult to obtain and there is an emerging need for the development of efficient approaches for parameter estimation. In this study we suggest a new method for parameter estimation, which is based on stochastic simulations and can be used when the number of molecules in the system is small. Our approach comprised the following steps: we start from the selection of parameters that lead to a good ordinary differential equation (ODE) fit. We continued by carrying out stochastic simulations for each of these parameters. Comparing the correlation structure of these simulations with the data, we finally could identify the best parameter set. The method was applied for a model of CD95-induced apoptosis, the new best identified parameters fit well to the experimental data. The best parameter set allowed us to get new insights into CD95 apoptosis regulation and can be applied for the comprehensive analysis of other signaling networks. The modeling approach allowed us to get new insights into network regulation, in particular, to identify robustness in CD95 apoptotic response. Taken together, this new method provides valuable predictions and can be applied for the analysis of other signaling networks.

  6. Computational phenotyping of two-person interactions reveals differential neural response to depth-of-thought.

    Directory of Open Access Journals (Sweden)

    Ting Xiang

    Full Text Available Reciprocating exchange with other humans requires individuals to infer the intentions of their partners. Despite the importance of this ability in healthy cognition and its impact in disease, the dimensions employed and computations involved in such inferences are not clear. We used a computational theory-of-mind model to classify styles of interaction in 195 pairs of subjects playing a multi-round economic exchange game. This classification produces an estimate of a subject's depth-of-thought in the game (low, medium, high, a parameter that governs the richness of the models they build of their partner. Subjects in each category showed distinct neural correlates of learning signals associated with different depths-of-thought. The model also detected differences in depth-of-thought between two groups of healthy subjects: one playing patients with psychiatric disease and the other playing healthy controls. The neural response categories identified by this computational characterization of theory-of-mind may yield objective biomarkers useful in the identification and characterization of pathologies that perturb the capacity to model and interact with other humans.

  7. Transcriptomic Analysis of Laribacter hongkongensis Reveals Adaptive Response Coupled with Temperature

    Science.gov (United States)

    Kong, Hoi-Kuan; Law, Hon-Wai; Liu, Xuan; Law, Carmen O. K.; Pan, Qing; Gao, Lin; Xiong, Lifeng; Lau, Susanna K. P.; Woo, Patrick C. Y.; Lau, Terrence chi kong

    2017-01-01

    Bacterial adaptation to different hosts requires transcriptomic alteration in response to the environmental conditions. Laribacter hongkongensis is a gram-negative, facultative anaerobic, urease-positive bacillus caused infections in liver cirrhosis patients and community-acquired gastroenteritis. It was also found in intestine from commonly consumed freshwater fishes and drinking water reservoirs. Since L. hongkongensis could survive as either fish or human pathogens, their survival mechanisms in two different habitats should be temperature-regulated and highly complex. Therefore, we performed transcriptomic analysis of L. hongkongensis at body temperatures of fish and human in order to elucidate the versatile adaptation mechanisms coupled with the temperatures. We identified numerous novel temperature-induced pathways involved in host pathogenesis, in addition to the shift of metabolic equilibriums and overexpression of stress-related proteins. Moreover, these pathways form a network that can be activated at a particular temperature, and change the physiology of the bacteria to adapt to the environments. In summary, the dynamic of transcriptomes in L. hongkongensis provides versatile strategies for the bacterial survival at different habitats and this alteration prepares the bacterium for the challenge of host immunity. PMID:28085929

  8. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

    2016-09-29

    The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

  9. Auditory steady-state responses reveal amplitude modulation gap detection thresholds

    Science.gov (United States)

    Ross, Bernhard; Pantev, Christo

    2004-05-01

    Auditory evoked magnetic fields were recorded from the left hemisphere of healthy subjects using a 37-channel magnetometer while stimulating the right ear with 40-Hz amplitude modulated (AM) tone-bursts with 500-Hz carrier frequency in order to study the time-courses of amplitude and phase of auditory steady-state responses (ASSRs). The stimulus duration of 300 ms and the duration of the silent periods (3-300 ms) between succeeding stimuli were chosen to address the question whether the time-course of the ASSR can reflect both temporal integration and temporal resolution in the central auditory processing. Long lasting perturbations of the ASSR were found after gaps in the AM sound, even for gaps of short duration. These were interpreted as evidences for an auditory reset mechanism. Concomitant psycho-acoustical tests corroborated that gap durations perturbing the ASSR were in the same range as the threshold for AM gap detection. Magnetic source localizations estimated the ASSR sources in the primary auditory cortex, suggesting that the processing of temporal structures in the sound is performed at or below the cortical level.

  10. Kinetic features revealed by top-hat electrostatic analysers: numerical simulations and instrument response results

    Science.gov (United States)

    De Marco, Rossana; Marcucci, Maria Federica; Brienza, Daniele; Bruno, Roberto; Consolini, Giuseppe; Perrone, Denise; Valentini, Franceso; Servidio, Sergio; Stabile, Sara; Pezzi, Oreste; Sorriso-Valvo, Luca; Lavraud, Benoit; De Keyser, Johan; Retinò, Alessandro; Fazakerley, Andrew; Wicks, Robert; Vaivads, Andris; Salatti, Mario; Veltri, Pierliugi

    2017-04-01

    Turbulence Heating ObserveR (THOR) is the first mission devoted to study energization, acceleration and heating of turbulent space plasmas, and designed to perform field and particle measurements at kinetic scales in different near-Earth regions and in the solar wind. Solar Orbiter (SolO), together with Solar Probe Plus, will provide the first comprehensive remote and in situ measurements which are critical to establish the fundamental physical links between the Sun's dynamic atmosphere and the turbulent solar wind. The fundamental process of turbulent dissipation is mediated by physical mechanism that occur at a variety of temporal and spatial scales, and most efficiently at the kinetics scales. Hybrid Vlasov-Maxwell simulations of solar-wind turbulence show that kinetic effects manifest as particle beams, production of temperature anisotropies and ring-like modulations, preferential heating of heavy ions. We use a numerical code able to reproduce the response of a typical electrostatic analyzer of top-hat type starting from velocity distribution functions (VDFs) generated by Hybrid Vlasov-Maxwell (HVM) numerical simulations. Here, we show how optimized particle measurements by top-hat analysers can capture the kinetic features injected by turbulence in the VDFs.

  11. The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants.

    Science.gov (United States)

    Mustafa, Ghada A; Abd-Elgawad, Amr; Ouf, Amged; Siam, Rania

    2016-07-01

    The Red Sea is considered one of the youngest oceanic systems, with unique physical, geochemical and biological characteristics. Tourism, industrialization, extensive fishing, oil processing and shipping are extensive sources of pollution in the Red Sea. We analyzed the geochemical characteristics and microbial community of sediments along the Egyptian coast of the Red Sea. Our sites mainly included 1) four ports used for shipping aluminum, ilmenite and phosphate; 2) a site previously reported to have suffered extensive oil spills; and 3) a site impacted by tourism. Two major datasets for the sediment of ten Red Sea coastal sites were generated; i) a chemical dataset included measurements of carbon, hydrogen, nitrogen and sulfur, metals and selected semi-volatile oil; and ii) a 16S rRNA Pyrotags bacterial metagenomic dataset. Based on the taxonomic assignments of the 16S rRNA Pyrotags to major bacterial groups, we report 30 taxa constituting an Egyptian Red Sea Coastal Microbiome. Bacteria that degrade hydrocarbons were predominant in the majority of the sites, particularly in two ports where they reached up to 76% of the total identified genera. In contrast, sulfate-reducing and sulfate-oxidizing bacteria dominated two lakes at the expense of other hydrocarbon metabolizers. Despite the reported "Egyptian Red Sea Coastal Microbiome," sites with similar anthropogenic pollutants showed unique microbial community abundances. This suggests that the abundance of a specific bacterial community is an evolutionary mechanism induced in response to selected anthropogenic pollutants.

  12. South Atlantic island record reveals a South Atlantic response to the 8.2 kyr event

    Directory of Open Access Journals (Sweden)

    K. Ljung

    2007-05-01

    Full Text Available One of the most distinct climate fluctuations during the Holocene is the short and rapid event centred around 8200 years ago, the 8.2 kyr event, which was most likely triggered by glacial melt-water forcing from the receding Laurentide ice-sheet. Evidence for this cooling has primarily been reported from sites around the North Atlantic, but an increasing number of observations imply a more wide-spread occurrence. Palaeoclimate archives from the Southern Hemisphere have hitherto failed to uncover a distinct climatic anomaly associated with the 8.2 kyr event. Here we present a lake sediment record from Nightingale Island in the central South Atlantic showing enhanced precipitation between 8275 and 8025 cal. yrs BP, most likely as a consequence of increased sea surface temperature (SST. We show that this is consistent with climate model projections of a warming of the South Atlantic in response to reduced north-ward energy transport during the 8.2 kyr event.

  13. Leaf Proteome Analysis Reveals Prospective Drought and Heat Stress Response Mechanisms in Soybean

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    Aayudh Das

    2016-01-01

    Full Text Available Drought and heat are among the major abiotic stresses that affect soybean crops worldwide. During the current investigation, the effect of drought, heat, and drought plus heat stresses was compared in the leaves of two soybean varieties, Surge and Davison, combining 2D-DIGE proteomic data with physiology and biochemical analyses. We demonstrated how 25 differentially expressed photosynthesis-related proteins affect RuBisCO regulation, electron transport, Calvin cycle, and carbon fixation during drought and heat stress. We also observed higher abundance of heat stress-induced EF-Tu protein in Surge. It is possible that EF-Tu might have activated heat tolerance mechanisms in the soybean. Higher level expressions of heat shock-related protein seem to be regulating the heat tolerance mechanisms. This study identifies the differential expression of various abiotic stress-responsive proteins that regulate various molecular processes and signaling cascades. One inevitable outcome from the biochemical and proteomics assays of this study is that increase of ROS levels during drought stress does not show significant changes at the phenotypic level in Davison and this seems to be due to a higher amount of carbonic anhydrase accumulation in the cell which aids the cell to become more resistant to cytotoxic concentrations of H2O2.

  14. Response of plasmaspheric configuration to substorms revealed by Chang’e 3

    Science.gov (United States)

    He, Han; Shen, Chao; Wang, Huaning; Zhang, Xiaoxin; Chen, Bo; Yan, Jun; Zou, Yongliao; Jorgensen, Anders M.; He, Fei; Yan, Yan; Zhu, Xiaoshuai; Huang, Ya; Xu, Ronglan

    2016-08-01

    The Moon-based Extreme Ultraviolet Camera (EUVC) of the Chang’e 3 mission provides a global and instantaneous meridian view (side view) of the Earth’s plasmasphere. The plasmasphere is one inner component of the whole magnetosphere, and the configuration of the plasmasphere is sensitive to magnetospheric activity (storms and substorms). However, the response of the plasmaspheric configuration to substorms is only partially understood, and the EUVC observations provide a good opportunity to investigate this issue. By reconstructing the global plasmaspheric configuration based on the EUVC images observed during 20–22 April 2014, we show that in the observing period, the plasmasphere had three bulges which were located at different geomagnetic longitudes. The inferred midnight transit times of the three bulges, using the rotation rate of the Earth, coincide with the expansion phase of three substorms, which implies a causal relationship between the substorms and the formation of the three bulges on the plasmasphere. Instead of leading to plasmaspheric erosion as geomagnetic storms do, substorms initiated on the nightside of the Earth cause local inflation of the plasmasphere in the midnight region.

  15. Long Term Salinity Stress Reveals Variety Specific Differences in Root Oxidative Stress Response

    Institute of Scientific and Technical Information of China (English)

    Prasad SENADHEERA; Shamala TIRIMANNE; Frans J M MAATHUIS

    2012-01-01

    Salinity stress induces oxidative stress caused by reactive oxygen species (ROS):superoxide radicals,hydrogen peroxide (H2O2) and hydroxyl radicals.Activities of both enzymatic and non-enzymatic components of the antioxidant system and related growth parameters were studied in the roots of the salt tolerant rice variety FL478 and the sensitive variety IR29 in response to long term stress (12 d) induced by 50 mmol/L NaCl.The comparative study showed that FL478maintained higher relative growth rate and lower Na+/K+ in the roots than IR29 due to a higher membrane stability index that effectively exclude Na+.Lower TBARS (thiobarbituric acid reactive substance) content in FL478 roots indicated that its membrane was relatively unaffected by ROS despite high H2O2 content recorded under the salinity stress.Relatively higher superoxide dismutase activity along with a parallel increase in transcript level of superoxide dismutase (Os07946990) in FL478 indicated that this protein might make a vital contribution to salt stress tolerance.Although the content of ascorbic acid remained unchanged in FL478,the activity of ascorbic peroxidases (APOXs) was reduced comparably in the both varieties.Transcriptomic data showed that a larger number of peroxidase genes were upregulated in FL478 compared to IR29 and several of which might provide engineering targets to improve rice salt tolerance.

  16. Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing

    Directory of Open Access Journals (Sweden)

    Colleen A Burge

    2013-07-01

    Full Text Available Coral reef communities are undergoing marked declines due to a variety of stressors including disease. The sea fan coral, Gorgonia ventalina, is a tractable study system to investigate mechanisms of immunity to a natural occurring pathogen. Functional studies in Gorgonia ventalina immunity indicate that several key pathways and cellular responses are involved in response to natural microbial invaders, although to date the functional and regulatory pathways remain largely un-described. This study used short-read sequencing (Illumina GAIIx to identify genes involved in the response of G. ventalina to a naturally occurring Aplanochytrium spp. parasite. De novo assembly of the G. ventalina transcriptome yielded 90,230 contigs of which 40,142 were annotated. RNA-Seq analysis revealed 210 differentially expressed genes in sea fans exposed to the Aplanochytrium parasite. Differentially expressed genes involved in immunity include pattern recognition molecules, anti-microbial peptides, and genes involved in wound repair and reactive oxygen species formation. Gene enrichment analysis indicated eight biological processes were enriched representing 36 genes, largely involved with protein translation and energy production. This is the first report using high-throughput sequencing to characterize the host response of a coral to a natural pathogen. Furthermore, we have generated the first transcriptome for a soft (octocoral or non-scleractinian coral species. Expression analysis revealed genes important in invertebrate innate immune pathways, as well as those whose role is previously un-described in cnidarians. This resource will be valuable in characterizing G. ventalina immune response to infection and co-infection of pathogens in the context of environmental change.

  17. The combined effect of salinity and heat reveals a specific physiological, biochemical and molecular response in tomato plants.

    Science.gov (United States)

    Rivero, Rosa M; Mestre, Teresa C; Mittler, Ron; Rubio, Francisco; Garcia-Sanchez, Francisco; Martinez, Vicente

    2014-05-01

    Many studies have described the response mechanisms of plants to salinity and heat applied individually; however, under field conditions some abiotic stresses often occur simultaneously. Recent studies revealed that the response of plants to a combination of two different stresses is specific and cannot be deduced from the stresses applied individually. Here, we report on the response of tomato plants to a combination of heat and salt stress. Interestingly, and in contrast to the expected negative effect of the stress combination on plant growth, our results show that the combination of heat and salinity provides a significant level of protection to tomato plants from the effects of salinity. We observed a specific response of plants to the stress combination that included accumulation of glycine betaine and trehalose. The accumulation of these compounds under the stress combination was linked to the maintenance of a high K(+) concentration and thus a lower Na(+) /K(+) ratio, with a better performance of the cell water status and photosynthesis as compared with salinity alone. Our findings unravel new and unexpected aspects of the response of plants to stress combination and provide a proposed list of enzymatic targets for improving crop tolerance to the abiotic field environment.

  18. Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum.

    Directory of Open Access Journals (Sweden)

    Andrea eVega

    2015-11-01

    Full Text Available Nitrogen (N is one of the main limiting nutrients for plant growth and crop yield. It is well documented that changes in nitrate availability, the main N source found in agricultural soils, influences a myriad of developmental programs and processes including the plant defense response. Indeed, many agronomical reports indicate that the plant N nutritional status influences their ability to respond effectively when challenged by different pathogens. However, the molecular mechanisms involved in N-modulation of plant susceptibility to pathogens are poorly characterized. In this work, we show that Solanum lycopersicum defense response to the necrotrophic fungus Botrytis cinerea is affected by plant N availability, with higher susceptibility in nitrate-limiting conditions. Global gene expression responses of tomato against B. cinerea under contrasting nitrate conditions reveals that plant primary metabolism is affected by the fungal infection regardless of N regimes. This result suggests that differential susceptibility to pathogen attack under contrasting N conditions is not only explained by a metabolic alteration. We used a systems biology approach to identify the transcriptional regulatory network implicated in plant response to the fungus infection under contrasting nitrate conditions. Interestingly, hub genes in this network are known key transcription factors involved in ethylene and jasmonic acid signaling. This result positions these hormones as key integrators of nitrate and defense against B. cinerea in tomato plants. Our results provide insights into potential crosstalk mechanisms between necrotrophic defense response and N status in plants.

  19. Application of xCELLigence RTCA Biosensor Technology for Revealing the Profile and Window of Drug Responsiveness in Real Time

    Directory of Open Access Journals (Sweden)

    Dan Kho

    2015-04-01

    Full Text Available The xCELLigence technology is a real-time cellular biosensor, which measures the net adhesion of cells to high-density gold electrode arrays printed on custom-designed E-plates. The strength of cellular adhesion is influenced by a myriad of factors that include cell type, cell viability, growth, migration, spreading and proliferation. We therefore hypothesised that xCELLigence biosensor technology would provide a valuable platform for the measurement of drug responses in a multitude of different experimental, clinical or pharmacological contexts. In this manuscript, we demonstrate how xCELLigence technology has been invaluable in the identification of (1 not only if cells respond to a particular drug, but (2 the window of drug responsiveness. The latter aspect is often left to educated guess work in classical end-point assays, whereas biosensor technology reveals the temporal profile of the response in real time, which enables both acute responses and longer term responses to be profiled within the same assay. In our experience, the xCELLigence biosensor technology is suitable for highly targeted drug assessment and also low to medium throughput drug screening, which produces high content temporal data in real time.

  20. Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation.

    Science.gov (United States)

    Yong-Villalobos, Lenin; González-Morales, Sandra Isabel; Wrobel, Kazimierz; Gutiérrez-Alanis, Dolores; Cervantes-Peréz, Sergio Alan; Hayano-Kanashiro, Corina; Oropeza-Aburto, Araceli; Cruz-Ramírez, Alfredo; Martínez, Octavio; Herrera-Estrella, Luis

    2015-12-29

    Phosphate (Pi) availability is a significant limiting factor for plant growth and productivity in both natural and agricultural systems. To cope with such limiting conditions, plants have evolved a myriad of developmental and biochemical strategies to enhance the efficiency of Pi acquisition and assimilation to avoid nutrient starvation. In the past decade, these responses have been studied in detail at the level of gene expression; however, the possible epigenetic components modulating plant Pi starvation responses have not been thoroughly investigated. Here, we report that an extensive remodeling of global DNA methylation occurs in Arabidopsis plants exposed to low Pi availability, and in many instances, this effect is related to changes in gene expression. Modifications in methylation patterns within genic regions were often associated with transcriptional activation or repression, revealing the important role of dynamic methylation changes in modulating the expression of genes in response to Pi starvation. Moreover, Arabidopsis mutants affected in DNA methylation showed that changes in DNA methylation patterns are required for the accurate regulation of a number of Pi-starvation-responsive genes and that DNA methylation is necessary to establish proper morphological and physiological phosphate starvation responses.

  1. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

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    Henry D Priest

    Full Text Available Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

  2. Strategies for achieving a high response rate in a home interview survey

    Directory of Open Access Journals (Sweden)

    Power Kevin

    2009-06-01

    Full Text Available Abstract Background Response rates in surveys have been falling over the last 20 years, leading to the need for novel approaches to enhance recruitment. This study describes strategies used to maximise recruitment to a home interview survey of mothers with young children living in areas of high deprivation. Methods Mothers of two year old children received a letter from their GP inviting them to take part in a survey on diet. Participants were subsequently recruited by a researcher. The researcher first tried to contact potential participants by telephone, to discuss the study and make an appointment to conduct a home interview. Where telephone numbers for women could not be obtained from GP records, web searches of publicly available databases were conducted. After obtaining correct telephone numbers, up to six attempts were made to establish contact by telephone. If this was unsuccessful, a postal request for telephone contact was made. Where no telephone contact was achieved, the researcher sent up to two appointments by post to conduct a home interview. Results Participating GPs invited 372 women to take part in a home based interview study. GP practices provided telephone numbers for 162 women, of which 134 were valid numbers. The researcher identified a further 187 numbers from electronic directories. Further searches of GP records by practice staff yielded another 38 telephone numbers. Thus, telephone numbers were obtained for 99% of potential participants. The recruitment rate from telephone contacts was 77%. Most of the gain was achieved within four calls. For the remaining women, contact by post and home visits resulted in 18 further interviews, corresponding to 35% of the women not recruited by telephone. The final interview rate was 82%. This was possible because personal contact was established with 95% of potential participants. Conclusion This study achieved a high response rate in a hard to reach group. This was mainly achieved

  3. Factors influencing identification of and response to intimate partner violence: a survey of physicians and nurses

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    Wathen C Nadine

    2007-01-01

    Full Text Available Abstract Background Intimate partner violence against women (IPV has been identified as a serious public health problem. Although the health care system is an important site for identification and intervention, there have been challenges in determining how health care professionals can best address this issue in practice. We surveyed nurses and physicians in 2004 regarding their attitudes and behaviours with respect to IPV, including whether they routinely inquire about IPV, as well as potentially relevant barriers, facilitators, experiential, and practice-related factors. Methods A modified Dillman Tailored Design approach was used to survey 1000 nurses and 1000 physicians by mail in Ontario, Canada. Respondents were randomly selected from professional directories and represented practice areas pre-identified from the literature as those most likely to care for women at the point of initial IPV disclosure: family practice, obstetrics and gynecology, emergency care, maternal/newborn care, and public health. The survey instrument had a case-based scenario followed by 43 questions asking about behaviours and resources specific to woman abuse. Results In total, 931 questionnaires were returned; 597 by nurses (59.7% response rate and 328 by physicians (32.8% response rate. Overall, 32% of nurses and 42% of physicians reported routinely initiating the topic of IPV in practice. Principal components analysis identified eight constructs related to whether routine inquiry was conducted: preparedness, self-confidence, professional supports, abuse inquiry, practitioner consequences of asking, comfort following disclosure, practitioner lack of control, and practice pressures. Each construct was analyzed according to a number of related issues, including clinician training and experience with woman abuse, area of practice, and type of health care provider. Preparedness emerged as a key construct related to whether respondents routinely initiated the topic of

  4. Deep sequencing reveals microRNAs predictive of antiangiogenic drug response

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    García-Donas, Jesús; Beuselinck, Benoit; Inglada-Pérez, Lucía; Graña, Osvaldo; Schöffski, Patrick; Wozniak, Agnieszka; Bechter, Oliver; Apellániz-Ruiz, Maria; Leandro-García, Luis Javier; Esteban, Emilio; Castellano, Daniel E.; González del Alba, Aranzazu; Climent, Miguel Angel; Hernando, Susana; Arranz, José Angel; Morente, Manuel; Pisano, David G.; Robledo, Mercedes

    2016-01-01

    The majority of metastatic renal cell carcinoma (RCC) patients are treated with tyrosine kinase inhibitors (TKI) in first-line treatment; however, a fraction are refractory to these antiangiogenic drugs. MicroRNAs (miRNAs) are regulatory molecules proven to be accurate biomarkers in cancer. Here, we identified miRNAs predictive of progressive disease under TKI treatment through deep sequencing of 74 metastatic clear cell RCC cases uniformly treated with these drugs. Twenty-nine miRNAs were differentially expressed in the tumors of patients who progressed under TKI therapy (P values from 6 × 10–9 to 3 × 10–3). Among 6 miRNAs selected for validation in an independent series, the most relevant associations corresponded to miR–1307-3p, miR–155-5p, and miR–221-3p (P = 4.6 × 10–3, 6.5 × 10–3, and 3.4 × 10–2, respectively). Furthermore, a 2 miRNA–based classifier discriminated individuals with progressive disease upon TKI treatment (AUC = 0.75, 95% CI, 0.64–0.85; P = 1.3 × 10–4) with better predictive value than clinicopathological risk factors commonly used. We also identified miRNAs significantly associated with progression-free survival and overall survival (P = 6.8 × 10–8 and 7.8 × 10–7 for top hits, respectively), and 7 overlapped with early progressive disease. In conclusion, this is the first miRNome comprehensive study, to our knowledge, that demonstrates a predictive value of miRNAs for TKI response and provides a new set of relevant markers that can help rationalize metastatic RCC treatment. PMID:27699216

  5. Genome-wide survey reveals predisposing diabetes type 2-related DNA methylation variations in human peripheral blood.

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    Toperoff, Gidon; Aran, Dvir; Kark, Jeremy D; Rosenberg, Michael; Dubnikov, Tatyana; Nissan, Batel; Wainstein, Julio; Friedlander, Yechiel; Levy-Lahad, Ephrat; Glaser, Benjamin; Hellman, Asaf

    2012-01-15

    Inter-individual DNA methylation variations were frequently hypothesized to alter individual susceptibility to Type 2 Diabetes Mellitus (T2DM). Sequence-influenced methylations were described in T2DM-associated genomic regions, but evidence for direct, sequence-independent association with disease risk is missing. Here, we explore disease-contributing DNA methylation through a stepwise study design: first, a pool-based, genome-scale screen among 1169 case and control individuals revealed an excess of differentially methylated sites in genomic regions that were previously associated with T2DM through genetic studies. Next, in-depth analyses were performed at selected top-ranking regions. A CpG site in the first intron of the FTO gene showed small (3.35%) but significant (P = 0.000021) hypomethylation of cases relative to controls. The effect was independent of the sequence polymorphism in the region and persists among individuals carrying the sequence-risk alleles. The odds of belonging to the T2DM group increased by 6.1% for every 1% decrease in methylation (OR = 1.061, 95% CI: 1.032-1.090), the odds ratio for decrease of 1 standard deviation of methylation (adjusted to gender) was 1.5856 (95% CI: 1.2824-1.9606) and the sensitivity (area under the curve = 0.638, 95% CI: 0.586-0.690; males = 0.675, females = 0.609) was better than that of the strongest known sequence variant. Furthermore, a prospective study in an independent population cohort revealed significant hypomethylation of young individuals that later progressed to T2DM, relative to the individuals who stayed healthy. Further genomic analysis revealed co-localization with gene enhancers and with binding sites for methylation-sensitive transcriptional regulators. The data showed that low methylation level at the analyzed sites is an early marker of T2DM and suggests a novel mechanism by which early-onset, inter-individual methylation variation at isolated non-promoter genomic sites predisposes to T2DM.

