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Sample records for survey responses revealed

  1. Puerto Rico Revealed Preference Survey Data 2004

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Revealed preference models provide insights into recreational angler behavior and the economic value of recreational fishing trips. Revealed preference data is...

  2. 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

  3. Survey of High Throughput RNA-Seq Data Reveals Potential Roles for lncRNAs during Development and Stress Response in Bread Wheat

    Directory of Open Access Journals (Sweden)

    Shumayla

    2017-06-01

    Full Text Available Long non-coding RNAs (lncRNAs are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of lncRNAs in certain plant species, but they are less known in Triticum aestivum (bread wheat. Herein, we analyzed 52 RNA seq data (>30 billion reads and identified 44,698 lncRNAs in T. aestivum genome, which were characterized in comparison to the coding sequences (mRNAs. Similar to the mRNAs, lncRNAs were also derived from each sub-genome and chromosome, and showed tissue developmental stage specific and differential expression, as well. The modulated expression of lncRNAs during abiotic stresses like heat, drought, and salt indicated their putative role in stress response. The co-expression of lncRNAs with vital mRNAs including various transcription factors and enzymes involved in Abscisic acid (ABA biosynthesis, and gene ontology mapping inferred their regulatory roles in numerous biological processes. A few lncRNAs were predicted as precursor (19 lncRNAs, while some as target mimics (1,047 lncRNAs of known miRNAs involved in various regulatory functions. The results suggested numerous functions of lncRNAs in T. aestivum, and unfolded the opportunities for functional characterization of individual lncRNA in future studies.

  4. Improving Survey Response Rates in Online Panels

    DEFF Research Database (Denmark)

    Pedersen, Mogens Jin; Nielsen, Christian Videbæk

    2016-01-01

    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...... 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...... 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...

  5. The new galaxy evolution paradigm revealed by the Herschel surveys

    Science.gov (United States)

    Eales, Stephen; Smith, Dan; Bourne, Nathan; Loveday, Jon; Rowlands, Kate; van der Werf, Paul; Driver, Simon; Dunne, Loretta; Dye, Simon; Furlanetto, Cristina; Ivison, R. J.; Maddox, Steve; Robotham, Aaron; Smith, Matthew W. L.; Taylor, Edward N.; Valiante, Elisabetta; Wright, Angus; Cigan, Philip; De Zotti, Gianfranco; Jarvis, Matt J.; Marchetti, Lucia; Michałowski, Michał J.; Phillipps, Steven; Viaene, Sebastien; Vlahakis, Catherine

    2018-01-01

    The Herschel Space Observatory has revealed a very different galaxyscape from that shown by optical surveys which presents a challenge for galaxy-evolution models. The Herschel surveys reveal (1) that there was rapid galaxy evolution in the very recent past and (2) that galaxies lie on a single Galaxy Sequence (GS) rather than a star-forming 'main sequence' and a separate region of 'passive' or 'red-and-dead' galaxies. The form of the GS is now clearer because far-infrared surveys such as the Herschel ATLAS pick up a population of optically red star-forming galaxies that would have been classified as passive using most optical criteria. The space-density of this population is at least as high as the traditional star-forming population. By stacking spectra of H-ATLAS galaxies over the redshift range 0.001 high stellar masses, high star-formation rates but, even several billion years in the past, old stellar populations - they are thus likely to be relatively recent ancestors of early-type galaxies in the Universe today. The form of the GS is inconsistent with rapid quenching models and neither the analytic bathtub model nor the hydrodynamical EAGLE simulation can reproduce the rapid cosmic evolution. We propose a new gentler model of galaxy evolution that can explain the new Herschel results and other key properties of the galaxy population.

  6. Northern goshawk broadcast surveys: Hawk response variables and survey cost

    Science.gov (United States)

    Suzanne M. Joy; Richard T. Reynolds; Douglas G. Leslie

    1994-01-01

    We examined responses of Northern Goshawks (Accipter gentilis) to taped broadcast calls of conspecifics in tree-harvest areas and around alternate goshawk nests on Kaibab National Forest, Arizona, in 1991 and 1992. Forest areas totaling 476 km2 were systematically surveyed for goshawks. Ninety responses by adult and juvenile goshawks were elicited...

  7. Effect of survey mode on response patterns

    DEFF Research Database (Denmark)

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

    2014-01-01

    .7%). Marital status, ethnic background and highest completed education were associated with non-response in both modes. Furthermore, sex and age were associated with non-response in the self-administered mode. No significant mode effects were observed for indicators related to use of health services......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...

  8. Response Strategies and Response Styles in Cross-Cultural Surveys

    NARCIS (Netherlands)

    Morren, M.H.; Gelissen, J.P.T.M.; Vermunt, J.K.

    2012-01-01

    This article addresses the following research questions: Do respondents participating in cross-cultural surveys differ in their response style when responding to attitude statements? If so, are characteristics of the response process associated with their ethnicity and generation of immigration? To

  9. Identifying Careless Responses in Survey Data

    Science.gov (United States)

    Meade, Adam W.; Craig, S. Bartholomew

    2012-01-01

    When data are collected via anonymous Internet surveys, particularly under conditions of obligatory participation (such as with student samples), data quality can be a concern. However, little guidance exists in the published literature regarding techniques for detecting careless responses. Previously several potential approaches have been…

  10. Survey of corporate social responsibility practices in Nigerian manufacturing sector

    OpenAIRE

    Akinyomi, Oladele John

    2013-01-01

    Based on stakeholders’ theory, this study examined the practice of corporate social responsibility by manufacturing companies in Nigeria. It employed survey research design to study 15 randomly selected companies in the food and beverages sector. A total of 225 questionnaires were administered to collect data. Data analysis revealed that CSR is a familiar concept in the sector as most of the companies do engage in CSR activities regularly. The major areas of focus of the CSR activities includ...

  11. A Comparison of Response Rate, Response Time, and Costs of Mail and Electronic Surveys.

    Science.gov (United States)

    Shannon, David M.; Bradshaw, Carol C.

    2002-01-01

    Compared response rates, response time, and costs of mail and electronic surveys using a sample of 377 college faculty members. Mail surveys yielded a higher response rate and a lower rate of undeliverable surveys, but response time was longer and costs were higher than for electronic surveys. (SLD)

  12. Non-response weighting adjustment approach in survey sampling ...

    African Journals Online (AJOL)

    Hence the discussion is illustrated with real examples from surveys (in particular 2003 KDHS) conducted by Central Bureau of Statistics (CBS) - Kenya. Some suggestions are made for improving the quality of non-response weighting. Keywords: Survey non-response; non-response adjustment factors; weighting; sampling ...

  13. Study of a twisted ATLAS SCT Barrel deformation as revealed by a photogrammetric survey

    CERN Document Server

    Dobson, E; Heinemann, F; Karagoz-Unel, M

    2007-01-01

    A photogrammetry survey on the SCT barrels was performed as an engineering check on the structure of the ATLAS Semiconductor Tracker (SCT) shortly after construction. Analysis of the data obtained revealed small scale elliptical deformation as well as a twist of the structure. The results of the survey are presented as well as interpolation of the measured targets to the module positions and a comparison with track based alignment measurements.

  14. 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.

  15. Survey reveals public open to ban on hand-held cell phone use and texting.

    Science.gov (United States)

    2013-01-01

    A study performed by the Bureau of Transportation Statistics (BTS) reveals that the public is open to a ban on hand-held cell phone use while driving. The study is based on data from 2009s Omnibus Household Survey (OHS), which is administered by B...

  16. Maximising nurses' and midwives' response rates to surveys.

    Science.gov (United States)

    Cooper, Alannah Louise; Brown, Janie

    2017-12-18

    Low response rates to surveys have been a long-standing issue in research. This includes research involving nurses and midwives. To gain representative samples, appropriate measures to maximise response rates need to be used. To explore ways to maximise response rates from nurses and midwives, using a hospital-wide survey as an example. All nurses and midwives at the study hospital were invited to participate in a survey. To encourage participation and elicit an adequate response rate, several strategies were used. A total of 1,000 surveys were distributed and 319 (32%) were returned. All the required age groups, levels of experience and types of nursing registration were represented in the responses and data saturation was achieved. It is important to pay attention to obtaining a representative sample. Further investigation of response rates to surveys by nurses and midwives is warranted. Strategies to maximise response rates from a target population should be used when conducting surveys. ©2017 RCN Publishing Company Ltd. All rights reserved. Not to be copied, transmitted or recorded in any way, in whole or part, without prior permission of the publishers.

  17. 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…

  18. Assessment of health surveys: fitting a multidimensional graded response model.

    Science.gov (United States)

    Depaoli, Sarah; Tiemensma, Jitske; Felt, John M

    The multidimensional graded response model, an item response theory (IRT) model, can be used to improve the assessment of surveys, even when sample sizes are restricted. Typically, health-based survey development utilizes classical statistical techniques (e.g. reliability and factor analysis). In a review of four prominent journals within the field of Health Psychology, we found that IRT-based models were used in less than 10% of the studies examining scale development or assessment. However, implementing IRT-based methods can provide more details about individual survey items, which is useful when determining the final item content of surveys. An example using a quality of life survey for Cushing's syndrome (CushingQoL) highlights the main components for implementing the multidimensional graded response model. Patients with Cushing's syndrome (n = 397) completed the CushingQoL. Results from the multidimensional graded response model supported a 2-subscale scoring process for the survey. All items were deemed as worthy contributors to the survey. The graded response model can accommodate unidimensional or multidimensional scales, be used with relatively lower sample sizes, and is implemented in free software (example code provided in online Appendix). Use of this model can help to improve the quality of health-based scales being developed within the Health Sciences.

  19. 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…

  20. The effectiveness of a monetary incentive offer on survey response rates and response completeness in a longitudinal study.

    Science.gov (United States)

    Yu, Shengchao; Alper, Howard E; Nguyen, Angela-Maithy; Brackbill, Robert M; Turner, Lennon; Walker, Deborah J; Maslow, Carey B; Zweig, Kimberly C

    2017-04-26

    Achieving adequate response rates is an ongoing challenge for longitudinal studies. The World Trade Center Health Registry is a longitudinal health study that periodically surveys a cohort of ~71,000 people exposed to the 9/11 terrorist attacks in New York City. Since Wave 1, the Registry has conducted three follow-up surveys (Waves 2-4) every 3-4 years and utilized various strategies to increase survey participation. A promised monetary incentive was offered for the first time to survey non-respondents in the recent Wave 4 survey, conducted 13-14 years after 9/11. We evaluated the effectiveness of a monetary incentive in improving the response rate five months after survey launch, and assessed whether or not response completeness was compromised due to incentive use. The study compared the likelihood of returning a survey for those who received an incentive offer to those who did not, using logistic regression models. Among those who returned surveys, we also examined whether those receiving an incentive notification had higher rate of response completeness than those who did not, using negative binomial regression models and logistic regression models. We found that a $10 monetary incentive offer was effective in increasing Wave 4 response rates. Specifically, the $10 incentive offer was useful in encouraging initially reluctant participants to respond to the survey. The likelihood of returning a survey increased by 30% for those who received an incentive offer (AOR = 1.3, 95% CI: 1.1, 1.4), and the incentive increased the number of returned surveys by 18%. Moreover, our results did not reveal any significant differences on response completeness between those who received an incentive offer and those who did not. In the face of the growing challenge of maintaining a high response rate for the World Trade Center Health Registry follow-up surveys, this study showed the value of offering a monetary incentive as an additional refusal conversion strategy. Our

  1. 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.

  2. Determination for energy response and directionality of neutron survey meters

    International Nuclear Information System (INIS)

    Chen Changmao; Liu Jinhua; Xie Jianlun; Su Jingling

    1992-01-01

    The energy response and directionality of neutron survey meter type MK7 and 2202D are determined. The reactor thermal column beam, reactor filtered beams (6 eV, 24.4 keV and 144 keV), 226 Ra-Be, 241 Am-Be, 252 Cf and its moderated sources are used for the measurement. The results shows: the survey meters are influenced obviously by the direction; the response of middle-energy region is large, the energy response of 2202D is better than MK7

  3. Comparing web and mail responses in a mixed mode survey in college alcohol use research

    Science.gov (United States)

    McCabe, Sean Esteban; Diez, Alison; Boyd, Carol J.; Nelson, Toben F.; Weitzman, Elissa R.

    2011-01-01

    Objective This exploratory study examined potential mode effects (web versus U.S. mail) in a mixed mode design survey of alcohol use at eight U.S. colleges. Methods Randomly selected students from eight U.S. colleges were invited to participate in a self-administered survey on their alcohol use in the spring of 2002. Data were collected initially by web survey (n =2619) and non-responders to this mode were mailed a hardcopy survey (n =628). Results College students who were male, living on-campus and under 21 years of age were significantly more likely to complete the initial web survey. Multivariate analyses revealed few substantive differences between survey modality and alcohol use measures. Conclusions The findings from this study provide preliminary evidence that web and mail surveys produce comparable estimates of alcohol use in a non-randomized mixed mode design. The results suggest that mixed mode survey designs could be effective at reaching certain college sub-populations and improving overall response rate while maintaining valid measurement of alcohol use. Web surveys are gaining popularity in survey research and more work is needed to examine whether these results can extend to web surveys generally or are specific to mixed mode designs. PMID:16460882

  4. Intentional exposure to loud music: the second MTV.com survey reveals an opportunity to educate.

    Science.gov (United States)

    Quintanilla-Dieck, Maria de Lourdes; Artunduaga, Maria Alexandra; Eavey, Roland D

    2009-10-01

    Music-induced hearing loss (MIHL), an unconsciously self-inflicted public health concern, could evolve into an epidemic because of the appeal of loud music. After media attention about a previous hearing-loss survey with Music Television (MTV.com), we hypothesized that a repeat survey could compare awareness and behavior trends. We incorporated the 2002 survey into the new 73-question instrument presented to random visitors on the MTV.com website in 2007. A P music exposure. Health care providers were the least likely source of MIHL awareness despite the respondents favoring provider education for hearing protection behavior modification. Most respondents still could not recall learning about prevention of potential hearing loss, although the media has become the most informative source. Most respondents indicated that they would adopt protective ear behavior if made aware of hearing loss risk, especially if informed by health care professionals, revealing an educational opportunity.

  5. 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...

  6. 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.

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

    KAUST Repository

    Kuo, Dwight; Tan, Kai; Zinman, Guy; Ravasi, Timothy; Bar-Joseph, Ziv; Ideker, Trey

    2010-01-01

    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.

  8. 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.

  9. 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.

  10. 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.

  11. Approximate median regression for complex survey data with skewed response.

    Science.gov (United States)

    Fraser, Raphael André; Lipsitz, Stuart R; Sinha, Debajyoti; Fitzmaurice, Garrett M; Pan, Yi

    2016-12-01

    The ready availability of public-use data from various large national complex surveys has immense potential for the assessment of population characteristics using regression models. Complex surveys can be used to identify risk factors for important diseases such as cancer. Existing statistical methods based on estimating equations and/or utilizing resampling methods are often not valid with survey data due to complex survey design features. That is, stratification, multistage sampling, and weighting. In this article, we accommodate these design features in the analysis of highly skewed response variables arising from large complex surveys. Specifically, we propose a double-transform-both-sides (DTBS)'based estimating equations approach to estimate the median regression parameters of the highly skewed response; the DTBS approach applies the same Box-Cox type transformation twice to both the outcome and regression function. The usual sandwich variance estimate can be used in our approach, whereas a resampling approach would be needed for a pseudo-likelihood based on minimizing absolute deviations (MAD). Furthermore, the approach is relatively robust to the true underlying distribution, and has much smaller mean square error than a MAD approach. The method is motivated by an analysis of laboratory data on urinary iodine (UI) concentration from the National Health and Nutrition Examination Survey. © 2016, The International Biometric Society.

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

    OpenAIRE

    Torres van Grinsven Vanessa; Bolko Irena; Bavdaž 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. 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 extrinsi...

  13. Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome

    Directory of Open Access Journals (Sweden)

    Ferrari Francesco

    2009-06-01

    Full Text Available Abstract Background Water stress during grain filling has a marked effect on grain yield, leading to a reduced endosperm cell number and thus sink capacity to accumulate dry matter. The bread wheat cultivar Chinese Spring (CS, a Chinese Spring terminal deletion line (CS_5AL-10 and the durum wheat cultivar Creso were subjected to transcriptional profiling after exposure to mild and severe drought stress at the grain filling stage to find evidences of differential stress responses associated to different wheat genome regions. Results The transcriptome analysis of Creso, CS and its deletion line revealed 8,552 non redundant probe sets with different expression levels, mainly due to the comparisons between the two species. The drought treatments modified the expression of 3,056 probe sets. Besides a set of genes showing a similar drought response in Creso and CS, cluster analysis revealed several drought response features that can be associated to the different genomic structure of Creso, CS and CS_5AL-10. Some drought-related genes were expressed at lower level (or not expressed in Creso (which lacks the D genome or in the CS_5AL-10 deletion line compared to CS. The chromosome location of a set of these genes was confirmed by PCR-based mapping on the D genome (or the 5AL-10 region. Many clusters were characterized by different level of expression in Creso, CS and CS_AL-10, suggesting that the different genome organization of the three genotypes may affect plant adaptation to stress. Clusters with similar expression trend were grouped and functional classified to mine the biological mean of their activation or repression. Genes involved in ABA, proline, glycine-betaine and sorbitol pathways were found up-regulated by drought stress. Furthermore, the enhanced expression of a set of transposons and retrotransposons was detected in CS_5AL-10. Conclusion Bread and durum wheat genotypes were characterized by a different physiological reaction to water

  14. 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…

  15. A questionnaire survey of senior house officers/registrars response ...

    African Journals Online (AJOL)

    A questionnaire survey of senior house officers/registrars response to their training at University College Hospital, Ibadan. ... A regular conduct of auditing of training programmes is recommended. Keywords: Questionnaire ... spécialistes. Nous proposons l'organisation régulière de la verification de programme de formation.

  16. Rising Mercury, Rising Hostility: How Heat Affects Survey Response

    Science.gov (United States)

    Cohen, Alexander H.; Krueger, James S.

    2016-01-01

    Recent social scientific research has examined connections between public opinion and weather conditions. This article contributes to this literature by analyzing the relationship between high temperature and survey response. Because hot temperatures are associated with aggression, irritation, and negativity, such conditions should lead to the…

  17. Mapping neighborhood scale survey responses with uncertainty metrics

    Directory of Open Access Journals (Sweden)

    Charles Robert Ehlschlaeger

    2016-12-01

    Full Text Available This paper presents a methodology of mapping population-centric social, infrastructural, and environmental metrics at neighborhood scale. This methodology extends traditional survey analysis methods to create cartographic products useful in agent-based modeling and geographic information analysis. It utilizes and synthesizes survey microdata, sub-upazila attributes, land use information, and ground truth locations of attributes to create neighborhood scale multi-attribute maps. Monte Carlo methods are employed to combine any number of survey responses to stochastically weight survey cases and to simulate survey cases' locations in a study area. Through such Monte Carlo methods, known errors from each of the input sources can be retained. By keeping individual survey cases as the atomic unit of data representation, this methodology ensures that important covariates are retained and that ecological inference fallacy is eliminated. These techniques are demonstrated with a case study from the Chittagong Division in Bangladesh. The results provide a population-centric understanding of many social, infrastructural, and environmental metrics desired in humanitarian aid and disaster relief planning and operations wherever long term familiarity is lacking. Of critical importance is that the resulting products have easy to use explicit representation of the errors and uncertainties of each of the input sources via the automatically generated summary statistics created at the application's geographic scale.

  18. 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.

  19. 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…

  20. Survey of French spine surgeons reveals significant variability in spine trauma practices in 2013.

    Science.gov (United States)

    Lonjon, G; Grelat, M; Dhenin, A; Dauzac, C; Lonjon, N; Kepler, C K; Vaccaro, A R

    2015-02-01

    In France, attempts to define common ground during spine surgery meetings have revealed significant variability in clinical practices across different schools of surgery and the two specialities involved in spine surgery, namely, neurosurgery and orthopaedic surgery. To objectively characterise this variability by performing a survey based on a fictitious spine trauma case. Our working hypothesis was that significant variability existed in trauma practices and that this variability was related to a lack of strong scientific evidence in spine trauma care. We performed a cross-sectional survey based on a clinical vignette describing a 31-year-old male with an L1 burst fracture and neurologic symptoms (numbness). Surgeons received the vignette and a 14-item questionnaire on the management of this patient. For each question, surgeons had to choose among five possible answers. Differences in answers across surgeons were assessed using the Index of Qualitative Variability (IQV), in which 0 indicates no variability and 1 maximal variability. Surgeons also received a questionnaire about their demographics and surgical experience. Of 405 invited spine surgeons, 200 responded to the survey. Five questions had an IQV greater than 0.9, seven an IQV between 0.5 and 0.9, and two an IQV lower than 0.5. Variability was greatest about the need for MRI (IQV=0.93), degree of urgency (IQV=0.93), need for fusion (IQV=0.92), need for post-operative bracing (IQV=0.91), and routine removal of instrumentation (IQV=0.94). Variability was lowest for questions about the need for surgery (IQV=0.42) and use of the posterior approach (IQV=0.36). Answers were influenced by surgeon specialty, age, experience level, and type of centre. Clinical practice regarding spine trauma varies widely in France. Little published evidence is available on which to base recommendations that would diminish this variability. Copyright © 2015. Published by Elsevier Masson SAS.

  1. A survey of optometry leadership: participation in disaster response.

    Science.gov (United States)

    Psoter, Walter J; Glotzer, David L; Weiserbs, Kera Fay; Baek, Linda S; Karloopia, Rajiv

    2012-01-01

    A study was completed to assess the academic and state-level professional optometry leadership views regarding optometry professionals as surge responders in the event of a catastrophic event. A cross-sectional survey was conducted using a 21-question, self-administered, structured questionnaire. All U.S. optometry school deans and state optometric association presidents were mailed a questionnaire and instructions to return it by mail on completion; 2 repeated mailings were made. Descriptive statistics were produced and differences between deans and association presidents were tested by Fisher exact test. The questionnaire response rate was 50% (25 returned/50 sent) for the state association presidents and 65% (11/17) for the deans. There were no statistically significant differences between the leadership groups for any survey questions. All agreed that optometrists have the skills, are ethically obligated to help, and that optometrists should receive additional training for participation in disaster response. There was general agreement that optometrists should provide first-aid, obtain medical histories, triage, maintain infection control, manage a point of distribution, prescribe medications, and counsel the "worried well." Starting intravenous lines, interpreting radiographs, and suturing were less favorably supported. There was some response variability between the 2 leadership groups regarding potential sources for training. The overall opinion of optometry professional leadership is that with additional training, optometrists can and should provide an important reserve pool of catastrophic event responders. Copyright © 2011 American Optometric Association. Published by Elsevier Inc. All rights reserved.

  2. Survey of system responsibility in the Nordic countries. Final report

    International Nuclear Information System (INIS)

    2005-02-01

    In September 2004 the Nordic Council of Ministers asked Nordel to perform some tasks and present the results to the Council on 1 March 2005. One of the tasks is to survey how system responsibility is defined and executed in the different Nordic countries. According to the Nordic Council of Ministers, the survey shall illuminate similarities and differences between the countries and assess the reasons for the differences. Nordel is asked to present a joint view system responsibility in the Nordic countries. Among other things, the responsibility for the system operators and the participants in the market shall be defined. The definition shall also include the distribution of costs between costs for network business and costs for business in competition. This shall be done in a way that creates a common platform for the further harmonisation work and continuous positive development of the Nordic electricity market. It is also important to identify the need for changes in e.g. legislation and guidelines in the different countries as a consequence of an implementation of a common definition in the Nordic countries. Areas to be included in the task are among others, balance settlement, security of supply, congestion management and system services. (BA)

  3. Neuropathological survey reveals underestimation of the prevalence of neuroinfectious diseases in cattle in Switzerland.

    Science.gov (United States)

    Truchet, Laura; Walland, Julia; Wüthrich, Daniel; Boujon, Céline L; Posthaus, Horst; Bruggmann, Rémy; Schüpbach-Regula, Gertraud; Oevermann, Anna; Seuberlich, Torsten

    2017-09-01

    Neuroinfectious diseases in livestock represent a severe threat to animal health, but their prevalence is not well documented and the etiology of disease often remains unidentified. The aims of this study were to generate baseline data on the prevalence of neuroinfectious diseases in cattle in Switzerland by neuropathological survey, and to identify disease-associated pathogens. The survey was performed over a 1-year period using a representative number of brainstem samples (n=1816) from fallen cattle. In total, 4% (n=73) of the animals had significant lesions, the most frequent types of which were indicative of viral (n=27) and bacterial (n=31) etiologies. Follow-up diagnostics by immunohistochemistry, PCR protocols and next-generation sequencing identified infection with Listeria monocytogenes (n=6), ovine herpesvirus 2 (n=7), bovine astrovirus CH13 (n=2), bovine herpesvirus 6 (n=6), bovine retrovirus CH15 (n=2), posavirus 1 (n=2), and porcine astroviruses (n=2). A retrospective questionnaire-based investigation indicated that animals' owners observed clinical signs of neurological disease in about one-third of cases with lesions, which was estimated to correspond to approximately 85 cases per year in the adult fallen cattle population in Switzerland. This estimate stands in sharp contrast to the number of cases reported to the authorities and reveals a gap in disease surveillance. Systematic neuropathological examination and follow-up molecular testing of neurologically diseased cattle could significantly enhance the efficiency of disease detection for the purposes of estimating the prevalence of endemic diseases, identifying new or re-emerging pathogens, and providing "early warnings" of disease outbreaks. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. 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.

  5. 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…

  6. 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.

  7. 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.

  8. 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.

  9. Responsive survey design, demographic data collection, and models of demographic behavior.

    Science.gov (United States)

    Axinn, William G; Link, Cynthia F; Groves, Robert M

    2011-08-01

    To address declining response rates and rising data-collection costs, survey methodologists have devised new techniques for using process data ("paradata") to address nonresponse by altering the survey design dynamically during data collection. We investigate the substantive consequences of responsive survey design-tools that use paradata to improve the representative qualities of surveys and control costs. By improving representation of reluctant respondents, responsive design can change our understanding of the topic being studied. Using the National Survey of Family Growth Cycle 6, we illustrate how responsive survey design can shape both demographic estimates and models of demographic behaviors based on survey data. By juxtaposing measures from regular and responsive data collection phases, we document how special efforts to interview reluctant respondents may affect demographic estimates. Results demonstrate the potential of responsive survey design to change the quality of demographic research based on survey data.

  10. Developing and testing the CHORDS: Characteristics of Responsible Drinking Survey.

    Science.gov (United States)

    Barry, Adam E; Goodson, Patricia

    2011-01-01

    Report on the development and psychometric testing of a theoretically and evidence-grounded instrument, the Characteristics of Responsible Drinking Survey (CHORDS). Instrument subjected to four phases of pretesting (cognitive validity, cognitive and motivational qualities, pilot test, and item evaluation) and a final posttest implementation. Large public university in Texas. Randomly selected convenience sample (n  =  729) of currently enrolled students. This 78-item questionnaire measures individuals' responsible drinking beliefs, motivations, intentions, and behaviors. Cronbach α, split-half reliability, principal components analysis and Spearman ρ were conducted to investigate reliability, stability, and validity. Measures in the CHORDS exhibited high internal consistency reliability and strong correlations of split-half reliability. Factor analyses indicated five distinct scales were present, as proposed in the theoretical model. Subscale composite scores also exhibited a correlation to alcohol consumption behaviors, indicating concurrent validity. The CHORDS represents the first instrument specifically designed to assess responsible drinking beliefs and behaviors. It was found to elicit valid and reliable data among a college student sample. This instrument holds much promise for practitioners who desire to empirically investigate dimensions of responsible drinking.

  11. Effects of Personalization and Invitation Email Length on Web-Based Survey Response Rates

    Science.gov (United States)

    Trespalacios, Jesús H.; Perkins, Ross A.

    2016-01-01

    Individual strategies to increase response rate and survey completion have been extensively researched. Recently, efforts have been made to investigate a combination of interventions to yield better response rates for web-based surveys. This study examined the effects of four different survey invitation conditions on response rate. From a large…

  12. Survey of tyrosine kinase signaling reveals ROS kinase fusions in human cholangiocarcinoma.

    Directory of Open Access Journals (Sweden)

    Ting-Lei Gu

    Full Text Available Cholangiocarcinoma, also known as bile duct cancer, is the second most common primary hepatic carcinoma with a median survival of less than 2 years. The molecular mechanisms underlying the development of this disease are not clear. To survey activated tyrosine kinases signaling in cholangiocarcinoma, we employed immunoaffinity profiling coupled to mass spectrometry and identified DDR1, EPHA2, EGFR, and ROS tyrosine kinases, along with over 1,000 tyrosine phosphorylation sites from about 750 different proteins in primary cholangiocarcinoma patients. Furthermore, we confirmed the presence of ROS kinase fusions in 8.7% (2 out of 23 of cholangiocarcinoma patients. Expression of the ROS fusions in 3T3 cells confers transforming ability both in vitro and in vivo, and is responsive to its kinase inhibitor. Our data demonstrate that ROS kinase is a promising candidate for a therapeutic target and for a diagnostic molecular marker in cholangiocarcinoma. The identification of ROS tyrosine kinase fusions in cholangiocarcinoma, along with the presence of other ROS kinase fusions in lung cancer and glioblastoma, suggests that a more broadly based screen for activated ROS kinase in cancer is warranted.