  6. Systems rebalancing of metabolism in response to sulfur deprivation, as revealed by metabolome analysis of Arabidopsis plants.

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    Nikiforova, Victoria J; Kopka, Joachim; Tolstikov, Vladimir; Fiehn, Oliver; Hopkins, Laura; Hawkesford, Malcolm J; Hesse, Holger; Hoefgen, Rainer

    2005-05-01

    Sulfur is an essential macro-element in plant and animal nutrition. Plants assimilate inorganic sulfate into two sulfur-containing amino acids, cysteine and methionine. Low supply of sulfate leads to decreased sulfur pools within plant tissues. As sulfur-related metabolites represent an integral part of plant metabolism with multiple interactions, sulfur deficiency stress induces a number of adaptive responses, which must be coordinated. To reveal the coordinating network of adaptations to sulfur deficiency, metabolite profiling of Arabidopsis has been undertaken. Gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry techniques revealed the response patterns of 6,023 peaks of nonredundant ion traces and relative concentration levels of 134 nonredundant compounds of known chemical structure. Here, we provide a catalogue of the detected metabolic changes and reconstruct the coordinating network of their mutual influences. The observed decrease in biomass, as well as in levels of proteins, chlorophylls, and total RNA, gives evidence for a general reduction of metabolic activity under conditions of depleted sulfur supply. This is achieved by a systemic adjustment of metabolism involving the major metabolic pathways. Sulfur/carbon/nitrogen are partitioned by accumulation of metabolites along the pathway O-acetylserine to serine to glycine, and are further channeled together with the nitrogen-rich compound glutamine into allantoin. Mutual influences between sulfur assimilation, nitrogen imbalance, lipid breakdown, purine metabolism, and enhanced photorespiration associated with sulfur-deficiency stress are revealed in this study. These responses may be assembled into a global scheme of metabolic regulation induced by sulfur nutritional stress, which optimizes resources for seed production.

  7. Tap water isotopes reveal the San Francisco Bay Area's plumbing and responses to a major drought

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    Tipple, B. J.; Jameel, M. Y.; Chau, T. H.; Mancuso, C. J.; Bowen, G. J.; Dufour, A.; Chesson, L. A.; Ehleringer, J. R.

    2016-12-01

    Water availability and sustainability in the Western United States is a major flashpoint among expanding communities, growing industries, and productive agricultural lands. This issue came to a head in 2015 in the State of California, when the State mandated a 25% reduction in urban water use following a multi-year drought that significantly depleted water resources. The demands for and challenges in supplying water are only expected to intensify as climate perturbations, such as the 2012-2015 California Drought, become more common. As a consequence, there is an increased need to understand linkages between population centers, water transport and usage, and the impacts of climate change on water resources and infrastructure. To better understand these relationships within a megalopolis in the Western United States, we collected and analyzed 723 tap waters from the San Francisco Bay Area during seven collection campaigns across 21 months during 2013-2015. San Francisco Bay Area was selected as it has well-known water management strategies and its water resources were dramatically affected by the 2012-2105 drought. Consistent with known water management strategies and previous reports of tap water isotope values, we found large spatiotemporal variations in the δ2H and δ18O values of tap waters, indicative of complex water transport systems and municipality-scale management decisions. We observed δ2H and δ18O values of tap water consistent with waters originating from snowmelt from the Sierra Nevada Mountains, local precipitation, ground water, and partially evaporated reservoir sources. A cluster analysis of measured tap water data grouped waters from 43 static sampling sites that were associated with specific water utility providers within the San Francisco Bay Area and known management practices. Water management responses to the drought, such as source switching, bringing in new sources, and conservation, could be observed within the isotope data from each of

  8. Virus-induced gene silencing reveals signal transduction components required for the Pvr9-mediated hypersensitive response in Nicotiana benthamiana.

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    Tran, Phu-Tri; Choi, Hoseong; Choi, Doil; Kim, Kook-Hyung

    2016-08-01

    Resistance to pathogens mediated by plant resistance (R) proteins requires different signaling transduction components and pathways. Our previous studies revealed that a potyvirus resistance gene in pepper, Pvr9, confers a hypersensitive response (HR) to pepper mottle virus in Nicotiana benthamiana. Our results show that the Pvr9-mediated HR against pepper mottle virus infection requires HSP90, SGT1, NDR1, but not EDS1. These results suggest that the Pvr9-mediated HR is possibly related to the SA pathway but not the ET, JA, ROS or NO pathways.

  9. History of the great Kanto earthquakes inferred from the ages of Holocene marine terraces revealed by a comprehensive drilling survey

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    Komori, Junki; Shishikura, Masanobu; Ando, Ryosuke; Yokoyama, Yusuke; Miyairi, Yosuke

    2017-08-01

    We measured the emergence ages of four marine terraces in the Chikura lowland, which lies to the southeast of the Boso Peninsula, in eastern Japan, to reevaluate the history of the great earthquake occurrences along the Sagami Trough over the past 10,000 years. The dates of the marine terraces are measured via radiocarbon dating of shell fossils obtained from the marine deposits. The sampling method employed in this study collects core samples using a dense and systematic drilling survey, which increased the reliability when correlating shell fossils with marine terraces. In addition, radiocarbon dating was performed with accelerator mass spectrometry, which produces more highly accurate measurements than those measured in previous studies. Moreover, we explored the surface profiles of the terraces with detailed digital elevation model (DEM) data obtained using LiDAR. The maximum emergence ages of the marine terraces were dated at 6300 cal yBP, 3000 cal yBP, and 2200 cal yBP from the top terrace excepting the lowest terrace (which was estimated at AD1703). In addition, another previously unrecognized terrace was detected between the highest and the second terrace in both the dating and the geomorphological analyses and was dated at 5800 cal yBP. The newly obtained ages are nearly a thousand of years younger than previously estimated ages; consequently, the intervals of the great earthquakes that occurred along the Sagami Trough are estimated to be much shorter and more varied than those of previous estimations. This result revises the data used in the current assessment of the probabilities of earthquakes along the Sagami Trough, which could devastate the Tokyo metropolitan area. Furthermore, it demonstrates that the current approach could be a powerful tool to increase the accuracy of assessments of the other areas with depositional marine terraces.

  10. Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts

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    Kang, Wenjing; Bang-Berthelsen, Claus Heiner; Holm, Anja; Houben, Anna J.S.; Müller, Anne Holt; Thymann, Thomas; Pociot, Flemming; Estivill, Xavier; Friedländer, Marc R.

    2017-01-01

    miRNAs are small 22-nucleotide RNAs that can post-transcriptionally regulate gene expression. It has been proposed that dietary plant miRNAs can enter the human bloodstream and regulate host transcripts; however, these findings have been widely disputed. We here conduct the first comprehensive meta-study in the field, surveying the presence and abundances of cross-species miRNAs (xenomiRs) in 824 sequencing data sets from various human tissues and body fluids. We find that xenomiRs are commonly present in tissues (17%) and body fluids (69%); however, the abundances are low, comprising 0.001% of host human miRNA counts. Further, we do not detect a significant enrichment of xenomiRs in sequencing data originating from tissues and body fluids that are exposed to dietary intake (such as liver). Likewise, there is no significant depletion of xenomiRs in tissues and body fluids that are relatively separated from the main bloodstream (such as brain and cerebro-spinal fluids). Interestingly, the majority (81%) of body fluid xenomiRs stem from rodents, which are a rare human dietary contribution but common laboratory animals. Body fluid samples from the same studies tend to group together when clustered by xenomiR compositions, suggesting technical batch effects. Last, we performed carefully designed and controlled animal feeding studies, in which we detected no transfer of plant miRNAs into rat blood, or bovine milk sequences into piglet blood. In summary, our comprehensive computational and experimental results indicate that xenomiRs originate from technical artifacts rather than dietary intake. PMID:28062594

  11. Survey of Ixodes pacificus Ticks in California Reveals a Diversity of Microorganisms and a Novel and Widespread Anaplasmataceae Species.

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    Mark W Eshoo

    Full Text Available Ixodes pacificus ticks can harbor a wide range of human and animal pathogens. To survey the prevalence of tick-borne known and putative pathogens, we tested 982 individual adult and nymphal I. pacificus ticks collected throughout California between 2007 and 2009 using a broad-range PCR and electrospray ionization mass spectrometry (PCR/ESI-MS assay designed to detect a wide range of tick-borne microorganisms. Overall, 1.4% of the ticks were found to be infected with Borrelia burgdorferi, 2.0% were infected with Borrelia miyamotoi and 0.3% were infected with Anaplasma phagocytophilum. In addition, 3.0% were infected with Babesia odocoilei. About 1.2% of the ticks were co-infected with more than one pathogen or putative pathogen. In addition, we identified a novel Anaplasmataceae species that we characterized by sequencing of its 16S rRNA, groEL, gltA, and rpoB genes. Sequence analysis indicated that this organism is phylogenetically distinct from known Anaplasma species with its closest genetic near neighbors coming from Asia. The prevalence of this novel Anaplasmataceae species was as high as 21% at one site, and it was detected in 4.9% of ticks tested statewide. Based upon this genetic characterization we propose that this organism be called 'Candidatus Cryptoplasma californiense'. Knowledge of this novel microbe will provide awareness for the community about the breadth of the I. pacificus microbiome, the concept that this bacterium could be more widely spread; and an opportunity to explore whether this bacterium also contributes to human or animal disease burden.

  12. Legacies of stream channel modification revealed using General Land Office surveys, with implications for water temperature and aquatic life

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    Seth M. White

    2017-02-01

    Full Text Available Land use legacies can have a discernible influence in present-day watersheds and should be accounted for when designing conservation strategies for riverine aquatic life. We describe the environmental history of three watersheds within the Grande Ronde subbasin of the Columbia River using General Land Office survey field notes from the 19th century. In the two watersheds severely impacted by Euro-American land use, stream channel widths—a metric representing habitat simplification—increased from an average historical width of 16.8 m to an average present width of 20.8 m in large streams; 4.3 m to 5.5 m in small, confined or partly confined streams; and 3.5 m to 6.5 m in small, laterally unconfined steams. Conversely, we did not detect significant change in stream widths in an adjacent, wilderness stream with minimal human impact. Using a mechanistic water temperature model and restoration scenarios based on the historical condition, we predicted that stream restoration in the impacted watersheds could notably decrease average water temperatures—especially when channel narrowing is coupled with riparian restoration—up to a 6.6°C reduction in the upper Grande Ronde River and 3.0°C in Catherine Creek. These reductions in water temperature translated to substantial changes in the percentage of stream network habitable to salmon and steelhead migration (from 29% in the present condition to 79% in the fully restored scenario and to core juvenile rearing (from 13% in the present condition to 36% in the fully restored scenario. We conclude that land use legacies leave an important footprint on the present landscape and are critical for understanding historic habitat-forming processes as a necessary first step towards restoration.

  13. Prophylactic Platelets in Dengue: Survey Responses Highlight Lack of an Evidence Base

    Science.gov (United States)

    Whitehorn, James; Roche, Rosmari Rodriguez; Guzman, Maria G.; Martinez, Eric; Villamil Gomez, Wilmar; Nainggolan, Leonard; Laksono, Ida Safitri; Mishra, Ajay; Lum, Lucy; Faiz, Abul; Sall, Amadou; Dawurung, Joshua; Borges, Alvaro; Leo, Yee-Sin; Blumberg, Lucille; Bausch, Daniel G.; Kroeger, Axel; Horstick, Olaf; Thwaites, Guy; Wertheim, Heiman; Larsson, Mattias; Hien, Tran Tinh; Peeling, Rosanna; Wills, Bridget; Simmons, Cameron; Farrar, Jeremy

    2012-01-01

    Dengue is the most important arboviral infection of humans. Thrombocytopenia is frequently observed in the course of infection and haemorrhage may occur in severe disease. The degree of thrombocytopenia correlates with the severity of infection, and may contribute to the risk of haemorrhage. As a result of this prophylactic platelet transfusions are sometimes advocated for the prevention of haemorrhage. There is currently no evidence to support this practice, and platelet transfusions are costly and sometimes harmful. We conducted a global survey to assess the different approaches to the use of platelets in dengue. Respondents were all physicians involved with the treatment of patients with dengue. Respondents were asked that their answers reflected what they would do if they were the treating physician. We received responses from 306 physicians from 20 different countries. The heterogeneity of the responses highlights the variation in clinical practice and lack of an evidence base in this area and underscores the importance of prospective clinical trials to address this key question in the clinical management of patients with dengue. PMID:22745847

  14. Prophylactic platelets in dengue: survey responses highlight lack of an evidence base.

    Directory of Open Access Journals (Sweden)

    James Whitehorn

    Full Text Available Dengue is the most important arboviral infection of humans. Thrombocytopenia is frequently observed in the course of infection and haemorrhage may occur in severe disease. The degree of thrombocytopenia correlates with the severity of infection, and may contribute to the risk of haemorrhage. As a result of this prophylactic platelet transfusions are sometimes advocated for the prevention of haemorrhage. There is currently no evidence to support this practice, and platelet transfusions are costly and sometimes harmful. We conducted a global survey to assess the different approaches to the use of platelets in dengue. Respondents were all physicians involved with the treatment of patients with dengue. Respondents were asked that their answers reflected what they would do if they were the treating physician. We received responses from 306 physicians from 20 different countries. The heterogeneity of the responses highlights the variation in clinical practice and lack of an evidence base in this area and underscores the importance of prospective clinical trials to address this key question in the clinical management of patients with dengue.

  15. Reliability, validity and responsiveness of a Norwegian version of the Chronic Sinusitis Survey

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    Røssberg Edna

    2006-05-01

    Full Text Available Abstract Background The Chronic Sinusitis Survey (CSS is a valid, disease-specific questionnaire for assessing health status and treatment effectiveness in chronic rhinosinusitis. In the present study, we developed a Norwegian version of the CSS and assessed its psychometric properties. Methods In the pooled data set of 65 patients from a trial of treatment for chronic sinusitis with long-standing symptoms and signs of sinusitis on computed tomography (CT, we assessed the reliability, validity and responsiveness of the CSS. Results Test-retest reliability of the two CSS scales and the total scale ranged 0.87–0.92, while internal consistency reliability ranged 0.31–0.55. CSS subscale scores were associated with other items on sinusitis symptoms, and with the Mental health and Bodily pain scale of the SF-36. There was little association of the CSS scale scores with sinus CT findings. The patients with chronic sinusitis had worse scores on all three CSS scales than a healthy reference population (n = 42 (p Conclusion The Norwegian version of the CSS had acceptable test-retest reliability, but lower internal consistency reliability than the accepted standard criteria. The results support the construct validity of the measure and the sinusitis symptoms subscale and the total scales were responsive to change. This supports the use of the questionnaire in interventions for chronic sinusitis, but points at problems with the internal consistency reliability.

  16. RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response.

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    Prunotto, Andrea; Stevenson, Brian J; Berthonneche, Corinne; Schüpfer, Fanny; Beckmann, Jacques S; Maurer, Fabienne; Bergmann, Sven

    2016-09-07

    The transcriptional response to many widely used drugs and its modulation by genetic variability is poorly understood. Here we present an analysis of RNAseq profiles from heart tissue of 18 inbred mouse strains treated with the β-blocker atenolol (ATE) and the β-agonist isoproterenol (ISO). Differential expression analyses revealed a large set of genes responding to ISO (n = 1770 at FDR = 0.0001) and a comparatively small one responding to ATE (n = 23 at FDR = 0.0001). At a less stringent definition of differential expression, the transcriptional responses to these two antagonistic drugs are reciprocal for many genes, with an overall anti-correlation of r = -0.3. This trend is also observed at the level of most individual strains even though the power to detect differential expression is significantly reduced. The inversely expressed gene sets are enriched with genes annotated for heart-related functions. Modular analysis revealed gene sets that exhibit coherent transcription profiles across some strains and/or treatments. Correlations between these modules and a broad spectrum of cardiovascular traits are stronger than expected by chance. This provides evidence for the overall importance of transcriptional regulation for these organismal responses and explicits links between co-expressed genes and the traits they are associated with. Gene set enrichment analysis of differentially expressed groups of genes pointed to pathways related to heart development and functionality. Our study provides new insights into the transcriptional response of the heart to perturbations of the β-adrenergic system, implicating several new genes that had not been associated to this system previously.

  17. Integrative proteome analysis of Brachypodium distachyon roots and leaves reveals a synergetic responsive network under H2O2 stress.

    Science.gov (United States)

    Bian, Yan-Wei; Lv, Dong-Wen; Cheng, Zhi-Wei; Gu, Ai-Qin; Cao, Hui; Yan, Yue-Ming

    2015-10-14

    The plant oxidative stress response is vital for defense against various abiotic and biotic stresses. In this study, ultrastructural changes and the proteomic response to H2O2 stress in roots and leaves of the model plant Brachypodium distachyon were studied. Transmission electron microscopy (TEM) showed that the ultrastructural damage in roots was more serious than in leaves. Particularly, the ultrastructures of organelles and the nucleus in root tip cells were damaged, leading to the inhibition of normal biological activities of roots, which then spread throughout the plant. Based on two-dimensional electrophoresis (2-DE) and MALDI-TOF/TOF-MS, 84 and 53 differentially accumulated protein (DAP) spots representing 75 and 45 unique proteins responsive to H2O2 stress in roots and leaves, respectively, were identified. These protein species were mainly involved in signal transduction, energy metabolism, redox homeostasis/stress defense, protein folding/degradation, and cell wall/cell structure. Interestingly, two 14-3-3 proteins (GF14-B and GF14-D) were identified as DAPs in both roots and leaves. Protein-protein interaction (PPI) analysis revealed a synergetic H2O2-responsive network.

  18. Tomato Transcriptional Changes in Response to Clavibacter michiganensis subsp. michiganensis Reveal a Role for Ethylene in Disease Development1[W

    Science.gov (United States)

    Balaji, Vasudevan; Mayrose, Maya; Sherf, Ofra; Jacob-Hirsch, Jasmine; Eichenlaub, Rudolf; Iraki, Naim; Manulis-Sasson, Shulamit; Rechavi, Gideon; Barash, Isaac; Sessa, Guido

    2008-01-01

    Clavibacter michiganensis subsp. michiganensis (Cmm) is a gram-positive actinomycete, causing bacterial wilt and canker disease in tomato (Solanum lycopersicum). Host responses to gram-positive bacteria and molecular mechanisms associated with the development of disease symptoms caused by Cmm in tomato are largely unexplored. To investigate plant responses activated during this compatible interaction, we used microarray analysis to monitor changes in host gene expression during disease development. This analysis was performed at 4 d postinoculation, when bacteria were actively multiplying and no wilt symptoms were yet visible; and at 8 d postinoculation, when bacterial growth approached saturation and typical wilt symptoms were observed. Of the 9,254 tomato genes represented on the array, 122 were differentially expressed in Cmm-infected plants, compared with mock-inoculated plants. Functional classification of Cmm-responsive genes revealed that Cmm activated typical basal defense responses in the host, including induction of defense-related genes, production and scavenging of free oxygen radicals, enhanced protein turnover, and hormone synthesis. Cmm infection also induced a subset of host genes involved in ethylene biosynthesis and response. After inoculation with Cmm, Never ripe (Nr) mutant plants, impaired in ethylene perception, and transgenic plants with reduced ethylene synthesis showed significant delay in the appearance of wilt symptoms, compared with wild-type plants. The retarded wilting in Nr plants was a specific effect of ethylene insensitivity, and was not due to altered expression of defense-related genes, reduced bacterial populations, or decreased ethylene synthesis. Taken together, our results indicate that host-derived ethylene plays an important role in regulation of the tomato susceptible response to Cmm. PMID:18245454

  19. Tomato transcriptional changes in response to Clavibacter michiganensis subsp. michiganensis reveal a role for ethylene in disease development.

    Science.gov (United States)

    Balaji, Vasudevan; Mayrose, Maya; Sherf, Ofra; Jacob-Hirsch, Jasmine; Eichenlaub, Rudolf; Iraki, Naim; Manulis-Sasson, Shulamit; Rechavi, Gideon; Barash, Isaac; Sessa, Guido

    2008-04-01

    Clavibacter michiganensis subsp. michiganensis (Cmm) is a gram-positive actinomycete, causing bacterial wilt and canker disease in tomato (Solanum lycopersicum). Host responses to gram-positive bacteria and molecular mechanisms associated with the development of disease symptoms caused by Cmm in tomato are largely unexplored. To investigate plant responses activated during this compatible interaction, we used microarray analysis to monitor changes in host gene expression during disease development. This analysis was performed at 4 d postinoculation, when bacteria were actively multiplying and no wilt symptoms were yet visible; and at 8 d postinoculation, when bacterial growth approached saturation and typical wilt symptoms were observed. Of the 9,254 tomato genes represented on the array, 122 were differentially expressed in Cmm-infected plants, compared with mock-inoculated plants. Functional classification of Cmm-responsive genes revealed that Cmm activated typical basal defense responses in the host, including induction of defense-related genes, production and scavenging of free oxygen radicals, enhanced protein turnover, and hormone synthesis. Cmm infection also induced a subset of host genes involved in ethylene biosynthesis and response. After inoculation with Cmm, Never ripe (Nr) mutant plants, impaired in ethylene perception, and transgenic plants with reduced ethylene synthesis showed significant delay in the appearance of wilt symptoms, compared with wild-type plants. The retarded wilting in Nr plants was a specific effect of ethylene insensitivity, and was not due to altered expression of defense-related genes, reduced bacterial populations, or decreased ethylene synthesis. Taken together, our results indicate that host-derived ethylene plays an important role in regulation of the tomato susceptible response to Cmm.

  20. Do postage stamps versus pre-paid envelopes increase responses to patient mail surveys? A randomised controlled trial

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    Campbell Malcolm

    2008-05-01

    Full Text Available Abstract Background Studies largely from the market research field suggest that the inclusion of a stamped addressed envelope, rather than a pre-paid business reply, increases the response rate to mail surveys. The evidence that this is also the case regarding patient mail surveys is limited. Methods The aim of this study is to investigate whether stamped addressed envelopes increase response rates to patient mail surveys compared to pre-paid business reply envelopes and compare the relative costs. A sample of 477 initial non-responders to a mail survey of patients attending breast clinics in Greater Manchester between 1/10/2002 – 31/7/2003 were entered into the trial: 239 were randomly allocated to receive a stamped envelope and 238 to receive a pre-paid envelope in with their reminder surveys. Overall cost and per item returned were calculated. Results The response to the stamped envelope group was 31.8% (95% CI: 25.9% – 37.7% compared to 26.9% (21.3% – 32.5% for the pre-paid group. The difference (4.9% 95% CI: -3.3% – 13.1% is not significant at α = 0.05 (χ2 = 1.39; 2 tailed test, d.f. = 1; P = 0.239. The stamped envelopes were cheaper in terms of cost per returned item (£1.20 than the pre-paid envelopes (£1.67. However if the set up cost for the licence to use the pre-paid service is excluded, the cost of the stamped envelopes is more expensive than pre-paid returns (£1.20 versus £0.73. Conclusion Compared with pre-paid business replies, stamped envelopes did not produce a statistically significant increase in response rate to this patient survey. However, the response gain of the stamped strategy (4.9% is similar to that demonstrated in a Cochrane review (5.3% of strategies to increase response to general mail surveys. Further studies and meta analyses of patient responses to mail surveys via stamped versus pre-paid envelopes are needed with sufficient power to detect response gains of this magnitude in a patient population.

  1. Physiological and proteomic analyses of leaves from the halophyte Tangut Nitraria reveals diverse response pathways critical for high salinity tolerance

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    Tielong eCheng

    2015-02-01

    Full Text Available Soil salinization poses a serious threat to the environment and agricultural productivity worldwide. Studies on the physiological and molecular mechanisms of salinity tolerance in halophytic plants provide valuable information to enhance their salt tolerance. Tangut Nitraria is a widely distributed halophyte in saline–alkali soil in the northern areas of China. In this study, we used a proteomic approach to investigate the molecular pathways of the high salt tolerance of T. Nitraria. We analyzed the changes in biomass, photosynthesis, and redox-related enzyme activities in T. Nitraria leaves from plant seedlings treated with high salt concentration. Comparative proteomic analysis of the leaves revealed that the expression of 71 proteins was significantly altered after salinity treatments of T. Nitraria. These salinity-responsive proteins were mainly involved in photosynthesis, redox homeostasis, stress/defense, carbohydrate and energy metabolism, protein metabolism, signal transduction, and membrane transport. Results showed that the reduction of photosynthesis under salt stress was attributed to the down-regulation of the enzymes and proteins involved in the light reaction and Calvin cycle. Protein–protein interaction analysis revealed that the proteins involved in redox homeostasis, photosynthesis, and energy metabolism constructed two types of response networks to high salt stress. T. Nitraria plants developed diverse mechanisms for scavenging reactive oxygen species in their leaves to cope with stress induced by high salinity. This study provides important information regarding the salt tolerance of the halophyte T. Nitraria.

  2. Adult responses to a survey of soil contact-related behaviors.

    Science.gov (United States)

    Garlock, T J; Shirai, J H; Kissel, J C

    1999-01-01

    Protocols used to assess human exposure to chemicals in soils at contaminated sites often include a dermal pathway. Use of default parameters to assess dermal exposure to soil can easily lead to risk projections that appear to warrant remedial action. However, because those default parameters are typically highly uncertain, risk estimates based upon them inspire little confidence. To better characterize assumptions regarding dermal exposures, a telephone survey instrument was developed to elicit information on behaviors relevant to assessment of dermal contact with soil and dust. Participation in four activities--gardening, other yard work, outdoor team sports, and home construction or repair involving digging--was investigated. Questions were also asked regarding clothing choices and post-activity bathing practices. The survey was administered to two populations of approximately 450 adult respondents each using random digit dialing. The first was a national (U.S.) sample. The second sample was drawn from counties surrounding the Hanford Nuclear Reservation. Seventy-nine percent of the regional respondents and 89% of the national respondents reported participating in at least one of the four targeted activities. Responses of doers regarding clothing choices suggest that median fractions of skin exposed during warm-weather activities typically exceed the 25% often assumed. The Hanford sample differed from the national sample in the fraction residing in single-family homes, the fraction describing their residential surroundings as rural, and in ethnic makeup. The Hanford population displayed greater rates of participation than the national sample in three activities that have an obvious link to residence in a single-family dwelling: home repair involving digging, gardening, and other yard work, but differences were not explained entirely by residence type. The regional population also reported greater frequency of participation in multiple activities. In contrast

  3. Revealing the cold dust in low-metallicity environments. I. Photometry analysis of the Dwarf Galaxy Survey with Herschel

    Science.gov (United States)

    Rémy-Ruyer, A.; Madden, S. C.; Galliano, F.; Hony, S.; Sauvage, M.; Bendo, G. J.; Roussel, H.; Pohlen, M.; Smith, M. W. L.; Galametz, M.; Cormier, D.; Lebouteiller, V.; Wu, R.; Baes, M.; Barlow, M. J.; Boquien, M.; Boselli, A.; Ciesla, L.; De Looze, I.; Karczewski, O. Ł.; Panuzzo, P.; Spinoglio, L.; Vaccari, M.; Wilson, C. D.

    2013-09-01

    Context. We present new photometric data from our Herschel guaranteed time key programme, the Dwarf Galaxy Survey (DGS), dedicated to the observation of the gas and dust in low-metallicity environments. A total of 48 dwarf galaxies were observed with the PACS and SPIRE instruments onboard the Herschel Space Observatory at 70, 100, 160, 250, 350, and 500 μm. Aims: The goal of this paper is to provide reliable far-infrared (FIR) photometry for the DGS sample and to analyse the FIR/submillimetre (submm) behaviour of the DGS galaxies. We focus on a systematic comparison of the derived FIR properties (FIR luminosity, LFIR, dust mass, Mdust, dust temperature, T, emissivity index, β) with more metal-rich galaxies and investigate the detection of a potential submm excess. Methods: The data reduction method is adapted for each galaxy in order to derive the most reliable photometry from the final maps. The derived PACS flux densities are compared with the Spitzer MIPS 70 and 160 μm bands. We use colour-colour diagrams to analyse the FIR/submm behaviour of the DGS galaxies and modified blackbody fitting procedures to determine their dust properties. To study the variation in these dust properties with metallicity, we also include galaxies from the Herschel KINGFISH sample, which contains more metal-rich environments, totalling 109 galaxies. Results: The location of the DGS galaxies on Herschel colour-colour diagrams highlights the differences in dust grain properties and/or global environments of low-metallicity dwarf galaxies. The dust in DGS galaxies is generally warmer than in KINGFISH galaxies (TDGS ~ 32 K and TKINGFISH ~ 23 K). The emissivity index, β, is ~1.7 in the DGS, however metallicity does not make a strong effect on β. The proportion of dust mass relative to stellar mass is lower in low-metallicity galaxies: Mdust/Mstar ~ 0.02% for the DGS versus 0.1% for KINGFISH. However, per unit dust mass, dwarf galaxies emit about six times more in the FIR/submm than

  4. Hydrophysical and hydrochemical features of Lake Issyk-Kul (Kyrgyzstan) as revealed by field survey of June, 2015

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    Zavialov, Peter; Makkaveev, Petr; Rimskiy-Korsakov, Nikolay; Alymkulov, Salmor; Izhitskiy, Alexander

    2016-04-01

    Lake Issyk-Kul is a major (volume 1700 km3, depth 668 m) terminal lake in Kyrgyzstan, Central Asia. The lake has a longstanding history of research and recently attracted international attention, in particular, as a potentially promising site for scientific drilling and reconstructing paleo-climate variability (e.g., Oberhansli and Molnar, 2012). However, the in situ hydrophysical and hydrochemical data collected from Issyk-Kul are still limited, and those available are somewhat outdated, given that the most recent field campaign reported in the literature dates back to about 15 years ago. A new field survey was conducted in June, 2015. The measurements included CTD profiling and water sampling at 19 stations in all parts of the lake, as well as continuous measurements by a pump-through system and an ultraviolet lidar along the ship's track. The water samples were analyzed for a variety of hydrochemical indicators, including nutrients, dissolved oxygen and methane. In addition, velocity meters were deployed at 3 mooring stations to investigate the synoptic variability of currents. The nitrates, nitrites, phosphorus and silica exhibited elevated surface concentrations in the central part of the lake, which is likely to be associated with the upwelling induced by the basin-wide cyclonic circulation gyre evident from the current measurements. At the same time, the coastal waters were characterized by very low content of nutrients, except the southeastern part of the lake exposed to significant continental discharges from the Tyup and the Dzhergalan rivers. In the areas of continental water influence, concentration of dissolved silica attained minimum values in the surface and intermediate layers. On the other hand, silica concentrations grew steadily from the depth of about 100 m down to the bottom. In general, concentrations of principal biogenic elements in the euphotic layer were relatively low - albeit not low enough to be a limiting factor for phytoplankton life

  5. Understanding barriers to medication adherence in the hypertensive population by evaluating responses to a telephone survey

    Directory of Open Access Journals (Sweden)

    Nair KV

    2011-04-01

    Full Text Available Kavita V Nair1, Daniel A Belletti3, Joseph J Doyle3, Richard R Allen4, Robert B McQueen1, Joseph J Saseen1, Joseph Vande Griend1, Jay V Patel5, Angela McQueen2, Saira Jan21School of Pharmacy, University of Colorado, Aurora, CO, USA; 2Horizon Blue Cross Blue Shield of New Jersey, Newark, NJ, USA; 3Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA, 4Peakstat Statistical Services, Evergreen, CO, USA; 5Care Management International, Marlborough, MA, USABackground: Although hypertension is a major risk factor for cardiovascular disease, adherence to hypertensive medications is low. Previous research identifying factors influencing adherence has focused primarily on broad, population-based approaches. Identifying specific barriers for an individual is more useful in designing meaningful targeted interventions. Using customized telephonic outreach, we examined specific patient-reported barriers influencing hypertensive patients' nonadherence to medication in order to identify targeted interventions.Methods: A telephone survey of 8692 nonadherent hypertensive patients was conducted. The patient sample comprised health plan members with at least two prescriptions for antihypertensive medications in 2008. The telephone script was based on the "target" drug associated with greatest nonadherence (medication possession ratio [MPR] <80% during the four-month period preceding the survey.Results: The response rate was 28.2% of the total sample, representing 63.8% of commercial members and 37.2% of Medicare members. Mean age was 63.4 years. Mean MPR was 61.0% for the target drug. Only 58.2% of Medicare respondents and 60.4% of commercial respondents reported "missing a dose of medication". The primary reason given was "forgetfulness" (61.8% Medicare, 60.8% commercial, followed by "being too busy" (2.7% Medicare, 18.5% commercial and "other reasons" (21.9% Medicare, 8.1% commercial including travel, hospitalization/sickness, disruption of daily events

  6. Transcriptome-wide survey of mouse CNS-derived cells reveals monoallelic expression within novel gene families.

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    Sierra M Li

    Full Text Available Monoallelic expression is an integral component of regulation of a number of essential genes and gene families. To probe for allele-specific expression in cells of CNS origin, we used next-generation sequencing (RNA-seq to analyze four clonal neural stem cell (NSC lines derived from Mus musculus C57BL/6 (B6×Mus musculus molossinus (JF1 adult female mice. We established a JF1 cSNP library, then ascertained transcriptome-wide expression from B6 vs. JF1 alleles in the NSC lines. Validating the assay, we found that 262 of 268 X-linked genes evaluable in at least one cell line showed monoallelic expression (at least 85% expression of the predominant allele, p-value<0.05. For autosomal genes 170 of 7,198 genes (2.4% of the total showed monoallelic expression in at least 2 evaluable cell lines. The group included eight known imprinted genes with the expected pattern of allele-specific expression. Among the other autosomal genes with monoallelic expression were five members of the glutathione transferase gene superfamily, which processes xenobiotic compounds as well as carcinogens and cancer therapeutic agents. Monoallelic expression within this superfamily thus may play a functional role in the response to diverse and potentially lethal exogenous factors, as is the case for the immunoglobulin and olfactory receptor superfamilies. Other genes and gene families showing monoallelic expression include the annexin gene family and the Thy1 gene, both linked to inflammation and cancer, as well as genes linked to alcohol dependence (Gabrg1 and epilepsy (Kcnma1. The annotated set of genes will provide a resource for investigation of mechanisms underlying certain cases of these and other major disorders.

  7. The Success of a Planned Bereavement Response--A Survey on Teacher Use of Bereavement Response Plans When Supporting Grieving Children in Danish Schools

    Science.gov (United States)

    Lytje, Martin

    2017-01-01

    This article investigates the strengths and weaknesses of the Danish Bereavement response plans. These are used by teachers to support grieving students and have been implemented in 96% of all Danish schools. The study is based on an Internet survey conducted with 967 teachers. Issues investigated are: "generalisation of grief",…

  8. Physiological Stress Responses in Amphibian Larvae to Multiple Stressors Reveal Marked Anthropogenic Effects even below Lethal Levels.

    Science.gov (United States)

    Burraco, Pablo; Gomez-Mestre, Ivan

    Natural and anthropogenic disturbances cause profound alterations in organisms, inducing physiological adjustments to avoid, reduce, or remedy the impact of disturbances. In vertebrates, the stress response is regulated via neuroendocrine pathways, including the hypothalamic-pituitary-interrenal axis that regulates the secretion of glucocorticoids. Glucocorticoids have cascading effects on multiple physiological pathways, affecting the metabolic rate, reactive oxygen species production, or immune system. Determining the extent to which natural and anthropogenic environmental factors induce stress responses in vertebrates is of great importance in ecology and conservation biology. Here we study the physiological stress response in spadefoot toad tadpoles (Pelobates cultripes) against three levels of a series of natural and anthropogenic stressors common to many aquatic systems: salinity (0, 6, and 9 ppt), herbicide (0, 1, and 2 mg/L acid equivalent of glyphosate), water acidity (pH 4.5, 7.0, and 9.5), predators (absent, native, and invasive), and temperature (21°, 25°, and 29°C). The physiological stress response was assessed examining corticosterone levels, standard metabolic rate, activity of antioxidant enzymes, oxidative cellular damage in lipids, and immunological status. We found that common stressors substantially altered the physiological state of tadpoles. In particular, salinity and herbicides cause dramatic physiological changes in tadpoles. Moreover, tadpoles reduced corticosterone levels in the presence of natural predators but did not do so against invasive predators, indicating a lack of innate recognition. Corticosterone and the antioxidant enzyme glutathione reductase were the most sensitive parameters to stress in this study. Anthropogenic perturbations of aquatic systems pose serious threats to larval amphibians even at nonlethal concentrations, judging from the marked physiological stress responses generated, and reveal the importance of

  9. Systems biology of tissue-specific response to Anaplasma phagocytophilum reveals differentiated apoptosis in the tick vector Ixodes scapularis.

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    Nieves Ayllón

    2015-03-01

    Full Text Available Anaplasma phagocytophilum is an emerging pathogen that causes human granulocytic anaplasmosis. Infection with this zoonotic pathogen affects cell function in both vertebrate host and the tick vector, Ixodes scapularis. Global tissue-specific response and apoptosis signaling pathways were characterized in I. scapularis nymphs and adult female midguts and salivary glands infected with A. phagocytophilum using a systems biology approach combining transcriptomics and proteomics. Apoptosis was selected for pathway-focused analysis due to its role in bacterial infection of tick cells. The results showed tissue-specific differences in tick response to infection and revealed differentiated regulation of apoptosis pathways. The impact of bacterial infection was more pronounced in tick nymphs and midguts than in salivary glands, probably reflecting bacterial developmental cycle. All apoptosis pathways described in other organisms were identified in I. scapularis, except for the absence of the Perforin ortholog. Functional characterization using RNA interference showed that Porin knockdown significantly increases tick colonization by A. phagocytophilum. Infection with A. phagocytophilum produced complex tissue-specific alterations in transcript and protein levels. In tick nymphs, the results suggested a possible effect of bacterial infection on the inhibition of tick immune response. In tick midguts, the results suggested that A. phagocytophilum infection inhibited cell apoptosis to facilitate and establish infection through up-regulation of the JAK/STAT pathway. Bacterial infection inhibited the intrinsic apoptosis pathway in tick salivary glands by down-regulating Porin expression that resulted in the inhibition of Cytochrome c release as the anti-apoptotic mechanism to facilitate bacterial infection. However, tick salivary glands may promote apoptosis to limit bacterial infection through induction of the extrinsic apoptosis pathway. These dynamic

  10. Transcriptomes of Eight Arabidopsis thaliana Accessions Reveal Core Conserved, Genotype- and Organ-Specific Responses to Flooding Stress1[OPEN

    Science.gov (United States)

    van Veen, Hans; Vashisht, Divya; Akman, Melis; Girke, Thomas; Mustroph, Angelika; Reinen, Emilie; Kooiker, Maarten; van Tienderen, Peter; Voesenek, Laurentius A.C.J.

    2016-01-01

    Climate change has increased the frequency and severity of flooding events, with significant negative impact on agricultural productivity. These events often submerge plant aerial organs and roots, limiting growth and survival due to a severe reduction in light reactions and gas exchange necessary for photosynthesis and respiration, respectively. To distinguish molecular responses to the compound stress imposed by submergence, we investigated transcriptomic adjustments to darkness in air and under submerged conditions using eight Arabidopsis (Arabidopsis thaliana) accessions differing significantly in sensitivity to submergence. Evaluation of root and rosette transcriptomes revealed an early transcriptional and posttranscriptional response signature that was conserved primarily across genotypes, although flooding susceptibility-associated and genotype-specific responses also were uncovered. Posttranscriptional regulation encompassed darkness- and submergence-induced alternative splicing of transcripts from pathways involved in the alternative mobilization of energy reserves. The organ-specific transcriptome adjustments reflected the distinct physiological status of roots and shoots. Root-specific transcriptome changes included marked up-regulation of chloroplast-encoded photosynthesis and redox-related genes, whereas those of the rosette were related to the regulation of development and growth processes. We identified a novel set of tolerance genes, recognized mainly by quantitative differences. These included a transcriptome signature of more pronounced gluconeogenesis in tolerant accessions, a response that included stress-induced alternative splicing. This study provides organ-specific molecular resolution of genetic variation in submergence responses involving interactions between darkness and low-oxygen constraints of flooding stress and demonstrates that early transcriptome plasticity, including alternative splicing, is associated with the ability to cope

  11. Arabidopsis thaliana natural variation reveals connections between UV radiation stress and plant pathogen-like defense responses.

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    Piofczyk, Thomas; Jeena, Ganga; Pecinka, Ales

    2015-08-01

    UV radiation is a ubiquitous component of solar radiation that affects plant growth and development. Here we studied growth related traits of 345 Arabidopsis thaliana accessions in response to UV radiation stress. We analyzed the genetic basis of this natural variation by genome-wide association studies, which suggested a specific candidate genomic region. RNA-sequencing of three sensitive and three resistant accessions combined with mutant analysis revealed five large effect genes. Mutations in PHE ammonia lyase 1 (PAL1) and putative kinase At1g76360 rendered Arabidopsis hypersensitive to UV stress, while loss of function from putative methyltransferase At4g22530, novel plant snare 12 (NPSN12) and defense gene activated disease resistance 2 (ADR2) conferred higher UV stress resistance. Three sensitive accessions showed strong ADR2 transcriptional activation, accumulation of salicylic acid (SA) and dwarf growth upon UV stress, while these phenotypes were much less affected in resistant plants. The phenotype of sensitive accessions resembles autoimmune reactions due to overexpression of defense related genes, and suggests that natural variation in response to UV radiation stress is driven by pathogen-like responses in Arabidopsis.

  12. Inducible ablation of melanopsin-expressing retinal ganglion cells reveals their central role in non-image forming visual responses.

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    Megumi Hatori

    Full Text Available Rod/cone photoreceptors of the outer retina and the melanopsin-expressing retinal ganglion cells (mRGCs of the inner retina mediate non-image forming visual responses including entrainment of the circadian clock to the ambient light, the pupillary light reflex (PLR, and light modulation of activity. Targeted deletion of the melanopsin gene attenuates these adaptive responses with no apparent change in the development and morphology of the mRGCs. Comprehensive identification of mRGCs and knowledge of their specific roles in image-forming and non-image forming photoresponses are currently lacking. We used a Cre-dependent GFP expression strategy in mice to genetically label the mRGCs. This revealed that only a subset of mRGCs express enough immunocytochemically detectable levels of melanopsin. We also used a Cre-inducible diphtheria toxin receptor (iDTR expression approach to express the DTR in mRGCs. mRGCs develop normally, but can be acutely ablated upon diphtheria toxin administration. The mRGC-ablated mice exhibited normal outer retinal function. However, they completely lacked non-image forming visual responses such as circadian photoentrainment, light modulation of activity, and PLR. These results point to the mRGCs as the site of functional integration of the rod/cone and melanopsin phototransduction pathways and as the primary anatomical site for the divergence of image-forming and non-image forming photoresponses in mammals.

  13. Global Gene Expression Analysis Reveals Crosstalk between Response Mechanisms to Cold and Drought Stresses in Cassava Seedlings.