  13. 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

    Directory of Open Access Journals (Sweden)

    Witt Julia

    2011-09-01

    Full Text Available Abstract Background 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. Methods 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. Results 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

  14. 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

  15. ROV advanced magnetic survey for revealing archaeological targets and estimating medium magnetization

    Science.gov (United States)

    Eppelbaum, Lev

    2013-04-01

    Magnetic survey is one of most applied geophysical method for searching and localization of any objects with contrast magnetic properties (for instance, in Israel detailed magneric survey has been succesfully applied at more than 60 archaeological sites (Eppelbaum, 2010, 2011; Eppelbaum et al., 2011, 2010)). However, land magnetic survey at comparatively large archaeological sites (with observation grids 0.5 x 0.5 or 1 x 1 m) may occupy 5-10 days. At the same time the new Remote Operation Vehicle (ROV) generation - small and maneuvering vehicles - can fly at levels of few (and even one) meters over the earth's surface (flowing the relief forms or straight). Such ROV with precise magnetic field measurements (with a frequency of 20-25 observations per second) may be performed during 10-30 minutes, moreover at different levels over the earth's surface. Such geophysical investigations should have an extremely low exploitation cost. Finally, measurements of geophysical fields at different observation levels could provide new unique geophysical-archaeological information (Eppelbaum, 2005; Eppelbaum and Mishne, 2011). The developed interpretation methodology for magnetic anomalies advanced analysis (Khesin et al., 1996; Eppelbaum et al., 2001; Eppelbaum et al., 2011) may be successfully applied for ROV magnetic survey for delineation of archaeological objects and estimation averaged magnetization of geological medium. This methodology includes: (1) non-conventional procedure for elimination of secondary effect of magnetic temporary variations, (2) calculation of rugged relief influence by the use of a correlation method, (3) estimation of medium magnetization, (4) application of various informational and wavelet algorithms for revealing low anomalous effects against the strong noise background, (5) advanced procedures for magnetic anomalies quantitative analysis (they are applicable in conditions of rugged relief, inclined magnetization, and an unknown level of the total

  16. 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.

  17. Visualization-based analysis of multiple response survey data

    Science.gov (United States)

    Timofeeva, Anastasiia

    2017-11-01

    During the survey, the respondents are often allowed to tick more than one answer option for a question. Analysis and visualization of such data have difficulties because of the need for processing multiple response variables. With standard representation such as pie and bar charts, information about the association between different answer options is lost. The author proposes a visualization approach for multiple response variables based on Venn diagrams. For a more informative representation with a large number of overlapping groups it is suggested to use similarity and association matrices. Some aggregate indicators of dissimilarity (similarity) are proposed based on the determinant of the similarity matrix and the maximum eigenvalue of association matrix. The application of the proposed approaches is well illustrated by the example of the analysis of advertising sources. Intersection of sets indicates that the same consumer audience is covered by several advertising sources. This information is very important for the allocation of the advertising budget. The differences between target groups in advertising sources are of interest. To identify such differences the hypothesis of homogeneity and independence are tested. Recent approach to the problem are briefly reviewed and compared. An alternative procedure is suggested. It is based on partition of a consumer audience into pairwise disjoint subsets and includes hypothesis testing of the difference between the population proportions. It turned out to be more suitable for the real problem being solved.

  18. Assessing Response Bias in a Web Survey at a University Faculty

    Science.gov (United States)

    Menachemi, Nir

    2011-01-01

    Online surveys are increasingly common due to the myriad of benefits they offer over traditional survey methods. However, research has shown that response rates to web-based surveys are typically lower than to traditional surveys and can possibly yield biased results. University-based faculty members are a unique cohort that may be ideally suited…

  19. 2003 Survey of Retired Military: Tabulations of Responses

    National Research Council Canada - National Science Library

    Kroeger; Ceervantes, Flores; Jones; Wilson

    2004-01-01

    .... Survey Content Topics covered in the survey primarily addressed the post-service employment and earnings experiences of military retirees, with emphasis on the effects of combat- related disabilities...

  20. Alcohol responsiveness in laryngeal dystonia: A survey study

    Science.gov (United States)

    Kirke, Diana N.; Frucht, Steven J.; Simonyan, Kristina

    2015-01-01

    Laryngeal dystonia (LD) is a task-specific focal dystonia of unknown pathophysiology affecting speech production. We examined the demographics of anecdotally reported alcohol use and its effects on LD symptoms using an online survey based on Research Electronic Data Capture (REDCap™) and National Spasmodic Dysphonia Association’s patient registry. From 641 participants, 531 were selected for data analysis, and 110 were excluded because of unconfirmed diagnosis. A total of 406 patients (76.5%) had LD and 125 (23.5%) had LD and voice tremor (LD/VT). The consumption of alcohol was reported by 374 LD (92.1%) and 109 LD/VT (87.2%) patients. Improvement of voice symptoms after alcohol ingestion was noted by 227 LD (55.9% of all patients) and 73 LD/VT (58.4%), which paralleled the improvement observed by patient’s family and/or friends in 214 LD (57.2%) and 69 LD/VT (63.3%) patients. The benefits lasted 1–3 hours in both groups with the maximum effect after 2 drinks in LD patients (p = 0.002), whereas LD/VT symptoms improved independent of the consumed amount (p = 0.48). Our data suggest that isolated dystonic symptoms, such as in LD, are responsive to alcohol intake and this responsiveness is not attributed to the presence of VT, which is known to have significant benefits from alcohol ingestion. Alcohol may modulate the pathophysiological mechanisms underlying abnormal neurotransmission of γ-aminobutyric acid (GABA) in dystonia and as such provide new avenues for novel therapeutic options in these patients. PMID:25929664

  1. 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.

  2. Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination

    OpenAIRE

    Li, Xi; Miao, Hongyu; Henn, Alicia; Topham, David J.; Wu, Hulin; Zand, Martin S.; Mosmann, Tim R.

    2012-01-01

    Although previous studies have found minimal changes in CD4 T cell responses after vaccination of adults with trivalent inactivated influenza vaccine, daily sampling and monitoring of the proliferation marker Ki-67 have now been used to reveal that a substantial fraction of influenza-specific CD4 T cells respond to vaccination. At 4–6 days after vaccination, there is a sharp rise in the numbers of Ki-67-expressing PBMC that produce IFNγ, IL-2 and/or TNFα in vitro in response to influenza vacc...

  3. 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...

  4. Synoptic sky surveys and the diffuse supernova neutrino background: Removing astrophysical uncertainties and revealing invisible supernovae

    International Nuclear Information System (INIS)

    Lien, Amy; Fields, Brian D.; Beacom, John F.

    2010-01-01

    The cumulative (anti)neutrino production from all core-collapse supernovae within our cosmic horizon gives rise to the diffuse supernova neutrino background (DSNB), which is on the verge of detectability. The observed flux depends on supernova physics, but also on the cosmic history of supernova explosions; currently, the cosmic supernova rate introduces a substantial (±40%) uncertainty, largely through its absolute normalization. However, a new class of wide-field, repeated-scan (synoptic) optical sky surveys is coming online, and will map the sky in the time domain with unprecedented depth, completeness, and dynamic range. We show that these surveys will obtain the cosmic supernova rate by direct counting, in an unbiased way and with high statistics, and thus will allow for precise predictions of the DSNB. Upcoming sky surveys will substantially reduce the uncertainties in the DSNB source history to an anticipated ±5% that is dominated by systematics, so that the observed high-energy flux thus will test supernova neutrino physics. The portion of the universe (z < or approx. 1) accessible to upcoming sky surveys includes the progenitors of a large fraction (≅87%) of the expected 10-26 MeV DSNB event rate. We show that precision determination of the (optically detected) cosmic supernova history will also make the DSNB into a strong probe of an extra flux of neutrinos from optically invisible supernovae, which may be unseen either due to unexpected large dust obscuration in host galaxies, or because some core-collapse events proceed directly to black hole formation and fail to give an optical outburst.

  5. Stochasticity in the enterococcal sex pheromone response revealed by quantitative analysis of transcription in single cells.

    Science.gov (United States)

    Breuer, Rebecca J; Bandyopadhyay, Arpan; O'Brien, Sofie A; Barnes, Aaron M T; Hunter, Ryan C; Hu, Wei-Shou; Dunny, Gary M

    2017-07-01

    In Enterococcus faecalis, sex pheromone-mediated transfer of antibiotic resistance plasmids can occur under unfavorable conditions, for example, when inducing pheromone concentrations are low and inhibiting pheromone concentrations are high. To better understand this paradox, we adapted fluorescence in situ hybridization chain reaction (HCR) methodology for simultaneous quantification of multiple E. faecalis transcripts at the single cell level. We present direct evidence for variability in the minimum period, maximum response level, and duration of response of individual cells to a specific inducing condition. Tracking of induction patterns of single cells temporally using a fluorescent reporter supported HCR findings. It also revealed subpopulations of rapid responders, even under low inducing pheromone concentrations where the overall response of the entire population was slow. The strong, rapid induction of small numbers of cells in cultures exposed to low pheromone concentrations is in agreement with predictions of a stochastic model of the enterococcal pheromone response. The previously documented complex regulatory circuitry controlling the pheromone response likely contributes to stochastic variation in this system. In addition to increasing our basic understanding of the biology of a horizontal gene transfer system regulated by cell-cell signaling, demonstration of the stochastic nature of the pheromone response also impacts any future efforts to develop therapeutic agents targeting the system. Quantitative single cell analysis using HCR also has great potential to elucidate important bacterial regulatory mechanisms not previously amenable to study at the single cell level, and to accelerate the pace of functional genomic studies.

  6. What do consumer surveys and experiments reveal and conceal about consumer preferences for genetically modified foods?

    Science.gov (United States)

    Colson, Gregory; Rousu, Matthew C

    2013-01-01

    Assessing consumer perceptions and willingness to pay for genetically modified (GM) foods has been one of the most active areas of empirical research in agricultural economics. Researchers over the past 15 years have delivered well over 100 estimates of consumers' willingness to pay for GM foods using surveys and experimental methods. In this review, we explore a number of unresolved issues related to three questions that are critical when considering the sum of the individual contributions that constitute the evidence on consumer preferences for GM foods.

  7. DOTD customer satisfaction survey frequency responses and cross-tabulations.

    Science.gov (United States)

    2004-01-01

    The Louisiana Department of Transportation and Development (DOTD) conducted this customer satisfaction survey to determine levels of satisfaction overall and with select components of the state maintained highway system. An A, B, C, D and F letter ga...

  8. 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)

  9. 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.

  10. 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.

  11. Relationships between drought, heat and air humidity responses revealed by transcriptome-metabolome co-analysis.

    Science.gov (United States)

    Georgii, Elisabeth; Jin, Ming; Zhao, Jin; Kanawati, Basem; Schmitt-Kopplin, Philippe; Albert, Andreas; Winkler, J Barbro; Schäffner, Anton R

    2017-07-10

    Elevated temperature and reduced water availability are frequently linked abiotic stresses that may provoke distinct as well as interacting molecular responses. Based on non-targeted metabolomic and transcriptomic measurements from Arabidopsis rosettes, this study aims at a systematic elucidation of relevant components in different drought and heat scenarios as well as relationships between molecular players of stress response. In combined drought-heat stress, the majority of single stress responses are maintained. However, interaction effects between drought and heat can be discovered as well; these relate to protein folding, flavonoid biosynthesis and growth inhibition, which are enhanced, reduced or specifically induced in combined stress, respectively. Heat stress experiments with and without supplementation of air humidity for maintenance of vapor pressure deficit suggest that decreased relative air humidity due to elevated temperature is an important component of heat stress, specifically being responsible for hormone-related responses to water deprivation. Remarkably, this "dry air effect" is the primary trigger of the metabolomic response to heat. In contrast, the transcriptomic response has a substantial temperature component exceeding the dry air component and including up-regulation of many transcription factors and protein folding-related genes. Data level integration independent of prior knowledge on pathways and condition labels reveals shared drought and heat responses between transcriptome and metabolome, biomarker candidates and co-regulation between genes and metabolic compounds, suggesting novel players in abiotic stress response pathways. Drought and heat stress interact both at transcript and at metabolite response level. A comprehensive, non-targeted view of this interaction as well as non-interacting processes is important to be taken into account when improving tolerance to abiotic stresses in breeding programs. Transcriptome and metabolome

  12. Survey of the July 17, 2006 Central Javan tsunami reveals 21m runup heights

    Science.gov (United States)

    Fritz, H.; Goff, J.; Harbitz, C.; McAdoo, B.; Moore, A.; Latief, H.; Kalligeris, N.; Kodjo, W.; Uslu, B.; Titov, V.; Synolakis, C.

    2006-12-01

    The Monday, July 17, 2006 Central Javan 7.7 earthquake triggered a substantial tsunami that killed 600 people along a 200km stretch of coastline. The earthquake was not reported felt along the coastline. While there was a warning issued by the PTWC, it did not trigger an evacuation warning (Synolakis, 2006). The Indian Ocean Tsunami Warning System announced by UNESCO as operational in a press release two weeks before the event did not function as promised. There were no seismic recordings transmitted to the PTWC, and two German tsunameter buoys had broken off their moorings and were not operational. Lifeguards along a tourist beach reported that while the observed the harbinger shoreline recession, they attributed to exteme storm waves that were pounding the beaches that day. Had the tsunami struck on the preceding Sunday, instead of Monday, the death toll would had been far higher. The International Tsunami Survey Team (ITST) surveyed the coastline measuring runup, inundation, flow depths and sediment deposition, with standard methods (Synolakis and Okal, 2004). Runup values ranged up to 21m with several readings over 10m, while sand sheets up to 15cm were deposited. The parent earthquake was similar, albeit of smaller magnitude, to the 1994 East Javan tsunami, which struck about 200km east (Synolakis, et al, 1995) and reached a maximum of 11m runup height only at one location on steep cliffs. The unusual distribution of runup heights, and the pronounced extreme values near Nusa Kambangan, suggest a local coseismic landslide may have triggered an additional tsunami (Okal and Synolakis, 2005). The ITST observed that many coastal villages were completely abandoned after the tsunami, even in locales where there were no casualties. Whether residents will return is uncertain, but it is clear that an education campaign in tsunami hazard mitigation is urgently needed. In the aftermath of the tsunami, the Government of Indonesia enforced urgent emergency preparedness

  13. 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.

  14. 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

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

    International Nuclear Information System (INIS)

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

    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 (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

  16. Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles

    Directory of Open Access Journals (Sweden)

    Cassandra Collins

    2017-09-01

    Full Text Available Armillaria mellea is a major plant pathogen. Yet, the strategies the organism uses to infect susceptible species, degrade lignocellulose and other plant material and protect itself against plant defences and its own glycodegradative arsenal are largely unknown. Here, we use a combination of gel and MS-based proteomics to profile A. mellea under conditions of oxidative stress and changes in growth matrix. 2-DE and LC-MS/MS were used to investigate the response of A. mellea to H2O2 and menadione/FeCl3 exposure, respectively. Several proteins were detected with altered abundance in response to H2O2, but not menadione/FeCl3 (i.e., valosin-containing protein, indicating distinct responses to these different forms of oxidative stress. One protein, cobalamin-independent methionine synthase, demonstrated a common response in both conditions, which may be a marker for a more general stress response mechanism. Further changes to the A. mellea proteome were investigated using MS-based proteomics, which identified changes to putative secondary metabolism (SM enzymes upon growth in agar compared to liquid cultures. Metabolomic analyses revealed distinct profiles, highlighting the effect of growth matrix on SM production. This establishes robust methods by which to utilize comparative proteomics to characterize this important phytopathogen.

  17. Global Transcription Profiling Reveals Comprehensive Insights into Hypoxic Response in Arabidopsis1[w

    Science.gov (United States)

    Liu, Fenglong; VanToai, Tara; Moy, Linda P.; Bock, Geoffrey; Linford, Lara D.; Quackenbush, John

    2005-01-01

    Plants have evolved adaptation mechanisms to sense oxygen deficiency in their environments and make coordinated physiological and structural adjustments to enhance their hypoxic tolerance. To gain insight into how plants respond to low-oxygen stress, gene expression profiling using whole-genome DNA amplicon microarrays was carried out at seven time points over 24 h, in wild-type and transgenic PSAG12:ipt Arabidopsis (Arabidopsis thaliana) plants under normoxic and hypoxic conditions. Transcript levels of genes involved in glycolysis and fermentation pathways, ethylene synthesis and perception, calcium signaling, nitrogen utilization, trehalose metabolism, and alkaloid synthesis were significantly altered in response to oxygen limitation. Analysis based on gene ontology assignments suggested a significant down-regulation of genes whose functions are associated with cell walls, nucleosome structures, water channels, and ion transporters and a significant up-regulation of genes involved in transcriptional regulation, protein kinase activity, and auxin responses under conditions of oxygen shortage. Promoter analysis on a cluster of up-regulated genes revealed a significant overrepresentation of the AtMYB2-binding motif (GT motif), a sugar response element-like motif, and a G-box-related sequence, and also identified several putative anaerobic response elements. Finally, quantitative real-time polymerase chain reactions using 29 selected genes independently verified the microarray results. This study represents one of the most comprehensive analyses conducted to date investigating hypoxia-responsive transcriptional networks in plants. PMID:15734912

  18. Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis.

    Science.gov (United States)

    Liu, Fenglong; Vantoai, Tara; Moy, Linda P; Bock, Geoffrey; Linford, Lara D; Quackenbush, John

    2005-03-01

    Plants have evolved adaptation mechanisms to sense oxygen deficiency in their environments and make coordinated physiological and structural adjustments to enhance their hypoxic tolerance. To gain insight into how plants respond to low-oxygen stress, gene expression profiling using whole-genome DNA amplicon microarrays was carried out at seven time points over 24 h, in wild-type and transgenic P(SAG12):ipt Arabidopsis (Arabidopsis thaliana) plants under normoxic and hypoxic conditions. Transcript levels of genes involved in glycolysis and fermentation pathways, ethylene synthesis and perception, calcium signaling, nitrogen utilization, trehalose metabolism, and alkaloid synthesis were significantly altered in response to oxygen limitation. Analysis based on gene ontology assignments suggested a significant down-regulation of genes whose functions are associated with cell walls, nucleosome structures, water channels, and ion transporters and a significant up-regulation of genes involved in transcriptional regulation, protein kinase activity, and auxin responses under conditions of oxygen shortage. Promoter analysis on a cluster of up-regulated genes revealed a significant overrepresentation of the AtMYB2-binding motif (GT motif), a sugar response element-like motif, and a G-box-related sequence, and also identified several putative anaerobic response elements. Finally, quantitative real-time polymerase chain reactions using 29 selected genes independently verified the microarray results. This study represents one of the most comprehensive analyses conducted to date investigating hypoxia-responsive transcriptional networks in plants.

  19. Functional Genomic Screening Reveals Core Modulators of Echinocandin Stress Responses in Candida albicans

    Directory of Open Access Journals (Sweden)

    Tavia Caplan

    2018-05-01

    Full Text Available Summary: Candida albicans is a leading cause of death due to fungal infection. Treatment of systemic candidiasis often relies on echinocandins, which disrupt cell wall synthesis. Resistance is readily acquired via mutations in the drug target gene, FKS1. Both basal tolerance and resistance to echinocandins require cellular stress responses. We performed a systematic analysis of 3,030 C. albicans mutants to define circuitry governing cellular responses to echinocandins. We identified 16 genes for which deletion or transcriptional repression enhanced echinocandin susceptibility, including components of the Pkc1-MAPK signaling cascade. We discovered that the molecular chaperone Hsp90 is required for the stability of Pkc1 and Bck1, establishing key mechanisms through which Hsp90 mediates echinocandin resistance. We also discovered that perturbation of the CCT chaperonin complex causes enhanced echinocandin sensitivity, altered cell wall architecture, and aberrant septin localization. Thus, we provide insights into the mechanisms by which cellular chaperones enable crucial responses to echinocandin-induced stress. : Caplan et al. screen 3,030 Candida albicans mutants to define circuitry governing cellular responses to echinocandins, the first-line therapy for systemic candidiasis. They reveal that the molecular chaperone Hsp90 is required for stability of Pkc1 and Bck1 and that the CCT chaperonin complex is a key modulator of echinocandin susceptibility. Keywords: fungal pathogen, Candida albicans, echinocandins, Hsp90, Pkc1, CCT complex, client protein, stress response, functional genomic screen, drug resistance

  20. Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum.

    Science.gov (United States)

    Kenyon, Amy; Gavriouchkina, Daria; Zorman, Jernej; Napolitani, Giorgio; Cerundolo, Vincenzo; Sauka-Spengler, Tatjana

    2017-07-26

    The mechanisms governing neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific in vivo biotinylation in zebrafish to analyse the initial response of neutrophils to Mycobacterium marinum, a close genetic relative of M. tuberculosis used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, NLRC3 ortholog (wu: fb15h11) and il1β. Crispr/Cas9-mediated knockout of caspase b, which acts by proteolytic processing of il1β, results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterial infection, thus impairing granuloma development. We also show that a number of immediate early response genes (IEGs) are responsible for orchestrating the initial neutrophil response to mycobacterial infection. Further perturbation of the IEGs exposes egr3 as a key transcriptional regulator controlling il1β transcription.

  1. Effects of various methodologic strategies: survey response rates among Canadian physicians and physicians-in-training.

    Science.gov (United States)

    Grava-Gubins, Inese; Scott, Sarah

    2008-10-01

    To increase the overall 2007 response rate of the National Physician Survey (NPS) from the survey's 2004 rate of response with the implementation of various methodologic strategies. Physicians were stratified to receive either a long version (12 pages) or a short version (6 pages) of the survey (38% and 62%, respectively). Mixed modes of contact were used-58% were contacted by e-mail and 42% by regular mail-with multiple modes of contact attempted for nonrespondents. The self-administered, confidential surveys were distributed in either English or French. Medical residents and students received e-mail surveys only and were offered a substantial monetary lottery incentive for completing their surveys. A professional communications firm assisted in marketing the survey and delivered advance notification of its impending distribution. Canada. A total of 62 441 practising physicians, 2627 second-year medical residents, and 9162 medical students in Canada. Of the practising physicians group, 60 811 participants were eligible and 19 239 replied, for an overall 2007 study response rate of 31.64% (compared with 35.85% in 2004). No difference in rate of response was found between the longer and shorter versions of the survey. If contacted by regular mail, the response rate was 34.1%; the e-mail group had a response rate of 29.9%. Medical student and resident response rates were 30.8% and 27.9%, respectively (compared with 31.2% and 35.6% in 2004). Despite shortening the questionnaires, contacting more physicians by e-mail, and enhancing marketing and follow-up, the 2007 NPS response rate for practising physicians did not surpass the 2004 NPS response rate. Offering a monetary lottery incentive to medical residents and students was also unsuccessful in increasing their response rates. The role of surveys in gathering information from physicians and physicians-in-training remains problematic. Researchers need to investigate alternative strategies for achieving higher rates of

  2. 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...... rearrangements. Integration of transcriptomic and proteomic data revealed a poor correlation between changes in the relative levels of transcripts and their corresponding proteins, but a large overlap in affected pathways at the levels of mRNA, protein, and phosphoprotein. This study provides an integrated view...

  3. 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

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. 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.

  7. A survey of pandemic influenza preparedness and response capabilities in Chicago area hospital security departments.

    Science.gov (United States)

    Kimmerly, David P

    2009-01-01

    This article is a summary based on a December 2007 paper prepared by the author in partial fulfillment of the requirements for a master's degree in business and organizational security management at Webster University. The project described was intended to assess Chicago-area healthcare organization security departments' preparedness and response capabilities for a potential influenza pandemic. While the author says healthcare organizations are learning from the pandemics of the past, little research has been conducted on the requirements necessary within hospital security departments. The article explores staffing, planning, preparation and response capabilities within a healthcare security context to determine existing resources available to the healthcare security community. Eleven completed surveys were received from hospital security managers throughout the geographical Chicago area. They reveal that hospital security managers are conscious of the risks of a pandemic influenza outbreak. Yet, it was found that several gaps existed within hospital security department staffing and response capabilities, as hospital security departments may not have the available resources necessary to adequately maintain their operations during a pandemic incident.

  8. Surveying and analyzing injection responses for patterns with horizontal wells

    Energy Technology Data Exchange (ETDEWEB)

    Fedenczuk, L.; Hoffman, K.

    1998-12-31

    A novel method for visualizing injection responses in patterns that include horizontal and/or vertical wells is described. Understanding fluid communication between the horizontal well and the surrounding injectors is essential to estimating the effectiveness of the waterflood. Armed with the understanding of responses, injection patterns can be optimized, production rates can be increased and more efficient oil recovery can be achieved. In this study the time lags of correlations and a new parameter, the waterflood response type is introduced. The response type is based on the oil and total fluid responses. In addition spider diagrams are introduced to help visualizing the correlations, time lags and response types. Integration of the results with geology, petrophysics and completion techniques can help to find the cause and effect rules in waterflood fields. 6 refs., 10 figs.

  9. 2012 Survey of Active Duty Spouses: Tabulations of Responses

    Science.gov (United States)

    2013-09-30

    Survey Reporting Tool. A team consisting of Deepika Batra, Malikah Dorvil, and Amy Campbell, SRA International, Inc., completed quality control for...would you prefer to take a virtual/ telecommuting position or an office/building position outside of your home...224 d. Not being able to stop or control worrying ........................................... 226 56. Patient Health Questionnaire (PHQ-4

  10. Experimental evolution reveals differences between phenotypic and evolutionary responses to population density.

    Science.gov (United States)

    McNamara, K B; Simmons, L W

    2017-09-01

    Group living can select for increased immunity, given the heightened risk of parasite transmission. Yet, it also may select for increased male reproductive investment, given the elevated risk of female multiple mating. Trade-offs between immunity and reproduction are well documented. Phenotypically, population density mediates both reproductive investment and immune function in the Indian meal moth, Plodia interpunctella. However, the evolutionary response of populations to these traits is unknown. We created two replicated populations of P. interpunctella, reared and mated for 14 generations under high or low population densities. These population densities cause plastic responses in immunity and reproduction: at higher numbers, both sexes invest more in one index of immunity [phenoloxidase (PO) activity] and males invest more in sperm. Interestingly, our data revealed divergence in PO and reproduction in a different direction to previously reported phenotypic responses. Males evolving at low population densities transferred more sperm, and both males and females displayed higher PO than individuals at high population densities. These positively correlated responses to selection suggest no apparent evolutionary trade-off between immunity and reproduction. We speculate that the reduced PO activity and sperm investment when evolving under high population density may be due to the reduced population fitness predicted under increased sexual conflict and/or to trade-offs between pre- and post-copulatory traits. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  11. Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination.

    Science.gov (United States)

    Li, Xi; Miao, Hongyu; Henn, Alicia; Topham, David J; Wu, Hulin; Zand, Martin S; Mosmann, Tim R

    2012-06-29

    Although previous studies have found minimal changes in CD4 T cell responses after vaccination of adults with trivalent inactivated influenza vaccine, daily sampling and monitoring of the proliferation marker Ki-67 have now been used to reveal that a substantial fraction of influenza-specific CD4 T cells respond to vaccination. At 4-6 days after vaccination, there is a sharp rise in the numbers of Ki-67-expressing PBMC that produce IFNγ, IL-2 and/or TNFα in vitro in response to influenza vaccine or peptide. Ki-67(+) cell numbers then decline rapidly, and 10 days after vaccination, both Ki-67(+) and overall influenza-specific cell numbers are similar to pre-vaccination levels. These results provide a tool for assessing the quality and quantity of CD4 T cell responses to different influenza vaccines, and raise the possibility that the anti-influenza T cell memory response may be qualitatively altered by vaccination, even if the overall memory cell numbers do not change significantly. Copyright © 2012. Published by Elsevier Ltd.

  12. RNA-Seq Reveals Extensive Transcriptional Response to Heat Stress in the Stony Coral Galaxea fascicularis

    Science.gov (United States)

    Hou, Jing; Xu, Tao; Su, Dingjia; Wu, Ying; Cheng, Li; Wang, Jun; Zhou, Zhi; Wang, Yan

    2018-01-01

    Galaxea fascicularis, a stony coral belonging to family Oculinidae, is widely distributed in Red Sea, the Gulf of Aden and large areas of the Indo-Pacific oceans. So far there is a lack of gene expression knowledge concerning this massive coral. In the present study, G. fascicularis was subjected to heat stress at 32.0 ± 0.5°C in the lab, we found that the density of symbiotic zooxanthellae decreased significantly; meanwhile apparent bleaching and tissue lysing were observed at 10 h and 18 h after heat stress. The transcriptome responses were investigated in the stony coral G. fascicularis during heat bleaching using RNA-seq. A total of 42,028 coral genes were assembled from over 439 million reads. Gene expressions were compared at 10 and 18 h after heat stress. The significantly upregulated genes found in the Control_10h vs. Heat_10h comparison, presented mainly in GO terms related with DNA integration and unfolded protein response; and for the Control_18h vs. Heat_18h comparison, the GO terms include DNA integration. In addition, comparison between groups of Control_10h vs. Heat_10h and Control_18h vs. Heat_18h revealed that 125 genes were significantly upregulated in common between the two groups, whereas 21 genes were significantly downregulated in common, all these differentially expressed genes were found to be involved in stress response, DNA integration and unfolded protein response. Taken together, our results suggest that high temperature could activate the stress response at the early stage, and subsequently induce the bleaching and lysing through DNA integration and unfolded protein response, which are able to disrupt the balance of coral-zooxanthella symbiosis in the stony coral G. fascicularis. PMID:29487614

  13. RNA-Seq Reveals Extensive Transcriptional Response to Heat Stress in the Stony Coral Galaxea fascicularis

    Directory of Open Access Journals (Sweden)

    Jing Hou

    2018-02-01

    Full Text Available Galaxea fascicularis, a stony coral belonging to family Oculinidae, is widely distributed in Red Sea, the Gulf of Aden and large areas of the Indo-Pacific oceans. So far there is a lack of gene expression knowledge concerning this massive coral. In the present study, G. fascicularis was subjected to heat stress at 32.0 ± 0.5°C in the lab, we found that the density of symbiotic zooxanthellae decreased significantly; meanwhile apparent bleaching and tissue lysing were observed at 10 h and 18 h after heat stress. The transcriptome responses were investigated in the stony coral G. fascicularis during heat bleaching using RNA-seq. A total of 42,028 coral genes were assembled from over 439 million reads. Gene expressions were compared at 10 and 18 h after heat stress. The significantly upregulated genes found in the Control_10h vs. Heat_10h comparison, presented mainly in GO terms related with DNA integration and unfolded protein response; and for the Control_18h vs. Heat_18h comparison, the GO terms include DNA integration. In addition, comparison between groups of Control_10h vs. Heat_10h and Control_18h vs. Heat_18h revealed that 125 genes were significantly upregulated in common between the two groups, whereas 21 genes were significantly downregulated in common, all these differentially expressed genes were found to be involved in stress response, DNA integration and unfolded protein response. Taken together, our results suggest that high temperature could activate the stress response at the early stage, and subsequently induce the bleaching and lysing through DNA integration and unfolded protein response, which are able to disrupt the balance of coral-zooxanthella symbiosis in the stony coral G. fascicularis.