    Science.gov (United States)

    Li, Shuxia; Yu, Xiang; Cheng, Zhihao; Yu, Xiaoling; Ruan, Mengbin; Li, Wenbin; Peng, Ming

    2017-01-01

    Abiotic stress negatively impacts cassava (Manihot esculenta) growth and yield. Several molecular mechanisms of plant response to cold and drought have been identified and described in the literature, however, little is known about the crosstalk of the responses of cassava to these two stresses. To elucidate this question, transcriptome analysis of cassava seedlings under cold or PEG-simulated drought stress treatment was performed. Our results showed that 6103 and 7462 transcripts were significantly regulated by cold and drought stress, respectively. Gene Ontology annotation revealed that the abscisic and jasmonic acid signaling pathways shared between the two stresses responses. We further identified 2434 common differentially expressed genes (DEGs), including 1130 up-regulated and 841 down-regulated DEGs by the two stresses. These co-induced or co-suppressed genes are grouped as stress signal perception and transduction, transcription factors (TFs), metabolism as well as transport facilitation according to the function annotation. Furthermore, a large proportion of well characterized protein kinases, TF families and ubiquitin proteasome system related genes, such as RLKs, MAPKs, AP2/ERFBPs, WRKYs, MYBs, E2 enzymes and E3 ligases, including three complexes of interacting proteins were shown as key points of crosstalk between cold and drought stress signaling transduction pathways in a hierarchical manner. Our research provides valuable information and new insights for genetically improving the tolerance of crops to multiple abiotic stresses.

  14. Global Gene Expression Analysis Reveals Crosstalk between Response Mechanisms to Cold and Drought Stresses in Cassava Seedlings

    Directory of Open Access Journals (Sweden)

    Shuxia Li

    2017-07-01

    Full Text Available Abiotic stress negatively impacts cassava (Manihot esculenta growth and yield. Several molecular mechanisms of plant response to cold and drought have been identified and described in the literature, however, little is known about the crosstalk of the responses of cassava to these two stresses. To elucidate this question, transcriptome analysis of cassava seedlings under cold or PEG-simulated drought stress treatment was performed. Our results showed that 6103 and 7462 transcripts were significantly regulated by cold and drought stress, respectively. Gene Ontology annotation revealed that the abscisic and jasmonic acid signaling pathways shared between the two stresses responses. We further identified 2434 common differentially expressed genes (DEGs, including 1130 up-regulated and 841 down-regulated DEGs by the two stresses. These co-induced or co-suppressed genes are grouped as stress signal perception and transduction, transcription factors (TFs, metabolism as well as transport facilitation according to the function annotation. Furthermore, a large proportion of well characterized protein kinases, TF families and ubiquitin proteasome system related genes, such as RLKs, MAPKs, AP2/ERFBPs, WRKYs, MYBs, E2 enzymes and E3 ligases, including three complexes of interacting proteins were shown as key points of crosstalk between cold and drought stress signaling transduction pathways in a hierarchical manner. Our research provides valuable information and new insights for genetically improving the tolerance of crops to multiple abiotic stresses.

  15. 520-d Isolation and confinement simulating a flight to Mars reveals heightened immune responses and alterations of leukocyte phenotype.

    Science.gov (United States)

    Yi, B; Rykova, M; Feuerecker, M; Jäger, B; Ladinig, C; Basner, M; Hörl, M; Matzel, S; Kaufmann, I; Strewe, C; Nichiporuk, I; Vassilieva, G; Rinas, K; Baatout, S; Schelling, G; Thiel, M; Dinges, D F; Morukov, B; Choukèr, A

    2014-08-01

    During interplanetary exploration, chronic stress caused by long term isolation and confinement in the spacecraft is one of the major concerns of physical and psychological health of space travelers. And for human on Earth, more and more people live in an isolated condition, which has become a common social problem in modern western society. Collective evidences have indicated prolonged chronic stress could bring big influence to human immune function, which may lead to a variety of health problems. However, to what extent long-term isolation can affect the immune system still remains largely unknow. A simulated 520-d Mars mission provided an extraordinary chance to study the effect of prolonged isolation. Six healthy males participated in this mission and their active neuroendocrine and immune conditions were studied with saliva and blood samples from all participants on chosen time points during the isolation period. As a typical neuroendocrine parameter, stress hormone cortisol was measured in the morning saliva samples. Immune phenotype changes were monitored through peripheral leukocyte phenotype analysis. Using an ex vivo viral infection simulation assay we assessed the immune response changes characterized by the ability to produce representative endogenous pro-inflammatory cytokines. The results of this study revealed elevated cortisol levels, increased lymphocyte amount and heightened immune responses, suggesting that prolonged isolation acting as chronic stressors are able to trigger leukocyte phenotype changes and poorly controlled immune responses.

  16. Microarray analysis of macrophage response to infection with Streptococcus oralis reveals the immunosuppressive effect of hydrogen peroxide.

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    Matsushima, Hitomi; Kumagai, Yutaro; Vandenbon, Alexis; Kataoka, Hideo; Kadena, Miki; Fukamachi, Haruka; Arimoto, Takafumi; Morisaki, Hirobumi; Fujiwara, Nagatoshi; Okahashi, Nobuo; Kuwata, Hirotaka

    2017-02-13

    Oral streptococci including mitis group streptococci are commensal residents and are also the first to colonize the oral cavity. However, various species of these oral streptococci have the potential to invade the host and occasionally lead to severe infectious disease such as cardiovascular diseases. Oral streptococci have close interactions with the host immune system including macrophages at the oral mucosal surface. One notable common trait of oral streptococcus including Streptococcus oralis (S. oralis) is the production of hydrogen peroxide (H2O2). Using a comprehensive microarray approach, we sought to understand the innate immune response profiling affected by H2O2 production from oral streptococci. We compared the gene expression patterns of macrophages infected with S. oralis wild type (WT) and streptococcal pyruvate oxidase knockout (SpxB-KO), a strain that does not produce H2O2. We found that H2O2 from S. oralis suppressed proinflammatory gene expression such as TNF-α, that is induced in response to infection, and activated the cellular stress genes such as Egr-1 in response to oxidative stress. A comparative gene ontology analysis of S. oralis WT and SpxB-KO strains revealed that during infection, down regulated genes were closely related to the processes involved in the host defense reaction and up regulated genes were related with the cellular stress responses. Using qPCR analysis, we also confirmed the same pattern of expression changes such as TNF-α, IL-6 and Egr-1. Furthermore, supernatant from SpxB-KO could not suppress the expression of TNF-α in macrophages stimulated with LPS. These findings suggested that H2O2 production from S. oralis leads to the suppression of inflammatory responses and NF-κB signaling pathways in macrophages as well as the induction of the oxidative stress response. We concluded that streptococcal H2O2 production has the beneficial effects of modulating the innate immune response, thereby stabilizing streptococcal

  17. Implementing medical revalidation in the United Kingdom: Findings about organisational changes and impacts from a survey of Responsible Officers

    Science.gov (United States)

    Boyd, Alan; Bryce, Marie; Luscombe, Kayleigh; Tazzyman, Abigail; Tredinnick-Rowe, John; Archer, Julian

    2017-01-01

    Objective To describe the implementation of medical revalidation in healthcare organisations in the United Kingdom and to examine reported changes and impacts on the quality of care. Design A cross-sectional online survey gathering both quantitative and qualitative data about structures and processes for medical revalidation and wider quality management in the organisations which employ or contract with doctors (termed ‘designated bodies’) from the senior doctor in each organisation with statutory responsibility for medical revalidation (termed the ‘Responsible Officer’). Setting United Kingdom Participants Responsible Officers in designated bodies in the United Kingdom. Five hundred and ninety-five survey invitations were sent and 374 completed surveys were returned (63%). Main outcome measures The role of Responsible Officers, the development of organisational mechanisms for quality assurance or improvement, decision-making on revalidation recommendations, impact of revalidation and mechanisms for quality assurance or improvement on clinical practice and suggested improvements to revalidation arrangements. Results Responsible Officers report that revalidation has had some impacts on the way medical performance is assured and improved, particularly strengthening appraisal and oversight of quality within organisations and having some impact on clinical practice. They suggest changes to make revalidation less ‘one size fits all’ and more responsive to individual, organisational and professional contexts. Conclusions Revalidation appears primarily to have improved systems for quality improvement and the management of poor performance to date. There is more to be done to ensure it produces wider benefits, particularly in relation to doctors who already perform well. PMID:28084166

  18. The Rapid Response Radiation Survey (R3S) Mission Using the HISat Conformal Satellite Architecture

    Science.gov (United States)

    Miller, Nathanael

    2015-01-01

    The Rapid Response Radiation Survey (R3S) experiment, designed as a quick turnaround mission to make radiation measurements in LEO, will fly as a hosted payload in partnership with NovaWurks using their Hyper-integrated Satlet (HiSat) architecture. The need for the mission arises as the Nowcast of Atmospheric Ionization Radiation for Aviation Safety (NAIRAS) model moves from a research effort into an operational radiation assessment tool. The data collected by R3S, in addition to the complementary data from a NASA Langley Research Center (LaRC) atmospheric balloon mission entitled Radiation Dosimetry Experiment (RaDX), will validate exposure prediction capabilities of NAIRAS. This paper discusses the development of the R3S experiment as made possible by use of the HiSat architecture. The system design and operational modes of the experiment are described, as well as the experiment interfaces to the HiSat satellite via the user defined adapter (UDA) provided by NovaWurks. This paper outlines the steps taken by the project to execute the R3S mission in the 4 months of design, build, and test. Finally, description of the engineering process is provided, including the use of facilitated rapid/concurrent engineering sessions, the associated documentation, and the review process employed.

  19. Developing Culturally Responsive Surveys: Lessons in Development, Implementation, and Analysis from Brazil's African Descent Communities

    Science.gov (United States)

    Bowen, Merle L.; Tillman, Ayesha S.

    2015-01-01

    Considerable empirical research, along with a growing body of conceptual and theoretical literature, exists on the role of culture and context in evaluation. Less scholarship has examined culturally responsive surveys in the context of international evaluation. In this article, the authors present lessons learned from the development,…

  20. Comparison of response patterns in different survey designs: a longitudinal panel with mixed-mode and online-only design.

    Science.gov (United States)

    Rübsamen, Nicole; Akmatov, Manas K; Castell, Stefanie; Karch, André; Mikolajczyk, Rafael T

    2017-01-01

    Increasing availability of the Internet allows using only online data collection for more epidemiological studies. We compare response patterns in a population-based health survey using two survey designs: mixed-mode (choice between paper-and-pencil and online questionnaires) and online-only design (without choice). We used data from a longitudinal panel, the Hygiene and Behaviour Infectious Diseases Study (HaBIDS), conducted in 2014/2015 in four regions in Lower Saxony, Germany. Individuals were recruited using address-based probability sampling. In two regions, individuals could choose between paper-and-pencil and online questionnaires. In the other two regions, individuals were offered online-only participation. We compared sociodemographic characteristics of respondents who filled in all panel questionnaires between the mixed-mode group (n = 1110) and the online-only group (n = 482). Using 134 items, we performed multinomial logistic regression to compare responses between survey designs in terms of type (missing, "do not know" or valid response) and ordinal regression to compare responses in terms of content. We applied the false discovery rates (FDR) to control for multiple testing and investigated effects of adjusting for sociodemographic characteristic. For validation of the differential response patterns between mixed-mode and online-only, we compared the response patterns between paper and online mode among the respondents in the mixed-mode group in one region (n = 786). Respondents in the online-only group were older than those in the mixed-mode group, but both groups did not differ regarding sex or education. Type of response did not differ between the online-only and the mixed-mode group. Survey design was associated with different content of response in 18 of the 134 investigated items; which decreased to 11 after adjusting for sociodemographic variables. In the validation within the mixed-mode, only two of those were among the 11 significantly

  1. Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium

    Directory of Open Access Journals (Sweden)

    Bhattacharyya-Pakrasi Maitrayee

    2010-08-01

    Full Text Available Abstract Background Cyanobacteria are the only known prokaryotes capable of oxygenic photosynthesis. They play significant roles in global biogeochemical cycles and carbon sequestration, and have recently been recognized as potential vehicles for production of renewable biofuels. Synechocystis sp. PCC 6803 has been extensively used as a model organism for cyanobacterial studies. DNA microarray studies in Synechocystis have shown varying degrees of transcriptome reprogramming under altered environmental conditions. However, it is not clear from published work how transcriptome reprogramming affects pre-existing networks of fine-tuned cellular processes. Results We have integrated 163 transcriptome data sets generated in response to numerous environmental and genetic perturbations in Synechocystis. Our analyses show that a large number of genes, defined as the core transcriptional response (CTR, are commonly regulated under most perturbations. The CTR contains nearly 12% of Synechocystis genes found on its chromosome. The majority of genes in the CTR are involved in photosynthesis, translation, energy metabolism and stress protection. Our results indicate that a large number of differentially regulated genes identified in most reported studies in Synechocystis under different perturbations are associated with the general stress response. We also find that a majority of genes in the CTR are coregulated with 25 regulatory genes. Some of these regulatory genes have been implicated in cellular responses to oxidative stress, suggesting that reactive oxygen species are involved in the regulation of the CTR. A Bayesian network, based on the regulation of various KEGG pathways determined from the expression patterns of their associated genes, has revealed new insights into the coordination between different cellular processes. Conclusion We provide here the first integrative analysis of transcriptome data sets generated in a cyanobacterium. This

  2. Secretome analysis revealed adaptive and non-adaptive responses of the Staphylococcus carnosus femB mutant.

    Science.gov (United States)

    Nega, Mulugeta; Dube, Linda; Kull, Melanie; Ziebandt, Anne-Kathrin; Ebner, Patrick; Albrecht, Dirk; Krismer, Bernhard; Rosenstein, Ralf; Hecker, Michael; Götz, Friedrich

    2015-04-01

    FemABX peptidyl transferases are involved in non-ribosomal pentaglycine interpeptide bridge biosynthesis. Here, we characterized the phenotype of a Staphylococcus carnosus femB deletion mutant, which was affected in growth and showed pleiotropic effects such as enhanced methicillin sensitivity, lysostaphin resistance, cell clustering, and decreased peptidoglycan cross-linking. However, comparative secretome analysis revealed a most striking difference in the massive secretion or release of proteins into the culture supernatant in the femB mutant than the wild type. The secreted proteins can be categorized into typical cytosolic proteins and various murein hydrolases. As the transcription of the murein hydrolase genes was up-regulated in the mutant, they most likely represent an adaption response to the life threatening mutation. Even though the transcription of the cytosolic protein genes was unaltered, their high abundance in the supernatant of the mutant is most likely due to membrane leakage triggered by the weakened murein sacculus and enhanced autolysins.

  3. Transcriptional profiling reveals the expression of novel genes in response to various stimuli in the human dermatophyte Trichophyton rubrum

    Directory of Open Access Journals (Sweden)

    Aquino-Ferreira Roseli

    2010-02-01

    Full Text Available Abstract Background Cutaneous mycoses are common human infections among healthy and immunocompromised hosts, and the anthropophilic fungus Trichophyton rubrum is the most prevalent microorganism isolated from such clinical cases worldwide. The aim of this study was to determine the transcriptional profile of T. rubrum exposed to various stimuli in order to obtain insights into the responses of this pathogen to different environmental challenges. Therefore, we generated an expressed sequence tag (EST collection by constructing one cDNA library and nine suppression subtractive hybridization libraries. Results The 1388 unigenes identified in this study were functionally classified based on the Munich Information Center for Protein Sequences (MIPS categories. The identified proteins were involved in transcriptional regulation, cellular defense and stress, protein degradation, signaling, transport, and secretion, among other functions. Analysis of these unigenes revealed 575 T. rubrum sequences that had not been previously deposited in public databases. Conclusion In this study, we identified novel T. rubrum genes that will be useful for ORF prediction in genome sequencing and facilitating functional genome analysis. Annotation of these expressed genes revealed metabolic adaptations of T. rubrum to carbon sources, ambient pH shifts, and various antifungal drugs used in medical practice. Furthermore, challenging T. rubrum with cytotoxic drugs and ambient pH shifts extended our understanding of the molecular events possibly involved in the infectious process and resistance to antifungal drugs.

  4. SWATH-MS Quantitative Proteomic Investigation Reveals a Role of Jasmonic Acid during Lead Response in Arabidopsis.

    Science.gov (United States)

    Zhu, Fu-Yuan; Chan, Wai-Lung; Chen, Mo-Xian; Kong, Ricky P W; Cai, Congxi; Wang, Qiaomei; Zhang, Jian-Hua; Lo, Clive

    2016-10-07

    Lead (Pb) pollution is a growing environment problem that continuously threatens the productivity of crops. To understand the molecular mechanisms of plant adaptation to Pb toxicity, we examined proteome changes in Arabidopsis seedlings following Pb treatment by SWATH-MS, a label-free quantitative proteomic platform. We identified and quantified the expression of 1719 proteins in water- and Pb-treated plants. Among them, 231 proteins showed significant abundance changes (151 elevated and 80 reduced) upon Pb exposure. Functional categorization revealed that most of the Pb-responsive proteins are involved in different metabolic processes. For example, down-regulation of photosynthesis and biosynthesis of isoprenoids and tetrapyrroles in chloroplasts were observed. On the contrary, pathways leading to glutathione, jasmonic acid (JA), glucosinolate (GSL), and phenylpropanoid production are up-regulated. Experimental characterizations demonstrated a rapid elevation of endogenic JA production in Pb-treated Arabidopsis seedlings, while a JA-deficient mutant and a JA-insensitive mutant showed hypersensitivity to root inhibition by Pb, implicating an essential role of JA during Pb responses. Consistently, methyl jasmonate supplementation alleviated Pb toxicity in the wild-type and JA-deficient mutant. Furthermore, GSL levels were substantially enhanced following Pb treatment, while such induction was not detected in the JA mutant, suggesting that the Pb-induced GSL accumulation is JA-dependent. Overall, our work represents the first SWATH-MS analysis in Arabidopsis and highlights a potential mediating role of JA during Pb stress.

  5. Chemosensory processing in the fruit fly, Drosophila melanogaster: Generalization of a feeding response reveals overlapping odour representations

    Indian Academy of Sciences (India)

    Sathees B C Chandra; Sandeep Singh

    2005-12-01

    Insects are capable of detecting, and discriminating between, a very large number of odours. The biological relevance of many of those odours, particularly those related to food, must first be learned. Given that the number of sensory receptors and antennal lobe (AL) glomeruli is limited relative to the number of odours that must be detectable, this ability implies that the olfactory system makes use of a combinatorial coding scheme whereby each sensory cell or AL projection neuron can participate in coding for several different odours. An important step in understanding this coding scheme is to behaviourally quantify the degree to which sets of odours are discriminable. Here we evaluate odour discriminability in the fruit fly, Drosophila melanogaster, by first conditioning individual flies to not respond to any of several odourants using a nonassociative conditioning protocol (habituation). We show that flies habituate unconditioned leg movement responses to both mechanosensory and olfactory stimulation over 25 unreinforceed trials. Habituation is retained for at least 2 h and is subject to dishabituation. Finally, we test the degree to which the conditioned response generalizes to other odourants based on molecular features of the odourants (e.g. carbon chain length and the presence of a target functional group). These tests reveal predictable generalization gradients across these molecular features. These data substantiate the claim that these features are relevant coding dimensions in the fruit fly olfactory system, as has been shown for other insect and vertebrate species.

  6. Long-term heat stress induces the inflammatory response in dairy cows revealed by plasma proteome analysis.

    Science.gov (United States)

    Min, Li; Zheng, Nan; Zhao, Shengguo; Cheng, Jianbo; Yang, Yongxin; Zhang, Yangdong; Yang, Hongjian; Wang, Jiaqi

    2016-03-04

    In this work we employed a comparative proteomic approach to evaluate seasonal heat stress and investigate proteomic alterations in plasma of dairy cows. Twelve lactating Holstein dairy cows were used and the treatments were: heat stress (n = 6) in hot summer (at the beginning of the moderate heat stress) and no heat stress (n = 6) in spring natural ambient environment, respectively. Subsequently, heat stress treatment lasted 23 days (at the end of the moderate heat stress) to investigate the alterations of plasma proteins, which might be employed as long-term moderate heat stress response in dairy cows. Changes in plasma proteins were analyzed by two-dimensional electrophoresis (2-DE) combined with mass spectrometry. Analysis of the properties of the identified proteins revealed that the alterations of plasma proteins were related to inflammation in long-term moderate heat stress. Furthermore, the increase in plasma tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) directly demonstrated that long-term moderate heat stress caused an inflammatory response in dairy cows.

  7. Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site

    Energy Technology Data Exchange (ETDEWEB)

    Chourey, Karuna [ORNL; Nissen, Silke [ORNL; Vishnivetskaya, T. [University of Tennessee, Knoxville (UTK); Shah, Manesh B [ORNL; Pffifner, Susan [University of Tennessee, Knoxville (UTK); Hettich, Robert {Bob} L [ORNL; Loeffler, Frank E [ORNL

    2013-01-01

    High performance mass spectrometry instrumentation coupled with improved protein extraction techniques enable metaproteomics to identify active members of soil and groundwater microbial communities. Metaproteomics workflows were applied to study the initial responses (i.e., 4 days post treatment) of the indigenous aquifer microbiota to biostimulation with emulsified vegetable oil (EVO) at a uranium-contaminated site. Members of the Betaproteobacteria (i.e., Dechloromonas, Ralstonia, Rhodoferax, Polaromonas, Delftia, Chromobacterium) and Firmicutes dominated the biostimulated aquifer community. Proteome characterization revealed distinct differences in protein expression between the microbial biomass collected from groundwater influenced by biostimulation and groundwater collected up-gradient of the EVO injection points. In particular, proteins involved in ammonium assimilation, EVO degradation, and polyhydroxybutyrate (PHB) granule formation were prominent following biostimulation. Interestingly, the atypical NosZ of a Dechloromonas sp. was highly expressed suggesting active nitrous oxide (N2O) respiration. c-type cytochromes were barely detected, as was citrate synthase, a biomarker for hexavalent uranium reduction activity, suggesting that metal reduction has not commenced 4 days post EVO delivery. Environmental metaproteomics identified microbial community responses to biostimulation and elucidated active pathways demonstrating the value of this technique for complementing nucleic acid-based approaches.

  8. Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response

    Science.gov (United States)

    Pang, Chi Nam Ignatius; Lai, Yu-Wen; Campbell, Leona T.; Chen, Sharon C.-A.; Carter, Dee A.; Wilkins, Marc R.