  14. 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

    2015-01-01

    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. PMID:26475115

  15. A complex scenario of tuberculosis transmission is revealed through genetic and epidemiological surveys in Porto.

    Science.gov (United States)

    Rito, Teresa; Matos, Carlos; Carvalho, Carlos; Machado, Henrique; Rodrigues, Gabriela; Oliveira, Olena; Ferreira, Eduarda; Gonçalves, Jorge; Maio, Lurdes; Morais, Clara; Ramos, Helena; Guimarães, João Tiago; Santos, Catarina L; Duarte, Raquel; Correia-Neves, Margarida

    2018-01-25

    Tuberculosis (TB) incidence is decreasing worldwide and eradication is becoming plausible. In low-incidence countries, intervention on migrant populations is considered one of the most important strategies for elimination. However, such measures are inappropriate in European areas where TB is largely endemic, such as Porto in Portugal. We aim to understand transmission chains in Porto through a genetic characterization of Mycobacterium tuberculosis strains and through a detailed epidemiological evaluation of cases. We genotyped the M. tuberculosis strains using the MIRU-VNTR system. We performed an evolutionary reconstruction of the genotypes with median networks, used in this context for the first time. TB cases from a period of two years were evaluated combining genetic, epidemiological and georeferencing information. The data reveal a unique complex scenario in Porto where the autochthonous population acts as a genetic reservoir of M. tuberculosis diversity with discreet episodes of transmission, mostly undetected using classical epidemiology alone. Although control policies have been successful in decreasing incidence in Porto, the discerned complexity suggests that, for elimination to be a realistic goal, strategies need to be adjusted and coupled with a continuous genetic characterization of strains and detailed epidemiological evaluation, in order to successfully identify and interrupt transmission chains.

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

    Directory of Open Access Journals (Sweden)

    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.

  17. [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.

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

    DEFF Research Database (Denmark)

    Kjøller, Mette; Thoning, Henrik

    2005-01-01

    BACKGROUND: The types and quantity of non-response in surveys influence the extent to which the results may be generalized. This study analysed trends in non-response in the Danish Health Interview Surveys from 1987 to 1994 and used the National Patient Registry to assess whether non-response bia......BACKGROUND: The types and quantity of non-response in surveys influence the extent to which the results may be generalized. This study analysed trends in non-response in the Danish Health Interview Surveys from 1987 to 1994 and used the National Patient Registry to assess whether non...... respondents before data collection but similar during and after data collection. The rate was higher during the whole period among ill or disabled non-respondents. Among people who could not be contacted during the data collection period a higher admission rate was only found immediately before and during...

  19. Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis.

    Science.gov (United States)

    Xie, Jianbo; Tian, Jiaxing; Du, Qingzhang; Chen, Jinhui; Li, Ying; Yang, Xiaohui; Li, Bailian; Zhang, Deqiang

    2016-05-01

    Gibberellins (GAs) regulate a wide range of important processes in plant growth and development, including photosynthesis. However, the mechanism by which GAs regulate photosynthesis remains to be understood. Here, we used multi-gene association to investigate the effect of genes in the GA-responsive pathway, as constructed by RNA sequencing, on photosynthesis, growth, and wood property traits, in a population of 435 Populus tomentosa By analyzing changes in the transcriptome following GA treatment, we identified many key photosynthetic genes, in agreement with the observed increase in measurements of photosynthesis. Regulatory motif enrichment analysis revealed that 37 differentially expressed genes related to photosynthesis shared two essential GA-related cis-regulatory elements, the GA response element and the pyrimidine box. Thus, we constructed a GA-responsive pathway consisting of 47 genes involved in regulating photosynthesis, including GID1, RGA, GID2, MYBGa, and 37 photosynthetic differentially expressed genes. Single nucleotide polymorphism (SNP)-based association analysis showed that 142 SNPs, representing 40 candidate genes in this pathway, were significantly associated with photosynthesis, growth, and wood property traits. Epistasis analysis uncovered interactions between 310 SNP-SNP pairs from 37 genes in this pathway, revealing possible genetic interactions. Moreover, a structural gene-gene matrix based on a time-course of transcript abundances provided a better understanding of the multi-gene pathway affecting photosynthesis. The results imply a functional role for these genes in mediating photosynthesis, growth, and wood properties, demonstrating the potential of combining transcriptome-based regulatory pathway construction and genetic association approaches to detect the complex genetic networks underlying quantitative traits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights

  20. Dissection of Ire1 functions reveals stress response mechanisms uniquely evolved in Candida glabrata.

    Directory of Open Access Journals (Sweden)

    Taiga Miyazaki

    2013-01-01

    Full Text Available Proper protein folding in the endoplasmic reticulum (ER is vital in all eukaryotes. When misfolded proteins accumulate in the ER lumen, the transmembrane kinase/endoribonuclease Ire1 initiates splicing of HAC1 mRNA to generate the bZIP transcription factor Hac1, which subsequently activates its target genes to increase the protein-folding capacity of the ER. This cellular machinery, called the unfolded protein response (UPR, is believed to be an evolutionarily conserved mechanism in eukaryotes. In this study, we comprehensively characterized mutant phenotypes of IRE1 and other related genes in the human fungal pathogen Candida glabrata. Unexpectedly, Ire1 was required for the ER stress response independently of Hac1 in this fungus. C. glabrata Ire1 did not cleave mRNAs encoding Hac1 and other bZIP transcription factors identified in the C. glabrata genome. Microarray analysis revealed that the transcriptional response to ER stress is not mediated by Ire1, but instead is dependent largely on calcineurin signaling and partially on the Slt2 MAPK pathway. The loss of Ire1 alone did not confer increased antifungal susceptibility in C. glabrata contrary to UPR-defective mutants in other fungi. Taken together, our results suggest that the canonical Ire1-Hac1 UPR is not conserved in C. glabrata. It is known in metazoans that active Ire1 nonspecifically cleaves and degrades a subset of ER-localized mRNAs to reduce the ER load. Intriguingly, this cellular response could occur in an Ire1 nuclease-dependent fashion in C. glabrata. We also uncovered the attenuated virulence of the C. glabrata Δire1 mutant in a mouse model of disseminated candidiasis. This study has unveiled the unique evolution of ER stress response mechanisms in C. glabrata.

  1. The transcriptome and proteome of the diatom Thalassiosira pseudonana reveal a diverse phosphorus stress response.

    Directory of Open Access Journals (Sweden)

    Sonya T Dyhrman

    Full Text Available Phosphorus (P is a critical driver of phytoplankton growth and ecosystem function in the ocean. Diatoms are an abundant class of marine phytoplankton that are responsible for significant amounts of primary production. With the control they exert on the oceanic carbon cycle, there have been a number of studies focused on how diatoms respond to limiting macro and micronutrients such as iron and nitrogen. However, diatom physiological responses to P deficiency are poorly understood. Here, we couple deep sequencing of transcript tags and quantitative proteomics to analyze the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. A total of 318 transcripts were differentially regulated with a false discovery rate of <0.05, and a total of 136 proteins were differentially abundant (p<0.05. Significant changes in the abundance of transcripts and proteins were observed and coordinated for multiple biochemical pathways, including glycolysis and translation. Patterns in transcript and protein abundance were also linked to physiological changes in cellular P distributions, and enzyme activities. These data demonstrate that diatom P deficiency results in changes in cellular P allocation through polyphosphate production, increased P transport, a switch to utilization of dissolved organic P through increased production of metalloenzymes, and a remodeling of the cell surface through production of sulfolipids. Together, these findings reveal that T. pseudonana has evolved a sophisticated response to P deficiency involving multiple biochemical strategies that are likely critical to its ability to respond to variations in environmental P availability.

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

    Directory of Open Access Journals (Sweden)

    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

  3. Comparative Transcriptomic Analysis Reveals Similarities and Dissimilarities in Saccharomyces cerevisiae Wine Strains Response to Nitrogen Availability

    Science.gov (United States)

    Barbosa, Catarina; García-Martínez, José; Pérez-Ortín, José E.; Mendes-Ferreira, Ana

    2015-01-01

    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 (12h, 24h and 96h). 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 12h, 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 nutrient in the grape

  4. 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.

  5. 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. © 2016 John Wiley & Sons Ltd.

  6. 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

  7. A survey of attitudes toward responsible pet ownership.

    Science.gov (United States)

    Selby, L A; Rhoades, J D; Hewett, J E; Irvin, J A

    1979-01-01

    The concerns of medical and community officials about responsible pet ownership have increased. Before a practical solution can be found for irresponsible ownership and community health problems associated with pet populations, the public's attitudes on issues related to responsible pet ownership must be determined. Such issues include attitudes on dog and cat overpopulation, potential public health problems associated with pet populations, and methods of controlling pet populations and stray animals. Responses to a questionnaire were used to evaluate the attitudes of 910 pet owners and nonowners toward factors comprising responsible pet ownership. The median age of the respondents was 33 years; 414 (45 percent) were men, and 496 (55 percent) were women. At the time of the study, 18 percent owned a cat and a dog, 35 percent owned only a dog, 11 percent showed only a cat, and 36 percent were nonowners. Not only the sex of the respondent but also the category of pet ownership affected opinions on overpopulation of dogs and cats, nuisance and pollution problems associated with these animals, and methods of controlling pet populations in the community. For example, owners agreed strongly on family planning for pets, but a majority of male owners stated that they would not have their dogs neutered. PMID:572978

  8. 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

  9. 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.

  10. Thyroid transcriptome analysis reveals different adaptive responses to cold environmental conditions between two chicken breeds.

    Science.gov (United States)

    Xie, Shanshan; Yang, Xukai; Wang, Dehe; Zhu, Feng; Yang, Ning; Hou, Zhuocheng; Ning, Zhonghua

    2018-01-01

    Selection for cold tolerance in chickens is important for improving production performance and animal welfare. The identification of chicken breeds with higher cold tolerance and production performance will help to target candidates for the selection. The thyroid gland plays important roles in thermal adaptation, and its function is influenced by breed differences and transcriptional plasticity, both of which remain largely unknown in the chicken thyroid transcriptome. In this study, we subjected Bashang Long-tail (BS) and Rhode Island Red (RIR) chickens to either cold or warm environments for 21 weeks and investigated egg production performance, body weight changes, serum thyroid hormone concentrations, and thyroid gland transcriptome profiles. RIR chickens had higher egg production than BS chickens under warm conditions, but BS chickens produced more eggs than RIRs under cold conditions. Furthermore, BS chickens showed stable body weight gain under cold conditions while RIRs did not. These results suggested that BS breed is a preferable candidate for cold-tolerance selection and that the cold adaptability of RIRs should be improved in the future. BS chickens had higher serum thyroid hormone concentrations than RIRs under both environments. RNA-Seq generated 344.3 million paired-end reads from 16 sequencing libraries, and about 90% of the processed reads were concordantly mapped to the chicken reference genome. Differential expression analysis identified 46-1,211 genes in the respective comparisons. With regard to breed differences in the thyroid transcriptome, BS chickens showed higher cell replication and development, and immune response-related activity, while RIR chickens showed higher carbohydrate and protein metabolism activity. The cold environment reduced breed differences in the thyroid transcriptome compared with the warm environment. Transcriptional plasticity analysis revealed different adaptive responses in BS and RIR chickens to cope with the cold

  11. 2012 Survey of Reserve Components Spouses (RCSS): Tabulations of Responses

    Science.gov (United States)

    2012-09-30

    injury/medical problems Child care problems Other family/personal obligation Maternity / paternity leave Labor dispute Weather affected job School...Did you interact with the unit or Service point of contact? ............................. 262  36.  How satisfied are you with the level of assistance...I did not interact with the unit or Service point of contact were tabulated separately, as responses to the constructed question Did you interact

  12. Effects of Mentioning the Incentive Prize in the Email Subject Line on Survey Response

    Directory of Open Access Journals (Sweden)

    Robert Janke

    2014-03-01

    Full Text Available Objective – This study examined the effects that mentioning the survey incentive prize in the subject line of a reminder email had on the response rate and data quality. To date, manipulation of the subject line, specifically in terms of mentioning the incentive prize, has received limited attention in the survey design literature. Methods – The delivery of the survey invitation is discussed in terms of the timing of the launch and reminder emails. Particular emphasis is given to the design of the email subject line and justification of the format. Weekly response rates from four LibQUAL+TM surveys were compared. In addition, weekly responses for one year were analyzed using SPSS to investigate if there were any between means differences in terms of three elements of data quality. The three elements were: length of time it took to complete the survey, the number of core questions with an N/A response, and the number of illogical responses where minimum scores were higher than desired. Results – The response rates for the second week were grouped together based on the presence or absence of the subject line manipulation. There was a significant difference between these means (4.75%, p 0.033. There was no statistical difference in regards to the measures of data quality as determined by a one-way ANOVA test. Conclusions – Reminding survey participants with an email that mentions the incentive prize in the subject line appears to increase response rates with no deleterious effects on data quality. The results of this investigation are encouraging, and those running the LibQUAL+TM survey in their universities should consider implementing this method to increase response rates. Further research to replicate these findings in other contexts and using an experimental design would be beneficial.

  13. 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

  14. Multiple surveys employing a new sample-processing protocol reveal the genetic diversity of placozoans in Japan.

    Science.gov (United States)

    Miyazawa, Hideyuki; Nakano, Hiroaki

    2018-03-01

    Placozoans, flat free-living marine invertebrates, possess an extremely simple bauplan lacking neurons and muscle cells and represent one of the earliest-branching metazoan phyla. They are widely distributed from temperate to tropical oceans. Based on mitochondrial 16S rRNA sequences, 19 haplotypes forming seven distinct clades have been reported in placozoans to date. In Japan, placozoans have been found at nine locations, but 16S genotyping has been performed at only two of these locations. Here, we propose a new processing protocol, "ethanol-treated substrate sampling," for collecting placozoans from natural environments. We also report the collection of placozoans from three new locations, the islands of Shikine-jima, Chichi-jima, and Haha-jima, and we present the distribution of the 16S haplotypes of placozoans in Japan. Multiple surveys conducted at multiple locations yielded five haplotypes that were not reported previously, revealing high genetic diversity in Japan, especially at Shimoda and Shikine-jima Island. The observed geographic distribution patterns were different among haplotypes; some were widely distributed, while others were sampled only from a single location. However, samplings conducted on different dates at the same sites yielded different haplotypes, suggesting that placozoans of a given haplotype do not inhabit the same site constantly throughout the year. Continued sampling efforts conducted during all seasons at multiple locations worldwide and the development of molecular markers within the haplotypes are needed to reveal the geographic distribution pattern and dispersal history of placozoans in greater detail.

  15. An examination of responses to surveys among Filipino-Australian migrants.

    Science.gov (United States)

    Maneze, Della; Everett, Bronwyn; DiGiacomo, Michelle; Davidson, Patricia M; Salamonson, Yenna

    2016-11-18

    Background Surveys are frequently used to collect data. Although paper surveys are commonly used, online surveys are gaining in popularity, with the inclusion of open-ended questions (OEQs) allowing respondents to freely express their views. Little is known about how Filipino-Australian migrants respond to surveys. There is some concern about the usefulness of OEQs administered to culturally and linguistically diverse migrants, who may have limited capacity to articulate their thoughts in writing. Aim To examine the responses of Filipino-Australian migrants to a survey. Discussion A total of 552 respondents were recruited, of whom 428 (78%) completed the questionnaire online. The overall response rate to the OEQs was 69%, with higher completion rates among those given a paper-based questionnaire and those with university educations. Conclusion Filipino migrants with functional English language skills responded well to the online survey. Paper-based administration elicited more OEQ responses, which is attributed to greater interaction between participants and researchers. Those with university educations may have more capacity to express themselves in English and were therefore more likely to complete the OEQs. Implications for practice The high response rate obtained in this study suggests that among Filipino-Australian migrants who rated their English language skills and educational level highly, the translation of OEQs may not be necessary. This has important implications for resources in research. Face-to-face interaction between participants and researchers is an important strategy for increasing the rates of response to OEQs.

  16. 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.

  17. 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. Copyright © 2014 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

  18. The Effects of Two Types of Appeal on Survey Response Rates.

    Science.gov (United States)

    Green, Kathy E.; And Others

    The effects of two cover letter manipulations and their interactions with demographic variables on response to the initial mailing of a survey were investigated. The two manipulations, type of appeal and type of respondent group identification, were intended to affect respondents' perceptions of their social responsibility and position. In all,…

  19. 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

  20. Growth and carbon isotopes of Mediterranean trees reveal contrasting responses to increased carbon dioxide and drought.

    Science.gov (United States)

    Granda, Elena; Rossatto, Davi Rodrigo; Camarero, J Julio; Voltas, Jordi; Valladares, Fernando

    2014-01-01

    Forest dynamics will depend upon the physiological performance of individual tree species under more stressful conditions caused by climate change. In order to compare the idiosyncratic responses of Mediterranean tree species (Quercus faginea, Pinus nigra, Juniperus thurifera) coexisting in forests of central Spain, we evaluated the temporal changes in secondary growth (basal area increment; BAI) and intrinsic water-use efficiency (iWUE) during the last four decades, determined how coexisting species are responding to increases in atmospheric CO2 concentrations (C(a)) and drought stress, and assessed the relationship among iWUE and growth during climatically contrasting years. All species increased their iWUE (ca. +15 to +21%) between the 1970s and the 2000s. This increase was positively related to C(a) for J. thurifera and to higher C(a) and drought for Q. faginea and P. nigra. During climatically favourable years the study species either increased or maintained their growth at rising iWUE, suggesting a higher CO2 uptake. However, during unfavourable climatic years Q. faginea and especially P. nigra showed sharp declines in growth at enhanced iWUE, likely caused by a reduced stomatal conductance to save water under stressful dry conditions. In contrast, J. thurifera showed enhanced growth also during unfavourable years at increased iWUE, denoting a beneficial effect of C(a) even under climatically harsh conditions. Our results reveal significant inter-specific differences in growth driven by alternative physiological responses to increasing drought stress. Thus, forest composition in the Mediterranean region might be altered due to contrasting capacities of coexisting tree species to withstand increasingly stressful conditions.

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

    Directory of Open Access Journals (Sweden)

    Elisabeth Fonteneau

    2008-03-01

    Full Text Available 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.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.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.

  2. 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 S; Halpern, Marnie E

    2014-04-01

    Environmental endocrine disruptors (EEDs) 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 (ERs) in the larval heart compared with 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 tissue-specific effects similar to those of BPA and genistein, or why some compounds preferentially target receptors in the heart. 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 ER genes by RNA in situ hybridization. We observed selective patterns of ER activation 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 was due to differences in the expression of ER subtypes. ERα was expressed in developing heart valves but not in the liver, whereas ERβ2 had the opposite profile. Accordingly, subtype-specific ER agonists activated the reporter in either the heart valves or the liver. The use of 5xERE:GFP transgenic zebrafish revealed an unexpected tissue-specific difference in the response to environmentally relevant estrogenic compounds. Exposure to estrogenic EEDs in utero was associated with adverse health effects, with the potentially unanticipated consequence of targeting developing heart valves.

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

    Directory of Open Access Journals (Sweden)

    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

  4. Online Physician Reviews Do Not Reflect Patient Satisfaction Survey Responses.

    Science.gov (United States)

    Widmer, R Jay; Maurer, Matthew J; Nayar, Veena R; Aase, Lee A; Wald, John T; Kotsenas, Amy L; Timimi, Farris K; Harper, Charles M; Pruthi, Sandhya

    2018-04-01

    Online physician reviews have become increasingly prevalent and are a common means by which patients explore medical options online. Currently, there are no data comparing physicians with negative online reviews and those without negative reviews. We sought to compare industry-vetted patient satisfaction surveys (PSSs), such as Press Ganey (PG) PSSs, between those physicians with negative online reviews and those without negative reviews. Overall, there were 113 unique individuals with negative online reviews from September 1, 2014, to December 31, 2014, with 8 being nonphysicians. We matched 113 physicians in similar departments/divisions. We obtained PG PSS scores of both groups and compared the mean scores of the 2 groups. Press Ganey PSS scores were available for 98 physicians with negative online reviews compared with 82 matched physicians without negative online reviews. The mean raw PG PSS scores were not different between the 2 groups (4.05; 95% CI, 3.99-4.11 vs 4.04; 95% CI, 3.97-4.11; P=.92). We also noted no difference in mean scores on questions related to physician-patient communication and interaction skills between those with poor online reviews and those without (4.38; 95% CI, 4.32-4.43 vs 4.41; 95% CI, 4.35-4.47; P=.42). However, there was a significantly lower non-physician-specific mean in those with negative online reviews (3.91; 95% CI, 3.84-3.97) vs those without negative online reviews (4.01; 95% CI, 3.95-4.09) (P=.02). Here, we provide data indicating that online physician reviews do not correlate to formal institutional PG PSS. Furthermore, physicians with negative online reviews have lower scores on non-physician-specific variables included in the PG PSSs, emphasizing that these discrepancies can negatively affect overall patient experience, online physician reviews, and physician reputation. It is prudent that an improved mechanism for online ratings be implemented to better inform patients about a physician's online reputation. Copyright

  5. Infectious diseases of marine molluscs and host responses as revealed by genomic tools

    Science.gov (United States)

    Ford, Susan E.

    2016-01-01

    More and more infectious diseases affect marine molluscs. Some diseases have impacted commercial species including MSX and Dermo of the eastern oyster, QPX of hard clams, withering syndrome of abalone and ostreid herpesvirus 1 (OsHV-1) infections of many molluscs. Although the exact transmission mechanisms are not well understood, human activities and associated environmental changes often correlate with increased disease prevalence. For instance, hatcheries and large-scale aquaculture create high host densities, which, along with increasing ocean temperature, might have contributed to OsHV-1 epizootics in scallops and oysters. A key to understanding linkages between the environment and disease is to understand how the environment affects the host immune system. Although we might be tempted to downplay the role of immunity in invertebrates, recent advances in genomics have provided insights into host and parasite genomes and revealed surprisingly sophisticated innate immune systems in molluscs. All major innate immune pathways are found in molluscs with many immune receptors, regulators and effectors expanded. The expanded gene families provide great diversity and complexity in innate immune response, which may be key to mollusc's defence against diverse pathogens in the absence of adaptive immunity. Further advances in host and parasite genomics should improve our understanding of genetic variation in parasite virulence and host disease resistance. PMID:26880838

  6. 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.

  7. Transcriptomics Reveal Several Gene Expression Patterns in the Piezophile Desulfovibrio hydrothermalis in Response to Hydrostatic Pressure

    Science.gov (United States)

    Amrani, Amira; Bergon, Aurélie; Holota, Hélène; Tamburini, Christian; Garel, Marc; Ollivier, Bernard; Imbert, Jean; Dolla, Alain; Pradel, Nathalie

    2014-01-01

    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. PMID:25215865

  8. 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.

  9. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Plant physiology and proteomics reveals the leaf response to drought in alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Aranjuelo, Iker; Molero, Gemma; Erice, Gorka; Avice, Jean Christophe; Nogués, Salvador

    2011-01-01

    Despite its relevance, protein regulation, metabolic adjustment, and the physiological status of plants under drought is not well understood in relation to the role of nitrogen fixation in nodules. In this study, nodulated alfalfa plants were exposed to drought conditions. The study determined the physiological, metabolic, and proteomic processes involved in photosynthetic inhibition in relation to the decrease in nitrogenase (N(ase)) activity. The deleterious effect of drought on alfalfa performance was targeted towards photosynthesis and N(ase) activity. At the leaf level, photosynthetic inhibition was mainly caused by the inhibition of Rubisco. The proteomic profile and physiological measurements revealed that the reduced carboxylation capacity of droughted plants was related to limitations in Rubisco protein content, activation state, and RuBP regeneration. Drought also decreased amino acid content such as asparagine, and glutamic acid, and Rubisco protein content indicating that N availability limitations were caused by N(ase) activity inhibition. In this context, drought induced the decrease in Rubisco binding protein content at the leaf level and proteases were up-regulated so as to degrade Rubisco protein. This degradation enabled the reallocation of the Rubisco-derived N to the synthesis of amino acids with osmoregulant capacity. Rubisco degradation under drought conditions was induced so as to remobilize Rubisco-derived N to compensate for the decrease in N associated with N(ase) inhibition. Metabolic analyses showed that droughted plants increased amino acid (proline, a major compound involved in osmotic regulation) and soluble sugar (D-pinitol) levels to contribute towards the decrease in osmotic potential (Ψ(s)). At the nodule level, drought had an inhibitory effect on N(ase) activity. This decrease in N(ase) activity was not induced by substrate shortage, as reflected by an increase in total soluble sugars (TSS) in the nodules. Proline accumulation

  12. Spatially Extensive Standardized Surveys Reveal Widespread, Multi-Decadal Increase in East Antarctic Adélie Penguin Populations.

    Science.gov (United States)

    Southwell, Colin; Emmerson, Louise; McKinlay, John; Newbery, Kym; Takahashi, Akinori; Kato, Akiko; Barbraud, Christophe; DeLord, Karine; Weimerskirch, Henri

    2015-01-01

    Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980's and have been increasing since the earliest counts in the 1960's. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

  13. Spatially Extensive Standardized Surveys Reveal Widespread, Multi-Decadal Increase in East Antarctic Adélie Penguin Populations.

    Directory of Open Access Journals (Sweden)

    Colin Southwell

    Full Text Available Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980's and have been increasing since the earliest counts in the 1960's. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

  14. 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.

  15. Evaluation and Monte Carlo modelling of the response function of the Leake neutron area survey instrument

    International Nuclear Information System (INIS)

    Tagziria, H.; Tanner, R.J.; Bartlett, D.T.; Thomas, D.J.

    2004-01-01

    All available measured data for the response characteristics of the Leake counter have been gathered together. These data, augmented by previously unpublished work, have been compared to Monte Carlo simulations of the instrument's response characteristics in the energy range from thermal to 20 MeV. A response function has been derived, which is recommended as the best currently available for the instrument. Folding this function with workplace energy distributions has enabled an assessment of the impact of this new response function to be made. Similar work, which will be published separately, has been carried out for the NM2 and the Studsvik 2202D neutron area survey instruments

  16. Response of six neutron survey meters in mixed fields of fast and thermal neutrons.

    Science.gov (United States)

    Kim, S I; Kim, B H; Chang, I; Lee, J I; Kim, J L; Pradhan, A S

    2013-10-01

    Calibration neutron fields have been developed at KAERI (Korea Atomic Energy Research Institute) to study the responses of commonly used neutron survey meters in the presence of fast neutrons of energy around 10 MeV. The neutron fields were produced by using neutrons from the (241)Am-Be sources held in a graphite pile and a DT neutron generator. The spectral details and the ambient dose equivalent rates of the calibration fields were established, and the responses of six neutron survey meters were evaluated. Four single-moderator-based survey meters exhibited an under-responses ranging from ∼9 to 55 %. DINEUTRUN, commonly used in fields around nuclear reactors, exhibited an over-response by a factor of three in the thermal neutron field and an under-response of ∼85 % in the mixed fields. REM-500 (tissue-equivalent proportional counter) exhibited a response close to 1.0 in the fast neutron fields and an under-response of ∼50 % in the thermal neutron field.

  17. Spaceflight Modifies Escherichia coli Gene Expression in Response to Antibiotic Exposure and Reveals Role of Oxidative Stress Response

    Directory of Open Access Journals (Sweden)

    Thomas R. Aunins

    2018-03-01

    Full Text Available Bacteria grown in space experiments under microgravity conditions have been found to undergo unique physiological responses, ranging from modified cell morphology and growth dynamics to a putative increased tolerance to antibiotics. A common theory for this behavior is the loss of gravity-driven convection processes in the orbital environment, resulting in both reduction of extracellular nutrient availability and the accumulation of bacterial byproducts near the cell. To further characterize the responses, this study investigated the transcriptomic response of Escherichia coli to both microgravity and antibiotic concentration. E. coli was grown aboard International Space Station in the presence of increasing concentrations of the antibiotic gentamicin with identical ground controls conducted on Earth. Here we show that within 49 h of being cultured, E. coli adapted to grow at higher antibiotic concentrations in space compared to Earth, and demonstrated consistent changes in expression of 63 genes in response to an increase in drug concentration in both environments, including specific responses related to oxidative stress and starvation response. Additionally, we find 50 stress-response genes upregulated in response to the microgravity when compared directly to the equivalent concentration in the ground control. We conclude that the increased antibiotic tolerance in microgravity may be attributed not only to diminished transport processes, but also to a resultant antibiotic cross-resistance response conferred by an overlapping effect of stress response genes. Our data suggest that direct stresses of nutrient starvation and acid-shock conveyed by the microgravity environment can incidentally upregulate stress response pathways related to antibiotic stress and in doing so contribute to the increased antibiotic stress tolerance observed for bacteria in space experiments. These results provide insights into the ability of bacteria to adapt under

  18. Spaceflight Modifies Escherichia coli Gene Expression in Response to Antibiotic Exposure and Reveals Role of Oxidative Stress Response.

    Science.gov (United States)

    Aunins, Thomas R; Erickson, Keesha E; Prasad, Nripesh; Levy, Shawn E; Jones, Angela; Shrestha, Shristi; Mastracchio, Rick; Stodieck, Louis; Klaus, David; Zea, Luis; Chatterjee, Anushree

    2018-01-01

    Bacteria grown in space experiments under microgravity conditions have been found to undergo unique physiological responses, ranging from modified cell morphology and growth dynamics to a putative increased tolerance to antibiotics. A common theory for this behavior is the loss of gravity-driven convection processes in the orbital environment, resulting in both reduction of extracellular nutrient availability and the accumulation of bacterial byproducts near the cell. To further characterize the responses, this study investigated the transcriptomic response of Escherichia coli to both microgravity and antibiotic concentration. E. coli was grown aboard International Space Station in the presence of increasing concentrations of the antibiotic gentamicin with identical ground controls conducted on Earth. Here we show that within 49 h of being cultured, E. coli adapted to grow at higher antibiotic concentrations in space compared to Earth, and demonstrated consistent changes in expression of 63 genes in response to an increase in drug concentration in both environments, including specific responses related to oxidative stress and starvation response. Additionally, we find 50 stress-response genes upregulated in response to the microgravity when compared directly to the equivalent concentration in the ground control. We conclude that the increased antibiotic tolerance in microgravity may be attributed not only to diminished transport processes, but also to a resultant antibiotic cross-resistance response conferred by an overlapping effect of stress response genes. Our data suggest that direct stresses of nutrient starvation and acid-shock conveyed by the microgravity environment can incidentally upregulate stress response pathways related to antibiotic stress and in doing so contribute to the increased antibiotic stress tolerance observed for bacteria in space experiments. These results provide insights into the ability of bacteria to adapt under extreme stress

  19. Spaceflight Modifies Escherichia coli Gene Expression in Response to Antibiotic Exposure and Reveals Role of Oxidative Stress Response

    Science.gov (United States)

    Aunins, Thomas R.; Erickson, Keesha E.; Prasad, Nripesh; Levy, Shawn E.; Jones, Angela; Shrestha, Shristi; Mastracchio, Rick; Stodieck, Louis; Klaus, David; Zea, Luis; Chatterjee, Anushree

    2018-01-01

    Bacteria grown in space experiments under microgravity conditions have been found to undergo unique physiological responses, ranging from modified cell morphology and growth dynamics to a putative increased tolerance to antibiotics. A common theory for this behavior is the loss of gravity-driven convection processes in the orbital environment, resulting in both reduction of extracellular nutrient availability and the accumulation of bacterial byproducts near the cell. To further characterize the responses, this study investigated the transcriptomic response of Escherichia coli to both microgravity and antibiotic concentration. E. coli was grown aboard International Space Station in the presence of increasing concentrations of the antibiotic gentamicin with identical ground controls conducted on Earth. Here we show that within 49 h of being cultured, E. coli adapted to grow at higher antibiotic concentrations in space compared to Earth, and demonstrated consistent changes in expression of 63 genes in response to an increase in drug concentration in both environments, including specific responses related to oxidative stress and starvation response. Additionally, we find 50 stress-response genes upregulated in response to the microgravity when compared directly to the equivalent concentration in the ground control. We conclude that the increased antibiotic tolerance in microgravity may be attributed not only to diminished transport processes, but also to a resultant antibiotic cross-resistance response conferred by an overlapping effect of stress response genes. Our data suggest that direct stresses of nutrient starvation and acid-shock conveyed by the microgravity environment can incidentally upregulate stress response pathways related to antibiotic stress and in doing so contribute to the increased antibiotic stress tolerance observed for bacteria in space experiments. These results provide insights into the ability of bacteria to adapt under extreme stress

  20. Response Burden in Official Business Surveys: Measurement and Reduction Practices of National Statistical Institutes

    Directory of Open Access Journals (Sweden)

    Bavdaž Mojca

    2015-12-01

    Full Text Available Response burden in business surveys has long been a concern for National Statistical Institutes (NSIs for three types of reasons: political reasons, because response burden is part of the total administrative burden governments impose on businesses; methodological reasons, because an excessive response burden may reduce data quality and increase data-collection costs; and strategic reasons, because it affects relations between the NSIs and the business community. This article investigates NSI practices concerning business response burden measurement and reduction actions based on a survey of 41 NSIs from 39 countries. Most NSIs monitor at least some burden aspects and have implemented some actions to reduce burden, but large differences exist between NSIs’ methodologies for burden measurement and actions taken to reduce burden. Future research should find ways to deal with methodological differences in burden conceptualization, operationalization, and measurement, and provide insights into the effectiveness and efficiency of burden-reduction actions.

  1. 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 (gas production, and (3) the frequent passage of tropical cyclones. In June 2014, a geophysical pilot study was conducted 8 km southwest of Southwest Pass, the distributary that currently receives the largest fraction of Mississippi River sediment supply. The resultant dataset encompasses 216 km of subbottom Chirp seismic profiles and a 60 km2 grid of bathymetry and sidescan data. Preliminary interpretation of these data shows the 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

  2. Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics

    Directory of Open Access Journals (Sweden)

    Yadetie Fekadu

    2012-02-01

    Full Text Available Abstract Background Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression responses to xenobiotics have not been well investigated in most invertebrates. Here, we performed genome survey for key defensome genes in Oikopleura dioica genome, and explored genome-wide gene expression using high density tiling arrays with over 2 million probes, in response to two model xenobiotic chemicals - the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP the pharmaceutical compound Clofibrate (Clo. Results Oikopleura genome surveys for key genes of the chemical defensome suggested a reduced repertoire. Not more than 23 cytochrome P450 (CYP genes could be identified, and neither CYP1 family genes nor their transcriptional activator AhR was detected. These two genes were present in deuterostome ancestors. As in vertebrates, the genotoxic compound BaP induced xenobiotic biotransformation and oxidative stress responsive genes. Notable exceptions were genes of the aryl hydrocarbon receptor (AhR signaling pathway. Clo also affected the expression of many biotransformation genes and markedly repressed genes involved in energy metabolism and muscle contraction pathways. Conclusions Oikopleura has the smallest number of CYP genes among sequenced animal genomes and lacks the AhR signaling pathway. However it appears to have basic xenobiotic inducible biotransformation genes such as a conserved genotoxic stress response gene set. Our genome survey and expression study does not support a role of AhR signaling pathway in the chemical defense of metazoans prior to the emergence of vertebrates.

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

    Science.gov (United States)

    Miura, Asako; Kobayashi, Tetsuro

    2016-01-01

    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. PMID:27803680

  4. Disclosure of Sexual Intercourse by Teenagers: Agreement Between Telephone Survey Responses and Annual Visit Disclosures

    Science.gov (United States)

    Alexander, Stewart C.; Fortenberry, J. Dennis; Pollak, Kathryn I.; Østbye, Truls; Bravender, Terrill; Tulsky, James A.; Dolor, Rowena; Shields, Cleveland G.

    2015-01-01

    Background Physicians can help guide teenagers in their emerging sexuality; however, teens rarely inform physicians about their sexual activity. Methods We audio-recorded annual visits between 365 teenagers and 49 physicians. sexual intercourse. Recordings were coded for teenage disclosures about previous sexual intercourse. We measured agreement between telephone survey responses and annual visit disclosures, and examined factors associated with agreement between the two. Results Fifty-six teenagers (15%) reported previous sexual intercourse in either the telephone survey or to their physician. Among those who reported sexual intercourse, 57% shared this information to both the telephone survey and their physician (κ = .72, confidence interval = 0.63–0.82). Conclusions Although a slight majority of teenagers disclosed their sexual activity to both the telephone survey and their doctor, a significant number disclosed to just one source. PMID:25857726

  5. Effect of mailed reminders on the response rate in surveys among patients in general practice

    DEFF Research Database (Denmark)

    Wensing, M; Mainz, Jan; Kramme, O

    1999-01-01

    Randomized trials were performed in Denmark and The Netherlands to determine the effect of mailed reminders on the response rate in surveys among patients in general practice. In both countries, general practitioners handed out questionnaires to 200 adult patients who came to visit them. An inter...

  6. Preparing for Success: One Institution's Aspirational and Student Focused Response to the National Student Survey

    Science.gov (United States)

    Flint, Abbi; Oxley, Anne; Helm, Paul; Bradley, Sally

    2009-01-01

    This paper describes quality enhancement (QE) focused response to the 2006 National Student Survey (NSS) by a post-1992 Higher Education Institution. Recognising the increasing importance of the NSS to a wide range of stakeholders, the University established a task team to explore, from a QE perspective, why the institution received particular…

  7. The International scale interval study: improving the comparability of responses to survey questions about happiness

    NARCIS (Netherlands)

    Veenhoven, R.

    2009-01-01

    This study is about survey questions on happiness using verbal response options, such as ‘very happy’ and ‘fairly happy’. The aim is to estimate what degrees of happiness are denoted by such terms in different questions and Languages. These degrees are expressed in numerical values on a 0 to 10

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

    NARCIS (Netherlands)

    ten Kleij, F; Musters, PAD

    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

  9. Understanding Response Rates to Surveys About Family Members' Psychological Symptoms After Patients' Critical Illness.

    Science.gov (United States)

    Long, Ann C; Downey, Lois; Engelberg, Ruth A; Nielsen, Elizabeth; Ciechanowski, Paul; Curtis, J Randall

    2017-07-01

    Achieving adequate response rates from family members of critically ill patients can be challenging, especially when assessing psychological symptoms. To identify factors associated with completion of surveys about psychological symptoms among family members of critically ill patients. Using data from a randomized trial of an intervention to improve communication between clinicians and families of critically ill patients, we examined patient-level and family-level predictors of the return of usable surveys at baseline, three months, and six months (n = 181, 171, and 155, respectively). Family-level predictors included baseline symptoms of psychological distress, decisional independence preference, and attachment style. We hypothesized that family with fewer symptoms of psychological distress, a preference for less decisional independence, and secure attachment style would be more likely to return questionnaires. We identified several predictors of the return of usable questionnaires. Better self-assessed family member health status was associated with a higher likelihood and stronger agreement with a support-seeking attachment style with a lower likelihood, of obtaining usable baseline surveys. At three months, family-level predictors of return of usable surveys included having usable baseline surveys, status as the patient's legal next of kin, and stronger agreement with a secure attachment style. The only predictor of receipt of surveys at six months was the presence of usable surveys at three months. We identified several predictors of the receipt of surveys assessing psychological symptoms in family of critically ill patients, including family member health status and attachment style. Using these characteristics to inform follow-up mailings and reminders may enhance response rates. Copyright © 2017 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

  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. Pre-notification letter type and response rate to a postal survey among women who have recently given birth.

    Science.gov (United States)

    Todd, Angela L; Porter, Maree; Williamson, Jennifer L; Patterson, Jillian A; Roberts, Christine L

    2015-12-01

    Surveys are commonly used in health research to assess patient satisfaction with hospital care. Achieving an adequate response rate, in the face of declining trends over time, threatens the quality and reliability of survey results. This paper evaluates a strategy to increase the response rate in a postal satisfaction survey with women who had recently given birth. A sample of 2048 Australian women who had recently given birth at seven maternity units in New South Wales were invited to participate in a postal survey about their recent experiences with maternity care. The study design included a randomised controlled trial that tested two types of pre-notification letter (with or without the option of opting out of the survey). The study also explored the acceptability of a request for consent to link survey data with existing routinely collected health data (omitting the latter data items from the survey reduced survey length and participant burden). This consent was requested of all women. The survey had an overall response rate of 46% (913 completed surveys returned, total sample 1989). Women receiving the pre-notification letter with the option of opting out of the survey were more likely to actively decline to participate than women receiving the letter without this option, although the overall numbers of women declining were small (27 versus 12). Letter type was not significantly associated with the return of a completed survey. Among women who completed the survey, 97% gave consent to link their survey data with existing health data. The two types of pre-notification letters used in our study did not influence the survey response rate. However, seeking consent for record linkage was highly acceptable to women who completed the survey, and represents an important strategy to add to the arsenal for designing and implementing effective surveys. In addition to aspects of survey design, future research should explore how to more effectively influence personal

  12. Altered Evoked Gamma-Band Responses Reveal Impaired Early Visual Processing in ADHD Children

    Science.gov (United States)

    Lenz, Daniel; Krauel, Kerstin; Flechtner, Hans-Henning; Schadow, Jeanette; Hinrichs, Hermann; Herrmann, Christoph S.

    2010-01-01

    Neurophysiological studies yield contrary results whether attentional problems of patients with attention-deficit/hyperactivity disorder (ADHD) are related to early visual processing deficits or not. Evoked gamma-band responses (GBRs), being among the first cortical responses occurring as early as 90 ms after visual stimulation in human EEG, have…

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

    DEFF Research Database (Denmark)

    Mahmood, Faisal; Johannesen, Helle H; Geertsen, Poul

    2017-01-01

    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 prospect......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...

  14. What impact do questionnaire length and monetary incentives have on mailed health psychology survey response?

    Science.gov (United States)

    Robb, Kathryn A; Gatting, Lauren; Wardle, Jane

    2017-11-01

    Response rates to health-related surveys are declining. This study tested two strategies to improve the response rate to a health psychology survey mailed through English general practices: (1) sending a shortened questionnaire and (2) offering a monetary incentive to return a completed questionnaire. Randomized controlled trial. Adults (n = 4,241) aged 45-59 years, from four General Practices in South-East England, were mailed a survey on attitudes towards bowel cancer screening. Using a 2 × 4 factorial design, participants were randomized to receive a 'short' (four A4 pages) or a 'long' (seven A4 pages) questionnaire, and one of four monetary incentives to return a completed questionnaire - (1) no monetary incentive, (2) £2.50 shop voucher, (3) £5.00 shop voucher, and (4) inclusion in a £250 shop voucher prize draw. Age, gender, and area-level deprivation were obtained from the General Practices. The overall response rate was 41% (n = 1,589). Response to the 'short' questionnaire (42%) was not significantly different from the 'long' questionnaire (40%). The £2.50 incentive (43%) significantly improved response rates in univariate analyses, and remained significant after controlling for age, gender, area-level deprivation, and questionnaire length. The £5.00 (42%) and £250 prize draw (41%) incentives had no significant impact on response rates compared to no incentive (38%). A small monetary incentive (£2.50) may slightly increase response to a mailed health psychology survey. The length of the questionnaire (four pages vs. seven pages) did not influence response. Although frequently used, entry into a prize draw did not increase response. Achieving representative samples remains a challenge for health psychology. Statement of contribution What is already known on this subject Response rates to mailed questionnaires continue to decline, threatening the representativeness of data. Prize draw incentives are frequently used but there is little evidence

  15. The Military and Domestic Disaster Response: Lead Role Revealed Through the Eye of Hurricane Katrina?

    National Research Council Canada - National Science Library

    Walker, Juliana M

    2006-01-01

    .... During and in the aftermath of Hurricane Katrina however the slow and perceived inept response to the massive disaster prompted a national debate on the appropriate role of the military in major domestic disasters...

  16. Quantitative proteomics and dynamic imaging of the nucleolus reveal distinct responses to UV and ionizing radiation.

    Science.gov (United States)

    Moore, Henna M; Bai, Baoyan; Boisvert, François-Michel; Latonen, Leena; Rantanen, Ville; Simpson, Jeremy C; Pepperkok, Rainer; Lamond, Angus I; Laiho, Marikki

    2011-10-01

    The nucleolus is a nuclear organelle that coordinates rRNA transcription and ribosome subunit biogenesis. Recent proteomic analyses have shown that the nucleolus contains proteins involved in cell cycle control, DNA processing and DNA damage response and repair, in addition to the many proteins connected with ribosome subunit production. Here we study the dynamics of nucleolar protein responses in cells exposed to stress and DNA damage caused by ionizing and ultraviolet (UV) radiation in diploid human fibroblasts. We show using a combination of imaging and quantitative proteomics methods that nucleolar substructure and the nucleolar proteome undergo selective reorganization in response to UV damage. The proteomic responses to UV include alterations of functional protein complexes such as the SSU processome and exosome, and paraspeckle proteins, involving both decreases and increases in steady state protein ratios, respectively. Several nonhomologous end-joining proteins (NHEJ), such as Ku70/80, display similar fast responses to UV. In contrast, nucleolar proteomic responses to IR are both temporally and spatially distinct from those caused by UV, and more limited in terms of magnitude. With the exception of the NHEJ and paraspeckle proteins, where IR induces rapid and transient changes within 15 min of the damage, IR does not alter the ratios of most other functional nucleolar protein complexes. The rapid transient decrease of NHEJ proteins in the nucleolus indicates that it may reflect a response to DNA damage. Our results underline that the nucleolus is a specific stress response organelle that responds to different damage and stress agents in a unique, damage-specific manner.

  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. 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.

  19. 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. © 2016 International Union of Psychological Science.

  20. Differential reproductive responses to stress reveal the role of life-history strategies within a species.

    Science.gov (United States)

    Schultner, J; Kitaysky, A S; Gabrielsen, G W; Hatch, S A; Bech, C

    2013-11-22

    Life-history strategies describe that 'slow'- in contrast to 'fast'-living species allocate resources cautiously towards reproduction to enhance survival. Recent evidence suggests that variation in strategies exists not only among species but also among populations of the same species. Here, we examined the effect of experimentally induced stress on resource allocation of breeding seabirds in two populations with contrasting life-history strategies: slow-living Pacific and fast-living Atlantic black-legged kittiwakes. We tested the hypothesis that reproductive responses in kittiwakes under stress reflect their life-history strategies. We predicted that in response to stress, Pacific kittiwakes reduce investment in reproduction compared with Atlantic kittiwakes. We exposed chick-rearing kittiwakes to a short-term (3-day) period of increased exogenous corticosterone (CORT), a hormone that is released during food shortages. We examined changes in baseline CORT levels, parental care and effects on offspring. We found that kittiwakes from the two populations invested differently in offspring when facing stress. In response to elevated CORT, Pacific kittiwakes reduced nest attendance and deserted offspring more readily than Atlantic kittiwakes. We observed lower chick growth, a higher stress response in offspring and lower reproductive success in response to CORT implantation in Pacific kittiwakes, whereas the opposite occurred in the Atlantic. Our findings support the hypothesis that life-history strategies predict short-term responses of individuals to stress within a species. We conclude that behaviour and physiology under stress are consistent with trade-off priorities as predicted by life-history theory. We encourage future studies to consider the pivotal role of life-history strategies when interpreting inter-population differences of animal responses to stressful environmental events.

  1. 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.

  2. Classification of frequency response areas in the inferior colliculus reveals continua not discrete classes.

    Science.gov (United States)

    Palmer, Alan R; Shackleton, Trevor M; Sumner, Christian J; Zobay, Oliver; Rees, Adrian

    2013-08-15

    A differential response to sound frequency is a fundamental property of auditory neurons. Frequency analysis in the cochlea gives rise to V-shaped tuning functions in auditory nerve fibres, but by the level of the inferior colliculus (IC), the midbrain nucleus of the auditory pathway, neuronal receptive fields display diverse shapes that reflect the interplay of excitation and inhibition. The origin and nature of these frequency receptive field types is still open to question. One proposed hypothesis is that the frequency response class of any given neuron in the IC is predominantly inherited from one of three major afferent pathways projecting to the IC, giving rise to three distinct receptive field classes. Here, we applied subjective classification, principal component analysis, cluster analysis, and other objective statistical measures, to a large population (2826) of frequency response areas from single neurons recorded in the IC of the anaesthetised guinea pig. Subjectively, we recognised seven frequency response classes (V-shaped, non-monotonic Vs, narrow, closed, tilt down, tilt up and double-peaked), that were represented at all frequencies. We could identify similar classes using our objective classification tools. Importantly, however, many neurons exhibited properties intermediate between these classes, and none of the objective methods used here showed evidence of discrete response classes. Thus receptive field shapes in the IC form continua rather than discrete classes, a finding consistent with the integration of afferent inputs in the generation of frequency response areas. The frequency disposition of inhibition in the response areas of some neurons suggests that across-frequency inputs originating at or below the level of the IC are involved in their generation.

  3. EEG neural oscillatory dynamics reveal semantic and response conflict at difference levels of conflict awareness.

    Science.gov (United States)

    Jiang, Jun; Zhang, Qinglin; Van Gaal, Simon

    2015-07-14

    Although previous work has shown that conflict can be detected in the absence of awareness, it is unknown how different sources of conflict (i.e., semantic, response) are processed in the human brain and whether these processes are differently modulated by conflict awareness. To explore this issue, we extracted oscillatory power dynamics from electroencephalographic (EEG) data recorded while human participants performed a modified version of the Stroop task. Crucially, in this task conflict awareness was manipulated by masking a conflict-inducing color word preceding a color patch target. We isolated semantic from response conflict by introducing four color words/patches, of which two were matched to the same response. We observed that both semantic as well as response conflict were associated with mid-frontal theta-band and parietal alpha-band power modulations, irrespective of the level of conflict awareness (high vs. low), although awareness of conflict increased these conflict-related power dynamics. These results show that both semantic and response conflict can be processed in the human brain and suggest that the neural oscillatory mechanisms in EEG reflect mainly "domain general" conflict processing mechanisms, instead of conflict source specific effects.

  4. EEG neural oscillatory dynamics reveal semantic and response conflict at difference levels of conflict awareness

    Science.gov (United States)

    Jiang, Jun; Zhang, Qinglin; Van Gaal, Simon

    2015-01-01

    Although previous work has shown that conflict can be detected in the absence of awareness, it is unknown how different sources of conflict (i.e., semantic, response) are processed in the human brain and whether these processes are differently modulated by conflict awareness. To explore this issue, we extracted oscillatory power dynamics from electroencephalographic (EEG) data recorded while human participants performed a modified version of the Stroop task. Crucially, in this task conflict awareness was manipulated by masking a conflict-inducing color word preceding a color patch target. We isolated semantic from response conflict by introducing four color words/patches, of which two were matched to the same response. We observed that both semantic as well as response conflict were associated with mid-frontal theta-band and parietal alpha-band power modulations, irrespective of the level of conflict awareness (high vs. low), although awareness of conflict increased these conflict-related power dynamics. These results show that both semantic and response conflict can be processed in the human brain and suggest that the neural oscillatory mechanisms in EEG reflect mainly “domain general” conflict processing mechanisms, instead of conflict source specific effects. PMID:26169473

  5. 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

    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......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...... 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...

  6. The human auditory brainstem response to running speech reveals a subcortical mechanism for selective attention.

    Science.gov (United States)

    Forte, Antonio Elia; Etard, Octave; Reichenbach, Tobias

    2017-10-10

    Humans excel at selectively listening to a target speaker in background noise such as competing voices. While the encoding of speech in the auditory cortex is modulated by selective attention, it remains debated whether such modulation occurs already in subcortical auditory structures. Investigating the contribution of the human brainstem to attention has, in particular, been hindered by the tiny amplitude of the brainstem response. Its measurement normally requires a large number of repetitions of the same short sound stimuli, which may lead to a loss of attention and to neural adaptation. Here we develop a mathematical method to measure the auditory brainstem response to running speech, an acoustic stimulus that does not repeat and that has a high ecological validity. We employ this method to assess the brainstem's activity when a subject listens to one of two competing speakers, and show that the brainstem response is consistently modulated by attention.

  7. 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

    across an experimental gradient. We characterized thermal reactionomes of two common ant species in the eastern U.S, the northern cool-climate Aphaenogaster picea and the southern warm-climate Aphaenogaster carolinensis, across 12 temperatures that spanned their entire thermal breadth.......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...

  8. 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.

  9. Vocal responses to noise reveal the presence of the Lombard effect in a frog

    NARCIS (Netherlands)

    Halfwerk, W.H.; Lea, A.M.; Guerra, M.A.; Page, R.A.; Ryan, M.J.

    2016-01-01

    Many animal communication systems have evolved signal flexibility depending on environmental conditions. A common strategy of vocal communication is to increase amplitude in response to increasing noise levels. This phenomenon, known as the Lombard effect, is a widespread trait among mammals and

  10. Thymus transcriptome reveals novel pathways in response to avian pathogenic Escherichia coli infection.

    Science.gov (United States)

    Sun, H; Liu, P; Nolan, L K; Lamont, S J

    2016-12-01

    Avian pathogenic Escherichia coli (APEC) can cause significant morbidity in chickens. The thymus provides the essential environment for T cell development; however, the thymus transcriptome has not been examined for gene expression in response to APEC infection. An improved understanding of the host genomic response to APEC infection could inform future breeding programs for disease resistance and APEC control. We therefore analyzed the transcriptome of the thymus of birds challenged with APEC, contrasting susceptible and resistant phenotypes. Thousands of genes were differentially expressed in birds of the 5-day post infection (dpi) challenged-susceptible group vs. 5 dpi non-challenged, in 5 dpi challenged-susceptible vs. 5 dpi challenged-resistant birds, as well as in 5 dpi vs. one dpi challenged-susceptible birds. The Toll-like receptor signaling pathway was the major innate immune response for birds to respond to APEC infection. Moreover, lysosome and cell adhesion molecules pathways were common mechanisms for chicken response to APEC infection. The T-cell receptor signaling pathway, cell cycle, and p53 signaling pathways were significantly activated in resistant birds to resist APEC infection. These results provide a comprehensive assessment of global gene networks and biological functionalities of differentially expressed genes in the thymus under APEC infection. These findings provide novel insights into key molecular genetic mechanisms that differentiate host resistance from susceptibility in this primary lymphoid tissue, the thymus. © The Author 2016. Published by Oxford University Press on behalf of Poultry Science Association.

  11. EEG neural oscillatory dynamics reveal semantic and response conflict at difference levels of conflict awareness

    NARCIS (Netherlands)

    Jiang, J.; Zhang, Q.; van Gaal, S.

    2015-01-01

    Although previous work has shown that conflict can be detected in the absence of awareness, it is unknown how different sources of conflict (i.e., semantic, response) are processed in the human brain and whether these processes are differently modulated by conflict awareness. To explore this issue,

  12. Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response.

    Science.gov (United States)

    Schmidt, Andreas; Trentini, Débora Broch; Spiess, Silvia; Fuhrmann, Jakob; Ammerer, Gustav; Mechtler, Karl; Clausen, Tim

    2014-02-01

    Arginine phosphorylation is an emerging protein modification implicated in the general stress response of Gram-positive bacteria. The modification is mediated by the arginine kinase McsB, which phosphorylates and inactivates the heat shock repressor CtsR. In this study, we developed a mass spectrometric approach accounting for the peculiar chemical properties of phosphoarginine. The improved methodology was used to analyze the dynamic changes in the Bacillus subtilis arginine phosphoproteome in response to different stress situations. Quantitative analysis showed that a B. subtilis mutant lacking the YwlE arginine phosphatase accumulated a strikingly large number of arginine phosphorylations (217 sites in 134 proteins), however only a minor fraction of these sites was increasingly modified during heat shock or oxidative stress. The main targets of McsB-mediated arginine phosphorylation comprise central factors of the stress response system including the CtsR and HrcA heat shock repressors, as well as major components of the protein quality control system such as the ClpCP protease and the GroEL chaperonine. These findings highlight the impact of arginine phosphorylation in orchestrating the bacterial stress response.

  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. 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.

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

    DEFF Research Database (Denmark)

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

    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......-30 years of age), single or in ‘other’ types of family relationships, and belong to a low-income bracket (annual household income ... 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...

  16. 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

  17. Quantitative proteomics reveals the central changes of wheat in response to powdery mildew.

    Science.gov (United States)

    Fu, Ying; Zhang, Hong; Mandal, Siddikun Nabi; Wang, Changyou; Chen, Chunhuan; Ji, Wanquan

    2016-01-01

    Powdery mildew (Pm), caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most important crop diseases, causing severe economic losses to wheat production worldwide. However, there are few reports about the proteomic response to Bgt infection in resistant wheat. Hence, quantitative proteomic analysis of N9134, a resistant wheat line, was performed to explore the molecular mechanism of wheat in defense against Bgt. Comparing the leaf proteins of Bgt-inoculated N9134 with that of mock-inoculated controls, a total of 2182 protein-species were quantified by iTRAQ at 24, 48 and 72h postinoculation (hpi) with Bgt, of which 394 showed differential accumulation. These differentially accumulated protein-species (DAPs) mainly included pathogenesis-related (PR) polypeptides, oxidative stress responsive proteins and components involved in primary metabolic pathways. KEGG enrichment analysis showed that phenylpropanoid biosynthesis, phenylalanine metabolism and photosynthesis-antenna proteins were the key pathways in response to Bgt infection. InterProScan 5 and the Gibbs Motif Sampler cluster 394 DAPs into eight conserved motifs, which shared leucine repeats and histidine sites in the sequence motifs. Moreover, eight separate protein-protein interaction (PPI) networks were predicted from STRING database. This study provides a powerful platform for further exploration of the molecular mechanism underlying resistant wheat responding to Bgt. Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive pathogenic disease in wheat-producing regions worldwide, resulting in severe yield reductions. Although many resistant wheat varieties have been cultivated, there are few reports about the proteomic response to Bgt infection in resistant wheat. Therefore, an iTRAQ-based quantitative proteomic analysis of a resistant wheat line (N9134) in response to Bgt infection has been performed. This paper provides new insights into the underlying molecular

  18. Increasing the Response Rate of the Patient Satisfaction Survey of Inpatients at National Naval Medical Center

    Science.gov (United States)

    1993-08-01

    identify a method to improve the effectiveness of the current survey process to increase the response rate of the patients being sampled. As health care... consumer must have adequate representation to provide meaningful information for decision making by the health care organization. Background of the...the Total Quality Management (TQM) philosophy into the health care industry has increased the importance of listening to the customer (Matthews, 1992

  19. A study of the responses of neutron dose equivalent survey meters with computer codes

    International Nuclear Information System (INIS)

    Sartori, D.E.; Beer, G.P. de

    1983-01-01

    The ANISN and DOT discrete-ordinates radiation transport codes for one and two dimensions have been proved as effective and simple techniques to study the response of dose equivalent neutron detectors. Comparisons between results of an experimental calibration of the Harwell 95/0075 survey meter and calculated results rendered satisfactory agreement, considering the different techniques and sources of error involved. Possible improvements in the methods and designs and causes of error are discussed. (author)

  20. What makes a place special? Interpretation of written survey responses in natural resource planning

    Science.gov (United States)

    Herbert W. Schroeder

    2000-01-01

    In an open-ended, written survey, I asked residents and visitors of the Black River area in northern Michigan to identify and describe places that were special to them. I conducted a thematic interpretation of the responses, using a set of indexing and cross-referencing marcos that I wrote in Word Perfect 5.1. The themes that emerged included the natural beauty ofthe...

  1. 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.

  2. 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.

  3. Linear and Non-Linear Dose-Response Functions Reveal a Hormetic Relationship Between Stress and Learning

    OpenAIRE

    Zoladz, Phillip R.; Diamond, David M.

    2008-01-01

    Over a century of behavioral research has shown that stress can enhance or impair learning and memory. In the present review, we have explored the complex effects of stress on cognition and propose that they are characterized by linear and non-linear dose-response functions, which together reveal a hormetic relationship between stress and learning. We suggest that stress initially enhances hippocampal function, resulting from amygdala-induced excitation of hippocampal synaptic plasticity, as ...

  4. Comment on "Satellites reveal contrasting responses of regional climate to the widespread greening of Earth".

    Science.gov (United States)

    Li, Yue; Zeng, Zhenzhong; Huang, Ling; Lian, Xu; Piao, Shilong

    2018-06-15

    Forzieri et al (Reports, 16 June 2017, p. 1180) used satellite data to show that boreal greening caused regional warming. We show that this positive sensitivity of temperature to the greening can be derived from the positive response of vegetation to boreal warming, which indicates that results from a statistical regression with satellite data should be carefully interpreted. Copyright © 2018, American Association for the Advancement of Science.