    2017-01-01

    Invasive fungal infections are difficult to treat. The few available antifungal drugs have problems with toxicity or efficacy, and resistance is increasing. To overcome these challenges, existing therapies may be enhanced by synergistic combination with another agent. Previously, we found amphotericin B (AMB) and the iron chelator, lactoferrin (LF), were synergistic against a range of different fungal pathogens. This study investigates the mechanism of AMB-LF synergy, using RNA-seq and network analyses. AMB treatment resulted in increased expression of genes involved in iron homeostasis and ATP synthesis. Unexpectedly, AMB-LF treatment did not lead to increased expression of iron and zinc homeostasis genes. However, genes involved in adaptive response to zinc deficiency and oxidative stress had decreased expression. The clustering of co-expressed genes and network analysis revealed that many iron and zinc homeostasis genes are targets of transcription factors Aft1p and Zap1p. The aft1Δ and zap1Δ mutants were hypersensitive to AMB and H2O2, suggesting they are key regulators of the drug response. Mechanistically, AMB-LF synergy could involve AMB affecting the integrity of the cell wall and membrane, permitting LF to disrupt intracellular processes. We suggest that Zap1p- and Aft1p-binding molecules could be combined with existing antifungals to serve as synergistic treatments. PMID:28079179

  9. Arabidopsis decuple mutant reveals the importance of SnRK2 kinases in osmotic stress responses in vivo

    KAUST Repository

    Fujii, Hiroaki

    2011-01-10

    Osmotic stress associated with drought or salinity is a major factor that limits plant productivity. Protein kinases in the SNF1-related protein kinase 2 (SnRK2) family are activated by osmotic stress, suggesting that the kinases are involved in osmotic stress signaling. However, due to functional redundancy, their contribution to osmotic stress responses remained unclear. In this report, we constructed an Arabidopsis line carrying mutations in all 10 members of the SnRK2 family. The decuple mutant snrk2.1/2/3/4/5/6/7/8/9/10 grew poorly under hyperosmotic stress conditions but was similar to the wild type in culture media in the absence of osmotic stress. The mutant was also defective in gene regulation and the accumulation of abscisic acid (ABA), proline, and inositol 1,4,5-trisphosphate under osmotic stress. In addition, analysis of mutants defective in the ABA-activated SnRK2s (snrk2.2/3/6) and mutants defective in the rest of the SnRK2s (snrk2.1/4/5/7/8/9/10) revealed that SnRK2s are a merging point of ABA-dependent and -independent pathways for osmotic stress responses. These results demonstrate critical functions of the SnRK2s in mediating osmotic stress signaling and tolerance.

  10. Effect of Pre-Stressing on the Acid-Stress Response in Bifidobacterium Revealed Using Proteomic and Physiological Approaches.

    Directory of Open Access Journals (Sweden)

    Junhua Jin

    Full Text Available Weak acid resistance limits the application of Bifidobacteria as a probiotic in food. The acid tolerance response (ATR, caused by pre-stressing cells at a sublethal pH, could improve the acid resistance of Bifidobacteria to subsequent acid stress. In this study, we used Bifidobacterium longum sub. longum BBMN68 to investigate the effect of the ATR on the acid stress response (ASR, and compared the difference between the ATR and the ASR by analyzing the two-dimensional-PAGE protein profiles and performing physiological tests. The results revealed that a greater abundance of proteins involved in carbohydrate metabolism and protein protection was present after the ASR than after the ATR in Bifidobacterium. Pre-stressing cells increased the abundance of proteins involved in energy production, amino acid metabolism, and peptidoglycan synthesis during the ASR of Bifidobacterium. Moreover, after the ASR, the content of ATP, NH3, thiols, and peptidoglycan, the activity of H+-ATPase, and the maintenance of the intracellular pH in the pre-stressed Bifidobacterium cells was significantly higher than in the uninduced cells. These results provide the first explanation as to why the resistance of Bifidobacterium to acid stress improved after pre-stressing.

  11. Deep sequencing-based transcriptome profiling reveals comprehensive insights into the responses of Nicotiana benthamiana to beet necrotic yellow vein virus infections containing or lacking RNA4.

    Directory of Open Access Journals (Sweden)

    Huiyan Fan

    Full Text Available BACKGROUND: Beet necrotic yellow vein virus (BNYVV, encodes either four or five plus-sense single stranded RNAs and is the causal agent of sugar beet rhizomania disease, which is widely distributed in most regions of the world. BNYVV can also infect Nicotiana benthamiana systemically, and causes severe curling and stunting symptoms in the presence of RNA4 or mild symptoms in the absence of RNA4. RESULTS: Confocal laser scanning microscopy (CLSM analyses showed that the RNA4-encoded p31 protein fused to the red fluorescent protein (RFP accumulated mainly in the nuclei of N. benthamiana epidermal cells. This suggested that severe RNA4-induced symptoms might result from p31-dependent modifications of the transcriptome. Therefore, we used next-generation sequencing technologies to analyze the transcriptome profile of N. benthamiana in response to infection with different isolates of BNYVV. Comparisons of the transcriptomes of mock, BN3 (RNAs 1+2+3, and BN34 (RNAs 1+2+3+4 infected plants identified 3,016 differentially expressed transcripts, which provided a list of candidate genes that potentially are elicited in response to virus infection. Our data indicate that modifications in the expression of genes involved in RNA silencing, ubiquitin-proteasome pathway, cellulose synthesis, and metabolism of the plant hormone gibberellin may contribute to the severe symptoms induced by RNA4 from BNYVV. CONCLUSIONS: These results expand our understanding of the genetic architecture of N. benthamiana as well as provide valuable clues to identify genes potentially involved in resistance to BNYVV infection. Our global survey of gene expression changes in infected plants reveals new insights into the complicated molecular mechanisms underlying symptom development, and aids research into new strategies to protect crops against viruses.

  12. QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite.

    Directory of Open Access Journals (Sweden)

    Adrien Zimmer

    Full Text Available Quantitative genetics and QTL mapping are efficient strategies for deciphering the genetic polymorphisms that explain the phenotypic differences of individuals within the same species. Since a decade, this approach has been applied to eukaryotic microbes such as Saccharomyces cerevisiae in order to find natural genetic variations conferring adaptation of individuals to their environment. In this work, a QTL responsible for lag phase duration in the alcoholic fermentation of grape juice was dissected by reciprocal hemizygosity analysis. After invalidating the effect of some candidate genes, a chromosomal translocation affecting the lag phase was brought to light using de novo assembly of parental genomes. This newly described translocation (XV-t-XVI involves the promoter region of ADH1 and the gene SSU1 and confers an increased expression of the sulfite pump during the first hours of alcoholic fermentation. This translocation constitutes another adaptation route of wine yeast to sulfites in addition to the translocation VIII-t-XVI previously described. A population survey of both translocation forms in a panel of domesticated yeast strains suggests that the translocation XV-t-XVI has been empirically selected by human activity.

  13. Comparative proteomic and physiological analyses reveal the protective effect of exogenous calcium on the germinating soybean response to salt stress.

    Science.gov (United States)

    Yin, Yongqi; Yang, Runqiang; Han, Yongbin; Gu, Zhenxin

    2015-01-15

    suppressed under salt stress condition. According to previous studies, exogenous calcium counters the harmful effect of salt stress and increases the biomass and GABA content of germinating soybeans. Nevertheless, the precise molecular mechanism underlying the role of calcium in resistance to salt stress is still unknown. This paper is the first study employing comparative proteomic and physiological analyses to reveal the protective effect of exogenous calcium in the germinating soybean response to salt stress. Our study links the biological events with proteomic information and provides detailed peptide information on all identified proteins. The functions of those significantly changed proteins are also analyzed. The physiological and comparative proteomic analyses revealed the putative molecular mechanism of exogenous calcium treatment induced salt stress responses. The findings from this paper are beneficial to high GABA-rich germinating soybean biomass. Additionally, these findings also might be applicable to the genetic engineering of soybean plants to improve stress tolerance.

  14. A Genome-Wide Analysis Reveals Stress and Hormone Responsive Patterns of TIFY Family Genes in Brassica rapa.

    Science.gov (United States)

    Saha, Gopal; Park, Jong-In; Kayum, Md Abdul; Nou, Ill-Sup

    2016-01-01

    The TIFY family is a plant-specific group of proteins with a diversity of functions and includes four subfamilies, viz. ZML, TIFY, PPD, and JASMONATE ZIM-domain (JAZ) proteins. TIFY family members, particularly JAZ subfamily proteins, play roles in biological processes such as development and stress and hormone responses in Arabidopsis, rice, chickpea, and grape. However, there is no information about this family in any Brassica crop. This study identifies 36 TIFY genes in Brassica rapa, an economically important crop species in the Brassicaceae. An extensive in silico analysis of phylogenetic grouping, protein motif organization and intron-exon distribution confirmed that there are four subfamilies of BrTIFY proteins. Out of 36 BrTIFY genes, we identified 21 in the JAZ subfamily, seven in the TIFY subfamily, six in ZML and two in PPD. Extensive expression profiling of 21 BrTIFY JAZs in various tissues, especially in floral organs and at different flower growth stages revealed constitutive expression patterns, which suggest that BrTIFY JAZ genes are important during growth and development of B. rapa flowers. A protein interaction network analysis also pointed to association of these proteins with fertility and defense processes of B. rapa. Using a low temperature-treated whole-genome microarray data set, most of the JAZ genes were found to have variable transcript abundance between the contrasting inbred lines Chiifu and Kenshin of B. rapa. Subsequently, the expression of all 21 BrTIFY JAZs in response to cold stress was characterized in the same two lines via qPCR, demonstrating that nine genes were up-regulated. Importantly, the BrTIFY JAZs showed strong and differential expression upon JA treatment, pointing to their probable involvement in JA-mediated growth regulatory functions, especially during flower development and stress responses. Additionally, BrTIFY JAZs were induced in response to salt, drought, Fusarium, ABA, and SA treatments, and six genes (BrTIFY3

  15. A model of estrogen-related gene expression reveals non-linear effects in transcriptional response to tamoxifen

    Directory of Open Access Journals (Sweden)

    Lebedeva Galina

    2012-11-01

    Full Text Available Abstract Background Estrogen receptors alpha (ER are implicated in many types of female cancers, and are the common target for anti-cancer therapy using selective estrogen receptor modulators (SERMs, such as tamoxifen. However, cell-type specific and patient-to-patient variability in response to SERMs (from suppression to stimulation of cancer growth, as well as frequent emergence of drug resistance, represents a serious problem. The molecular processes behind mixed effects of SERMs remain poorly understood, and this strongly motivates application of systems approaches. In this work, we aimed to establish a mathematical model of ER-dependent gene expression to explore potential mechanisms underlying the variable actions of SERMs. Results We developed an equilibrium model of ER binding with 17β-estradiol, tamoxifen and DNA, and linked it to a simple ODE model of ER-induced gene expression. The model was parameterised on the broad range of literature available experimental data, and provided a plausible mechanistic explanation for the dual agonism/antagonism action of tamoxifen in the reference cell line used for model calibration. To extend our conclusions to other cell types we ran global sensitivity analysis and explored model behaviour in the wide range of biologically plausible parameter values, including those found in cancer cells. Our findings suggest that transcriptional response to tamoxifen is controlled in a complex non-linear way by several key parameters, including ER expression level, hormone concentration, amount of ER-responsive genes and the capacity of ER-tamoxifen complexes to stimulate transcription (e.g. by recruiting co-regulators of transcription. The model revealed non-monotonic dependence of ER-induced transcriptional response on the expression level of ER, that was confirmed experimentally in four variants of the MCF-7 breast cancer cell line. Conclusions We established a minimal mechanistic model of ER-dependent gene

  16. Transcriptional response of zebrafish embryos exposed to neurotoxic compounds reveals a muscle activity dependent hspb11 expression.

    Directory of Open Access Journals (Sweden)

    Nils Klüver

    Full Text Available Acetylcholinesterase (AChE inhibitors are widely used as pesticides and drugs. Their primary effect is the overstimulation of cholinergic receptors which results in an improper muscular function. During vertebrate embryonic development nerve activity and intracellular downstream events are critical for the regulation of muscle fiber formation. Whether AChE inhibitors and related neurotoxic compounds also provoke specific changes in gene transcription patterns during vertebrate development that allow them to establish a mechanistic link useful for identification of developmental toxicity pathways has, however, yet not been investigated. Therefore we examined the transcriptomic response of a known AChE inhibitor, the organophosphate azinphos-methyl (APM, in zebrafish embryos and compared the response with two non-AChE inhibiting unspecific control compounds, 1,4-dimethoxybenzene (DMB and 2,4-dinitrophenol (DNP. A highly specific cluster of APM induced gene transcripts was identified and a subset of strongly regulated genes was analyzed in more detail. The small heat shock protein hspb11 was found to be the most sensitive induced gene in response to AChE inhibitors. Comparison of expression in wildtype, ache and sop(fixe mutant embryos revealed that hspb11 expression was dependent on the nicotinic acetylcholine receptor (nAChR activity. Furthermore, modulators of intracellular calcium levels within the whole embryo led to a transcriptional up-regulation of hspb11 which suggests that elevated intracellular calcium levels may regulate the expression of this gene. During early zebrafish development, hspb11 was specifically expressed in muscle pioneer cells and Hspb11 morpholino-knockdown resulted in effects on slow muscle myosin organization. Our findings imply that a comparative toxicogenomic approach and functional analysis can lead to the identification of molecular mechanisms and specific marker genes for potential neurotoxic compounds.

  17. RNA arbitrarily primed PCR and fourier transform infrared spectroscopy reveal plasticity in the acid tolerance response of Streptococcus macedonicus.

    Science.gov (United States)

    Papadimitriou, Konstantinos; Boutou, Effrossyni; Zoumpopoulou, Georgia; Tarantilis, Petros A; Polissiou, Moschos; Vorgias, Constantinos E; Tsakalidou, Effie

    2008-10-01

    We have previously reported that an acid tolerance response (ATR) can be induced in Streptococcus macedonicus cells at mid-log phase after autoacidification, transient exposure to acidic pH, or acid habituation, as well as at stationary phase. Here, we compared the transcriptional profiles of these epigenetic phenotypes, by RNA arbitrarily primed PCR (RAP-PCR), and their whole-cell chemical compositions, by Fourier transform infrared spectroscopy (FT-IR). RAP-PCR fingerprints revealed significant differences among the phenotypes, indicating that gene expression during the ATR is influenced not only by the growth phase but also by the treatments employed to induce the response. The genes coding for the mannose-specific IID component, the 1,2-diacylglycerol 3-glucosyltransferase, the 3-oxoacyl-acyl carrier protein, the large subunit of carbamoyl-phosphate synthase, and a hypothetical protein were found to be induced at least under some of the acid-adapting conditions. Furthermore, principal component analysis of the second-derivative-transformed FT-IR spectra segregated S. macedonicus phenotypes individually in all spectral regions that are characteristic for major cellular constituents like the polysaccharides of the cell wall, fatty acids of the cell membrane, proteins, and other compounds that absorb in these regions. These findings provide evidence for major changes in cellular composition due to acid adaptation that were clearly different to some extent among the phenotypes. Overall, our data demonstrate the plasticity in the ATR of S. macedonicus, which reflects the inherent ability of the bacterium to adjust the response to the distinctiveness of the imposed stress condition, probably to maximize its adaptability.

  18. Publishers' Responses to the E-Book Phenomenon: Survey Results from Three "Small Language" Markets

    Science.gov (United States)

    Wilson, T. D.; Maceviciute, Elena

    2016-01-01

    Introduction: This paper reports on a study of publishers' attitudes towards e-books in the context of the global situation of e-book publishing. Comparative data are drawn from a replication of a survey carried out in Sweden, in Lithuania and in Croatia. Method: A self-completed questionnaire survey was undertaken, offering respondents the choice…

  19. U.S. Geological Survey response to flooding in Texas, May–June 2015

    Science.gov (United States)

    East, Jeffery W.

    2016-04-26

    As a Federal science agency within the Department of the Interior, the U.S. Geological Survey (USGS) collects and disseminates streamflow stage and discharge information along with other types of water information as a major part of its Water mission area. Data collected at USGS streamflow-gaging stations (hereinafter referred to as “streamgages”) are used for a variety of purposes including flood warning, engineering design, management of water resources, and scientific research.During flood events, the need for timely, accurate, and complete streamflow data is underscored because these data are relied on by local, State, and Federal emergency management personnel for flood response purposes. For example, the National Weather Service uses the data from USGS streamgages to develop flood forecasts for specific locations on a river. Tasks that the USGS performs in response to floods include monitoring the operation of gages and responding to any interruptions in data collection, calibrating and verifying stage-discharge ratings, and documenting extreme events including peak stage and peak discharge.Frequent, severe storms during May and June 2015 caused widespread flooding in Texas. By various measures, the storms that caused the flooding were extreme and persistent. May 2015 was the wettest month on record for Texas, with a statewide average precipitation of 9.06 inches. In comparison, the long-term statewide average monthly precipitation is 3.37 inches, with the previous record average monthly precipitation reported as 6.66 inches during June 2004. The Office of the Texas State Climatologist compiled monthly precipitation amounts for 19 selected cities throughout Texas and for 1 city in Louisiana; the total monthly precipitation amounts exceeded the monthly normal precipitation for 18 of the 19 selected cities in Texas, with 5 of these cities exceeding their previous record for the month of May.The onset of abundant precipitation in May 2015 resulted in the

  20. "Suntelligence" Survey

    Science.gov (United States)

    ... to the American Academy of Dermatology's "Suntelligence" sun-smart survey. Please answer the following questions to measure ... be able to view a ranking of major cities suntelligence based on residents' responses to this survey. ...

  1. A dose-response strategy reveals differences between normal-weight and obese men in their metabolic and inflammatory responses to a high-fat meal.

    Science.gov (United States)

    Schwander, Flurina; Kopf-Bolanz, Katrin A; Buri, Caroline; Portmann, Reto; Egger, Lotti; Chollet, Magali; McTernan, Philip G; Piya, Milan K; Gijs, Martin A M; Vionnet, Nathalie; Pralong, François; Laederach, Kurt; Vergères, Guy

    2014-10-01

    A dose-response strategy may not only allow investigation of the impact of foods and nutrients on human health but may also reveal differences in the response of individuals to food ingestion based on their metabolic health status. In a randomized crossover study, we challenged 19 normal-weight (BMI: 20-25 kg/m(2)) and 18 obese (BMI: >30 kg/m(2)) men with 500, 1000, and 1500 kcal of a high-fat (HF) meal (60.5% energy from fat). Blood was taken at baseline and up to 6 h postprandially and analyzed for a range of metabolic, inflammatory, and hormonal variables, including plasma glucose, lipids, and C-reactive protein and serum insulin, glucagon-like peptide-1, interleukin-6 (IL-6), and endotoxin. Insulin was the only variable that could differentiate the postprandial response of normal-weight and obese participants at each of the 3 caloric doses. A significant response of the inflammatory marker IL-6 was only observed in the obese group after ingestion of the HF meal containing 1500 kcal [net incremental AUC (iAUC) = 22.9 ± 6.8 pg/mL × 6 h, P = 0.002]. Furthermore, the net iAUC for triglycerides significantly increased from the 1000 to the 1500 kcal meal in the obese group (5.0 ± 0.5 mmol/L × 6 h vs. 6.0 ± 0.5 mmol/L × 6 h; P = 0.015) but not in the normal-weight group (4.3 ± 0.5 mmol/L × 6 h vs. 4.8 ± 0.5 mmol/L × 6 h; P = 0.31). We propose that caloric dose-response studies may contribute to a better understanding of the metabolic impact of food on the human organism. This study was registered at clinicaltrials.gov as NCT01446068. © 2014 American Society for Nutrition.

  2. A Dose-Response Strategy Reveals Differences between Normal-Weight and Obese Men in Their Metabolic and Inflammatory Responses to a High-Fat Meal123

    Science.gov (United States)

    Schwander, Flurina; Kopf-Bolanz, Katrin A.; Buri, Caroline; Portmann, Reto; Egger, Lotti; Chollet, Magali; McTernan, Philip G.; Piya, Milan K.; Gijs, Martin A. M.; Vionnet, Nathalie; Pralong, François; Laederach, Kurt; Vergères, Guy

    2014-01-01

    A dose-response strategy may not only allow investigation of the impact of foods and nutrients on human health but may also reveal differences in the response of individuals to food ingestion based on their metabolic health status. In a randomized crossover study, we challenged 19 normal-weight (BMI: 20–25 kg/m2) and 18 obese (BMI: >30 kg/m2) men with 500, 1000, and 1500 kcal of a high-fat (HF) meal (60.5% energy from fat). Blood was taken at baseline and up to 6 h postprandially and analyzed for a range of metabolic, inflammatory, and hormonal variables, including plasma glucose, lipids, and C-reactive protein and serum insulin, glucagon-like peptide-1, interleukin-6 (IL-6), and endotoxin. Insulin was the only variable that could differentiate the postprandial response of normal-weight and obese participants at each of the 3 caloric doses. A significant response of the inflammatory marker IL-6 was only observed in the obese group after ingestion of the HF meal containing 1500 kcal [net incremental AUC (iAUC) = 22.9 ± 6.8 pg/mL × 6 h, P = 0.002]. Furthermore, the net iAUC for triglycerides significantly increased from the 1000 to the 1500 kcal meal in the obese group (5.0 ± 0.5 mmol/L × 6 h vs. 6.0 ± 0.5 mmol/L × 6 h; P = 0.015) but not in the normal-weight group (4.3 ± 0.5 mmol/L × 6 h vs. 4.8 ± 0.5 mmol/L × 6 h; P = 0.31). We propose that caloric dose-response studies may contribute to a better understanding of the metabolic impact of food on the human organism. This study was registered at clinicaltrials.gov as NCT01446068. PMID:24812072

  3. Unconventional microarray design reveals the response to obesity is largely tissue specific: analysis of common and divergent responses to diet-induced obesity in insulin-sensitive tissues.

    Science.gov (United States)

    Lee, Robyn K; Hittel, Dustin S; Nyamandi, Vongai Z; Kang, Li; Soh, Jung; Sensen, Christoph W; Shearer, Jane

    2012-04-01

    Obesity is a chronic condition involving the excessive accumulation of adipose tissue that adversely affects all systems in the body. The aim of the present study was to employ an unbiased, genome-wide assessment of transcript abundance in order to identify common gene expression pathways within insulin-sensitive tissues in response to dietary-induced diabetes. Following 20 weeks of chow or high-fat feeding (60% kcal), age-matched mice underwent a euglycemic-hyperinsulinemic clamp to assess insulin sensitivity. High-fat-fed animals were obese and highly insulin resistant, disposing of ∼75% less glucose compared with their chow-fed counterparts. Tissues were collected, and gene expression was examined by microarray in 4 tissues known to exhibit obesity-related metabolic disturbances: white adipose tissue, skeletal muscle, liver, and heart. A total of 463 genes were differentially expressed between diets. Analysis of individual tissues showed skeletal muscle to exhibit the largest number of differentially expressed genes (191) in response to high-fat feeding, followed by adipose tissue (169), liver (115), and heart (65). Analyses revealed that the response of individual genes to obesity is distinct and largely tissue specific, with less than 10% of transcripts being shared among tissues. Although transcripts are largely tissue specific, a systems approach shows numerous commonly activated pathways, including those involved in signal transduction, inflammation, oxidative stress, substrate transport, and metabolism. This suggests a coordinated attempt by tissues to limit metabolic perturbations occurring in early-stage obesity. Many identified genes were associated with a variety of disorders, thereby serving as potential links between obesity and its related health risks.