  5. Specific gene expression responses to parasite genotypes reveal redundancy of innate immunity in vertebrates.

    Directory of Open Access Journals (Sweden)

    David Haase

    Full Text Available Vertebrate innate immunity is the first line of defense against an invading pathogen and has long been assumed to be largely unspecific with respect to parasite/pathogen species. However, recent phenotypic evidence suggests that immunogenetic variation, i.e. allelic variability in genes associated with the immune system, results in host-parasite genotype-by-genotype interactions and thus specific innate immune responses. Immunogenetic variation is common in all vertebrate taxa and this reflects an effective immunological function in complex environments. However, the underlying variability in host gene expression patterns as response of innate immunity to within-species genetic diversity of macroparasites in vertebrates is unknown. We hypothesized that intra-specific variation among parasite genotypes must be reflected in host gene expression patterns. Here we used high-throughput RNA-sequencing to examine the effect of parasite genotypes on gene expression patterns of a vertebrate host, the three-spined stickleback (Gasterosteus aculeatus. By infecting naïve fish with distinct trematode genotypes of the species Diplostomum pseudospathaceum we show that gene activity of innate immunity in three-spined sticklebacks depended on the identity of an infecting macroparasite genotype. In addition to a suite of genes indicative for a general response against the trematode we also find parasite-strain specific gene expression, in particular in the complement system genes, despite similar infection rates of single clone treatments. The observed discrepancy between infection rates and gene expression indicates the presence of alternative pathways which execute similar functions. This suggests that the innate immune system can induce redundant responses specific to parasite genotypes.

  6. EEG neural oscillatory dynamics reveal semantic and response conflict at difference levels of conflict awareness

    OpenAIRE

    Jun Jiang; Qinglin Zhang; Simon Van Gaal

    2015-01-01

    Although previous work has shown that conflict can be detected in the absence of awareness, it is unknown how different sources of conflict (i.e., semantic, response) are processed in the human brain and whether these processes are differently modulated by conflict awareness. To explore this issue, we extracted oscillatory power dynamics from electroencephalographic (EEG) data recorded while human participants performed a modified version of the Stroop task. Crucially, in this task conflict a...

  7. Consistency Over Flattery: Self-Verification Processes Revealed in Implicit and Behavioral Responses to Feedback

    OpenAIRE

    Ayduk, O; Gyurak, A; Akinola, M; Mendes, WB

    2013-01-01

    Negative social feedback is often a source of distress. However, self-verification theory provides the counterintuitive explanation that negative feedback leads to less distress when it is consistent with chronic self-views. Drawing from this work, the present study examined the impact of receiving self-verifying feedback on outcomes largely neglected in prior research: implicit responses (i.e., physiological reactivity, facial expressions) that are difficult to consciously regulate and downs...

  8. Experimentally induced spermatophore production and immune responses reveal a trade-off in crickets

    OpenAIRE

    Angela M. Kerr; Susan N. Gershman; Scott K. Sakaluk

    2010-01-01

    The energetic demands of the immune system and reproduction are often high and can lead to trade-offs between these 2 life-history traits. In decorated crickets, Gryllodes sigillatus, much of a male's reproductive effort is devoted to calling, and to the synthesis of a spermatophylax, a large, gelatinous, non--sperm-containing mass forming part of the spermatophore and consumed by the female after mating. We employed a reciprocal design in which we experimentally induced an immune response in...

  9. Classification of frequency response areas in the inferior colliculus reveals continua not discrete classes

    OpenAIRE

    Palmer, Alan R; Shackleton, Trevor M; Sumner, Christian J; Zobay, Oliver; Rees, Adrian

    2013-01-01

    A differential response to sound frequency is a fundamental property of auditory neurons. Frequency analysis in the cochlea gives rise to V-shaped tuning functions in auditory nerve fibres, but by the level of the inferior colliculus (IC), the midbrain nucleus of the auditory pathway, neuronal receptive fields display diverse shapes that reflect the interplay of excitation and inhibition. The origin and nature of these frequency receptive field types is still open to question. One proposed hy...

  10. The influence of response competition on cerebral asymmetries for processing hierarchical stimuli revealed by ERP recordings

    OpenAIRE

    Malinowski, Peter; Hübner, Ronald; Keil, Andreas; Gruber, Thomas

    2002-01-01

    It is widely accepted that the left and right hemispheres differ with respect to the processing of global and local aspects of visual stimuli. Recently, behavioural experiments have shown that this processing asymmetry strongly depends on the response competition between the global and local levels of a stimulus. Here we report electrophysiological data that underline this observation. Hemispheric differences for global/local processing were mainly observed for responseincompatible stimuli an...

  11. Electro-responsivity of ionic liquid boundary layers in a polar solvent revealed by neutron reflectance

    Science.gov (United States)

    Pilkington, Georgia A.; Harris, Kathryn; Bergendal, Erik; Reddy, Akepati Bhaskar; Palsson, Gunnar K.; Vorobiev, Alexei; Antzutkin, Oleg. N.; Glavatskih, Sergei; Rutland, Mark W.

    2018-05-01

    Using neutron reflectivity, the electro-responsive structuring of the non-halogenated ionic liquid (IL) trihexyl(tetradecyl)phosphonium-bis(mandelato)borate, [P6,6,6,14][BMB], has been studied at a gold electrode surface in a polar solvent. For a 20% w/w IL mixture, contrast matched to the gold surface, distinct Kiessig fringes were observed for all potentials studied, indicative of a boundary layer of different composition to that of the bulk IL-solvent mixture. With applied potential, the amplitudes of the fringes from the gold-boundary layer interface varied systematically. These changes are attributable to the differing ratios of cations and anions in the boundary layer, leading to a greater or diminished contrast with the gold electrode, depending on the individual ion scattering length densities. Such electro-responsive changes were also evident in the reflectivities measured for the pure IL and a less concentrated (5% w/w) IL-solvent mixture at the same applied potentials, but gave rise to less pronounced changes. These measurements, therefore, demonstrate the enhanced sensitivity achieved by contrast matching the bulk solution and that the structure of the IL boundary layers formed in mixtures is strongly influenced by the bulk concentration. Together these results represent an important step in characterising IL boundary layers in IL-solvent mixtures and provide clear evidence of electro-responsive structuring of IL ions in their solutions with applied potential.

  12. Transcriptome profiling reveals the immune response of goose T cells under selenium stimuli.

    Science.gov (United States)

    Cao, Nan; Li, Wanyan; Li, Bingxin; Tian, Yunbo; Xu, Danning

    2017-12-01

    The goose is an economically important poultry species and a principal natural host of avian viruses. This study aimed to determine the effects of selenium on the immune response of geese. Under selenium stimulation, gene expression profiling was investigated using transcriptome sequencing. The selenoproteins were promoted by selenium stimulation, while the heat shock proteins, interleukin and interferons were mainly down-regulated. After comparison, 2228 differentially expressed genes were primarily involved in immune and environmental response, and infectious disease and genetic information processing related pathways were identified. Specifically, the enzymes of the lysosomes which acted as a safeguard in preventing pathogens were mostly up-regulated and six randomly selected differentially expressed genes were validated by quantitative polymerase chain reaction. In addition, the most proportional increased transcription factor family basic helix-loop-helix (bHLH) located in the 5' flank of selenoprotein P-like protein for selenium metabolism was identified by response to the selenium stimulation in this study. These analyses show that selenium can promote immune function by activating selenoproteins, transcript factors and lysosome pathway related genes, while weakening cytokine content genes in geese. © 2017 Japanese Society of Animal Science.

  13. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Metabolomics Reveals Metabolically Healthy and Unhealthy Obese Individuals Differ in their Response to a Caloric Challenge.

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    Flavia Badoud

    Full Text Available To determine if metabolically healthy obese (MHO individuals have a different metabolic response to a standardized diet compared to lean healthy (LH and metabolically unhealthy obese (MUO individuals.Thirty adults (35-70 yrs were classified as LH, MHO, and MUO according to anthropometric and clinical measurements. Participants consumed a standardized high calorie meal (~1330 kcal. Blood glucose and insulin were measured at fasting, and 15, 30, 60, 90 and 120 min postprandially. Additional blood samples were collected for the targeted analysis of amino acids (AAs and derivatives, and fatty acids (FAs.The postprandial response (i.e., area under the curve, AUC for serum glucose and insulin were similar between MHO and LH individuals, and significantly lower than MUO individuals (p < 0.05. Minor differences were found in postprandial responses for AAs between MHO and MUO individuals, while three polyunsaturated FAs (linoleic acid, γ-linolenic acid, arachidonic acid showed smaller changes in serum after the meal in MHO individuals compared to MUO. Fasting levels for various AAs (notably branched-chain AA and FAs (e.g., saturated myristic and palmitic acids were found to correlate with glucose and insulin AUC.MHO individuals show preserved insulin sensitivity and a greater ability to adapt to a caloric challenge compared to MUO individuals.

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

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    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.

  16. Differential stress response of Saccharomyces hybrids revealed by monitoring Hsp104 aggregation and disaggregation.

    Science.gov (United States)

    Kempf, Claudia; Lengeler, Klaus; Wendland, Jürgen

    2017-07-01

    Proteotoxic stress may occur upon exposure of yeast cells to different stress conditions. The induction of stress response mechanisms is important for cells to adapt to changes in the environment and ensure survival. For example, during exposure to elevated temperatures the expression of heat shock proteins such as Hsp104 is induced in yeast. Hsp104 extracts misfolded proteins from aggregates to promote their refolding. We used an Hsp104-GFP reporter to analyze the stress profiles of Saccharomyces species hybrids. To this end a haploid S. cerevisiae strain, harboring a chromosomal HSP104-GFP under control of its endogenous promoter, was mated with stable haploids of S. bayanus, S. cariocanus, S. kudriavzevii, S. mikatae, S. paradoxus and S. uvarum. Stress response behaviors in these hybrids were followed over time by monitoring the appearance and dissolution of Hsp104-GFP foci upon heat shock. General stress tolerance of these hybrids was related to the growth rate detected during exposure to e.g. ethanol and oxidizing agents. We observed that hybrids were generally more resistant to high temperature and ethanol stress compared to their parental strains. Amongst the hybrids differential responses regarding the appearance of Hsp104-foci and the time required for dissolving these aggregates were observed. The S. cerevisiae/S. paradoxus hybrid, combining the two most closely related strains, performed best under these conditions. Copyright © 2017 Elsevier GmbH. All rights reserved.

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

    Science.gov (United States)

    Voelz, Kerstin; Gratacap, Remi L; Wheeler, Robert T

    2015-11-01

    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 as a live whole

  18. 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

  19. 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

  20. Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation

    Science.gov (United States)

    Li, Xiaoping; Schilkey, Faye; Smith, Geoffrey B.

    2018-01-01

    Natural ionizing background radiation has exerted a constant pressure on organisms since the first forms of life appeared on Earth, so that cells have developed molecular mechanisms to avoid or repair damages caused directly by radiation or indirectly by radiation-induced reactive oxygen species (ROS). In the present study, we investigated the transcriptional effect of depriving Shewanella oneidensis cultures of background levels of radiation by growing the cells in a mine 655 m underground, thus reducing the dose rate from 72.1 to 0.9 nGy h-1 from control to treatment, respectively. RNASeq transcriptome analysis showed the differential expression of 4.6 and 7.6% of the S. oneidensis genome during early- and late-exponential phases of growth, respectively. The greatest change observed in the treatment was the downregulation of ribosomal proteins (21% of all annotated ribosomal protein genes during early- and 14% during late-exponential) and tRNA genes (14% of all annotated tRNA genes in early-exponential), indicating a marked decrease in protein translation. Other significant changes were the upregulation of membrane transporters, implying an increase in the traffic of substrates across the cell membrane, as well as the up and downregulation of genes related to respiration, which could be interpreted as a response to insufficient oxidants in the cells. In other reports, there is evidence in multiple species that some ROS not just lead to oxidative stress, but act as signaling molecules to control cellular metabolism at the transcriptional level. Consistent with these reports, several genes involved in the metabolism of carbon and biosynthesis of amino acids were also regulated, lending support to the idea of a wide metabolic response. Our results indicate that S. oneidensis is sensitive to the withdrawal of background levels of ionizing radiation and suggest that a transcriptional response is required to maintain homeostasis and retain normal growth. PMID:29768440

  1. 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.

  2. 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.

  3. Meta-analysis reveals profound responses of plant traits to glacial CO2 levels

    OpenAIRE

    Temme, A A; Cornwell, W K; Cornelissen, J H C; Aerts, R

    2013-01-01

    A general understanding of the links between atmospheric CO2 concentration and the functioning of the terrestrial biosphere requires not only an understanding of plant trait responses to the ongoing transition to higher CO2 but also the legacy effects of past low CO2. An interesting question is whether the transition from current to higher CO2 can be thought of as a continuation of the past trajectory of low to current CO2 levels. Determining this trajectory requires quantifying the effect si...

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

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    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

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

    Science.gov (United States)

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

    2016-03-22

    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.

  7. Analysis of Natural Variation in Bermudagrass (Cynodon dactylon) Reveals Physiological Responses Underlying Drought Tolerance

    Science.gov (United States)

    Cheng, Zhangmin; Ye, Tiantian; Chan, Zhulong

    2012-01-01

    Bermudagrass (Cynodon dactylon) is a widely used warm-season turfgrass and one of the most drought tolerant species. Dissecting the natural variation in drought tolerance and physiological responses will bring us powerful basis and novel insight for plant breeding. In the present study, we evaluated the natural variation of drought tolerance among nine bermudagrass varieties by measuring physiological responses after drought stress treatment through withholding water. Three groups differing in drought tolerance were identified, including two tolerant, five moderately tolerant and two susceptible varieties. Under drought stress condition, drought sensitive variety (Yukon) showed relative higher water loss, more severe cell membrane damage (EL), and more accumulation of hydrogen peroxide (H2O2) and malondialdehyde (MDA), while drought tolerant variety (Tifgreen) exhibited significantly higher antioxidant enzymes activities. Further results indicated that drought induced cell injury in different varieties (Yukon, SR9554 and Tifgreen) exhibited liner correlation with leaf water content (LWC), H2O2 content, MDA content and antioxidant enzyme activities. Additionally, Tifgreen plants had significantly higher levels of osmolytes (proline level and soluble sugars) when compared with Yukon and SR9554 under drought stress condition. Taken together, our results indicated that natural variation of drought stress tolerance in bermudagrass varieties might be largely related to the induced changes of water status, osmolyte accumulation and antioxidant defense system. PMID:23285294

  8. Time-Resolved Fast Mammalian Behavior Reveals the Complexity of Protective Pain Responses

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    Liam E. Browne

    2017-07-01

    Full Text Available Potentially harmful stimuli are detected at the skin by nociceptor sensory neurons that drive rapid protective withdrawal reflexes and pain. We set out to define, at a millisecond timescale, the relationship between the activity of these sensory neurons and the resultant behavioral output. Brief optogenetic activation of cutaneous nociceptors was found to activate only a single action potential in each fiber. This minimal input was used to determine high-speed behavioral responses in freely behaving mice. The localized stimulus generated widespread dynamic repositioning and alerting sub-second behaviors whose nature and timing depended on the context of the animal and its position, activity, and alertness. Our findings show that the primary response to injurious stimuli is not limited, fixed, or localized, but is dynamic, and that it involves recruitment and gating of multiple circuits distributed throughout the central nervous system at a sub-second timescale to effectively both alert to the presence of danger and minimize risk of harm.

  9. Meta-Analysis of High-Throughput Datasets Reveals Cellular Responses Following Hemorrhagic Fever Virus Infection

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    Gavin C. Bowick

    2011-05-01

    Full Text Available The continuing use of high-throughput assays to investigate cellular responses to infection is providing a large repository of information. Due to the large number of differentially expressed transcripts, often running into the thousands, the majority of these data have not been thoroughly investigated. Advances in techniques for the downstream analysis of high-throughput datasets are providing additional methods for the generation of additional hypotheses for further investigation. The large number of experimental observations, combined with databases that correlate particular genes and proteins with canonical pathways, functions and diseases, allows for the bioinformatic exploration of functional networks that may be implicated in replication or pathogenesis. Herein, we provide an example of how analysis of published high-throughput datasets of cellular responses to hemorrhagic fever virus infection can generate additional functional data. We describe enrichment of genes involved in metabolism, post-translational modification and cardiac damage; potential roles for specific transcription factors and a conserved involvement of a pathway based around cyclooxygenase-2. We believe that these types of analyses can provide virologists with additional hypotheses for continued investigation.

  10. Comprehensive proteome analysis of lysosomes reveals the diverse function of macrophages in immune responses.

    Science.gov (United States)

    Gao, Yanpan; Chen, Yanyu; Zhan, Shaohua; Zhang, Wenhao; Xiong, Feng; Ge, Wei

    2017-01-31

    Phagocytosis and autophagy in macrophages have been shown to be essential to both innate and adaptive immunity. Lysosomes are the main catabolic subcellular organelles responsible for degradation and recycling of both extracellular and intracellular material, which are the final steps in phagocytosis and autophagy. However, the molecular mechanisms underlying lysosomal functions after infection remain obscure. In this study, we conducted a quantitative proteomics analysis of the changes in constitution and glycosylation of proteins in lysosomes derived from murine RAW 264.7 macrophage cells treated with different types of pathogens comprising examples of bacteria (Listeria monocytogenes, L. m), DNA viruses (herpes simplex virus type-1, HSV-1) and RNA viruses (vesicular stomatitis virus, VSV). In total, 3,704 lysosome-related proteins and 300 potential glycosylation sites on 193 proteins were identified. Comparative analysis showed that the aforementioned pathogens induced distinct alterations in the proteome of the lysosome, which is closely associated with the immune functions of macrophages, such as toll-like receptor activation, inflammation and antigen-presentation. The most significant changes in proteins and fluctuations in glycosylation were also determined. Furthermore, Western blot analysis showed that the changes in expression of these proteins were undetectable at the whole cell level. Thus, our study provides unique insights into the function of lysosomes in macrophage activation and immune responses.

  11. Analysis of natural variation in bermudagrass (Cynodon dactylon) reveals physiological responses underlying drought tolerance.

    Science.gov (United States)

    Shi, Haitao; Wang, Yanping; Cheng, Zhangmin; Ye, Tiantian; Chan, Zhulong

    2012-01-01

    Bermudagrass (Cynodon dactylon) is a widely used warm-season turfgrass and one of the most drought tolerant species. Dissecting the natural variation in drought tolerance and physiological responses will bring us powerful basis and novel insight for plant breeding. In the present study, we evaluated the natural variation of drought tolerance among nine bermudagrass varieties by measuring physiological responses after drought stress treatment through withholding water. Three groups differing in drought tolerance were identified, including two tolerant, five moderately tolerant and two susceptible varieties. Under drought stress condition, drought sensitive variety (Yukon) showed relative higher water loss, more severe cell membrane damage (EL), and more accumulation of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA), while drought tolerant variety (Tifgreen) exhibited significantly higher antioxidant enzymes activities. Further results indicated that drought induced cell injury in different varieties (Yukon, SR9554 and Tifgreen) exhibited liner correlation with leaf water content (LWC), H₂O₂ content, MDA content and antioxidant enzyme activities. Additionally, Tifgreen plants had significantly higher levels of osmolytes (proline level and soluble sugars) when compared with Yukon and SR9554 under drought stress condition. Taken together, our results indicated that natural variation of drought stress tolerance in bermudagrass varieties might be largely related to the induced changes of water status, osmolyte accumulation and antioxidant defense system.

  12. Integrated approach reveals diet, APOE genotype and sex affect immune response in APP mice.

    Science.gov (United States)

    Nam, Kyong Nyon; Wolfe, Cody M; Fitz, Nicholas F; Letronne, Florent; Castranio, Emilie L; Mounier, Anais; Schug, Jonathan; Lefterov, Iliya; Koldamova, Radosveta

    2018-01-01

    Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder that is influenced by genetic and environmental risk factors, such as inheritance of ε4 allele of APOE (APOE4), sex and diet. Here, we examined the effect of high fat diet (HFD) on amyloid pathology and expression profile in brains of AD model mice expressing human APOE isoforms (APP/E3 and APP/E4 mice). APP/E3 and APP/E4 mice were fed HFD or Normal diet for 3months. We found that HFD significantly increased amyloid plaques in male and female APP/E4, but not in APP/E3 mice. To identify differentially expressed genes and gene-networks correlated to diet, APOE isoform and sex, we performed RNA sequencing and applied Weighted Gene Co-expression Network Analysis. We determined that the immune response network with major hubs Tyrobp/DAP12, Csf1r, Tlr2, C1qc and Laptm5 correlated significantly and positively to the phenotype of female APP/E4-HFD mice. Correspondingly, we found that in female APP/E4-HFD mice, microglia coverage around plaques, particularly of larger size, was significantly reduced. This suggests altered containment of the plaque growth and sex-dependent vulnerability in response to diet. The results of our study show concurrent impact of diet, APOE isoform and sex on the brain transcriptome and AD-like phenotype. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

    Czech Academy of Sciences Publication Activity Database

    Helguera, M.; Rivarola, M.; Clavijo, B.; Martis, M.M.; Vanzetti, L.S.; Gonzalez, S.; Garbus, I.; LeRoy, P.; Šimková, Hana; Valárik, Miroslav; Caccamo, M.; Doležel, Jaroslav; Mayer, K. F. X.; Feuillet, C.; Tranquilli, G.; Paniego, N.; Echenique, V.

    2015-01-01

    Roč. 233, APR 2015 (2015), s. 200-212 ISSN 0168-9452 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Chromosome 4D survey sequence * Gene annotation * Gene content Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.362, year: 2015

  14. Long-term changes in abundances of Sonoran Desert lizards reveal complex responses to climatic variation.

    Science.gov (United States)

    Flesch, Aaron D; Rosen, Philip C; Holm, Peter

    2017-12-01

    Understanding how climatic variation affects animal populations and communities is essential for addressing threats posed by climate change, especially in systems where impacts are projected to be high. We evaluated abundance dynamics of five common species of diurnal lizards over 25 years in a Sonoran Desert transition zone where precipitation decreased and temperature increased across time, and assessed hypotheses for the influence of climatic flux on spatiotemporal variation in abundances. We repeatedly surveyed lizards in spring and summer of each year at up to 32 sites, and used hierarchical mixture models to estimate detection probabilities, abundances, and population growth rates. Among terrestrial species, abundances of a short-lived, winter-spring breeder increased markedly by an estimated 237%-285% across time, while two larger spring-summer breeders with higher thermal preferences declined by up to 64%. Abundances of two arboreal species that occupy shaded and thus sheltered microhabitats fluctuated but did not decline systematically. Abundances of all species increased with precipitation at short lag times (1-1.5 years) likely due to enhanced food availability, but often declined after periods of high precipitation at longer lag times (2-4 years) likely due to predation and other biotic pressures. Although rising maximum daily temperatures (T max ) are expected to drive global declines of lizards, associations with T max were variable and weak for most species. Instead, abundances of all species declined with rising daily minimum temperatures, suggesting degradation of cool refugia imposed widespread metabolic or other costs. Our results suggest climate warming and drying are having major impacts on lizard communities by driving declines in species with traits that augment exposure to abiotic extremes and by modifying species interactions. The complexity of patterns we report indicates that evaluating and responding to the influence of climate change

  15. 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.

  16. 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

  17. 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.

  18. Variant allele frequency enrichment analysis in vitro reveals sonic hedgehog pathway to impede sustained temozolomide response in GBM.

    Science.gov (United States)

    Biswas, Nidhan K; Chandra, Vikas; Sarkar-Roy, Neeta; Das, Tapojyoti; Bhattacharya, Rabindra N; Tripathy, Laxmi N; Basu, Sunandan K; Kumar, Shantanu; Das, Subrata; Chatterjee, Ankita; Mukherjee, Ankur; Basu, Pryiadarshi; Maitra, Arindam; Chattopadhyay, Ansuman; Basu, Analabha; Dhara, Surajit

    2015-01-21

    Neoplastic cells of Glioblastoma multiforme (GBM) may or may not show sustained response to temozolomide (TMZ) chemotherapy. We hypothesize that TMZ chemotherapy response in GBM is predetermined in its neoplastic clones via a specific set of mutations that alter relevant pathways. We describe exome-wide enrichment of variant allele frequencies (VAFs) in neurospheres displaying contrasting phenotypes of sustained versus reversible TMZ-responses in vitro. Enrichment of VAFs was found on genes ST5, RP6KA1 and PRKDC in cells showing sustained TMZ-effect whereas on genes FREM2, AASDH and STK36, in cells showing reversible TMZ-effect. Ingenuity pathway analysis (IPA) revealed that these genes alter cell-cycle, G2/M-checkpoint-regulation and NHEJ pathways in sustained TMZ-effect cells whereas the lysine-II&V/phenylalanine degradation and sonic hedgehog (Hh) pathways in reversible TMZ-effect cells. Next, we validated the likely involvement of the Hh-pathway in TMZ-response on additional GBM neurospheres as well as on GBM patients, by extracting RNA-sequencing-based gene expression data from the TCGA-GBM database. Finally, we demonstrated TMZ-sensitization of a TMZ non-responder neurosphere in vitro by treating them with the FDA-approved pharmacological Hh-pathway inhibitor vismodegib. Altogether, our results indicate that the Hh-pathway impedes sustained TMZ-response in GBM and could be a potential therapeutic target to enhance TMZ-response in this malignancy.

  19. RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus

    Science.gov (United States)

    2011-01-01

    Background In a context of climate change, phenotypic plasticity provides long-lived species, such as trees, with the means to adapt to environmental variations occurring within a single generation. In eucalyptus plantations, water availability is a key factor limiting productivity. However, the molecular mechanisms underlying the adaptation of eucalyptus to water shortage remain unclear. In this study, we compared the molecular responses of two commercial eucalyptus hybrids during the dry season. Both hybrids differ in productivity when grown under water deficit. Results Pyrosequencing of RNA extracted from shoot apices provided extensive transcriptome coverage - a catalog of 129,993 unigenes (49,748 contigs and 80,245 singletons) was generated from 398 million base pairs, or 1.14 million reads. The pyrosequencing data enriched considerably existing Eucalyptus EST collections, adding 36,985 unigenes not previously represented. Digital analysis of read abundance in 14,460 contigs identified 1,280 that were differentially expressed between the two genotypes, 155 contigs showing differential expression between treatments (irrigated vs. non irrigated conditions during the dry season), and 274 contigs with significant genotype-by-treatment interaction. The more productive genotype displayed a larger set of genes responding to water stress. Moreover, stress signal transduction seemed to involve different pathways in the two genotypes, suggesting that water shortage induces distinct cellular stress cascades. Similarly, the response of functional proteins also varied widely between genotypes: the most productive genotype decreased expression of genes related to photosystem, transport and secondary metabolism, whereas genes related to primary metabolism and cell organisation were over-expressed. Conclusions For the most productive genotype, the ability to express a broader set of genes in response to water availability appears to be a key characteristic in the maintenance

  20. 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

  1. Conventional and technical diving surveys reveal elevated biomass and differing fish community composition from shallow and upper mesophotic zones of a remote United States coral reef.

    Directory of Open Access Journals (Sweden)

    Roldan C Muñoz

    Full Text Available The world's coral reefs appear to be in a global decline, yet most previous research on coral reefs has taken place at depths shallower than 30 m. Mesophotic coral ecosystem (depths deeper than ~30 m studies have revealed extensive, productive habitats and rich communities. Despite recent advances, mesophotic coral ecosystems remain understudied due to challenges with sampling at deeper depths. The few previous studies of mesophotic coral ecosystems have shown variation across locations in depth-specific species composition and assemblage shifts, potentially a response to differences in habitat or light availability/water clarity. This study utilized scuba to examine fish and benthic communities from shallow and upper mesophotic (to 45 m zones of Flower Garden Banks National Marine Sanctuary (FGBNMS, 28°0'N; 93°50'W from 2010-2012. Dominant planktivores were ubiquitous in shallow and upper mesophotic habitats, and comparisons with previous shallow research suggest this community distribution has persisted for over 30 years. Planktivores were abundant in shallow low-relief habitats on the periphery of the coral reef, and some of these sites that contained habitat transitioning from high to low relief supported high biomass of benthic predators. These peripheral sites at FGBNMS may be important for the trophic transfer of oceanic energy to the benthic coral reef. Distinct differences between upper mesophotic and shallow communities were also observed. These included greater overall fish (as well as apex predator biomass in the upper mesophotic, differences in apex predator community composition between depth zones, and greater percent cover of algae, rubble, sand, and sponges in the upper mesophotic. Greater fish biomass in the upper mesophotic and similar fish community composition between depth zones provide preliminary support that upper mesophotic habitats at FGBNMS have the capacity to serve as refugia for the shallow-water reefs. Diving

  2. Conventional and technical diving surveys reveal elevated biomass and differing fish community composition from shallow and upper mesophotic zones of a remote United States coral reef.

    Science.gov (United States)

    Muñoz, Roldan C; Buckel, Christine A; Whitfield, Paula E; Viehman, Shay; Clark, Randy; Taylor, J Christopher; Degan, Brian P; Hickerson, Emma L

    2017-01-01

    The world's coral reefs appear to be in a global decline, yet most previous research on coral reefs has taken place at depths shallower than 30 m. Mesophotic coral ecosystem (depths deeper than ~30 m) studies have revealed extensive, productive habitats and rich communities. Despite recent advances, mesophotic coral ecosystems remain understudied due to challenges with sampling at deeper depths. The few previous studies of mesophotic coral ecosystems have shown variation across locations in depth-specific species composition and assemblage shifts, potentially a response to differences in habitat or light availability/water clarity. This study utilized scuba to examine fish and benthic communities from shallow and upper mesophotic (to 45 m) zones of Flower Garden Banks National Marine Sanctuary (FGBNMS, 28°0'N; 93°50'W) from 2010-2012. Dominant planktivores were ubiquitous in shallow and upper mesophotic habitats, and comparisons with previous shallow research suggest this community distribution has persisted for over 30 years. Planktivores were abundant in shallow low-relief habitats on the periphery of the coral reef, and some of these sites that contained habitat transitioning from high to low relief supported high biomass of benthic predators. These peripheral sites at FGBNMS may be important for the trophic transfer of oceanic energy to the benthic coral reef. Distinct differences between upper mesophotic and shallow communities were also observed. These included greater overall fish (as well as apex predator) biomass in the upper mesophotic, differences in apex predator community composition between depth zones, and greater percent cover of algae, rubble, sand, and sponges in the upper mesophotic. Greater fish biomass in the upper mesophotic and similar fish community composition between depth zones provide preliminary support that upper mesophotic habitats at FGBNMS have the capacity to serve as refugia for the shallow-water reefs. Diving surveys of the

  3. What's missing in missing data? Omissions in survey responses among parents of children with advanced cancer.

    Science.gov (United States)

    Rosenberg, Abby R; Dussel, Veronica; Orellana, Liliana; Kang, Tammy; Geyer, J Russel; Feudtner, Chris; Wolfe, Joanne

    2014-08-01

    Missing data is a common phenomenon with survey-based research; patterns of missing data may elucidate why participants decline to answer certain questions. To describe patterns of missing data in the Pediatric Quality of Life and Evaluation of Symptoms Technology (PediQUEST) study, and highlight challenges in asking sensitive research questions. Cross-sectional, survey-based study embedded within a randomized controlled trial. Three large children's hospitals: Dana-Farber/Boston Children's Cancer and Blood Disorders Center (DF/BCCDC); Children's Hospital of Philadelphia (CHOP); and Seattle Children's Hospital (SCH). At the time of their child's enrollment, parents completed the Survey about Caring for Children with Cancer (SCCC), including demographics, perceptions of prognosis, treatment goals, quality of life, and psychological distress. Eighty-six of 104 parents completed surveys (83% response). The proportion of missing data varied by question type. While 14 parents (16%) left demographic fields blank, over half (n=48; 56%) declined to answer at least one question about their child's prognosis, especially life expectancy. The presence of missing data was unrelated to the child's diagnosis, time from progression, time to death, or parent distress (p>0.3 for each). Written explanations in survey margins suggested that addressing a child's life expectancy is particularly challenging for parents. Parents of children with cancer commonly refrain from answering questions about their child's prognosis, however, they may be more likely to address general cure likelihood than explicit life expectancy. Understanding acceptability of sensitive questions in survey-based research will foster higher quality palliative care research.

  4. Nonlinear responses within the medial prefrontal cortex reveal when specific implicit information influences economic decision making.

    Science.gov (United States)

    Deppe, Michael; Schwindt, Wolfram; Kugel, Harald; Plassmann, Hilke; Kenning, Peter

    2005-04-01

    The authors used functional magnetic resonance imaging (fMRI) to investigate how individual economic decisions are influenced by implicit memory contributions. Twenty-two participants were asked to make binary decisions between different brands of sensorily nearly undistinguishable consumer goods. Changes of brain activity comparing decisions in the presence or absence of a specific target brand were detected by fMRI. Only when the tar get brand was the participant's favorite one did the authors find reduced activation in the dorsolateral prefrontal, posterior parietal, and occipital cortices and the left premotor area (Brodmann areas [BA] 9, 46, 7/19, and 6). Simultaneously, activity was increased in the inferior precuneus and posterior cingulate (BA 7), right superior frontal gyrus (BA 10), right supramarginal gyrus (BA 40), and, most pronounced, in the ventromedial prefrontal cortex (BA 10). For products mainly distinguishable by brand information, the authors revealed a nonlinear winner-take-all effect for a participant's favorite brand characterized, on one hand, by reduced activation in brain areas associated with working memory and reasoning and, on the other hand, increased activation in areas involved in processing of emotions and self-reflections during decision making.

  5. Geographical gradients in selection can reveal genetic constraints for evolutionary responses to ocean acidification.

    Science.gov (United States)

    Gaitán-Espitia, Juan Diego; Marshall, Dustin; Dupont, Sam; Bacigalupe, Leonardo D; Bodrossy, Levente; Hobday, Alistair J

    2017-02-01

    Geographical gradients in selection can shape different genetic architectures in natural populations, reflecting potential genetic constraints for adaptive evolution under climate change. Investigation of natural pH/pCO 2 variation in upwelling regions reveals different spatio-temporal patterns of natural selection, generating genetic and phenotypic clines in populations, and potentially leading to local adaptation, relevant to understanding effects of ocean acidification (OA). Strong directional selection, associated with intense and continuous upwellings, may have depleted genetic variation in populations within these upwelling regions, favouring increased tolerances to low pH but with an associated cost in other traits. In contrast, diversifying or weak directional selection in populations with seasonal upwellings or outside major upwelling regions may have resulted in higher genetic variances and the lack of genetic correlations among traits. Testing this hypothesis in geographical regions with similar environmental conditions to those predicted under climate change will build insights into how selection may act in the future and how populations may respond to stressors such as OA. © 2017 The Author(s).

  6. Integrative Genomics Reveals Mechanisms of Copy Number Alterations Responsible for Transcriptional Deregulation in Colorectal Cancer

    Science.gov (United States)

    Camps, Jordi; Nguyen, Quang Tri; Padilla-Nash, Hesed M.; Knutsen, Turid; McNeil, Nicole E.; Wangsa, Danny; Hummon, Amanda B.; Grade, Marian; Ried, Thomas; Difilippantonio, Michael J.

    2016-01-01

    To evaluate the mechanisms and consequences of chromosomal aberrations in colorectal cancer (CRC), we used a combination of spectral karyotyping, array comparative genomic hybridization (aCGH), and array-based global gene expression profiling on 31 primary carcinomas and 15 established cell lines. Importantly, aCGH showed that the genomic profiles of primary tumors are recapitulated in the cell lines. We revealed a preponderance of chromosome breakpoints at sites of copy number variants (CNVs) in the CRC cell lines, a novel mechanism of DNA breakage in cancer. The integration of gene expression and aCGH led to the identification of 157 genes localized within high-level copy number changes whose transcriptional deregulation was significantly affected across all of the samples, thereby suggesting that these genes play a functional role in CRC. Genomic amplification at 8q24 was the most recurrent event and led to the overexpression of MYC and FAM84B. Copy number dependent gene expression resulted in deregulation of known cancer genes such as APC, FGFR2, and ERBB2. The identification of only 36 genes whose localization near a breakpoint could account for their observed deregulated expression demonstrates that the major mechanism for transcriptional deregulation in CRC is genomic copy number changes resulting from chromosomal aberrations. PMID:19691111

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Dynamic crossmodal links revealed by steady-state responses in auditory-visual divided attention.

    Science.gov (United States)

    de Jong, Ritske; Toffanin, Paolo; Harbers, Marten

    2010-01-01

    Frequency tagging has been often used to study intramodal attention but not intermodal attention. We used EEG and simultaneous frequency tagging of auditory and visual sources to study intermodal focused and divided attention in detection and discrimination performance. Divided-attention costs were smaller, but still significant, in detection than in discrimination. The auditory steady-state response (SSR) showed no effects of attention at frontocentral locations, but did so at occipital locations where it was evident only when attention was divided between audition and vision. Similarly, the visual SSR at occipital locations was substantially enhanced when attention was divided across modalities. Both effects were equally present in detection and discrimination. We suggest that both effects reflect a common cause: An attention-dependent influence of auditory information processing on early cortical stages of visual information processing, mediated by enhanced effective connectivity between the two modalities under conditions of divided attention. Copyright (c) 2009 Elsevier B.V. All rights reserved.

  9. Molecular Dynamics Simulation and Statistics Analysis Reveals the Defense Response Mechanism in Plants

    Science.gov (United States)

    Liu, Zhichao; Zhao, Yunjie; Zeng, Chen; Computational Biophysics Lab Team

    As the main protein of the bacterial flagella, flagellin plays an important role in perception and defense response. The newly discovered locus, FLS2, is ubiquitously expressed. FLS2 encodes a putative receptor kinase and shares many homologies with some plant resistance genes and even with some components of immune system of mammals and insects. In Arabidopsis, FLS2 perception is achieved by the recognition of epitope flg22, which induces FLS2 heteromerization with BAK1 and finally the plant immunity. Here we use both analytical methods such as Direct Coupling Analysis (DCA) and Molecular Dynamics (MD) Simulations to get a better understanding of the defense mechanism of FLS2. This may facilitate a redesign of flg22 or de-novo design for desired specificity and potency to extend the immune properties of FLS2 to other important crops and vegetables.

  10. The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs.

    Science.gov (United States)

    Gálvez, José Héctor; Tai, Helen H; Lagüe, Martin; Zebarth, Bernie J; Strömvik, Martina V

    2016-05-19

    Nitrogen (N) is the most important nutrient for the growth of potato (Solanum tuberosum L.). Foliar gene expression in potato plants with and without N supplementation at 180 kg N ha(-1) was compared at mid-season. Genes with consistent differences in foliar expression due to N supplementation over three cultivars and two developmental time points were examined. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed with supplemented N. Functional relationships between over-expressed genes were found. The main metabolic pathway represented among differentially expressed genes was amino acid metabolism. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed and nine overrepresented motifs were found using three motif discovery algorithms (Seeder, Weeder and MEME). These results point to coordinated gene regulation at the transcriptional level controlling steady state potato responses to N sufficiency.

  11. Serine Proteolytic Pathway Activation Reveals an Expanded Ensemble of Wound Response Genes in Drosophila

    Science.gov (United States)

    Patterson, Rachel A.; Juarez, Michelle T.; Hermann, Anita; Sasik, Roman; Hardiman, Gary; McGinnis, William

    2013-01-01

    After injury to the animal epidermis, a variety of genes are transcriptionally activated in nearby cells to regenerate the missing cells and facilitate barrier repair. The range and types of diffusible wound signals that are produced by damaged epidermis and function to activate repair genes during epidermal regeneration remains a subject of very active study in many animals. In Drosophila embryos, we have discovered that serine protease function is locally activated around wound sites, and is also required for localized activation of epidermal repair genes. The serine protease trypsin is sufficient to induce a striking global epidermal wound response without inflicting cell death or compromising the integrity of the epithelial barrier. We developed a trypsin wounding treatment as an amplification tool to more fully understand the changes in the Drosophila transcriptome that occur after epidermal injury. By comparing our array results with similar results on mammalian skin wounding we can see which evolutionarily conserved pathways are activated after epidermal wounding in very diverse animals. Our innovative serine protease-mediated wounding protocol allowed us to identify 8 additional genes that are activated in epidermal cells in the immediate vicinity of puncture wounds, and the functions of many of these genes suggest novel genetic pathways that may control epidermal wound repair. Additionally, our data augments the evidence that clean puncture wounding can mount a powerful innate immune transcriptional response, with different innate immune genes being activated in an interesting variety of ways. These include puncture-induced activation only in epidermal cells in the immediate vicinity of wounds, or in all epidermal cells, or specifically in the fat body, or in multiple tissues. PMID:23637905

  12. 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

    2014-06-03

    '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 (Pvisual 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. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

  13. High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection.

    Science.gov (United States)

    Florez, Juan Carlos; Mofatto, Luciana Souto; do Livramento Freitas-Lopes, Rejane; Ferreira, Sávio Siqueira; Zambolim, Eunize Maciel; Carazzolle, Marcelo Falsarella; Zambolim, Laércio; Caixeta, Eveline Teixeira

    2017-12-01

    We provide a transcriptional profile of coffee rust interaction and identified putative up regulated resistant genes Coffee rust disease, caused by the fungus Hemileia vastatrix, is one of the major diseases in coffee throughout the world. The use of resistant cultivars is considered to be the most effective control strategy for this disease. To identify candidate genes related to different mechanism defense in coffee, we present a time-course comparative gene expression profile of Caturra (susceptible) and Híbrido de Timor (HdT, resistant) in response to H. vastatrix race XXXIII infection. The main objectives were to obtain a global overview of transcriptome in both interaction, compatible and incompatible, and, specially, analyze up-regulated HdT specific genes with inducible resistant and defense signaling pathways. Using both Coffea canephora as a reference genome and de novo assembly, we obtained 43,159 transcripts. At early infection events (12 and 24 h after infection), HdT responded to the attack of H. vastatrix with a larger number of up-regulated genes than Caturra, which was related to prehaustorial resistance. The genes found in HdT at early hours were involved in receptor-like kinases, response ion fluxes, production of reactive oxygen species, protein phosphorylation, ethylene biosynthesis and callose deposition. We selected 13 up-regulated HdT-exclusive genes to validate by real-time qPCR, which most of them confirmed their higher expression in HdT than in Caturra at early stage of infection. These genes have the potential to assist the development of new coffee rust control strategies. Collectively, our results provide understanding of expression profiles in coffee-H. vastatrix interaction over a time course in susceptible and resistant coffee plants.

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

    Directory of Open Access Journals (Sweden)

    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. High-resolution tide projections reveal extinction threshold in response to sea-level rise.

    Science.gov (United States)

    Field, Christopher R; Bayard, Trina S; Gjerdrum, Carina; Hill, Jason M; Meiman, Susan; Elphick, Chris S

    2017-05-01

    Sea-level rise will affect coastal species worldwide, but models that aim to predict these effects are typically based on simple measures of sea level that do not capture its inherent complexity, especially variation over timescales shorter than 1 year. Coastal species might be most affected, however, by floods that exceed a critical threshold. The frequency and duration of such floods may be more important to population dynamics than mean measures of sea level. In particular, the potential for changes in the frequency and duration of flooding events to result in nonlinear population responses or biological thresholds merits further research, but may require that models incorporate greater resolution in sea level than is typically used. We created population simulations for a threatened songbird, the saltmarsh sparrow (Ammodramus caudacutus), in a region where sea level is predictable with high accuracy and precision. We show that incorporating the timing of semidiurnal high tide events throughout the breeding season, including how this timing is affected by mean sea-level rise, predicts a reproductive threshold that is likely to cause a rapid demographic shift. This shift is likely to threaten the persistence of saltmarsh sparrows beyond 2060 and could cause extinction as soon as 2035. Neither extinction date nor the population trajectory was sensitive to the emissions scenarios underlying sea-level projections, as most of the population decline occurred before scenarios diverge. Our results suggest that the variation and complexity of climate-driven variables could be important for understanding the potential responses of coastal species to sea-level rise, especially for species that rely on coastal areas for reproduction. © 2016 John Wiley & Sons Ltd.

  16. The Influence of the Design of Web Survey Questionnaires on the Quality of Responses

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    Stéphane Ganassali

    2008-03-01

    Full Text Available he first objective of this article is to propose a conceptual framework of the effects of on-line questionnaire design on the quality of collected responses. Secondly, we present the results of an experiment where different protocols have been tested and compared in a randomised design using the basis of several quality indexes. Starting from some previous categorizations, and from the main factors identified in the literature, we first propose an initial global framework of the questionnaire and question characteristics in a web survey, divided into five groups of factors. Our framework was built to follow the response process successive stages of the contact between the respondent and the questionnaire itself. Then, because it has been studied in the survey methodology literature in a very restricted way, the concept of `response quality' is discussed and extended with some more `qualitative' criteria that could be helpful for researchers and practitioners, in order to obtain a deeper assessment of the survey output. As an experiment, on the basis of the factors chosen as major characteristics of the questionnaire design, eight versions of a questionnaire related to young people's consumption patterns were created. The links to these on-line questionnaires were sent in November 2005 to a target of 10,000 young people. The article finally presents the results of our study and discusses the conclusions. Very interesting results come to light; especially regarding the influence of length, interaction and question wording dimensions on response quality. We discuss the effects of Web-questionnaire design characteristics on the quality of data.

  17. 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.

  18. [On the front line: survey on shared responsibility. General practitioners and schizophrenia].

    Science.gov (United States)

    Stip, Emmanuel; Boyer, Richard; Sepehry, Amir Ali; Rodriguez, Jean Pierre; Umbricht, Daniel; Tempier, Adrien; Simon, Andor E

    2007-01-01

    General practitioners (GP) play a preponderant role in the treatment of patients suffering of schizophrenia. Discovering the number of patients with schizophrenia who are treated by GPs ; the needs and attitudes of GPs, their knowledge concerning diagnosis, and the treatment they provide. A postal survey was conducted with Quebec GPs who were randomly chosen. A total of 1003 GPs have participated in the survey. Among them, a small percentage have to treat an early onset schizophrenia and the GPs have expressed their wish to be more informed on the accessibility of specialized services. Results pertaining to questions on diagnoses and knowledge on treatments are inconsistent. The majority of GPs treat the first psychotic episodes with antipsychotic medication. Only a third of GPs surveyed propose maintaining the treatment after a first psychotic episode, in accordance with international recommendations and the recent Canadian guidelines on practices that recommends at least 6 to 12 months of treatment after a partial or complete clinical response. Time given by male GPs to a first contact varies between 10 and 20 minutes, while 80 % of female GPs spend at least 20 minutes. The adverse effects of antipsychotic medication that raise most concern is weight gain before neurological signs. some of this survey's data should be considered by various professional and governmental associations, in order to improve the place of GPs in a health plan destined to treat schizophrenia.

  19. 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.

  20. 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

    2016-09-29

    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 CO 2 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.

  1. Functional analysis of rice HOMEOBOX4 (Oshox4) gene reveals a negative function in gibberellin responses.

    Science.gov (United States)

    Dai, Mingqiu; Hu, Yongfeng; Ma, Qian; Zhao, Yu; Zhou, Dao-Xiu

    2008-02-01

    The homeodomain-leucine zipper (HD-Zip) putative transcription factor genes are divided into 4 families. In this work, we studied the function of a rice HD-Zip I gene, H OME O BO X4 (Oshox4). Oshox4 transcripts were detected in leaf and floral organ primordia but excluded from the shoot apical meristem and the protein was nuclear localized. Over-expression of Oshox4 in rice induced a semi-dwarf phenotype that could not be complemented by applied GA3. The over-expression plants accumulated elevated levels of bioactive GA, while the GA catabolic gene GA2ox3 was upregulated in the transgenic plants. In addition, over-expression of Oshox4 blocked GA-dependent alpha-amylase production. However, down-regulation of Oshox4 in RNAi transgenic plants induced no phenotypic alteration. Interestingly, the expression of YAB1 that is involved in the negative feedback regulation of the GA biosynthesis was upregulated in the Oshox4 over-expressing plants. One-hybrid assays showed that Oshox4 could interact with YAB1 promoter in yeast. In addition, Oshox4 expression was upregulated by GA. These data together suggest that Oshox4 may be involved in the negative regulation of GA signalling and may play a role to fine tune GA responses in rice.

  2. Robust dynamic classes revealed by measuring the response function of a social system.

    Science.gov (United States)

    Crane, Riley; Sornette, Didier

    2008-10-14

    We study the relaxation response of a social system after endogenous and exogenous bursts of activity using the time series of daily views for nearly 5 million videos on YouTube. We find that most activity can be described accurately as a Poisson process. However, we also find hundreds of thousands of examples in which a burst of activity is followed by an ubiquitous power-law relaxation governing the timing of views. We find that these relaxation exponents cluster into three distinct classes and allow for the classification of collective human dynamics. This is consistent with an epidemic model on a social network containing two ingredients: a power-law distribution of waiting times between cause and action and an epidemic cascade of actions becoming the cause of future actions. This model is a conceptual extension of the fluctuation-dissipation theorem to social systems [Ruelle, D (2004) Phys Today 57:48-53] and [Roehner BM, et al., (2004) Int J Mod Phys C 15:809-834], and provides a unique framework for the investigation of timing in complex systems.

  3. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Network Analysis Reveals a Common Host–Pathogen Interaction Pattern in Arabidopsis Immune Responses

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    Hong Li

    2017-05-01

    Full Text Available Many plant pathogens secrete virulence effectors into host cells to target important proteins in host cellular network. However, the dynamic interactions between effectors and host cellular network have not been fully understood. Here, an integrative network analysis was conducted by combining Arabidopsis thaliana protein–protein interaction network, known targets of Pseudomonas syringae and Hyaloperonospora arabidopsidis effectors, and gene expression profiles in the immune response. In particular, we focused on the characteristic network topology of the effector targets and differentially expressed genes (DEGs. We found that effectors tended to manipulate key network positions with higher betweenness centrality. The effector targets, especially those that are common targets of an individual effector, tended to be clustered together in the network. Moreover, the distances between the effector targets and DEGs increased over time during infection. In line with this observation, pathogen-susceptible mutants tended to have more DEGs surrounding the effector targets compared with resistant mutants. Our results suggest a common plant–pathogen interaction pattern at the cellular network level, where pathogens employ potent local impact mode to interfere with key positions in the host network, and plant organizes an in-depth defense by sequentially activating genes distal to the effector targets.

  5. 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.

  6. Molecular profiling of prostate cancer derived exosomes may reveal a predictive signature for response to docetaxel.

    Science.gov (United States)

    Kharaziha, Pedram; Chioureas, Dimitris; Rutishauser, Dorothea; Baltatzis, George; Lennartsson, Lena; Fonseca, Pedro; Azimi, Alireza; Hultenby, Kjell; Zubarev, Roman; Ullén, Anders; Yachnin, Jeffrey; Nilsson, Sten; Panaretakis, Theocharis

    2015-08-28

    Docetaxel is a cornerstone treatment for metastatic, castration resistant prostate cancer (CRPC) which remains a leading cause of cancer-related deaths, worldwide. The clinical usage of docetaxel has resulted in modest gains in survival, primarily due to the development of resistance. There are currently no clinical biomarkers available that predict whether a CRPC patient will respond or acquire resistance to this therapy. Comparative proteomics analysis of exosomes secreted from DU145 prostate cancer cells that are sensitive (DU145 Tax-Sen) or have acquired resistance (DU145 Tax-Res) to docetaxel, demonstrated significant differences in the amount of exosomes secreted and in their molecular composition. A panel of proteins was identified by proteomics to be differentially enriched in DU145 Tax-Res compared to DU145 Tax-Sen exosomes and was validated by western blotting. Importantly, we identified MDR-1, MDR-3, Endophilin-A2 and PABP4 that were enriched only in DU145 Tax-Res exosomes. We validated the presence of these proteins in the serum of a small cohort of patients. DU145 cells that have uptaken DU145 Tax-Res exosomes show properties of increased matrix degradation. In summary, exosomes derived from DU145 Tax-Res cells may be a valuable source of biomarkers for response to therapy.

  7. Leaf Proteome Analysis Reveals Prospective Drought and Heat Stress Response Mechanisms in Soybean

    Directory of Open Access Journals (Sweden)

    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.

  8. A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria.

    Science.gov (United States)

    Fahlgren, Noah; Feldman, Maximilian; Gehan, Malia A; Wilson, Melinda S; Shyu, Christine; Bryant, Douglas W; Hill, Steven T; McEntee, Colton J; Warnasooriya, Sankalpi N; Kumar, Indrajit; Ficor, Tracy; Turnipseed, Stephanie; Gilbert, Kerrigan B; Brutnell, Thomas P; Carrington, James C; Mockler, Todd C; Baxter, Ivan

    2015-10-05

    Phenotyping has become the rate-limiting step in using large-scale genomic data to understand and improve agricultural crops. Here, the Bellwether Phenotyping Platform for controlled-environment plant growth and automated multimodal phenotyping is described. The system has capacity for 1140 plants, which pass daily through stations to record fluorescence, near-infrared, and visible images. Plant Computer Vision (PlantCV) was developed as open-source, hardware platform-independent software for quantitative image analysis. In a 4-week experiment, wild Setaria viridis and domesticated Setaria italica had fundamentally different temporal responses to water availability. While both lines produced similar levels of biomass under limited water conditions, Setaria viridis maintained the same water-use efficiency under water replete conditions, while Setaria italica shifted to less efficient growth. Overall, the Bellwether Phenotyping Platform and PlantCV software detected significant effects of genotype and environment on height, biomass, water-use efficiency, color, plant architecture, and tissue water status traits. All ∼ 79,000 images acquired during the course of the experiment are publicly available. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

  9. Satisfaction and responsiveness with health-care services in Qatar--evidence from a survey.

    Science.gov (United States)

    Ali, Faleh Mohamed Hussain; Nikoloski, Zlatko; Reka, Husein

    2015-11-01

    Satisfaction and responsiveness with health care are some of the main outcome variables of a health system. Although health outcomes have been studied in countries with different levels of economic development, there is limited information on the health provision/satisfaction/responsiveness nexus in countries where rapid transitions from middle to high-income status have occurred. Using a 2012 survey conducted in Qatar (amongst both Qatari and non-Qatari respondents), we analysed satisfaction and responsiveness of health care. The sample consisted of 4083 respondents. We use logit analysis [as well as robustness checks involving ordered logit, ordered probit, ordinary least squares (OLS) and probit analysis] in order to estimate the determinants of satisfaction and responsiveness. Both, satisfaction and responsiveness rates were high. Gender, nationality and, to some extent, income and age were significant sociodemographic determinants of satisfaction, with non-Qataris and females, having higher levels of satisfaction. Cost, previous experience with the same health provider and provision of medical insurance for a particular health provider were the attributes significantly correlated with general satisfaction. The results are consistent when the analysis is applied to the correlates of responsiveness. Sociodemographic factors explain the satisfaction with quality of health care in the state of Qatar (both from the general population point of view and from the patient point of view). Copyright © 2015. Published by Elsevier Ireland Ltd.

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

    Science.gov (United States)

    Keyvanara, Mahmoud; Sajadi, Haniye Sadat

    2015-01-01

    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. PMID:26340391

  11. 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.

  12. No Correlation Between Press Ganey Survey Responses and Outcomes in Post-Total Hip Arthroplasty Patients.

    Science.gov (United States)

    Chughtai, Morad; Gwam, Chukwuweike U; Khlopas, Anton; Sodhi, Nipun; Delanois, Ronald E; Spindler, Kurt P; Mont, Michael A

    2018-03-01

    In the era of the online orthopedic market, patients tend to equate publicly available online satisfaction surveys with what they presume their ultimate surgical outcome will be. Therefore, the purpose of this study was to assess whether there is a correlation between Press Ganey (PG) scores and (1) Hip Western Ontario and McMaster Universities Osteoarthritis Index and Harris Hip Score; (2) Short Form-12 and Short Form-36 scores; (3) University of California Los Angeles and Visual Analog Scale scores assessed at a mean of 3 years (range, 1 to 6 years) after surgery. In addition, we assessed whether (4) these correlations persist in patients who were evaluated under 2 years and 3 or more years after surgery. Six-hundred ninety-two patients from November 2009 to January 2015 were identified from our institutional PG database. One-hundred ninety (27%) responded to the survey. One-hundred forty-nine (78%) patients were given the total hip arthroplasty assessment tools at a minimum of 2-year follow-up, and 33 patients (17%) completed their survey before 2 years after surgery. We assessed whether overall hospital rating scores correlated with the above assessment tools. Pearson correlation analysis revealed no correlation between the PG survey score and the assessment tools. HHS had the highest correlation coefficient (r = .120; P = .316); however, this was not significant. After removing the patients who had their follow-up survey administered under 2 years after surgery (33 patients), there was still no statistically significant correlation between the above-mentioned outcome scores and PG overall hospital rating (P > .05). No statistically significant relationship was found between commonly used total hip arthroplasty assessment tools and the PG overall hospital rating. Based on these results, PG surveys may not be a suitable implementation of the Center for Medicare and Medicaid services. A set of measures that can be widely collected and reported by hospitals for

  13. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

    Directory of Open Access Journals (Sweden)

    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.

  14. A ChIP-chip approach reveals a novel role for transcription factor IRF1 in the DNA damage response.

    Science.gov (United States)

    Frontini, Mattia; Vijayakumar, Meeraa; Garvin, Alexander; Clarke, Nicole

    2009-03-01

    IRF1 is a transcription factor that regulates key processes in the immune system and in tumour suppression. To gain further insight into IRF1's role in these processes, we searched for new target genes by performing chromatin immunoprecipitation coupled to a CpG island microarray (ChIP-chip). Using this approach we identified 202 new IRF1-binding sites with high confidence. Functional categorization of the target genes revealed a surprising cadre of new roles that can be linked to IRF1. One of the major functional categories was the DNA damage response pathway. In order to further validate our findings, we show that IRF1 can regulate the mRNA expression of a number of the DNA damage response genes in our list. In particular, we demonstrate that the mRNA and protein levels of the DNA repair protein BRIP1 [Fanconi anemia gene J (FANC J)] are upregulated after IRF1 over-expression. We also demonstrate that knockdown of IRF1 by siRNA results in loss of BRIP1 expression, abrogation of BRIP1 foci after DNA interstrand crosslink (ICL) damage and hypersensitivity to the DNA crosslinking agent, melphalan; a characteristic phenotype of FANC J cells. Taken together, our data provides a more complete understanding of the regulatory networks controlled by IRF1 and reveals a novel role for IRF1 in regulating the ICL DNA damage response.

  15. A ChIP–chip approach reveals a novel role for transcription factor IRF1 in the DNA damage response

    Science.gov (United States)

    Frontini, Mattia; Vijayakumar, Meeraa; Garvin, Alexander; Clarke, Nicole

    2009-01-01

    IRF1 is a transcription factor that regulates key processes in the immune system and in tumour suppression. To gain further insight into IRF1's role in these processes, we searched for new target genes by performing chromatin immunoprecipitation coupled to a CpG island microarray (ChIP–chip). Using this approach we identified 202 new IRF1-binding sites with high confidence. Functional categorization of the target genes revealed a surprising cadre of new roles that can be linked to IRF1. One of the major functional categories was the DNA damage response pathway. In order to further validate our findings, we show that IRF1 can regulate the mRNA expression of a number of the DNA damage response genes in our list. In particular, we demonstrate that the mRNA and protein levels of the DNA repair protein BRIP1 [Fanconi anemia gene J (FANC J)] are upregulated after IRF1 over-expression. We also demonstrate that knockdown of IRF1 by siRNA results in loss of BRIP1 expression, abrogation of BRIP1 foci after DNA interstrand crosslink (ICL) damage and hypersensitivity to the DNA crosslinking agent, melphalan; a characteristic phenotype of FANC J cells. Taken together, our data provides a more complete understanding of the regulatory networks controlled by IRF1 and reveals a novel role for IRF1 in regulating the ICL DNA damage response. PMID:19129219

  16. Use of structured personality survey techniques to indicate operator response to stressful situations

    International Nuclear Information System (INIS)

    Waller, M.A.