  4. Complex adaptive responses during antagonistic coevolution between Tribolium castaneum and its natural parasite Nosema whitei revealed by multiple fitness components

    Directory of Open Access Journals (Sweden)

    Bérénos Camillo

    2012-01-01

    Full Text Available Abstract Background Host-parasite coevolution can lead to local adaptation of either parasite or host if there is specificity (GxG interactions and asymmetric evolutionary potential between host and parasite. This has been demonstrated both experimentally and in field studies, but a substantial proportion of studies fail to detect such clear-cut patterns. One explanation for this is that adaptation can be masked by counter-adaptation by the antagonist. Additionally, genetic architecture underlying the interaction is often highly complex thus preventing specific adaptive responses. Here, we have employed a reciprocal cross-infection experiment to unravel the adaptive responses of two components of fitness affecting both parties with different complexities of the underlying genetic architecture (i.e. mortality and spore load. Furthermore, our experimental coevolution of hosts (Tribolium castaneum and parasites (Nosema whitei included paired replicates of naive hosts from identical genetic backgrounds to allow separation between host- and parasite-specific responses. Results In hosts, coevolution led to higher resistance and altered resistance profiles compared to paired control lines. Host genotype × parasite genotype interactions (GH × GP were observed for spore load (the trait of lower genetic complexity, but not for mortality. Overall parasite performance correlated with resistance of its matching host coevolution background reflecting a directional and unspecific response to strength of selection during coevolution. Despite high selective pressures exerted by the obligatory killing parasite, and host- and parasite-specific mortality profiles, no general pattern of local adaptation was observed, but one case of parasite maladaptation was consistently observed on both coevolved and control host populations. In addition, the use of replicate control host populations in the assay revealed one case of host maladaptation and one case of parasite

  5. De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana.

    Science.gov (United States)

    Rao, Guodong; Sui, Jinkai; Zeng, Yanfei; He, Caiyun; Duan, Aiguo; Zhang, Jianguo

    2014-01-01

    Salix matsudana Koidz. is a deciduous, rapidly growing, and drought resistant tree and is one of the most widely distributed and commonly cultivated willow species in China. Currently little transcriptomic and small RNAomic data are available to reveal the genes involve in the stress resistant in S. matsudana. Here, we report the RNA-seq analysis results of both transcriptome and small RNAome data using Illumina deep sequencing of shoot tips from two willow variants(Salix. matsudana and Salix matsudana Koidz. cultivar 'Tortuosa'). De novo gene assembly was used to generate the consensus transcriptome and small RNAome, which contained 106,403 unique transcripts with an average length of 944 bp and a total length of 100.45 MB, and 166 known miRNAs representing 35 miRNA families. Comparison of transcriptomes and small RNAomes combined with quantitative real-time PCR from the two Salix libraries revealed a total of 292 different expressed genes(DEGs) and 36 different expressed miRNAs (DEMs). Among the DEGs and DEMs, 196 genes and 24 miRNAs were up regulated, 96 genes and 12 miRNA were down regulated in S. matsudana. Functional analysis of DEGs and miRNA targets showed that many genes were involved in stress resistance in S. matsudana. Our global gene expression profiling presents a comprehensive view of the transcriptome and small RNAome which provide valuable information and sequence resources for uncovering the stress response genes in S. matsudana. Moreover the transcriptome and small RNAome data provide a basis for future study of genetic resistance in Salix.

  6. De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana.

    Directory of Open Access Journals (Sweden)

    Guodong Rao

    Full Text Available Salix matsudana Koidz. is a deciduous, rapidly growing, and drought resistant tree and is one of the most widely distributed and commonly cultivated willow species in China. Currently little transcriptomic and small RNAomic data are available to reveal the genes involve in the stress resistant in S. matsudana. Here, we report the RNA-seq analysis results of both transcriptome and small RNAome data using Illumina deep sequencing of shoot tips from two willow variants(Salix. matsudana and Salix matsudana Koidz. cultivar 'Tortuosa'. De novo gene assembly was used to generate the consensus transcriptome and small RNAome, which contained 106,403 unique transcripts with an average length of 944 bp and a total length of 100.45 MB, and 166 known miRNAs representing 35 miRNA families. Comparison of transcriptomes and small RNAomes combined with quantitative real-time PCR from the two Salix libraries revealed a total of 292 different expressed genes(DEGs and 36 different expressed miRNAs (DEMs. Among the DEGs and DEMs, 196 genes and 24 miRNAs were up regulated, 96 genes and 12 miRNA were down regulated in S. matsudana. Functional analysis of DEGs and miRNA targets showed that many genes were involved in stress resistance in S. matsudana. Our global gene expression profiling presents a comprehensive view of the transcriptome and small RNAome which provide valuable information and sequence resources for uncovering the stress response genes in S. matsudana. Moreover the transcriptome and small RNAome data provide a basis for future study of genetic resistance in Salix.

  7. Effects of incentive size and timing on response rates to a follow-up wave of a longitudinal mailed survey.

    Science.gov (United States)

    Collins, R L; Ellickson, P L; Hays, R D; McCaffrey, D F

    2000-08-01

    Young adults who had previously participated in a longitudinal survey of youth were sent a questionnaire. They were randomly assigned to receive a $20 prepayment, a $20 postpayment, or a $25 postpayment for participation in the latest survey. Those in the large incentive condition were 7 percentage points more likely to return a survey than those in the smaller, postpayment group. Prepayment had a smaller, less reliable effect. Effects of incentive magnitude and timing were consistent at each month of the study period; only better high school grades distinguished early responders from late responders. Nonresponders had characteristics suggestive of low social conformity and were more likely than responders to be African American and male and have low SES. The discussion centers on motivations for participating in research and differences in the incentives likely to promote continued response versus initial study enrollment.

  8. Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell lines

    Science.gov (United States)

    2014-01-01

    Background Despite promising progress in targeted breast cancer therapy, drug resistance remains challenging. The monoclonal antibody drugs trastuzumab and pertuzumab as well as the small molecule inhibitor erlotinib were designed to prevent ErbB-2 and ErbB-1 receptor induced deregulated protein signalling, contributing to tumour progression. The oncogenic potential of ErbB receptors unfolds in case of overexpression or mutations. Dimerisation with other receptors allows to bypass pathway blockades. Our intention is to reconstruct the ErbB network to reveal resistance mechanisms. We used longitudinal proteomic data of ErbB receptors and downstream targets in the ErbB-2 amplified breast cancer cell lines BT474, SKBR3 and HCC1954 treated with erlotinib, trastuzumab or pertuzumab, alone or combined, up to 60 minutes and 30 hours, respectively. In a Boolean modelling approach, signalling networks were reconstructed based on these data in a cell line and time course specific manner, including prior literature knowledge. Finally, we simulated network response to inhibitor combinations to detect signalling nodes reflecting growth inhibition. Results The networks pointed to cell line specific activation patterns of the MAPK and PI3K pathway. In BT474, the PI3K signal route was favoured, while in SKBR3, novel edges highlighted MAPK signalling. In HCC1954, the inferred edges stimulated both pathways. For example, we uncovered feedback loops amplifying PI3K signalling, in line with the known trastuzumab resistance of this cell line. In the perturbation simulations on the short-term networks, we analysed ERK1/2, AKT and p70S6K. The results indicated a pathway specific drug response, driven by the type of growth factor stimulus. HCC1954 revealed an edgetic type of PIK3CA-mutation, contributing to trastuzumab inefficacy. Drug impact on the AKT and ERK1/2 signalling axes is mirrored by effects on RB and RPS6, relating to phenotypic events like cell growth or proliferation

  9. Gene expression profiling reveals biological pathways responsible for phenotypic heterogeneity between UK and Sri Lankan oral squamous cell carcinomas.

    Science.gov (United States)

    Saeed, Anas A; Sims, Andrew H; Prime, Stephen S; Paterson, Ian; Murray, Paul G; Lopes, Victor R

    2015-03-01

    It is well recognized that oral squamous cell carcinoma (OSCC) cases from Asia that are associated with betel quid chewing are phenotypically distinct to those from Western countries that are predominantly caused by smoking/drinking, but the molecular basis of these differences are largely unknown. The aim of this study is to examine gene expression, related carcinogenic pathways and molecular processes that might be responsible for the phenotypic heterogeneity of OSCC between UK and Sri Lankan population groups. We have compared the gene expression profiles of OSCCs and normal oral mucosal tissues from both Sri Lankan and UK individuals using Affymetrix gene expression arrays. The generated data was interrogated using significance analysis of microarrays and Ingenuity Pathway Analysis (IPA). The gene expression profiles of UK and Sri Lankan OSCC are similar in many respects to other oral cancer expression profiles reported in the literature and were mainly similar to each other. However, genes involved in tumor invasion, metastasis and recurrence were more obviously associated with UK tumors as opposed to those from Sri Lanka. The development of OSCCs in both UK and Sri Lankan populations appears largely mediated by similar biological pathways despite the differences related to race, ethnicity, lifestyle, and/or exposure to environmental carcinogens. However, IPA revealed a highly activated "Cell-mediated Immune Response" in Sri Lankan normal and tumor samples relative to UK cohorts. It seems likely, therefore, that any future attempts to personalize treatment for OSCC patients will need to be different in Western and Asian countries to reflect differences in gene expression and the immune status of the patients. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Self-reported responsiveness to direct-to-consumer drug advertising and medication use: results of a national survey

    Directory of Open Access Journals (Sweden)

    Somes Grant W

    2011-09-01

    Full Text Available Abstract Background Direct-to-consumer (DTC marketing of pharmaceuticals is controversial, yet effective. Little is known relating patterns of medication use to patient responsiveness to DTC. Methods We conducted a secondary analysis of data collected in national telephone survey on knowledge of and attitudes toward DTC advertisements. The survey of 1081 U.S. adults (response rate = 65% was conducted by the Food and Drug Administration (FDA. Responsiveness to DTC was defined as an affirmative response to the item: "Has an advertisement for a prescription drug ever caused you to ask a doctor about a medical condition or illness of your own that you had not talked to a doctor about before?" Patients reported number of prescription and over-the-counter (OTC medicines taken as well as demographic and personal health information. Results Of 771 respondents who met study criteria, 195 (25% were responsive to DTC. Only 7% respondents taking no prescription were responsive, whereas 45% of respondents taking 5 or more prescription medications were responsive. This trend remained significant (p trend .0009 even when controlling for age, gender, race, educational attainment, income, self-reported health status, and whether respondents "liked" DTC advertising. There was no relationship between the number of OTC medications taken and the propensity to discuss health-related problems in response to DTC advertisements (p = .4. Conclusion There is a strong cross-sectional relationship between the number of prescription, but not OTC, drugs used and responsiveness to DTC advertising. Although this relationship could be explained by physician compliance with patient requests for medications, it is also plausible that DTC advertisements have a particular appeal to patients prone to taking multiple medications. Outpatients motivated to discuss medical conditions based on their exposure to DTC advertising may require a careful medication history to evaluate for

  11. Sex-specific automatic responses to infant cries: TMS reveals greater excitability in females than males in motor evoked potentials

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    Irene eMessina

    2016-01-01

    Full Text Available Neuroimaging reveals that infant cries activate parts of the premotor cortical system. To validate this effect in a more direct way, we used event-related transcranial magnetic stimulation (TMS. Here, we investigated the presence and the time course of modulation of motor cortex excitability in young adults who listened to infant cries. Specifically, we recorded motor evoked potentials (MEPs from the biceps brachii (BB and interosseus dorsalis primus (ID1 muscles as produced by TMS delivered from 0 to 250 ms from sound onset in six steps of 50 ms in 10 females and 10 males. We observed an excitatory modulation of MEPs at 100 ms from the onset of the infant cry specific to females and to the ID1 muscle. We regard this modulation as a response to natural cry sounds because it was delayed, attenuated to stimuli increasingly different from natural cry, and was absent in a separate group of females who listened to non-cry stimuli physically matched to natural infant cries. Furthermore, the 100-ms latency of this modulation is not compatible with a voluntary reaction to the stimulus but suggests an automatic, bottom-up audiomotor association. The brains of adult females appear to be tuned to respond to infant cries with automatic motor excitation. This effect may reflect the greater and longstanding burden on females in caregiving infants.

  12. Host and Non-Host roots in rice: cellular and molecular approaches reveal differential responses to arbuscular mycorrhizal fungi.

    Directory of Open Access Journals (Sweden)

    Valentina eFiorilli

    2015-08-01

    Full Text Available Oryza sativa, a model plant for Arbuscular Mycorrhizal (AM symbiosis, has both host and non-host roots. Large lateral (LLR and fine lateral (FLR roots display opposite responses: LLR support AM colonization, but FLR do not. Our research aimed to study the molecular, morphological and physiological aspects related to the non-host behavior of FLR. RNA-seq analysis revealed that LLR and FLR displayed divergent expression profiles, including changes in many metabolic pathways. Compared with LLR, FLR showed down-regulation of genes instrumental for AM establishment and gibberellin signaling, and a higher expression of nutrient transporters. Consistent with the transcriptomic data, FLR had higher phosphorus content. Light and electron microscopy demonstrated that, surprisingly, in the Selenio cultivar, FLR have a two-layered cortex, which is theoretically compatible with AM colonization. According to RNA-seq, a gibberellin inhibitor treatment increased anticlinal divisions leading to a higher number of cortex cells in FLR.We propose that some of the differentially regulated genes that lead to the anatomical and physiological properties of the two root types also function as genetic factors regulating fungal colonization. The rice root apparatus offers a unique tool to study AM symbiosis, allowing direct comparisons of host and non-host roots in the same individual plant.

  13. Host and non-host roots in rice: cellular and molecular approaches reveal differential responses to arbuscular mycorrhizal fungi.

    Science.gov (United States)

    Fiorilli, Valentina; Vallino, Marta; Biselli, Chiara; Faccio, Antonella; Bagnaresi, Paolo; Bonfante, Paola

    2015-01-01

    Oryza sativa, a model plant for Arbuscular Mycorrhizal (AM) symbiosis, has both host and non-host roots. Large lateral (LLR) and fine lateral (FLR) roots display opposite responses: LLR support AM colonization, but FLR do not. Our research aimed to study the molecular, morphological and physiological aspects related to the non-host behavior of FLR. RNA-seq analysis revealed that LLR and FLR displayed divergent expression profiles, including changes in many metabolic pathways. Compared with LLR, FLR showed down-regulation of genes instrumental for AM establishment and gibberellin signaling, and a higher expression of nutrient transporters. Consistent with the transcriptomic data, FLR had higher phosphorus content. Light and electron microscopy demonstrated that, surprisingly, in the Selenio cultivar, FLR have a two-layered cortex, which is theoretically compatible with AM colonization. According to RNA-seq, a gibberellin inhibitor treatment increased anticlinal divisions leading to a higher number of cortex cells in FLR. We propose that some of the differentially regulated genes that lead to the anatomical and physiological properties of the two root types also function as genetic factors regulating fungal colonization. The rice root apparatus offers a unique tool to study AM symbiosis, allowing direct comparisons of host and non-host roots in the same individual plant.

  14. Phenotypic and transcriptional profiling in Entamoeba histolytica reveal costs to fitness and adaptive responses associated with metronidazole resistance

    Directory of Open Access Journals (Sweden)

    Gil M Penuliar

    2015-05-01

    Full Text Available Antimicrobial chemotherapy is critical in the fight against infectious diseases caused by Entamoeba histolytica. Among the drugs available for the treatment of amebiasis, metronidazole (MTZ is considered the drug of choice. Recently, in vitro studies have described MTZ resistance and the potential mechanisms involved. Costs to fitness and adaptive responses associated with resistance, however, have not been investigated. In this study we generated an HM-1 derived strain resistant to 12 µM MTZ (MTZR. We examined its phenotypic and transcriptional profile to determine the consequences and mRNA level changes associated with MTZ resistance. Our results indicated increased cell size and granularity, and decreased rates in cell division, adhesion, phagocytosis, cytopathogenicity, and glucose consumption. Transcriptome analysis revealed 142 differentially expressed genes in MTZR. In contrast to other MTZ resistant parasites, MTZR did not down-regulate pyruvate:ferredoxin oxidoreductase, but showed increased expression of genes for a hypothetical protein (HP1 and several iron-sulfur flavoproteins, and downregulation of genes for leucine-rich proteins. Fisher’s exact test showed 24 significantly enriched GO terms in MTZR, and a 3-way comparison of modulated genes in MTZR against those of MTZR cultured without MTZ and HM-1 cultured with MTZ, showed that 88 genes were specific to MTZR. Overall, our findings suggested that MTZ resistance is associated with specific transcriptional changes and decreased parasite virulence.

  15. Phenotypic and transcriptional profiling in Entamoeba histolytica reveal costs to fitness and adaptive responses associated with metronidazole resistance

    Science.gov (United States)

    Penuliar, Gil M.; Nakada-Tsukui, Kumiko; Nozaki, Tomoyoshi

    2015-01-01

    Antimicrobial chemotherapy is critical in the fight against infectious diseases caused by Entamoeba histolytica. Among the drugs available for the treatment of amebiasis, metronidazole (MTZ) is considered the drug of choice. Recently, in vitro studies have described MTZ resistance and the potential mechanisms involved. Costs to fitness and adaptive responses associated with resistance, however, have not been investigated. In this study we generated an HM-1 derived strain resistant to 12 μM MTZ (MTZR). We examined its phenotypic and transcriptional profile to determine the consequences and mRNA level changes associated with MTZ resistance. Our results indicated increased cell size and granularity, and decreased rates in cell division, adhesion, phagocytosis, cytopathogenicity, and glucose consumption. Transcriptome analysis revealed 142 differentially expressed genes in MTZR. In contrast to other MTZ resistant parasites, MTZR did not down-regulate pyruvate:ferredoxin oxidoreductase, but showed increased expression of genes for a hypothetical protein (HP1) and several iron-sulfur flavoproteins, and downregulation of genes for leucine-rich proteins. Fisher's exact test showed 24 significantly enriched GO terms in MTZR, and a 3-way comparison of modulated genes in MTZR against those of MTZR cultured without MTZ and HM-1 cultured with MTZ, showed that 88 genes were specific to MTZR. Overall, our findings suggested that MTZ resistance is associated with specific transcriptional changes and decreased parasite virulence. PMID:25999919

  16. Transcriptomic analysis reveals importance of ROS and phytohormones in response to short-term salinity stress in Populus tomentosa

    Directory of Open Access Journals (Sweden)

    Lingyu eZheng

    2015-09-01

    Full Text Available Populus tomentosa (Chinese white poplar is well adapted to various extreme environments, and is considered an important species to study the effects of salinity stress on poplar trees. To decipher the mechanism of poplar’s rapid response to short-term salinity stress, we firstly detected the changes in H2O2 and hormone, and then profiled the gene expression pattern of ten-week-old seedling roots treated with 200 mM NaCl for 0, 6, 12 and 24 hours (h by RNA-seq on the Illumina-Solexa platform. Physiological determination showed that the significant increase in H2O2 began at 6 h, while that in hormone ABA was at 24 h, under salt stress. Compared with controls (0 h, 3991, 4603 and 4903 genes were up regulated, and 1408, 2206 and 3461 genes were down regulated (adjusted P-value ≤ 0.05 and |log2Ratio|≥1 at 6, 12, and 24 h time points, respectively. The Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG pathway annotation revealed that the differentially expressed genes (DEGs were highly enriched in hormone- and reactive oxygen species-related biological processes, including ‘response to oxidative stress or abiotic stimulus’, ‘peroxidase activity’, ‘regulation of transcription’, ‘hormone synthetic and metabolic process’, ‘hormone signal transduction’, ‘antioxidant activity’ and ‘transcription factor activity’. Moreover, K-means clustering demonstrated that DEGs (total RPKM value>12 from four time points could be categorized into four kinds of expression trends: quick up/down over 6 h or 12 h, and slow up/down over 24 h. Of these, DEGs involved in H2O2- and hormone- producing and signal-related genes were further enriched in this analysis, which indicated that the two kinds of small molecules, hormones and H2O2, play pivotal roles in the short-term salt stress response in poplar. This study provides a basis for future studies of the molecular adaptation of poplar and other tree species to salinity

  17. Regal phylogeography: Range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean

    KAUST Repository

    Coleman, Richard R.

    2016-04-08

    The regal angelfish (Pygoplites diacanthus; family Pomacanthidae) occupies reefs from the Red Sea to the central Pacific, with an Indian Ocean/Rea Sea color morph distinct from a Pacific Ocean morph. To assess population differentiation and evaluate the possibility of cryptic evolutionary partitions in this monotypic genus, we surveyed mtDNA cytochrome b and two nuclear introns (S7 and RAG2) in 547 individuals from 15 locations. Phylogeographic analyses revealed four mtDNA lineages (d = 0.006 – 0.015) corresponding to the Pacific Ocean, the Red Sea, and two admixed lineages in the Indian Ocean, a pattern consistent with known biogeographical barriers. Christmas Island in the eastern Indian Ocean had both Indian and Pacific lineages. Both S7 and RAG2 showed strong population-level differentiation between the Red Sea, Indian Ocean, and Pacific Ocean (ΦST = 0.066 – 0.512). The only consistent population sub-structure within these three regions was at the Society Islands (French Polynesia), where surrounding oceanographic conditions may reinforce isolation. Coalescence analyses indicate the Pacific (1.7 Ma) as the oldest extant lineage followed by the Red Sea lineage (1.4 Ma). Results from a median-joining network suggest radiations of two lineages from the Red Sea that currently occupy the Indian Ocean (0.7 – 0.9 Ma). Persistence of a Red Sea lineage through Pleistocene glacial cycles suggests a long-term refuge in this region. The affiliation of Pacific and Red Sea populations, apparent in cytochrome b and S7 (but equivocal in RAG2) raises the hypthosis that the Indian Ocean was recolonized from the Red Sea, possibly more than once. Assessing the genetic architecture of this widespread monotypic genus reveals cryptic evolutionary diversity that merits subspecific recognition.

  18. Regal phylogeography: Range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean.

    Science.gov (United States)

    Coleman, Richard R; Eble, Jeffrey A; DiBattista, Joseph D; Rocha, Luiz A; Randall, John E; Berumen, Michael L; Bowen, Brian W

    2016-07-01

    The regal angelfish (Pygoplites diacanthus; family Pomacanthidae) occurs on reefs from the Red Sea to the central Pacific, with an Indian Ocean/Rea Sea color morph distinct from a Pacific Ocean morph. To assess population differentiation and evaluate the possibility of cryptic evolutionary partitions in this monotypic genus, we surveyed mtDNA cytochrome b and two nuclear introns (S7 and RAG2) in 547 individuals from 15 locations. Phylogeographic analyses revealed four mtDNA lineages (d=0.006-0.015) corresponding to the Pacific Ocean, the Red Sea, and two admixed lineages in the Indian Ocean, a pattern consistent with known biogeographic barriers. Christmas Island in the eastern Indian Ocean had both Indian and Pacific lineages. Both S7 and RAG2 showed strong population-level differentiation between the Red Sea, Indian Ocean, and Pacific Ocean (ΦST=0.066-0.512). The only consistent population sub-structure within these three regions was at the Society Islands (French Polynesia), where surrounding oceanographic conditions may reinforce isolation. Coalescence analyses indicate the Pacific (1.7Ma) as the oldest extant lineage followed by the Red Sea lineage (1.4Ma). Results from a median-joining network suggest radiations of two lineages from the Red Sea that currently occupy the Indian Ocean (0.7-0.9Ma). Persistence of a Red Sea lineage through Pleistocene glacial cycles suggests a long-term refuge in this region. The affiliation of Pacific and Red Sea populations, apparent in cytochrome b and S7 (but equivocal in RAG2) raises the hypothesis that the Indian Ocean was recolonized from the Red Sea, possibly more than once. Assessing the genetic architecture of this widespread monotypic genus reveals cryptic evolutionary diversity that merits subspecific recognition. We recommend P.d. diacanthus and P.d. flavescens for the Pacific and Indian Ocean/Red Sea forms.

  19. The influence of labels associated with anchor points of Likert-type response scales in survey questionnaires.

    Science.gov (United States)

    Blais, Jean-Guy; Grondin, Julie

    2011-01-01

    Survey questionnaires are among the most used data gathering techniques in the social sciences researchers' toolbox and many factors can influence respondents' answers on items and affect data validity. Among these factors, research has accumulated which demonstrates that verbal and numeric labels associated with item's response categories in such questionnaire may influence substantially the way in which respondents operate their choices within the proposed response format. In line with these findings, the focus of this article is to use Andrich's Rating scale model to illustrate what kind of influence the quantifier adverb "totally," used to label or emphasize extreme categories, could have on respondents' answers.

  20. Global Gene-expression Analysis of the Response of Salmonella Enteritidis to Egg White Exposure Reveals Multiple Egg White-imposed Stress Responses

    Directory of Open Access Journals (Sweden)

    Florence Baron

    2017-05-01

    Full Text Available Chicken egg white protects the embryo from bacterial invaders by presenting an assortment of antagonistic activities that combine together to both kill and inhibit growth. The key features of the egg white anti-bacterial system are iron restriction, high pH, antibacterial peptides and proteins, and viscosity. Salmonella enterica serovar Enteritidis is the major pathogen responsible for egg-borne infection in humans, which is partly explained by its exceptional capacity for survival under the harsh conditions encountered within egg white. However, at temperatures up to 42°C, egg white exerts a much stronger bactericidal effect on S. Enteritidis than at lower temperatures, although the mechanism of egg white-induced killing is only partly understood. Here, for the first time, the impact of exposure of S. Enteritidis to egg white under bactericidal conditions (45°C is explored by global-expression analysis. A large-scale (18.7% of genome shift in transcription is revealed suggesting major changes in specific aspects of S. Enteritidis physiology: induction of egg white related stress-responses (envelope damage, exposure to heat and alkalinity, and translation shutdown; shift in energy metabolism from respiration to fermentation; and enhanced micronutrient provision (due to iron and biotin restriction. Little evidence of DNA damage or redox stress was obtained. Instead, data are consistent with envelope damage resulting in cell death by lysis. A surprise was the high degree of induction of hexonate/hexuronate utilization genes, despite no evidence indicating the presence of these substrates in egg white.

  1. Climate Change and Infectious Disease Risk in Western Europe: A Survey of Dutch Expert Opinion on Adaptation Responses and Actors.

    Science.gov (United States)

    Akin, Su-Mia; Martens, Pim; Huynen, Maud M T E

    2015-08-18

    There is growing evidence of climate change affecting infectious disease risk in Western Europe. The call for effective adaptation to this challenge becomes increasingly stronger. This paper presents the results of a survey exploring Dutch expert perspectives on adaptation responses to climate change impacts on infectious disease risk in Western Europe. Additionally, the survey explores the expert sample's prioritization of mitigation and adaptation, and expert views on the willingness and capacity of relevant actors to respond to climate change. An integrated view on the causation of infectious disease risk is employed, including multiple (climatic and non-climatic) factors. The results show that the experts consider some adaptation responses as relatively more cost-effective, like fostering interagency and community partnerships, or beneficial to health, such as outbreak investigation and response. Expert opinions converge and diverge for different adaptation responses. Regarding the prioritization of mitigation and adaptation responses expert perspectives converge towards a 50/50 budgetary allocation. The experts consider the national government/health authority as the most capable actor to respond to climate change-induced infectious disease risk. Divergence and consensus among expert opinions can influence adaptation policy processes. Further research is necessary to uncover prevailing expert perspectives and their roots, and compare these.

  2. Climate Change and Infectious Disease Risk in Western Europe: A Survey of Dutch Expert Opinion on Adaptation Responses and Actors

    Science.gov (United States)

    Akin, Su-Mia; Martens, Pim; Huynen, Maud M.T.E.

    2015-01-01

    There is growing evidence of climate change affecting infectious disease risk in Western Europe. The call for effective adaptation to this challenge becomes increasingly stronger. This paper presents the results of a survey exploring Dutch expert perspectives on adaptation responses to climate change impacts on infectious disease risk in Western Europe. Additionally, the survey explores the expert sample’s prioritization of mitigation and adaptation, and expert views on the willingness and capacity of relevant actors to respond to climate change. An integrated view on the causation of infectious disease risk is employed, including multiple (climatic and non-climatic) factors. The results show that the experts consider some adaptation responses as relatively more cost-effective, like fostering interagency and community partnerships, or beneficial to health, such as outbreak investigation and response. Expert opinions converge and diverge for different adaptation responses. Regarding the prioritization of mitigation and adaptation responses expert perspectives converge towards a 50/50 budgetary allocation. The experts consider the national government/health authority as the most capable actor to respond to climate change-induced infectious disease risk. Divergence and consensus among expert opinions can influence adaptation policy processes. Further research is necessary to uncover prevailing expert perspectives and their roots, and compare these. PMID:26295247

  3. Climate Change and Infectious Disease Risk in Western Europe: A Survey of Dutch Expert Opinion on Adaptation Responses and Actors

    Directory of Open Access Journals (Sweden)

    Su-Mia Akin

    2015-08-01

    Full Text Available There is growing evidence of climate change affecting infectious disease risk in Western Europe. The call for effective adaptation to this challenge becomes increasingly stronger. This paper presents the results of a survey exploring Dutch expert perspectives on adaptation responses to climate change impacts on infectious disease risk in Western Europe. Additionally, the survey explores the expert sample’s prioritization of mitigation and adaptation, and expert views on the willingness and capacity of relevant actors to respond to climate change. An integrated view on the causation of infectious disease risk is employed, including multiple (climatic and non-climatic factors. The results show that the experts consider some adaptation responses as relatively more cost-effective, like fostering interagency and community partnerships, or beneficial to health, such as outbreak investigation and response. Expert opinions converge and diverge for different adaptation responses. Regarding the prioritization of mitigation and adaptation responses expert perspectives converge towards a 50/50 budgetary allocation. The experts consider the national government/health authority as the most capable actor to respond to climate change-induced infectious disease risk. Divergence and consensus among expert opinions can influence adaptation policy processes. Further research is necessary to uncover prevailing expert perspectives and their roots, and compare these.

  4. A randomised controlled trial to determine the effect on response of including a lottery incentive in health surveys [ISRCTN32203485

    Directory of Open Access Journals (Sweden)

    Bridge P

    2004-11-01

    Full Text Available Abstract Background Postal questionnaires are an economical and simple method of data collection for research purposes but are subject to non-response bias. Several studies have explored the effect of monetary and non-monetary incentives on response. Recent meta-analyses conclude that financial incentives are an effective way of increasing response rates. However, large surveys rarely have the resources to reward individual participants. Three previous papers report on the effectiveness of lottery incentives with contradictory results. This study aimed to determine the effect of including a lottery-style incentive on response rates to a postal health survey. Methods Randomised controlled trial. Setting: North and West Birmingham. 8,645 patients aged 18 or over randomly selected from registers of eight general practices (family physician practices. Intervention: Inclusion of a flyer and letter with a health questionnaire informing patients that returned questionnaires would be entered into a lottery-style draw for £100 of gift vouchers. Control: Health questionnaire accompanied only by standard letter of explanation. Main outcome measures: Response rate and completion rate to questionnaire. Results 5,209 individuals responded with identical rates in both groups (62.1%. Practice, patient age, sex and Townsend score (a postcode based deprivation measure were identified as predictive of response, with higher response related to older age, being female and living in an area with a lower Townsend score (less deprived. Conclusion This RCT, using a large community based sample, found that the offer of entry into a lottery style draw for £100 of High Street vouchers has no effect on response rates to a postal health questionnaire.

  5. Individual and culture-level components of survey response styles: A multi-level analysis using cultural models of selfhood.

    Science.gov (United States)

    Smith, Peter B; Vignoles, Vivian L; Becker, Maja; Owe, Ellinor; Easterbrook, Matthew J; Brown, Rupert; Bourguignon, David; Garðarsdóttir, Ragna B; Kreuzbauer, Robert; Cendales Ayala, Boris; Yuki, Masaki; Zhang, Jianxin; Lv, Shaobo; Chobthamkit, Phatthanakit; Jaafar, Jas Laile; Fischer, Ronald; Milfont, Taciano L; Gavreliuc, Alin; Baguma, Peter; Bond, Michael Harris; Martin, Mariana; Gausel, Nicolay; Schwartz, Seth J; Des Rosiers, Sabrina E; Tatarko, Alexander; González, Roberto; Didier, Nicolas; Carrasco, Diego; Lay, Siugmin; Nizharadze, George; Torres, Ana; Camino, Leoncio; Abuhamdeh, Sami; Macapagal, Ma Elizabeth J; Koller, Silvia H; Herman, Ginette; Courtois, Marie; Fritsche, Immo; Espinosa, Agustín; Villamar, Juan A; Regalia, Camillo; Manzi, Claudia; Brambilla, Maria; Zinkeng, Martina; Jalal, Baland; Kusdil, Ersin; Amponsah, Benjamin; Çağlar, Selinay; Mekonnen, Kassahun Habtamu; Möller, Bettina; Zhang, Xiao; Schweiger Gallo, Inge; Prieto Gil, Paula; Lorente Clemares, Raquel; Campara, Gabriella; Aldhafri, Said; Fülöp, Márta; Pyszczynski, Tom; Kesebir, Pelin; Harb, Charles

    2016-12-01

    Variations in acquiescence and extremity pose substantial threats to the validity of cross-cultural research that relies on survey methods. Individual and cultural correlates of response styles when using 2 contrasting types of response mode were investigated, drawing on data from 55 cultural groups across 33 nations. Using 7 dimensions of self-other relatedness that have often been confounded within the broader distinction between independence and interdependence, our analysis yields more specific understandings of both individual- and culture-level variations in response style. When using a Likert-scale response format, acquiescence is strongest among individuals seeing themselves as similar to others, and where cultural models of selfhood favour harmony, similarity with others and receptiveness to influence. However, when using Schwartz's (2007) portrait-comparison response procedure, acquiescence is strongest among individuals seeing themselves as self-reliant but also connected to others, and where cultural models of selfhood favour self-reliance and self-consistency. Extreme responding varies less between the two types of response modes, and is most prevalent among individuals seeing themselves as self-reliant, and in cultures favouring self-reliance. As both types of response mode elicit distinctive styles of response, it remains important to estimate and control for style effects to ensure valid comparisons. © 2016 International Union of Psychological Science.

  6. High-throughput sequencing reveals differing immune responses in the intestinal mucosa of two inbred lines afflicted with necrotic enteritis.

    Science.gov (United States)

    Truong, Anh Duc; Hong, Yeong Ho; Lillehoj, Hyun S

    2015-08-15

    We investigated the necrotic enteritis (NE)-induced transcripts of immune-related genes in the intestinal mucosa of two highly inbred White Leghorn chicken lines, line 6.3 and line 7.2, which share the same MHC haplotype and show different levels of NE susceptibility using high-throughput RNA sequencing (RNA-Seq) technology. NE was induced by the previously described co-infection model using Eimeria maxima and Clostridium perfringens. The RNA-Seq generated over 38 million sequence reads for Marek's disease (MD)-resistant line 6.3 and over 40 million reads for the MD-susceptible line 7.2. Alignment of these sequences with the Gallus gallus genome database revealed the expression of over 29,900 gene transcripts induced by NE in these two lines, among which 7,841 genes were significantly upregulated and 2,919 genes were downregulated in line 6.3 chickens and 6,043 genes were significantly upregulated and 2,764 genes were downregulated in NE-induced line 7.2 compared with their uninfected controls. Analysis of 560 differentially expressed genes (DEGs) using the gene ontology database revealed annotations for 246 biological processes, 215 molecular functions, and 81 cellular components. Among the 53 cytokines and 96 cytokine receptors, 15 cytokines and 29 cytokine receptors were highly expressed in line 6.3, whereas the expression of 15 cytokines and 15 cytokine receptors was higher in line 7.2 than in line 6.3 (fold change ≥ 2, p<0.01). In a hierarchical cluster analysis of novel mRNAs, the novel mRNA transcriptome showed higher expression in line 6.3 than in line 7.2, which is consistent with the expression profile of immune-related target genes. In qRT-PCR and RNA-Seq analysis, all the genes examined showed similar responses to NE (correlation coefficient R=0.85-0.89, p<0.01) in both lines 6.3 and 7.2. This study is the first report describing NE-induced DEGs and novel transcriptomes using RNA-seq data from two inbred chicken lines showing different levels of NE

  7. Correcting for non-response bias in contingent valuation surveys concerning environmental non-market goods

    DEFF Research Database (Denmark)

    Bonnichsen, Ole; Olsen, Søren Bøye

    2016-01-01

    to be part of an Internet panel and subsequently whether they wish to participate in the survey, thereby introducing two elements of potential self-selection. These elements may be correlated with preferences, thus making the respondents a non-random and non-representative sample, ultimately biasing results....... This paper analyses a sample used for an Internet contingent valuation method survey eliciting preferences for improvements in water quality of a river. We find that some variables that affect the survey participation decision also affect willingness-to-pay, consequently biasing our welfare estimates. We...... show how adjusting willingness-to-pay for this bias can be accomplished by using a grouped data model incorporating a correlation parameter to account for selection....

  8. Balancing the dual responsibilities of business unit controllers: field and survey evidence

    NARCIS (Netherlands)

    Maas, V.S.; Matejka, M.

    2009-01-01

    We examine how business unit (BU) controllers balance their dual roles of providing information for both local decision-making (local responsibility) and corporate control (functional responsibility). The existing literature suggests that organizations can improve the quality of financial reporting

  9. Transcriptome analysis of proton pump inhibitor-responsive esophageal eosinophilia reveals proton pump inhibitor-reversible allergic inflammation.

    Science.gov (United States)

    Wen, Ting; Dellon, Evan S; Moawad, Fouad J; Furuta, Glenn T; Aceves, Seema S; Rothenberg, Marc E

    2015-01-01

    Esophageal eosinophilia can be proton pump inhibitor (PPI) resistant or responsive, representing 2 entities known as eosinophilic esophagitis (EoE) and PPI-responsive esophageal eosinophilia (PPI-REE), respectively. Although they present with similar clinical features, EoE is accepted to be an antigen-driven, TH2-associated allergic disorder, whereas the cause of PPI-REE remains a mystery. In this study, our aim was to investigate the pathogenesis of PPI-REE by using a recently described EoE diagnostic panel (EDP) composed of a set of 94 esophageal transcripts and to determine whether PPI therapy reverses any esophageal transcriptional abnormalities. We evaluated the EDP signature in biopsy samples obtained from adult and pediatric patients with PPI-REE from 4 institutions and compared the pre- and post-PPI therapy expression profiles of these subjects with those of patients with active EoE. The EDP differentiated patients with EoE from control subjects with 100% accuracy among the 4 clinical sites. Bioinformatics analysis revealed largely overlapping transcriptomes between patients with PPI-REE and those with EoE, including the genes for eosinophil chemotaxis (eotaxin 3, CCL26), barrier molecules (desmoglein 1, DSG1), tissue remodeling (periostin, POSTN), and mast cells (carboxypeptidase A, CPA3). PPI monotherapy alone almost completely reversed the allergic inflammatory transcriptome of patients with PPI-REE. Furthermore, we identified a set of candidate genes to differentiate patients with EoE from those with PPI-REE before treatment. These findings provide definitive evidence that PPI-REE is a disease entity with significant molecular overlap with EoE, suggesting that many patients with PPI-REE represent a continuum of the same pathogenic allergic mechanisms that underlie EoE and thus might constitute a subphenotype of patients with EoE. The ability of PPI therapy to nearly entirely reverse gene expression associated with PPI-REE, particularly that associated

  10. Transcriptional response of P. pastoris in fed-batch cultivations to Rhizopus oryzae lipase production reveals UPR induction

    Directory of Open Access Journals (Sweden)

    Valero Francisco

    2007-07-01

    Full Text Available Abstract Background The analysis of transcriptional levels of the genes involved in protein synthesis and secretion is a key factor to understand the host organism's responses to recombinant protein production, as well as their interaction with the cultivation conditions. Novel techniques such as the sandwich hybridization allow monitoring quantitatively the dynamic changes of specific RNAs. In this study, the transcriptional levels of some genes related to the unfolded protein response (UPR and central metabolism of Pichia pastoris were analysed during batch and fed-batch cultivations using an X-33-derived strain expressing a Rhizopus oryzae lipase under control of the formaldehyde dehydrogenase promoter (FLD1, namely the alcohol oxidase gene AOX1, the formaldehyde dehydrogenase FLD1, the protein disulfide isomerase PDI, the KAR2 gene coding for the BiP chaperone, the 26S rRNA and the R. oryzae lipase gene ROL. Results The transcriptional levels of the selected set of genes were first analysed in P. pastoris cells growing in shake flask cultures containing different carbon and nitrogen sources combinations, glycerol + ammonium, methanol + methylamine and sorbitol + methylamine. The transcriptional levels of the AOX1 and FLD1 genes were coherent with the known regulatory mechanism of C1 substrates in P. pastoris, whereas ROL induction lead to the up-regulation of KAR2 and PDI transcriptional levels, thus suggesting that ROL overexpression triggers the UPR. This was further confirmed in fed-batch cultivations performed at different growth rates. Transcriptional levels of the analysed set of genes were generally higher at higher growth rates. Nevertheless, when ROL was overexpressed in a strain having the UPR constitutively activated, significantly lower relative induction levels of these marker genes were detected. Conclusion The bead-based sandwich hybridization assay has shown its potential as a reliable instrument for quantification of

  11. Transcriptome-wide analysis reveals candidate genes responsible for the asymmetric pigment pattern in scallop Patinopecten yessoensis

    Directory of Open Access Journals (Sweden)

    XJ Sun

    2016-09-01

    Full Text Available Transcriptome-wide analysis reveals candidate genes responsible for the asymmetric pigment pattern in scallop Patinopecten yessoensis XJ Sun, LQ Zhou, ZH Liu, B Wu, AG Yang Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China Accepted September 14, 2016 Abstract Yesso scallop Patinopecten yessoensis is an economically important marine bivalve species in aquaculture and fishery in Asian countries. The colors of the left and right shells are obviously distinct, typically having reddish-brown for the left and white for the right. This left-right asymmetric pigment pattern is a very unique phenomenon among invertebrates, whereas the molecular mechanisms that control regional differences in pigmentation are not clear. To better understand the left-right asymmetric pigment pattern, we apply Illumina digital gene expression (DGE to characterize the gene expression profiles in left and right mantle tissues, and identify five differentially expressed genes, including Cytochrome P450 and other four unknown genes. Among the five genes, one gene shows significantly higher expression in the right mantle, while other four exhibit significantly higher expression in the left mantle. We further validate the DGE results by using quantitative real-time PCR for P450, resulting in approximately 32-fold higher expression in the left mantle than that in the right mantle. These findings will not only help assist our understanding of the sophisticated processes of shell pigmentation in scallops, but also provide new insights into the adaptive evolution of phenotypes to maximize survival that underlie the left-right asymmetric pigment pattern in molluscs.

  12. The early asthmatic response is associated with glycolysis, calcium binding and mitochondria activity as revealed by proteomic analysis in rats

    Directory of Open Access Journals (Sweden)

    Xu Yu-Dong

    2010-08-01

    Full Text Available Abstract Background The inhalation of allergens by allergic asthmatics results in the early asthmatic response (EAR, which is characterized by acute airway obstruction beginning within a few minutes. The EAR is the earliest indicator of the pathological progression of allergic asthma. Because the molecular mechanism underlying the EAR is not fully defined, this study will contribute to a better understanding of asthma. Methods In order to gain insight into the molecular basis of the EAR, we examined changes in protein expression patterns in the lung tissue of asthmatic rats during the EAR using 2-DE/MS-based proteomic techniques. Bioinformatic analysis of the proteomic data was then performed using PPI Spider and KEGG Spider to investigate the underlying molecular mechanism. Results In total, 44 differentially expressed protein spots were detected in the 2-DE gels. Of these 44 protein spots, 42 corresponded to 36 unique proteins successfully identified using mass spectrometry. During subsequent bioinformatic analysis, the gene ontology classification, the protein-protein interaction networking and the biological pathway exploration demonstrated that the identified proteins were mainly involved in glycolysis, calcium binding and mitochondrial activity. Using western blot and semi-quantitative RT-PCR, we confirmed the changes in expression of five selected proteins, which further supports our proteomic and bioinformatic analyses. Conclusions Our results reveal that the allergen-induced EAR in asthmatic rats is associated with glycolysis, calcium binding and mitochondrial activity, which could establish a functional network in which calcium binding may play a central role in promoting the progression of asthma.

  13. Lipidomic profiling of Saccharomyces cerevisiae and Zygosaccharomyces bailii reveals critical changes in lipid composition in response to acetic acid stress.

    Science.gov (United States)

    Lindberg, Lina; Santos, Aline Xs; Riezman, Howard; Olsson, Lisbeth; Bettiga, Maurizio

    2013-01-01

    When using microorganisms as cell factories in the production of bio-based fuels or chemicals from lignocellulosic hydrolysate, inhibitory concentrations of acetic acid, released from the biomass, reduce the production rate. The undissociated form of acetic acid enters the cell by passive diffusion across the lipid bilayer, mediating toxic effects inside the cell. In order to elucidate a possible link between lipid composition and acetic acid stress, the present study presents detailed lipidomic profiling of the major lipid species found in the plasma membrane, including glycerophospholipids, sphingolipids and sterols, in Saccharomyces cerevisiae (CEN.PK 113_7D) and Zygosaccharomyces bailii (CBS7555) cultured with acetic acid. Detailed physiological characterization of the response of the two yeasts to acetic acid has also been performed in aerobic batch cultivations using bioreactors. Physiological characterization revealed, as expected, that Z. bailii is more tolerant to acetic acid than S. cerevisiae. Z. bailii grew at acetic acid concentrations above 24 g L(-1), while limited growth of S. cerevisiae was observed after 11 h when cultured with only 12 g L(-1) acetic acid. Detailed lipidomic profiling using electrospray ionization, multiple-reaction-monitoring mass spectrometry (ESI-MRM-MS) showed remarkable changes in the glycerophospholipid composition of Z. bailii, including an increase in saturated glycerophospholipids and considerable increases in complex sphingolipids in both S. cerevisiae (IPC 6.2×, MIPC 9.1×, M(IP)2C 2.2×) and Z. bailii (IPC 4.9×, MIPC 2.7×, M(IP)2C 2.7×), when cultured with acetic acid. In addition, the basal level of complex sphingolipids was significantly higher in Z. bailii than in S. cerevisiae, further emphasizing the proposed link between lipid saturation, high sphingolipid levels and acetic acid tolerance. The results also suggest that acetic acid tolerance is associated with the ability of a given strain to generate large

  14. High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment

    Energy Technology Data Exchange (ETDEWEB)

    Handley, Kim M.; Wrighton, Kelly E.; Piceno, Y. M.; Anderson, Gary L.; DeSantis, Todd; Williams, Kenneth H.; Wilkins, Michael J.; N' Guessan, A. L.; Peacock, Aaron; Bargar, John R.; Long, Philip E.; Banfield, Jillian F.