    1990-01-01

    Under given circumstances, a person will tend to operate in one of four dominant orientations: (1) to perform tasks; (2) to achieve consensus; (3) to achieve understanding, or (4) to maintain structure. Historically, personality survey techniques, such as the Myers-Briggs type indicator, have been used to determine these tendencies. While these techniques can accurately reflect a person's orientation under normal social situations, under different sets of conditions, the same person may exhibit other tendencies, displaying a similar or entirely different orientation. While most do not exhibit extreme tendencies or changes of orientation, the shift in personality from normal to stressful conditions can be rather dramatic, depending on the individual. Structured personality survey techniques have been used to indicate operator response to stressful situations. These techniques have been extended to indicate the balance between orientations that the control room team has through the various levels of cognizance

  17. Different responses to heat shock stress revealed heteromorphic adaptation strategy of Pyropia haitanensis (Bangiales, Rhodophyta).

    Science.gov (United States)

    Luo, Qijun; Zhu, Zhenggang; Zhu, Zhujun; Yang, Rui; Qian, Feijian; Chen, Haimin; Yan, Xiaojun

    2014-01-01

    Pyropia has a unique heteromorphic life cycle with alternation stages between thallus and conchocelis, which lives at different water temperatures in different seasons. To better understand the different adaptation strategies for temperature stress, we tried to observe comparative biochemical changes of Pyropia haitanensis based on a short term heat shock model. The results showed that: (1) At normal temperature, free-living conchocelis contains significantly higher levels of H2O2, fatty acid-derived volatiles, the copy number of Phrboh and Phhsp70 genes,the activities of NADPH oxidase and floridoside than those in thallus. The released H2O2 and NADPH oxidase activity of conchocelis were more than 7 times higher than those of thallus. The copy number of Phrboh in conchocelis was 32 times that in thallus. (2) After experiencing heat shock at 35°C for 30 min, the H2O2 contents, the mRNA levels of Phrboh and Phhsp70, NADPH oxidase activity and the floridoside content in thallus were all significantly increased. The mRNA levels of Phrboh increased 5.78 times in 5 min, NADPH oxidase activity increased 8.45 times in 20 min. (3) Whereas, in conchocelis, the changes in fatty acids and their down-stream volatiles predominated, significantly increasing levels of saturated fatty acids and decreasing levels of polyunsaturated fatty acids occurred, and the 8-carbon volatiles were accumulated. However, the changes in H2O2 content and expression of oxidant-related genes and enzymatic activity were not obvious. Overall, these results indicate that conchocelis maintains a high level of active protective apparatus to endure its survival at high temperature, while thallus exhibit typical stress responses to heat shock. It is concluded that Pyropia haitanensis has evolved a delicate strategy for temperature adaptation for its heteromorphic life cycle.

  18. Different responses to heat shock stress revealed heteromorphic adaptation strategy of Pyropia haitanensis (Bangiales, Rhodophyta.

    Directory of Open Access Journals (Sweden)

    Qijun Luo

    Full Text Available Pyropia has a unique heteromorphic life cycle with alternation stages between thallus and conchocelis, which lives at different water temperatures in different seasons. To better understand the different adaptation strategies for temperature stress, we tried to observe comparative biochemical changes of Pyropia haitanensis based on a short term heat shock model. The results showed that: (1 At normal temperature, free-living conchocelis contains significantly higher levels of H2O2, fatty acid-derived volatiles, the copy number of Phrboh and Phhsp70 genes,the activities of NADPH oxidase and floridoside than those in thallus. The released H2O2 and NADPH oxidase activity of conchocelis were more than 7 times higher than those of thallus. The copy number of Phrboh in conchocelis was 32 times that in thallus. (2 After experiencing heat shock at 35°C for 30 min, the H2O2 contents, the mRNA levels of Phrboh and Phhsp70, NADPH oxidase activity and the floridoside content in thallus were all significantly increased. The mRNA levels of Phrboh increased 5.78 times in 5 min, NADPH oxidase activity increased 8.45 times in 20 min. (3 Whereas, in conchocelis, the changes in fatty acids and their down-stream volatiles predominated, significantly increasing levels of saturated fatty acids and decreasing levels of polyunsaturated fatty acids occurred, and the 8-carbon volatiles were accumulated. However, the changes in H2O2 content and expression of oxidant-related genes and enzymatic activity were not obvious. Overall, these results indicate that conchocelis maintains a high level of active protective apparatus to endure its survival at high temperature, while thallus exhibit typical stress responses to heat shock. It is concluded that Pyropia haitanensis has evolved a delicate strategy for temperature adaptation for its heteromorphic life cycle.

  19. 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.

  20. Linear and non-linear dose-response functions reveal a hormetic relationship between stress and learning.

    Science.gov (United States)

    Zoladz, Phillip R; Diamond, David M

    2008-10-16

    Over a century of behavioral research has shown that stress can enhance or impair learning and memory. In the present review, we have explored the complex effects of stress on cognition and propose that they are characterized by linear and non-linear dose-response functions, which together reveal a hormetic relationship between stress and learning. We suggest that stress initially enhances hippocampal function, resulting from amygdala-induced excitation of hippocampal synaptic plasticity, as well as the excitatory effects of several neuromodulators, including corticosteroids, norepinephrine, corticotropin-releasing hormone, acetylcholine and dopamine. We propose that this rapid activation of the amygdala-hippocampus brain memory system results in a linear dose-response relation between emotional strength and memory formation. More prolonged stress, however, leads to an inhibition of hippocampal function, which can be attributed to compensatory cellular responses that protect hippocampal neurons from excitotoxicity. This inhibition of hippocampal functioning in response to prolonged stress is potentially relevant to the well-described curvilinear dose-response relationship between arousal and memory. Our emphasis on the temporal features of stress-brain interactions addresses how stress can activate, as well as impair, hippocampal functioning to produce a hormetic relationship between stress and learning.

  1. Application of xCELLigence RTCA Biosensor Technology for Revealing the Profile and Window of Drug Responsiveness in Real Time

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    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.

  2. Comprehensive transcriptome analyses correlated with untargeted metabolome reveal differentially expressed pathways in response to cell wall alterations.

    Science.gov (United States)

    Reem, Nathan T; Chen, Han-Yi; Hur, Manhoi; Zhao, Xuefeng; Wurtele, Eve Syrkin; Li, Xu; Li, Ling; Zabotina, Olga

    2018-03-01

    This research provides new insights into plant response to cell wall perturbations through correlation of transcriptome and metabolome datasets obtained from transgenic plants expressing cell wall-modifying enzymes. Plants respond to changes in their cell walls in order to protect themselves from pathogens and other stresses. Cell wall modifications in Arabidopsis thaliana have profound effects on gene expression and defense response, but the cell signaling mechanisms underlying these responses are not well understood. Three transgenic Arabidopsis lines, two with reduced cell wall acetylation (AnAXE and AnRAE) and one with reduced feruloylation (AnFAE), were used in this study to investigate the plant responses to cell wall modifications. RNA-Seq in combination with untargeted metabolome was employed to assess differential gene expression and metabolite abundance. RNA-Seq results were correlated with metabolite abundances to determine the pathways involved in response to cell wall modifications introduced in each line. The resulting pathway enrichments revealed the deacetylation events in AnAXE and AnRAE plants induced similar responses, notably, upregulation of aromatic amino acid biosynthesis and changes in regulation of primary metabolic pathways that supply substrates to specialized metabolism, particularly those related to defense responses. In contrast, genes and metabolites of lipid biosynthetic pathways and peroxidases involved in lignin polymerization were downregulated in AnFAE plants. These results elucidate how primary metabolism responds to extracellular stimuli. Combining the transcriptomics and metabolomics datasets increased the power of pathway prediction, and demonstrated the complexity of pathways involved in cell wall-mediated signaling.

  3. The effect of a monetary incentive for administrative assistants on the survey response rate: a randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Arnav Agarwal

    2016-08-01

    Full Text Available Abstract Background There is sufficient evidence that monetary incentives are effective in increasing survey response rates in the general population as well as with physicians. The objective of this study was to assess the impact of a monetary incentive intended for administrative assistants on the survey response rate of physicians in leadership positions. Methods This was an ancillary study to a national survey of chairs of academic Departments of Medicine in the United States about measuring faculty productivity. We randomized survey participants to receive or not receive a $5 gift card enclosed in the survey package. The cover letter explained that the gift card was intended for the administrative assistants as a “thank you for their time.” We compared the response rates between the 2 study arms using the Chi-square test. Results Out of 152 participants to whom survey packages were mailed to, a total of 78 responses were received (51 % response rate. The response rates were 59 % in the incentive arm and 46 % in the no incentive arm. The relative effect of the incentive compared to no monetary incentive was borderline statistically significant (relative risk (RR = 1.36, 95 % confidence interval (CI 0.99 to 1.87; p = 0.055. Conclusion Monetary incentives intended for administrative assistants likely increase the response rate of physicians in leadership positions.

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    Takashi Ikeda

    Full Text Available 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.

  6. Aerogeophysical survey over Sør Rondane Mountains and its implications for revealing the tectonic evolution of East Antarctica

    Science.gov (United States)

    Mieth, Matthias; Steinhage, Daniel; Ruppel, Antonia; Damaske, Detlef; Jokat, Wilfried

    2013-04-01

    We are presenting new magnetic and gravity data of a high-resolution aerogephysical survey over the area of the Sør Rondane Mountains in the eastern Dronning Maud Land (DML). The aircraft survey is part of the joint geological and geophysical GEA campaign (Geodynamic Evolution of East Antarctica) of the Federal Agency for Geosciences and Natural Resources (BGR) and Alfred-Wegener-Institute for Polar and Marine Research (AWI), in cooperation with the Universities of Ghent, Bremen and Bergen. It was completed during the Antarctic summer season 2012/13, covering an area of more than 100000 square kilometer with a line spacing of 5 km. The data will be correlated with geological structures exposed in the mountain range as well as matched and merged with the data sets of the eastern and southern DML (acquired by AWI during the last decade) for comparison and discussion in the greater context of the tectonic evolution of East Antarctica. Preliminary results show that the magnetic anomaly pattern over the Sør Rondane Mountains differs from the pattern found over the central DML mountains as well as from the low amplitude pattern in between both regions, indicating a significant difference in the evolution of this region, which is in accordance with latest geological findings in this region.

  7. Swiss national community survey on functioning after spinal cord injury : Protocol, characteristics of participants and determinants of non-response

    NARCIS (Netherlands)

    Brinkhof, Martin W G; Fekete, Christine; Chamberlain, Jonviea D; Post, Marcel W M; Gemperli, Armin

    2016-01-01

    OBJECTIVE: To detail the protocol, recruitment, study population, response, and data quality of the first population-based community survey of the Swiss Spinal Cord Injury (SwiSCI) Cohort Study. DESIGN: The survey consisted of 3 successive modules administered between September 2011 and March 2013.

  8. Swiss national community survey on functioning after spinal cord injury : Protocol, characteristics of participants and determinants of non-response

    NARCIS (Netherlands)

    Brinkhof, Martin W. G.; Fekete, Christine; Chamberlain, Jonviea D.; Post, Marcel W. M.; Gemperli, Armin

    Objective: To detail the protocol, recruitment, study population, response, and data quality of the first population-based community survey of the Swiss Spinal Cord Injury (SwiSCI) Cohort Study. Design: The survey consisted of 3 successive modules administered between September 2011 and March 2013.

  9. 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.

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

    International Nuclear Information System (INIS)

    Rosensteel, B.A.; Awl, D.J.

    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

  11. Systems biology integration of proteomic data in rodent models of depression reveals involvement of the immune response and glutamatergic signaling.

    Science.gov (United States)

    Carboni, Lucia; Nguyen, Thanh-Phuong; Caberlotto, Laura

    2016-12-01

    The pathophysiological basis of major depression is incompletely understood. Recently, numerous proteomic studies have been performed in rodent models of depression to investigate the molecular underpinnings of depressive-like behaviours with an unbiased approach. The objective of the study is to integrate the results of these proteomic studies in depression models to shed light on the most relevant molecular pathways involved in the disease. Network analysis is performed integrating preexisting proteomic data from rodent models of depression. The IntAct mouse and the HRPD are used as reference protein-protein interaction databases. The functionality analyses of the networks are then performed by testing overrepresented GO biological process terms and pathways. Functional enrichment analyses of the networks revealed an association with molecular processes related to depression in humans, such as those involved in the immune response. Pathways impacted by clinically effective antidepressants are modulated, including glutamatergic signaling and neurotrophic responses. Moreover, dysregulations of proteins regulating energy metabolism and circadian rhythms are implicated. The comparison with protein pathways modulated in depressive patients revealed significant overlapping. This systems biology study supports the notion that animal models can contribute to the research into the biology and therapeutics of depression. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Responsibility for managing musculoskeletal disorders--a cross-sectional postal survey of attitudes.

    Science.gov (United States)

    Larsson, Maria E H; Nordholm, Lena A

    2008-08-05

    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. 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. 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 disorders and investigated background variables were that

  13. 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

  14. 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

  15. 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.

  16. The failing measurement of attitudes: How semantic determinants of individual survey responses come to replace measures of attitude strength.

    Science.gov (United States)

    Arnulf, Jan Ketil; Larsen, Kai Rune; Martinsen, Øyvind Lund; Egeland, Thore

    2018-01-12

    The traditional understanding of data from Likert scales is that the quantifications involved result from measures of attitude strength. Applying a recently proposed semantic theory of survey response, we claim that survey responses tap two different sources: a mixture of attitudes plus the semantic structure of the survey. Exploring the degree to which individual responses are influenced by semantics, we hypothesized that in many cases, information about attitude strength is actually filtered out as noise in the commonly used correlation matrix. We developed a procedure to separate the semantic influence from attitude strength in individual response patterns, and compared these results to, respectively, the observed sample correlation matrices and the semantic similarity structures arising from text analysis algorithms. This was done with four datasets, comprising a total of 7,787 subjects and 27,461,502 observed item pair responses. As we argued, attitude strength seemed to account for much information about the individual respondents. However, this information did not seem to carry over into the observed sample correlation matrices, which instead converged around the semantic structures offered by the survey items. This is potentially disturbing for the traditional understanding of what survey data represent. We argue that this approach contributes to a better understanding of the cognitive processes involved in survey responses. In turn, this could help us make better use of the data that such methods provide.

  17. 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.

  18. Survey of public knowledge and responses to educational slogans regarding cold-water immersion.

    Science.gov (United States)

    Giesbrecht, Gordon G; Pretorius, Thea

    2008-01-01

    Cold water temperature is a significant factor in North American drownings. These deaths are usually attributed to hypothermia. Survey questions were administered to 661 attendees of cold-stress seminars-including medical, rescue, law enforcement and lay attendees-to determine general knowledge of the effects of ice water immersion and responses to 2 public service educational slogans. Five questions were posed at the beginning of seminars to 8 groups (ranging in size from 46 to 195) during a 2-year period. Pi(2) analyses were used to determine if responses within any occupational category differed from the group responses. A high portion of respondents greatly underestimated the time to become hypothermic in ice water (correct answer >30 minutes; 84% stated 15 minutes or less) and the time until cooling was life threatening (correct answer >60 minutes; 85% stated 30 minutes or less). There were no occupational differences in these responses. Most of the respondents identified a correct cause of death during cold stress (81% stated cardiac arrest, hypothermia, or drowning). Although both educational slogans had some advantages, between 40% (Slogan #1) to 50% (Slogan #2) of respondents did not respond correctly. The majority of respondents underestimated the time available for survival during ice water immersion. It is important to educate the public accurately to decrease the probability of panic under these circumstances. More work is required to develop effective educational slogans that provide proper information and actions for victims of cold-water immersion.

  19. Analysis of Transcriptional Signatures in Response to Listeria monocytogenes Infection Reveals Temporal Changes That Result from Type I Interferon Signaling

    Science.gov (United States)

    Potempa, Krzysztof; Graham, Christine M.; Moreira-Teixeira, Lucia; McNab, Finlay W.; Howes, Ashleigh; Stavropoulos, Evangelos; Pascual, Virginia; Banchereau, Jacques; Chaussabel, Damien; O’Garra, Anne

    2016-01-01

    Analysis of the mouse transcriptional response to Listeria monocytogenes infection reveals that a large set of genes are perturbed in both blood and tissue and that these transcriptional responses are enriched for pathways of the immune response. Further we identified enrichment for both type I and type II interferon (IFN) signaling molecules in the blood and tissues upon infection. Since type I IFN signaling has been reported widely to impair bacterial clearance we examined gene expression from blood and tissues of wild type (WT) and type I IFNαβ receptor-deficient (Ifnar1-/-) mice at the basal level and upon infection with L. monocytogenes. Measurement of the fold change response upon infection in the absence of type I IFN signaling demonstrated an upregulation of specific genes at day 1 post infection. A less marked reduction of the global gene expression signature in blood or tissues from infected Ifnar1-/- as compared to WT mice was observed at days 2 and 3 after infection, with marked reduction in key genes such as Oasg1 and Stat2. Moreover, on in depth analysis, changes in gene expression in uninfected mice of key IFN regulatory genes including Irf9, Irf7, Stat1 and others were identified, and although induced by an equivalent degree upon infection this resulted in significantly lower final gene expression levels upon infection of Ifnar1-/- mice. These data highlight how dysregulation of this network in the steady state and temporally upon infection may determine the outcome of this bacterial infection and how basal levels of type I IFN-inducible genes may perturb an optimal host immune response to control intracellular bacterial infections such as L. monocytogenes. PMID:26918359

  20. Structural characteristics around the frontal thrust along the Nankai Trough revealed by bathymetric and seismic reflection survey

    Science.gov (United States)

    Yamashita, M.; Nakanishi, A.; Moore, G. F.; Kodaira, S.; Nakamura, Y.; Miura, S.; Kaneda, Y.

    2016-12-01

    Great earthquakes with tsunamis with recurrence intervals of 100-200 years have occurred along the Nankai Trough near central Japan where the Shikoku Basin is subducting with thick sediments on the Philippine Sea plate. To predict the exact height of the tsunami on the coast region generated by these large ruptures, it is important to estimate the vertical deformation that occurs on the seaward end of the rupture area. Recent drilling results have also yielded evidence not only of splay faults that generate tsunamigenic rupture, but also new evidence of tsunamigenic rupture along the frontal thrust at the trench axis in the Nankai Trough. In order to understand the deformation around the frontal thrust at the trench axis, we conducted a dense high-resolution seismic reflection survey with 10-20 km spacing over 1500 km of line length during 2013 and 2014. Clear seismic reflection images of frontal thrusts in the accretionary prism and subducting Shikoku Basin, image deformation along the trench axis between off Muroto Cape and off Ashizuri Cape. The cumulative displacement along the frontal thrust and second thrust are measured from picked distinct reflectors in depth-converted profiles. The average value of cumulative displacement of the frontal thrust is more than 100 m within 2 km depth beneath the seafloor. The location of highest displacement of 300 m displacement agree with the seaward end of slip distribution of the 1946 Nankai event calculated by numerical simulations. We also evaluate the seaward structure for understanding the future rupture distribution. The protothrust zone (PTZ) consisting of many incipient thrusts is identifiable in the portion of trough-fill sediments seaward of the frontal thrust. In order to emphasize the characteristics of frontal thrust and PTZ, we construct the detailed relief image for focusing on the lineated slope of the PTZ at the trough axis. Although our surveys covered a part of Nankai seismogenic zone, it is important to

  1. Within-person analysis of welfare transitions in a longitudinal panel survey reveals change in mental health service use.

    Science.gov (United States)

    Pymont, C; Schofield, T P; Butterworth, P

    2017-12-01

    While international research shows that receipt of welfare benefits is associated with poor mental health, less is known about the relationship between welfare receipt and mental health service use. We investigate whether within-person change in welfare recipient status is associated with change in mental health service use. Analysis of two waves of data from an Australian national household survey. Random- and fixed-effect models considered the effect of change in welfare receipt status, and assessed whether change in mental health service use differed by type of welfare benefit or the direction of welfare transition. Individuals were more likely to report greater mental health service use at times of welfare receipt. These associations were attenuated, but remained significant, after adjusting for mental health. Increased health service use was not tied to specific types of welfare benefits. The increase in mental health service use associated with a transition onto welfare benefits was much greater than the decline in service use associated with the transition off benefits. Within individuals, welfare receipt is associated with greater mental health service use. While this does reflect poorer mental health at the time of welfare receipt, other factors seem to facilitate health service use. © The Author 2016. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. The COS-AGN survey: Revealing the nature of circum-galactic gas around hosts of active galactic nuclei

    Science.gov (United States)

    Berg, Trystyn A. M.; Ellison, Sara L.; Tumlinson, Jason; Oppenheimer, Benjamin D.; Horton, Ryan; Bordoloi, Rongmon; Schaye, Joop

    2018-04-01

    Active galactic nuclei (AGN) are thought to play a critical role in shaping galaxies, but their effect on the circumgalactic medium (CGM) is not well studied. We present results from the COS-AGN survey: 19 quasar sightlines that probe the CGM of 20 optically-selected AGN host galaxies with impact parameters 80 frame equivalent widths EW≥124 mÅ) whilst many of the metal ions are not detected in individual sightlines. A sightline-by-sightline comparison between COS-AGN and the control sample yields no significant difference in EW distribution. However, stacked spectra of the COS-AGN and control samples show significant (>3σ) enhancements in the EW of both Siiii And Lyα at impact parameters >164 kpc by a factor of +0.45 ± 0.05 dex and >+0.75 dex respectively. The lack of detections of both high-ionization species near the AGN and strong kinematic offsets between the absorption systemic galaxy redshifts indicates that neither the AGN's ionization nor its outflows are the origin of these differences. Instead, we suggest the observed differences could result from either AGN hosts residing in haloes with intrinsically distinct gas properties, or that their CGM has been affected by a previous event, such as a starburst, which may also have fuelled the nuclear activity.

  3. Long-term In Vivo Calcium Imaging of Astrocytes Reveals Distinct Cellular Compartment Responses to Sensory Stimulation.

    Science.gov (United States)

    Stobart, Jillian L; Ferrari, Kim David; Barrett, Matthew J P; Stobart, Michael J; Looser, Zoe J; Saab, Aiman S; Weber, Bruno

    2018-01-01

    Localized, heterogeneous calcium transients occur throughout astrocytes, but the characteristics and long-term stability of these signals, particularly in response to sensory stimulation, remain unknown. Here, we used a genetically encoded calcium indicator and an activity-based image analysis scheme to monitor astrocyte calcium activity in vivo. We found that different subcellular compartments (processes, somata, and endfeet) displayed distinct signaling characteristics. Closer examination of individual signals showed that sensory stimulation elevated the number of specific types of calcium peaks within astrocyte processes and somata, in a cortical layer-dependent manner, and that the signals became more synchronous upon sensory stimulation. Although mice genetically lacking astrocytic IP3R-dependent calcium signaling (Ip3r2-/-) had fewer signal peaks, the response to sensory stimulation was sustained, suggesting other calcium pathways are also involved. Long-term imaging of astrocyte populations revealed that all compartments reliably responded to stimulation over several months, but that the location of the response within processes may vary. These previously unknown characteristics of subcellular astrocyte calcium signals provide new insights into how astrocytes may encode local neuronal circuit activity. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice

    Directory of Open Access Journals (Sweden)

    Riaño-Pachón Diego

    2007-08-01

    Full Text Available Abstract Background In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs, ABRE and CE3, in thale cress (Arabidopsis thaliana and rice (Oryza sativa. Results Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Conclusion Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of

  5. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.

    Science.gov (United States)

    Gómez-Porras, Judith L; Riaño-Pachón, Diego Mauricio; Dreyer, Ingo; Mayer, Jorge E; Mueller-Roeber, Bernd

    2007-08-01

    In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be

  6. History of the great Kanto earthquakes inferred from the ages of Holocene marine terraces revealed by a comprehensive drilling survey

    Science.gov (United States)

    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.

  7. Legacies of stream channel modification revealed using General Land Office surveys, with implications for water temperature and aquatic life

    Directory of Open Access Journals (Sweden)

    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.

  8. Characterizing interstellar filaments as revealed by the Herschel Gould Belt survey: Insights into the initial conditions for star formation

    International Nuclear Information System (INIS)

    Arzoumanian, Doris

    2012-01-01

    This thesis aims to characterize the physical properties of interstellar filaments imaged in nearby molecular clouds with the Herschel Space Observatory as part of the Herschel Gould Belt survey. In order to get insight into the formation and evolution of interstellar filaments I analyzed, during my PhD work, a large sample of filaments detected in various nearby clouds. The observed density profiles of the filaments show a power law behavior at large radii and their dust temperature profiles show a drop towards the center. The filaments are characterized by a narrow distribution of de-convolved inner widths, centered around a typical value of ∼ 0.1 pc, while they span more than three orders of magnitude in central column density. This typical filament width corresponds to the sonic scale below which interstellar turbulence becomes subsonic in diffuse gas, which may suggest that the filaments form as a result of the dissipation of large-scale turbulence. While the turbulent fragmentation picture provides a plausible mechanism for forming interstellar filaments, the fact that pre-stellar cores tend to form in dense, gravitationally unstable filaments suggests that gravity is a major driver in the subsequent evolution of the dense supercritical filaments. The latter hypothesis is supported by molecular line observations with the IRAM 30 m telescope, which show an increase in the non-thermal velocity dispersion of supercritical filaments as a function of their central column density, suggesting that self gravitating filaments grow in mass per unit length by accretion of background material while at the same time fragmenting into star-forming cores. (author) [fr

  9. Differential proteomic analysis reveals sequential heat stress-responsive regulatory network in radish (Raphanus sativus L.) taproot.

    Science.gov (United States)

    Wang, Ronghua; Mei, Yi; Xu, Liang; Zhu, Xianwen; Wang, Yan; Guo, Jun; Liu, Liwang

    2018-05-01

    Differential abundance protein species (DAPS) involved in reducing damage and enhancing thermotolerance in radish were firstly identified. Proteomic analysis and omics association analysis revealed a HS-responsive regulatory network in radish. Heat stress (HS) is a major destructive factor influencing radish production and supply in summer, for radish is a cool season vegetable crop being susceptible to high temperature. In this study, the proteome changes of radish taproots under 40 °C treatment at 0 h (Control), 12 h (Heat12) and 24 h (Heat24) were analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification) approach. In total, 2258 DAPS representing 1542 differentially accumulated uniprotein species which respond to HS were identified. A total of 604, 910 and 744 DAPS was detected in comparison of Control vs. Heat12, Control vs. Heat24, and Heat12 vs. Heat24, respectively. Gene ontology and pathway analysis showed that annexin, ubiquitin-conjugating enzyme, ATP synthase, heat shock protein (HSP) and other stress-related proteins were predominately enriched in signal transduction, stress and defense pathways, photosynthesis and energy metabolic pathways, working cooperatively to reduce stress-induced damage in radish. Based on iTRAQ combined with the transcriptomics analysis, a schematic model of a sequential HS-responsive regulatory network was proposed. The initial sensing of HS occurred at the plasma membrane, and then key components of stress signal transduction triggered heat-responsive genes in the plant protective metabolism to re-establish homeostasis and enhance thermotolerance. These results provide new insights into characteristics of HS-responsive DAPS and facilitate dissecting the molecular mechanisms underlying heat tolerance in radish and other root crops.

  10. Adding Postal Follow-Up to a Web-Based Survey of Primary Care and Gastroenterology Clinic Physician Chiefs Improved Response Rates but not Response Quality or Representativeness.

    Science.gov (United States)

    Partin, Melissa R; Powell, Adam A; Burgess, Diana J; Haggstrom, David A; Gravely, Amy A; Halek, Krysten; Bangerter, Ann; Shaukat, Aasma; Nelson, David B

    2015-09-01

    This study assessed whether postal follow-up to a web-based physician survey improves response rates, response quality, and representativeness. We recruited primary care and gastroenterology chiefs at 125 Veterans Affairs medical facilities to complete a 10-min web-based survey on colorectal cancer screening and diagnostic practices in 2010. We compared response rates, response errors, and representativeness in the primary care and gastroenterology samples before and after adding postal follow-up. Adding postal follow-up increased response rates by 20-25 percentage points; markedly greater increases than predicted from a third e-mail reminder. In the gastroenterology sample, the mean number of response errors made by web responders (0.25) was significantly smaller than the mean number made by postal responders (2.18), and web responders provided significantly longer responses to open-ended questions. There were no significant differences in these outcomes in the primary care sample. Adequate representativeness was achieved before postal follow-up in both samples, as indicated by the lack of significant differences between web responders and the recruitment population on facility characteristics. We conclude adding postal follow-up to this web-based physician leader survey improved response rates but not response quality or representativeness. © The Author(s) 2013.