    2012-06-13

    There is increasing interest in harnessing the functional diversity of indigenous microbial communities to transform and remediate a wide range of environmental contaminants. Understanding the response of communities to stimulation, including flanking taxa, presents important opportunities for optimizing remediation approaches. We used high-density PhyloChip microarray analysis to comprehensively determine community membership and abundance patterns amongst a suite of samples from U(VI) bioremediation experiments. Samples were unstimulated or collected during Fe(III) and sulfate reduction from an acetate-augmented aquifer in Rifle, Colorado, and from laboratory experiments using field-collected materials. Results showed the greatest diversity in abundant SRB lineages was present in naturally-reduced sediment. Desulfuromonadales and Desulfobacterales were consistently identified as the dominant Fe(III)- and sulfate-reducing bacteria (IRB and SRB) throughout acetate amendment experiments. Stimulated communities also exhibited a high degree of functional redundancy amongst enriched flanking members. Not surprisingly, competition for both sulfate and iron was evident amongst abundant taxa, but the distribution and abundance of these ancillary SRB (Peptococcaceae, Desulfovibrionales and Syntrophobacterales), and lineages containing IRB (excluding Desulfobacteraceae) was heterogeneous amongst sample types. Interesting, amongst the most abundant taxa, particularly during sulfate reduction, were Epsilonproteobacteria that perform microaerobic or nitrate-dependant sulfur oxidation, and a number of bacteria other than Geobacteraceae that may enzymatically reduce U(VI). Finally, in depth community probing with PhyloChip determined the efficacy of experimental approaches, notably revealing striking similarity amongst stimulated sediment (from drill cores and in-situ columns) and groundwater communities, and demonstrating that sediment-packed in-situ (down-well) columns served

  15. Lipidomic Profiling of Saccharomyces cerevisiae and Zygosaccharomyces bailii Reveals Critical Changes in Lipid Composition in Response to Acetic Acid Stress

    Science.gov (United States)

    Riezman, Howard; Olsson, Lisbeth; Bettiga, Maurizio

    2013-01-01

    When using microorganisms as cell factories in the production of bio-based fuels or chemicals from lignocellulosic hydrolysate, inhibitory concentrations of acetic acid, released from the biomass, reduce the production rate. The undissociated form of acetic acid enters the cell by passive diffusion across the lipid bilayer, mediating toxic effects inside the cell. In order to elucidate a possible link between lipid composition and acetic acid stress, the present study presents detailed lipidomic profiling of the major lipid species found in the plasma membrane, including glycerophospholipids, sphingolipids and sterols, in Saccharomyces cerevisiae (CEN.PK 113_7D) and Zygosaccharomyces bailii (CBS7555) cultured with acetic acid. Detailed physiological characterization of the response of the two yeasts to acetic acid has also been performed in aerobic batch cultivations using bioreactors. Physiological characterization revealed, as expected, that Z. bailii is more tolerant to acetic acid than S. cerevisiae. Z. bailii grew at acetic acid concentrations above 24 g L−1, while limited growth of S. cerevisiae was observed after 11 h when cultured with only 12 g L−1 acetic acid. Detailed lipidomic profiling using electrospray ionization, multiple-reaction-monitoring mass spectrometry (ESI-MRM-MS) showed remarkable changes in the glycerophospholipid composition of Z. bailii, including an increase in saturated glycerophospholipids and considerable increases in complex sphingolipids in both S. cerevisiae (IPC 6.2×, MIPC 9.1×, M(IP)2C 2.2×) and Z. bailii (IPC 4.9×, MIPC 2.7×, M(IP)2C 2.7×), when cultured with acetic acid. In addition, the basal level of complex sphingolipids was significantly higher in Z. bailii than in S. cerevisiae, further emphasizing the proposed link between lipid saturation, high sphingolipid levels and acetic acid tolerance. The results also suggest that acetic acid tolerance is associated with the ability of a given strain to generate large

  16. Lipidomic profiling of Saccharomyces cerevisiae and Zygosaccharomyces bailii reveals critical changes in lipid composition in response to acetic acid stress.

    Directory of Open Access Journals (Sweden)

    Lina Lindberg

    Full Text Available When using microorganisms as cell factories in the production of bio-based fuels or chemicals from lignocellulosic hydrolysate, inhibitory concentrations of acetic acid, released from the biomass, reduce the production rate. The undissociated form of acetic acid enters the cell by passive diffusion across the lipid bilayer, mediating toxic effects inside the cell. In order to elucidate a possible link between lipid composition and acetic acid stress, the present study presents detailed lipidomic profiling of the major lipid species found in the plasma membrane, including glycerophospholipids, sphingolipids and sterols, in Saccharomyces cerevisiae (CEN.PK 113_7D and Zygosaccharomyces bailii (CBS7555 cultured with acetic acid. Detailed physiological characterization of the response of the two yeasts to acetic acid has also been performed in aerobic batch cultivations using bioreactors. Physiological characterization revealed, as expected, that Z. bailii is more tolerant to acetic acid than S. cerevisiae. Z. bailii grew at acetic acid concentrations above 24 g L(-1, while limited growth of S. cerevisiae was observed after 11 h when cultured with only 12 g L(-1 acetic acid. Detailed lipidomic profiling using electrospray ionization, multiple-reaction-monitoring mass spectrometry (ESI-MRM-MS showed remarkable changes in the glycerophospholipid composition of Z. bailii, including an increase in saturated glycerophospholipids and considerable increases in complex sphingolipids in both S. cerevisiae (IPC 6.2×, MIPC 9.1×, M(IP2C 2.2× and Z. bailii (IPC 4.9×, MIPC 2.7×, M(IP2C 2.7×, when cultured with acetic acid. In addition, the basal level of complex sphingolipids was significantly higher in Z. bailii than in S. cerevisiae, further emphasizing the proposed link between lipid saturation, high sphingolipid levels and acetic acid tolerance. The results also suggest that acetic acid tolerance is associated with the ability of a given strain to

  17. European survey on laboratory preparedness, response and diagnostic capacity for crimean-congo haemorrhagic fever, 2012

    NARCIS (Netherlands)

    M.D. Fernandez-Garcia (Maria Dolores); A. Negredo; A. Papa (Anna); O. Donoso-Mantke; M. Niedrig; H. Zeller; A. Tenorio; L. Franco (Leticia); S.W. Aberle (Stephan W.); M. van Esbroeck (M.); I. Christova; A. Markotic (Alemka); I.-C. Kurolt (Ivan-Christian); H. Zelena (Hana); I. Golovljova; D. Pannetier (Delphine); R. Charrel (Remi); J. Schmidt-Chanasit (Jonas); R. Wölfel (Roman); A. Papa (Anna); M.R. Capobianchi (Maria Rosaria); X. Jakupi (Xhevat); J. Storozenko (Jelena); A. Griskevicius (Algis); G. Bosevska (Golubinka); C. Muscat (Clive); M. Schutten (Martin); S.G. Dudman (Susanne Gjeruldsen); M.J. Alves (M. João); C.S. Ceianu; A. Platonov (Alexander); B. Bozovic (Bojana); B. Klempa; T. Avsic (Tatjana); A. Tenorio; Å. Lundkvist (Åke); P. Cherpillod (Pascal); G. Korukluoglu; D.W.G. Brown (D. W G); T. Brooks (Tim)

    2014-01-01

    textabstractCrimean-Congo haemorrhagic fever (CCHF) is an infectious viral disease that has (re-)emerged in the last decade in south-eastern Europe, and there is a risk for further geographical expansion to western Europe. Here we report the results of a survey covering 28 countries, conducted in 20

  18. Testing the Canon: Student Responses to Texts by Medieval Women in English Literature Surveys.

    Science.gov (United States)

    Hawkins, Ann R.

    While there has been a great deal of debate about enlarging the canon, less attention has been paid to how students respond to "new" literary figures such as Margery Kempe and Julian of Norwich, or to how instructors should incorporate them into an already cramped literature survey course. Instructors must consider some questions that…

  19. The Development of an Emotional Response to Writing Measure: The Affective Cognition Writing Survey

    Science.gov (United States)

    Fischer, Ronald G.; Fischer, Jerome M.; Jain, Sachin

    2010-01-01

    This study was designed to develop and initiate the validation of the Affective Cognition Writing Survey (ACWS), a psychological instrument used to measure emotional expression through writing. Procedures for development and validation of the instrument are reported. Subsequently, factor analysis extracted six factors: Positive Processing,…

  20. Framing Higher Education: Questions and Responses in the British Social Attitudes Survey, 1983-2010

    Science.gov (United States)

    Mountford-Zimdars, Anna; Jones, Steven; Sullivan, Alice; Heath, Anthony

    2013-01-01

    This article focuses on questions and attitudes towards higher education in the British Social Attitudes (BSA) survey series. First, we analyse the changing BSA questions (1983-2010) in the context of key policy reports. Our results show that changes in the framing of higher education questions correspond with changes in the macro-discourse of…

  1. 2011 Workplace and Equal Opportunity Survey of Reserve Component Members: Tabulations of Responses

    Science.gov (United States)

    2014-03-01

    230  2011 Workplace and Equal Opportunity Survey of Reserve Component Members DMDC ix b.  Feeling down, depressed , or hopeless... Depression scale: Constructed from Q59. Depression is a common mental disorder characterized by depressed mood, loss of interest or pleasure...graffiti, music , stories) which were racist or showed your race/ethnicity negatively

  2. Crisis Response in the Public Schools: A Survey of School Psychologists' Experiences and Perceptions

    Science.gov (United States)

    Adamson, Austin D.; Peacock, Gretchen Gimpel

    2007-01-01

    In this study, 228 school psychologists completed a survey regarding crisis intervention teams and plans. The majority of respondents indicated their schools had crisis plans (95.1%) and teams (83.6%). The most common team activities endorsed by participants involved providing direct assistance and services to students, staff, and the media. The…

  3. Austin Community College Management Response to Employee Satisfaction Survey, Spring 2000.

    Science.gov (United States)

    Austin Community Coll., TX.

    Findings from an Employee Satisfaction Survey conducted in spring 2000 at Austin Community College (ACC) (Texas) indicate that: (1) staff in many areas need customer service training; (2) telephones are not used effectively by many offices; (3) many areas are not able to respond quickly to the needs of college staff; and (4) 18 highly used areas…

  4. Measuring subjective response to aircraft noise: The effects of survey context

    NARCIS (Netherlands)

    Kroesen, M.; Molin, E.J.E.; Van Wee, G.P.

    2013-01-01

    In applied research, noise annoyance is often used as indicator of subjective reaction to aircraft noise in residential areas. The present study aims to show that the meaning which respondents attach to the concept of aircraft noise annoyance is partly a function of survey context. To this purpose a

  5. Are Divorce Studies Trustworthy? The Effects of Survey Nonresponse and Response Errors

    Science.gov (United States)

    Mitchell, Colter

    2010-01-01

    Researchers rely on relationship data to measure the multifaceted nature of families. This article speaks to relationship data quality by examining the ramifications of different types of error on divorce estimates, models predicting divorce behavior, and models employing divorce as a predictor. Comparing matched survey and divorce certificate…

  6. Rates, Delays, and Completeness of General Practitioners’ Responses to a Postal Versus Web-Based Survey: A Randomized Trial

    Science.gov (United States)

    Maisonneuve, Hubert; Cerutti, Bernard; Fournier, Jean Pascal; Senn, Nicolas; Haller, Dagmar M

    2017-01-01

    Background Web-based surveys have become a new and popular method for collecting data, but only a few studies have directly compared postal and Web-based surveys among physicians, and none to our knowledge among general practitioners (GPs). Objective Our aim is to compare two modes of survey delivery (postal and Web-based) in terms of participation rates, response times, and completeness of questionnaires in a study assessing GPs’ preventive practices. Methods This randomized study was conducted in Western Switzerland (Geneva and Vaud) and in France (Alsace and Pays de la Loire) in 2015. A random selection of community-based GPs (1000 GPs in Switzerland and 2400 GPs in France) were randomly allocated to receive a questionnaire about preventive care activities either by post (n=700 in Switzerland, n=400 in France) or by email (n=300 in Switzerland, n=2000 in France). Reminder messages were sent once in the postal group and twice in the Web-based group. Any GPs practicing only complementary and alternative medicine were excluded from the study. Results Among the 3400 contacted GPs, 764 (22.47%, 95% CI 21.07%-23.87%) returned the questionnaire. Compared to the postal group, the participation rate in the Web-based group was more than four times lower (246/2300, 10.70% vs 518/1100, 47.09%, Pparticipation in surveys while reducing costs. PMID:28330830

  7. Quantitative Transcriptomics Reveals the Growth- and Nutrient-Dependent Response of a Streamlined Marine Methylotroph to Methanol and Naturally Occurring Dissolved Organic Matter.

    Science.gov (United States)

    Gifford, Scott M; Becker, Jamie W; Sosa, Oscar A; Repeta, Daniel J; DeLong, Edward F

    2016-11-22

    substantial influence on marine organic matter flux, yet the carbon components targeted by specific bacterial groups, as well as how those groups' metabolic activities change under different conditions, are not well understood. Gene expression studies of model organisms can identify these responses under defined conditions, which can then be compared to environmental transcriptomes to elucidate in situ activities. This integration, however, is limited by the data's relative nature. Here, we report the fully quantitative transcriptome of a marine bacterium, providing a genome-wide survey of cellular transcript abundances and how they change with different states of growth, nutrient conditions, and carbon substrates. The results revealed the dynamic metabolic strategies this methylotroph has for processing both simple one-carbon compounds and the complex multicarbon substrates of naturally derived marine organic matter and provide baseline quantitative data for identifying their in situ activities and impact on the marine carbon cycle.

  8. The Grism Lens-amplified Survey from Space (Glass). IX. The Dual Origin of Low-mass Cluster Galaxies as Revealed by New Structural Analyses

    Science.gov (United States)

    Morishita, Takahiro; Abramson, Louis E.; Treu, Tommaso; Vulcani, Benedetta; Schmidt, Kasper B.; Dressler, Alan; Poggianti, Bianca M.; Malkan, Matthew A.; Wang, Xin; Huang, Kuang-Han; Trenti, Michele; Bradač, Maruša; Hoag, Austin

    2017-02-01

    Using deep Hubble Frontier Fields imaging and slitless spectroscopy from the Grism Survey from Space, we study 2200 cluster and 1748 field galaxies at 0.2≤slant z≤slant 0.7 to determine the impact of environment on galaxy size and structure at stellar masses {log}{M}* /{M}ȯ > 7.8, an unprecedented limit at these redshifts. Based on simple assumptions—{r}e=f({M}* )—we find no significant differences in half-light radii (r e ) between equal-mass cluster or field systems. More complex analyses—{r}e=f({M}* ,U-V,n,z,{{Σ }})—reveal local density (Σ) to induce only a 7% ± 3% (95% confidence) reduction in r e beyond what can be accounted for by U ‑ V color, Sérsic index (n), and redshift (z) effects. Almost any size difference between galaxies in high- and low-density regions is thus attributable to their different distributions in properties other than environment. Indeed, we find a clear color–r e correlation in low-mass passive cluster galaxies ({log}{M}* /{M}ȯ star-forming galaxies. We take this as evidence that large-r e low-mass passive cluster galaxies are recently acquired systems that have been environmentally quenched without significant structural transformation (e.g., by ram pressure stripping or starvation). Conversely, ∼20% of small-r e low-mass passive cluster galaxies appear to have been in place since z≳ 3. Given the consistency of the small-r e galaxies’ stellar surface densities (and even colors) with those of systems more than ten times as massive, our findings suggest that clusters mark places where galaxy evolution is accelerated for an ancient base population spanning most masses, with late-time additions quenched by environment-specific mechanisms mainly restricted to the lowest masses.

  9. The crustal structure of continental shelf in northern South China Sea: revealed by joint onshore-offshore wide-angle seismic survey

    Science.gov (United States)

    Cao, Jinghe; Sun, Jinlong; Xia, Shaohong; Wan, Kuiyuan; Xu, Huilong

    2017-04-01

    Known as a significant region for studying tectonic relationship between South China block and South China Sea (SCS) block and evolution of rifted basin in continental margin, the continental shelf of northern SCS not only preserved the information about intensive tectonic deformation and magmatism generated by the west Pacific subducted to Eurasian Plate in late Mesozoic, but also recorded the process from continental margin rifting to seafloor spreading of SCS in Cenozoic for the same mechanical property. To investigate crustal structure of continental shelf in northern SCS, a wide-angle onshore-offshore seismic experiment and a coincident multi-channel seismic (MCS) profile were carried out across the onshore-offshore transitional zone in northern SCS, 2010. A total of 14 stations consisted of ocean bottom seismometers, portable and permanent land stations were deployed during the survey. The two-dimensional precise crustal structure model of central continental shelf in northern SCS was constructed from onshore to offshore. The model reveals that South China block is a typical continental crust with a 30-32 km Moho depth, and a localized high-velocity anomaly in middle-lower crust under land area near Hong Kong was imaged, which may reflect magma underplating caused by subduction of paleo-Pacific plate in late Mesozoic. The Littoral Fault Zone (LFZ) lies 12 km south of Dangan Island with a width of 18-20 km low-velocity fracture zone from surface to Moho discontinuity. The shelf zone south of LFZ was consisted of a differential thinning upper and lower continental crust, which indicate stretch thinning of passive continent margin during the Cenozoic spreading of the SCS. All these results appear to further confirm that the northern margin of SCS experienced a transition from active margin to passive one during late Mesozoic and Cenozoic.

  10. Monitoring physiology trainee needs to focus professional society responses: the APS Trainee Needs Surveys.

    Science.gov (United States)

    Matyas, Marsha L; Lowy, Melinda E; Sweazea, Karen L; Alvarez, Diego F

    2011-06-01

    In 2004 and 2007, the American Physiological Society (APS) Trainee Advisory Committee (TAC) conducted surveys of graduate students, postdoctoral fellows, and new investigators in physiology to identify topics and issues important to those trainees. Two major trends emerged from the data. First, trainees in 2007 expressed somewhat greater interest in professional development information than did those in 2004. Second, needs expressed by trainees in both years were closely related to their specific career development stage. Survey findings guided the TAC and other APS committees and groups to focus their efforts toward the issues that were of the greatest interest to trainees. It also led to improved communication with trainees and increased involvement of trainees in APS governance.

  11. A survey of some ovarian abnormalities responsible for sterility in Damascus goats

    Directory of Open Access Journals (Sweden)

    A survey of some ovarian abnormalities responsible for sterility in Damascus goats M. Roukbi

    2013-12-01

    Full Text Available A survey of some ovarian abnormalities in 13 Damascus goats with normal to masculinized genitalia, aged 1.5 to 6 years was conducted to determine some types of disorders affecting the ovaries in light of their morphological findings with reference to obstetrics and gynecology literature. The results showed persistent follicles and cystic ovarian disease in phenotypically females, epidermal neoplasms, gonads dysgenesis and dysgenesic gonad tumors in goats with intersex appearance, similar to ovarian tumors in women

  12. Too Many Blood Donors – Response Bias in the Swiss Health Survey 2012

    Science.gov (United States)

    Volken, Thomas; Bänziger, Andreas; Buser, Andreas; Castelli, Damiano; Fontana, Stefano; Frey, Beat M.; Sarraj, Amira; Sigle, Jörg; Thierbach, Jutta; Weingand, Tina; Mansouri-Taleghani, Behrouz

    2016-01-01

    Background Data on blood donor status obtained from general surveys and health interview surveys have been widely used. However, the integrity of data on self-reported blood donor status from surveys may be threatened by sampling and non-sampling error. Our study aimed to compare self-reported blood donors (including one-time as well as regular donors) from the Swiss Health Survey 2012 (SHS) with register-based blood donors recorded by blood establishments and evaluate the direction and magnitude of bias in the SHS. Methods We compared population-weighted SHS point estimates of the number of blood donors with their corresponding 95% confidence intervals to the respective figures from blood donor registries (birth cohorts 1978-1993) and estimates of donors based on period donor tables derived from blood donor registries (birth cohorts 1920-1993). Results In the birth cohorts 1978-1993, the SHS-predicted number of donors was 1.8 times higher than the respective number of donors based on registry data. Adjusting for foreign and naturalized Swiss nationals that immigrated after their 18th birthday, the SHS overall predicted number of donors was 1.6 times higher. Similarly, SHS estimates for the 1920-1993 birth cohorts were 2.4 and 2.1 times higher as compared to register-based estimates. Generally, the differences between SHS and register-based donors were more pronounced in men than in women. Conclusion Self-reported blood donor status in the SHS is biased. Estimates of blood donors are substantially higher than respective estimates based on blood donor registries. PMID:27994526

  13. 2015 Workplace and Gender Relations Survey of Reserve Component Members: Tabulations of Responses

    Science.gov (United States)

    2016-03-17

    3 gender , relationship status, and race/ethnicity. 2. Time Reference— Important key events to provide frame of reference for respondents on the time...enforcing sexual harassment or Equal Opportunity regulations (Q63c/Q63d). NR: Not reportable NA: Not applicable 2015 Workplace and Gender Relations... Equal Opportunity regulations (Q63c/Q63d). NR: Not reportable NA: Not applicable 2015 Workplace and Gender Relations Survey of Reserve Component

  14. 2012 Workplace and Gender Relations Survey of Active Duty Members. Tabulations of Responses

    Science.gov (United States)

    2013-04-01

    enjoyment , and the opportunity to acquire valuable skills .................................................. 96 15. Overall, how well prepared...538 87. Suppose you see a Service member, who you do not know very well, getting drunk at a party. Someone tells you that one of...The composite measure includes survey items on sense of pride, use of skills, work enjoyment , and the opportunity to acquire valuable skills (Q14a-d

  15. Survey and online discussion groups to develop a patient-rated outcome measure on acceptability of treatment response in vitiligo.

    Science.gov (United States)

    Tour, Selina K; Thomas, Kim S; Walker, Dawn-Marie; Leighton, Paul; Yong, Adrian Sw; Batchelor, Jonathan M

    2014-06-14

    Vitiligo is a chronic depigmenting skin disorder which affects around 0.5-1% of the world's population. The outcome measures used most commonly in trials to judge treatment success focus on repigmentation. Patient-reported outcome measures of treatment success are rarely used, although recommendations have been made for their inclusion in vitiligo trials. This study aimed to evaluate the face validity of a new patient-reported outcome measure of treatment response, for use in future trials and clinical practice. An online survey to gather initial views on what constitutes treatment success for people with vitiligo or their parents/carers, followed by online discussion groups with patients to reach consensus on what constitutes treatment success for individuals with vitiligo, and how this can be assessed in the context of trials. Participants were recruited from an existing database of vitiligo patients and through posts on the social network sites Facebook and Twitter. A total of 202 survey responses were received, of which 37 were excluded and 165 analysed. Three main themes emerged as important in assessing treatment response: a) the match between vitiligo and normal skin (how well it blends in); b) how noticeable the vitiligo is and c) a reduction in the size of the white patches. The majority of respondents said they would consider 80% or more repigmentation to be a worthwhile treatment response after 9 months of treatment. Three online discussion groups involving 12 participants led to consensus that treatment success is best measured by asking patients how noticeable their vitiligo is after treatment. This was judged to be best answered using a 5-point Likert scale, on which a score of 4 or 5 represents treatment success. This study represents the first step in developing a patient reported measure of treatment success in vitiligo trials. Further work is now needed to assess its construct validity and responsiveness to change.

  16. Responses to language barriers in consultations with refugees and asylum seekers: a telephone survey of Irish general practitioners.

    LENUS (Irish Health Repository)

    MacFarlane, Anne

    2008-01-01

    BACKGROUND: Refugees and asylum seekers experience language barriers in general practice. Qualitative studies have found that responses to language barriers in general practice are ad hoc with use of both professional interpreters and informal interpreters (patients\\' relatives or friends). However, the scale of the issues involved is unknown. This study quantifies the need for language assistance in general practice consultations and examines the experience of, and satisfaction with, methods of language assistance utilized. METHODS: Data were collected by telephone survey with general practitioners in a regional health authority in Ireland between July-August 2004. Each respondent was asked a series of questions about consulting with refugees and asylum seekers, the need for language assistance and the kind of language assistance used. RESULTS: There was a 70% (n = 56\\/80) response