  11. A survey of utility experience with real time pricing: implications for policymakers seeking price responsive demand

    International Nuclear Information System (INIS)

    Barbose, Galen; Goldman, Charles; Neenan, Bernard

    2005-01-01

    Economists and policy makers frequently propose real time pricing (RTP) as a strategy for facilitating price responsive demand, thereby improving the performance of electricity markets and regional networks. While theoretically appealing, many practical and empirical issues related to RTP remain unresolved or poorly understood. Over the past two decades, more than 70 utilities in the U.S. have offered voluntary RTP tariffs, on either a pilot or permanent basis. However, most have operated in relative obscurity, and little information has made its way into the public domain. To address this gap, we conducted a conducted a comprehensive review of voluntary RTP programs in the U.S. by surveying 43 U.S. utilities and reviewing regulatory documents, tariffs, program evaluations, and other publicly available sources. Based on this review of RTP program experience, we identify key trends related to utilities' motivations and goals for implementing RTP, evolution of RTP tariff design, program participation, participant price response, and program outlook. Experience with voluntary RTP programs has been mixed. Several utilities have demonstrated that voluntary RTP programs are capable of generating significant load reductions. However, most programs have attracted relatively few participants and therefore have generated quite limited load reductions. About 2700 non-residential customers were enrolled in RTP programs in 2003, representing more than 11 000 MW of load. We then draw from these findings to identify implications for policy makers and regulators that are currently considering RTP as a strategy for facilitating price responsive demand

  12. Asymmetrical structure, hydrothermal system and edifice stability: The case of Ubinas volcano, Peru, revealed by geophysical surveys

    Science.gov (United States)

    Gonzales, Katherine; Finizola, Anthony; Lénat, Jean-François; Macedo, Orlando; Ramos, Domingo; Thouret, Jean-Claude; Fournier, Nicolas; Cruz, Vicentina; Pistre, Karine

    2014-04-01

    Ubinas volcano, the historically most active volcano in Peru straddles a low-relief high plateau and the flank of a steep valley. A multidisciplinary geophysical study has been performed to investigate the internal structure and the fluids flow within the edifice. We conducted 10 self-potential (SP) radial (from summit to base) profiles, 15 audio magnetotelluric (AMT) soundings on the west flank and a detailed survey of SP and soil temperature measurements on the summit caldera floor. The typical “V” shape of the SP radial profiles has been interpreted as the result of a hydrothermal zone superimposed on a hydrogeological zone in the upper parts of the edifice, and depicts a sub-circular SP positive anomaly, about 6 km in diameter. The latter is centred on the summit, and is characterised by a larger extension on the western flank located on the low-relief high plateau. The AMT resistivity model shows the presence of a conductive body beneath the summit at a depth comparable to that of the bottom of the inner south crater in the present-day caldera, where intense hydrothermal manifestations occur. The lack of SP and temperature anomalies on the present caldera floor suggests a self-sealed hydrothermal system, where the inner south crater acts as a pressure release valve. Although no resistivity data exists on the eastern flank, we presume, based on the asymmetry of the basement topography, and the amplitude of SP anomalies on the east flank, which are approximately five fold that on the west flank, that gravitational flow of hydrothermal fluids may occur towards the deep valley of Ubinas. This hypothesis, supported by the presence of hot springs and faults on the eastern foot of the edifice, reinforces the idea that a large part of the southeast flank of the Ubinas volcano may be altered by hydrothermal activity and will tend to be less stable. One of the major findings that stems from this study is that the slope of the basement on which a volcano has grown

  13. Comparison of Self-Reported Telephone Interviewing and Web-Based Survey Responses: Findings From the Second Australian Young and Well National Survey

    Science.gov (United States)

    Davenport, Tracey A; Burns, Jane M; Hickie, Ian B

    2017-01-01

    Background Web-based self-report surveying has increased in popularity, as it can rapidly yield large samples at a low cost. Despite this increase in popularity, in the area of youth mental health, there is a distinct lack of research comparing the results of Web-based self-report surveys with the more traditional and widely accepted computer-assisted telephone interviewing (CATI). Objective The Second Australian Young and Well National Survey 2014 sought to compare differences in respondent response patterns using matched items on CATI versus a Web-based self-report survey. The aim of this study was to examine whether responses varied as a result of item sensitivity, that is, the item’s susceptibility to exaggeration on underreporting and to assess whether certain subgroups demonstrated this effect to a greater extent. Methods A subsample of young people aged 16 to 25 years (N=101), recruited through the Second Australian Young and Well National Survey 2014, completed the identical items on two occasions: via CATI and via Web-based self-report survey. Respondents also rated perceived item sensitivity. Results When comparing CATI with the Web-based self-report survey, a Wilcoxon signed-rank analysis showed that respondents answered 14 of the 42 matched items in a significantly different way. Significant variation in responses (CATI vs Web-based) was more frequent if the item was also rated by the respondents as highly sensitive in nature. Specifically, 63% (5/8) of the high sensitivity items, 43% (3/7) of the neutral sensitivity items, and 0% (0/4) of the low sensitivity items were answered in a significantly different manner by respondents when comparing their matched CATI and Web-based question responses. The items that were perceived as highly sensitive by respondents and demonstrated response variability included the following: sexting activities, body image concerns, experience of diagnosis, and suicidal ideation. For high sensitivity items, a regression

  14. Comparison of Self-Reported Telephone Interviewing and Web-Based Survey Responses: Findings From the Second Australian Young and Well National Survey.

    Science.gov (United States)

    Milton, Alyssa C; Ellis, Louise A; Davenport, Tracey A; Burns, Jane M; Hickie, Ian B

    2017-09-26

    Web-based self-report surveying has increased in popularity, as it can rapidly yield large samples at a low cost. Despite this increase in popularity, in the area of youth mental health, there is a distinct lack of research comparing the results of Web-based self-report surveys with the more traditional and widely accepted computer-assisted telephone interviewing (CATI). The Second Australian Young and Well National Survey 2014 sought to compare differences in respondent response patterns using matched items on CATI versus a Web-based self-report survey. The aim of this study was to examine whether responses varied as a result of item sensitivity, that is, the item's susceptibility to exaggeration on underreporting and to assess whether certain subgroups demonstrated this effect to a greater extent. A subsample of young people aged 16 to 25 years (N=101), recruited through the Second Australian Young and Well National Survey 2014, completed the identical items on two occasions: via CATI and via Web-based self-report survey. Respondents also rated perceived item sensitivity. When comparing CATI with the Web-based self-report survey, a Wilcoxon signed-rank analysis showed that respondents answered 14 of the 42 matched items in a significantly different way. Significant variation in responses (CATI vs Web-based) was more frequent if the item was also rated by the respondents as highly sensitive in nature. Specifically, 63% (5/8) of the high sensitivity items, 43% (3/7) of the neutral sensitivity items, and 0% (0/4) of the low sensitivity items were answered in a significantly different manner by respondents when comparing their matched CATI and Web-based question responses. The items that were perceived as highly sensitive by respondents and demonstrated response variability included the following: sexting activities, body image concerns, experience of diagnosis, and suicidal ideation. For high sensitivity items, a regression analysis showed respondents who were male

  15. Amygdala subnuclei connectivity in response to violence reveals unique influences of individual differences in psychopathic traits in a nonforensic sample.

    Science.gov (United States)

    Yoder, Keith J; Porges, Eric C; Decety, Jean

    2015-04-01

    Atypical amygdala function and connectivity have reliably been associated with psychopathy. However, the amygdala is not a unitary structure. To examine how psychopathic traits in a nonforensic sample are linked to amygdala response to violence, this study used probabilistic tractography to classify amygdala subnuclei based on anatomical projections to and from amygdala subnuclei in a group of 43 male participants. The segmentation identified the basolateral complex (BLA; lateral, basal, and accessory basal subnuclei) and the central subnucleus (CE), which were used as seeds in a functional connectivity analysis to identify differences in neuronal coupling specific to observed violence. While a full amygdala seed showed significant connectivity only to right middle occipital gyrus, subnuclei seeds revealed unique connectivity patterns. BLA showed enhanced coupling with anterior cingulate and prefrontal regions, while CE showed increased connectivity with the brainstem, but reduced connectivity with superior parietal and precentral gyrus. Further, psychopathic personality factors were related to specific patterns of connectivity. Fearless Dominance scores on the psychopathic personality inventory predicted increased coupling between the BLA seed and sensory integration cortices, and increased connectivity between the CE seed and posterior insula. Conversely, Self-Centered Impulsivity scores were negatively correlated with coupling between BLA and ventrolateral prefrontal cortex, and Coldheartedness scores predicted increased functional connectivity between BLA and dorsal anterior cingulate cortex. Taken together, these findings demonstrate how subnuclei segmentations reveal important functional connectivity differences that are otherwise inaccessible. Such an approach yields a better understanding of amygdala dysfunction in psychopathy. © 2014 Wiley Periodicals, Inc.

  16. Omics approaches on fresh-cut lettuce reveal global molecular responses to sodium hypochlorite and peracetic acid treatment.

    Science.gov (United States)

    Daddiego, Loretta; Bianco, Linda; Capodicasa, Cristina; Carbone, Fabrizio; Dalmastri, Claudia; Daroda, Lorenza; Del Fiore, Antonella; De Rossi, Patrizia; Di Carli, Mariasole; Donini, Marcello; Lopez, Loredana; Mengoni, Alessio; Paganin, Patrizia; Perrotta, Gaetano; Bevivino, Annamaria

    2018-01-01

    Lettuce is a leafy vegetable that is extensively commercialized as a ready-to-eat product because of its widespread use in human nutrition as salad. It is well known that washing treatments can severely affect the quality and shelf-life of ready-to-eat vegetables. The study presented here evaluated the effect of two washing procedures on fresh-cut lettuce during storage. An omics approach was applied to reveal global changes at molecular level induced by peracetic acid washing in comparison with sodium hypochlorite treatment. Microbiological analyses were also performed to quantify total bacterial abundance and composition. The study revealed wide metabolic alterations induced by the two sanitizers. In particular, transcriptomic and proteomic analyses pointed out a number of transcripts and proteins differentially accumulated in response to peracetic acid washing, mainly occurring on the first day of storage. In parallel, different microbiota composition and significant reduction in total bacterial load following washing were also observed. The results provide useful information for the fresh-cut industry to select an appropriate washing procedure preserving fresh-like attributes as much as possible during storage of the end product. Molecular evidence indicated peracetic acid to be a valid alternative to sodium hypochlorite as sanitizer solution. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  17. 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.

  18. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

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    Meghann K. Devlin-Durante

    2017-11-01

    Full Text Available The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

  19. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata.

    Science.gov (United States)

    Devlin-Durante, Meghann K; Baums, Iliana B

    2017-01-01

    The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata , to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

  20. Effects of the leakage magnetic field from an analog meter on the response of scintillation survey meters

    International Nuclear Information System (INIS)

    Abe, Toshiaki; Yamamoto, Hisao; Norimura, Toshiyuki; Katase, Akira

    2003-01-01

    Effects of the weak leakage magnetic field are studied on the response of two kinds of scintillation survey meters: an ordinary type for γ-rays and that optimized for the detection of low-energy photons from 125 I. In the presence of the magnetic field, the response of the optimized survey meter decreases to the photons from 125 I, and increases considerably to the background radiations. On the other hand, the response of the ordinary survey meter decreases slightly to both the γ-rays from 131 I and the background radiations. From analysis of the pulse-height spectra for the radiations, such variations of the response are ascribed to the reduction of the amplification factor of photomultiplier tubes by the magnetic field. (author)

  1. 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.

  2. What Factors are Important to Patients when Assessing Treatment Response: An International Cross-sectional Survey.

    Science.gov (United States)

    von Kobyletzki, Laura B; Thomas, Kim S; Schmitt, Jochen; Chalmers, Joanne R; Deckert, Stefanie; Aoki, Valeria; Weisshaar, Elke; Ojo, Jumoke Ahubelem; Svensson, Åke

    2017-01-04

    This study investigated the perspective of international patients on individual symptoms of atopic dermatitis (eczema) in determining treatment response. A questionnaire was developed to evaluate the importance of symptoms from the patient's perspective. Patients were asked: "How important are these features in deciding whether or not a treatment is working?", and rated symptoms on a 5-point Likert scale. Patients were approached via Harmonising Outcome Measures for Eczema (HOME) collaborators and self-selected to take part in the on-line survey. Patients from 34 countries (n = 1,111) completed the survey; of these, 423 (38.3%) were parents of children with eczema. Nine items were rated as being "quite important" or "very important" by more than 80% of the respondents: itch, pain/soreness, skin feels hot or inflamed, bleeding, involvement of visible or sensitive body sites, cracks, sleep difficulties, amount of body affected, and weeping/oozing. These results may be of use in determining the face validity of scales from a cross-cultural patients' perspective.

  3. Interactive Fuzzy Goal Programming approach in multi-response stratified sample surveys

    Directory of Open Access Journals (Sweden)

    Gupta Neha

    2016-01-01

    Full Text Available In this paper, we applied an Interactive Fuzzy Goal Programming (IFGP approach with linear, exponential and hyperbolic membership functions, which focuses on maximizing the minimum membership values to determine the preferred compromise solution for the multi-response stratified surveys problem, formulated as a Multi- Objective Non Linear Programming Problem (MONLPP, and by linearizing the nonlinear objective functions at their individual optimum solution, the problem is approximated to an Integer Linear Programming Problem (ILPP. A numerical example based on real data is given, and comparison with some existing allocations viz. Cochran’s compromise allocation, Chatterjee’s compromise allocation and Khowaja’s compromise allocation is made to demonstrate the utility of the approach.

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

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    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.

  5. Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes

    Directory of Open Access Journals (Sweden)

    Paules Richard S

    2007-11-01

    Full Text Available Abstract Background A common observation in the analysis of gene expression data is that many genes display similarity in their expression patterns and therefore appear to be co-regulated. However, the variation associated with microarray data and the complexity of the experimental designs make the acquisition of co-expressed genes a challenge. We developed a novel method for Extracting microarray gene expression Patterns and Identifying co-expressed Genes, designated as EPIG. The approach utilizes the underlying structure of gene expression data to extract patterns and identify co-expressed genes that are responsive to experimental conditions. Results Through evaluation of the correlations among profiles, the magnitude of variation in gene expression profiles, and profile signal-to-noise ratio's, EPIG extracts a set of patterns representing co-expressed genes. The method is shown to work well with a simulated data set and microarray data obtained from time-series studies of dauer recovery and L1 starvation in C. elegans and after ultraviolet (UV or ionizing radiation (IR-induced DNA damage in diploid human fibroblasts. With the simulated data set, EPIG extracted the appropriate number of patterns which were more stable and homogeneous than the set of patterns that were determined using the CLICK or CAST clustering algorithms. However, CLICK performed better than EPIG and CAST with respect to the average correlation between clusters/patterns of the simulated data. With real biological data, EPIG extracted more dauer-specific patterns than CLICK. Furthermore, analysis of the IR/UV data revealed 18 unique patterns and 2661 genes out of approximately 17,000 that were identified as significantly expressed and categorized to the patterns by EPIG. The time-dependent patterns displayed similar and dissimilar responses between IR and UV treatments. Gene Ontology analysis applied to each pattern-related subset of co-expressed genes revealed underlying

  6. Water, sanitation, and hygiene access in southern Syria: analysis of survey data and recommendations for response.

    Science.gov (United States)

    Sikder, Mustafa; Daraz, Umar; Lantagne, Daniele; Saltori, Roberto

    2018-01-01

    Water, sanitation, and hygiene (WASH) are immediate priorities for human survival and dignity in emergencies. In 2010, > 90% of Syrians had access to improved drinking water. In 2011, armed conflict began and currently 12 million people need WASH services. We analyzed data collected in southern Syria to identify effective WASH response activities for this context. Cross-sectional household surveys were conducted in 2016 and 2017 in 17 sub-districts of two governorates in opposition controlled southern Syria. During the survey, household water was tested for free chlorine residual (FCR). Descriptive statistics were calculated, and mixed effect logistic regressions were completed to determine associations between demographic and WASH variables with outcomes of FCR > 0.1 mg/L in household water and reported diarrhea in children market-available hygiene items were unaffordable. FCR > 0.1 mg/L increased from 4.1% to 27.9% over this time, with Water Safety Plan (WSP) programming strongly associated with FCR (mOR: 24.16; 95% CI: 5.93-98.5). The proportion of households with childhood diarrhea declined from 32.8% to 20.4% over this time; sanitation and hygiene access were protective against childhood diarrhea. The private sector has effectively replaced decaying infrastructure in Syria, although at high cost and uncertain quality. Allowing market forces to manage WASH services and quantity, and targeting emergency response activities on increasing affordability with well-targeted subsidies and improving water quality and regulation via WSPs can be an effective, scalable, and cost-effective strategy to guarantee water and sanitation access in protracted emergencies with local markets.

  7. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. 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.

  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. Transcriptome-wide survey of mouse CNS-derived cells reveals monoallelic expression within novel gene families.

    Directory of Open Access Journals (Sweden)

    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.

  11. Transcriptomics of the rice blast fungus Magnaporthe oryzae in response to the bacterial antagonist Lysobacter enzymogenes reveals candidate fungal defense response genes.

    Directory of Open Access Journals (Sweden)

    Sandra M Mathioni

    Full Text Available Plants and animals have evolved a first line of defense response to pathogens called innate or basal immunity. While basal defenses in these organisms are well studied, there is almost a complete lack of understanding of such systems in fungal species, and more specifically, how they are able to detect and mount a defense response upon pathogen attack. Hence, the goal of the present study was to understand how fungi respond to biotic stress by assessing the transcriptional profile of the rice blast pathogen, Magnaporthe oryzae, when challenged with the bacterial antagonist Lysobacter enzymogenes. Based on microscopic observations of interactions between M. oryzae and wild-type L. enzymogenes strain C3, we selected early and intermediate stages represented by time-points of 3 and 9 hours post-inoculation, respectively, to evaluate the fungal transcriptome using RNA-seq. For comparative purposes, we also challenged the fungus with L. enzymogenes mutant strain DCA, previously demonstrated to be devoid of antifungal activity. A comparison of transcriptional data from fungal interactions with the wild-type bacterial strain C3 and the mutant strain DCA revealed 463 fungal genes that were down-regulated during attack by C3; of these genes, 100 were also found to be up-regulated during the interaction with DCA. Functional categorization of genes in this suite included those with roles in carbohydrate metabolism, cellular transport and stress response. One gene in this suite belongs to the CFEM-domain class of fungal proteins. Another CFEM class protein called PTH11 has been previously characterized, and we found that a deletion in this gene caused advanced lesion development by C3 compared to its growth on the wild-type fungus. We discuss the characterization of this suite of 100 genes with respect to their role in the fungal defense response.

  12. Brain transcriptional responses to high-fat diet in Acads-deficient mice reveal energy sensing pathways.

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    Claudia Kruger

    Full Text Available How signals from fatty acid metabolism are translated into changes in food intake remains unclear. Previously we reported that mice with a genetic inactivation of Acads (acyl-coenzyme A dehydrogenase, short-chain, the enzyme responsible for mitochondrial beta-oxidation of C4-C6 short-chain fatty acids (SCFAs, shift consumption away from fat and toward carbohydrate when offered a choice between diets. In the current study, we sought to indentify candidate genes and pathways underlying the effects of SCFA oxidation deficiency on food intake in Acads-/- mice.We performed a transcriptional analysis of gene expression in brain tissue of Acads-/- and Acads+/+ mice fed either a high-fat (HF or low-fat (LF diet for 2 d. Ingenuity Pathway Analysis revealed three top-scoring pathways significantly modified by genotype or diet: oxidative phosphorylation, mitochondrial dysfunction, and CREB signaling in neurons. A comparison of statistically significant responses in HF Acads-/- vs. HF Acads+/+ (3917 and Acads+/+ HF vs. LF Acads+/+ (3879 revealed 2551 genes or approximately 65% in common between the two experimental comparisons. All but one of these genes were expressed in opposite direction with similar magnitude, demonstrating that HF-fed Acads-deficient mice display transcriptional responses that strongly resemble those of Acads+/+ mice fed LF diet. Intriguingly, genes involved in both AMP-kinase regulation and the neural control of food intake followed this pattern. Quantitative RT-PCR in hypothalamus confirmed the dysregulation of genes in these pathways. Western blotting showed an increase in hypothalamic AMP-kinase in Acads-/- mice and HF diet increased, a key protein in an energy-sensing cascade that responds to depletion of ATP.Our results suggest that the decreased beta-oxidation of short-chain fatty acids in Acads-deficient mice fed HF diet produces a state of energy deficiency in the brain and that AMP-kinase may be the cellular energy

  13. Expression Profiling during Arabidopsis/Downy Mildew Interaction Reveals a Highly-Expressed Effector That Attenuates Responses to Salicylic Acid

    Science.gov (United States)

    Asai, Shuta; Caillaud, Marie-Cécile; Furzer, Oliver J.; Ishaque, Naveed; Wirthmueller, Lennart; Fabro, Georgina; Shirasu, Ken; Jones, Jonathan D. G.

    2014-01-01

    Plants have evolved strong innate immunity mechanisms, but successful pathogens evade or suppress plant immunity via effectors delivered into the plant cell. Hyaloperonospora arabidopsidis (Hpa) causes downy mildew on Arabidopsis thaliana, and a genome sequence is available for isolate Emoy2. Here, we exploit the availability of genome sequences for Hpa and Arabidopsis to measure gene-expression changes in both Hpa and Arabidopsis simultaneously during infection. Using a high-throughput cDNA tag sequencing method, we reveal expression patterns of Hpa predicted effectors and Arabidopsis genes in compatible and incompatible interactions, and promoter elements associated with Hpa genes expressed during infection. By resequencing Hpa isolate Waco9, we found it evades Arabidopsis resistance gene RPP1 through deletion of the cognate recognized effector ATR1. Arabidopsis salicylic acid (SA)-responsive genes including PR1 were activated not only at early time points in the incompatible interaction but also at late time points in the compatible interaction. By histochemical analysis, we found that Hpa suppresses SA-inducible PR1 expression, specifically in the haustoriated cells into which host-translocated effectors are delivered, but not in non-haustoriated adjacent cells. Finally, we found a highly-expressed Hpa effector candidate that suppresses responsiveness to SA. As this approach can be easily applied to host-pathogen interactions for which both host and pathogen genome sequences are available, this work opens the door towards transcriptome studies in infection biology that should help unravel pathogen infection strategies and the mechanisms by which host defense responses are overcome. PMID:25329884

  14. Proteomic analysis reveals contrasting stress response to uranium in two nitrogen-fixing Anabaena strains, differentially tolerant to uranium

    Energy Technology Data Exchange (ETDEWEB)

    Panda, Bandita; Basu, Bhakti; Acharya, Celin; Rajaram, Hema; Apte, Shree Kumar, E-mail: aptesk@barc.gov.in

    2017-01-15

    Highlights: • Response of two native cyanobacterial strains to uranium exposure was studied. • Anabaena L-31 exhibited higher tolerance to uranium as compared to Anabaena 7120. • Uranium exposure differentially affected the proteome profiles of the two strains. • Anabaena L-31 showed better sustenance of photosynthesis and carbon metabolism. • Anabaena L-31 displayed superior oxidative stress defense than Anabaena 7120. - Abstract: Two strains of the nitrogen-fixing cyanobacterium Anabaena, native to Indian paddy fields, displayed differential sensitivity to exposure to uranyl carbonate at neutral pH. Anabaena sp. strain PCC 7120 and Anabaena sp. strain L-31 displayed 50% reduction in survival (LD{sub 50} dose), following 3 h exposure to 75 μM and 200 μM uranyl carbonate, respectively. Uranium responsive proteome alterations were visualized by 2D gel electrophoresis, followed by protein identification by MALDI-ToF mass spectrometry. The two strains displayed significant differences in levels of proteins associated with photosynthesis, carbon metabolism, and oxidative stress alleviation, commensurate with their uranium tolerance. Higher uranium tolerance of Anabaena sp. strain L-31 could be attributed to sustained photosynthesis and carbon metabolism and superior oxidative stress defense, as compared to the uranium sensitive Anabaena sp. strain PCC 7120. Significance: Uranium responsive proteome modulations in two nitrogen-fixing strains of Anabaena, native to Indian paddy fields, revealed that rapid adaptation to better oxidative stress management, and maintenance of metabolic and energy homeostasis underlies superior uranium tolerance of Anabaena sp. strain L-31 compared to Anabaena sp. strain PCC 7120.

  15. 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.

  16. Serum metabolomics reveals betaine and phosphatidylcholine as potential biomarkers for the toxic responses of processed Aconitum carmichaelii Debx.

    Science.gov (United States)

    Tan, Yong; Ko, Joshua; Liu, Xinru; Lu, Cheng; Li, Jian; Xiao, Cheng; Li, Li; Niu, Xuyan; Jiang, Miao; He, Xiaojuan; Zhao, Hongyan; Zhang, Zhongxiao; Bian, Zhaoxiang; Yang, Zhijun; Zhang, Ge; Zhang, Weidong; Lu, Aiping

    2014-07-29

    We recently reported that processed Aconitum carmichaelii Debx (Bai-Fu-Pian in Chinese, BFP) elicits differential toxic responses in rats under various health conditions. The present study aimed to determine the graded toxicity of BFP so as to derive a safe therapeutic rationale in clinical practice. Sensitive and reliable biomarkers of toxicity were also identified, with the corresponding metabolic pathways being unveiled. Thirty male Sprague-Dawley rats were divided into five groups (n = 6) and received oral administration of BFP extract (0.32, 0.64, 1.28 or 2.56 g kg(-1) per day) or an equal volume of drinking water (control) for 15 days. The metabolomic profiles of rat serum were analyzed by liquid chromatography quadruple time-of-flight mass spectrometry (LC-Q-TOF-MS). Linear regression analysis and Ingenuity Pathway Analysis (IPA) were used to elucidate the differentiated altered metabolites and associated network relationships. Results from biochemical and histopathological examinations revealed that BFP could induce prominent toxicity in the heart, liver and kidneys at a dose of 2.56 g kg(-1) per day. Betaine up-regulation and phosphatidylcholine down-regulation were detected in the serum samples of drug-treated groups in a dose-dependent manner. In summary, betaine and phosphatidylcholine could be regarded as sensitive biomarkers for the toxic responses of BFP. Perturbations of RhoA signaling, choline metabolism and free radical scavenging were found to be partly responsible for the toxic effects of the herbal drug. Based on the metabolomics findings, we could establish a safe therapeutic range in the clinical use of BFP, with promising predictions of possible drug toxicity.

  17. Expression profiling during arabidopsis/downy mildew interaction reveals a highly-expressed effector that attenuates responses to salicylic acid.

    Directory of Open Access Journals (Sweden)

    Shuta Asai

    2014-10-01

    Full Text Available Plants have evolved strong innate immunity mechanisms, but successful pathogens evade or suppress plant immunity via effectors delivered into the plant cell. Hyaloperonospora arabidopsidis (Hpa causes downy mildew on Arabidopsis thaliana, and a genome sequence is available for isolate Emoy2. Here, we exploit the availability of genome sequences for Hpa and Arabidopsis to measure gene-expression changes in both Hpa and Arabidopsis simultaneously during infection. Using a high-throughput cDNA tag sequencing method, we reveal expression patterns of Hpa predicted effectors and Arabidopsis genes in compatible and incompatible interactions, and promoter elements associated with Hpa genes expressed during infection. By resequencing Hpa isolate Waco9, we found it evades Arabidopsis resistance gene RPP1 through deletion of the cognate recognized effector ATR1. Arabidopsis salicylic acid (SA-responsive genes including PR1 were activated not only at early time points in the incompatible interaction but also at late time points in the compatible interaction. By histochemical analysis, we found that Hpa suppresses SA-inducible PR1 expression, specifically in the haustoriated cells into which host-translocated effectors are delivered, but not in non-haustoriated adjacent cells. Finally, we found a highly-expressed Hpa effector candidate that suppresses responsiveness to SA. As this approach can be easily applied to host-pathogen interactions for which both host and pathogen genome sequences are available, this work opens the door towards transcriptome studies in infection biology that should help unravel pathogen infection strategies and the mechanisms by which host defense responses are overcome.

  18. Factors influencing identification of and response to intimate partner violence: a survey of physicians and nurses

    Directory of Open Access Journals (Sweden)

    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

  19. Utilizing the Total Design Method in medicine: maximizing response rates in long, non-incentivized, personal questionnaire postal surveys.

    Science.gov (United States)

    Kazzazi, Fawz; Haggie, Rebecca; Forouhi, Parto; Kazzazi, Nazar; Malata, Charles M

    2018-01-01

    Maximizing response rates in questionnaires can improve their validity and quality by reducing non-response bias. A comprehensive analysis is essential for producing reasonable conclusions in patient-reported outcome research particularly for topics of a sensitive nature. This often makes long (≥7 pages) questionnaires necessary but these have been shown to reduce response rates in mail surveys. Our work adapted the "Total Design Method," initially produced for commercial markets, to raise response rates in a long (total: 11 pages, 116 questions), non-incentivized, very personal postal survey sent to almost 350 women. A total of 346 women who had undergone mastectomy and immediate breast reconstruction from 2008-2014 (inclusive) at Addenbrooke's University Hospital were sent our study pack (Breast-Q satisfaction questionnaire and support documents) using our modified "Total Design Method." Participants were sent packs and reminders according to our designed schedule. Of the 346 participants, we received 258 responses, an overall response rate of 74.5% with a useable response rate of 72.3%. One hundred and six responses were received before the week 1 reminder (30.6%), 120 before week 3 (34.6%), 225 before the week 7 reminder (64.6%) and the remainder within 3 weeks of the final pack being sent. The median age of patients that the survey was sent to, and the median age of the respondents, was 54 years. In this study, we have demonstrated the successful implementation of a novel approach to postal surveys. Despite the length of the questionnaire (nine pages, 116 questions) and limitations of expenses to mail a survey to ~350 women, we were able to attain a response rate of 74.6%.

  20. Participation and factors associated with late or non-response to an online survey in primary care.

    Science.gov (United States)

    Aerny-Perreten, Nicole; Domínguez-Berjón, Ma Felicitas; Esteban-Vasallo, María D; García-Riolobos, Carmen

    2015-08-01

    Online surveys have several advantages, but a low response rate is common and it is uncertain how results are affected. Response inducement techniques can be used to overcome this problem. The objectives of this study were to describe the percentage of change in the response rate after reminders and to analyse the characteristics associated with non-response and late response based on the survey results, as well as by applying archival and extrapolation techniques. In the Autonomous Community of Madrid, an online questionnaire about cancer prevention was sent to a random sample of primary care health professionals (3586 physicians and nurses). Two reminders were sent later. The percentage of change in response rates after reminders, global and by demographic and health care characteristics of participants; and factors associated with non-response and late response were analysed using response rates and odds ratios (ORs). After the reminders, the response rate increased from 22.6% to 32.9% and to 39.4%. Non-response was associated with age [OR: 3.14; confidence interval (CI) 95%: 2.23-4.42 for aged >60 years], gender and functional area. Further, a higher response rate after reminders was observed in professionals with heavier workloads (OR: 1.46; CI 95%: 1.08-1.97) and in those who stated a lower relevance of cancer prevention in primary care. After electronic reminders, the response rate increased, especially among professionals with the highest workloads and a minor interest in the survey topic. However, possible bias associated with non-response remains and the factors behind this should be examined in future research. © 2015 John Wiley & Sons, Ltd.

  1. Prophylactic platelets in dengue: survey responses highlight lack of an evidence base.

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    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.

  2. De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana.

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    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.

  3. 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

  4. 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.

  5. Distinct herpesvirus resistances and immune responses of three gynogenetic clones of gibel carp revealed by comprehensive transcriptomes.

    Science.gov (United States)

    Gao, Fan-Xiang; Wang, Yang; Zhang, Qi-Ya; Mou, Cheng-Yan; Li, Zhi; Deng, Yuan-Sheng; Zhou, Li; Gui, Jian-Fang

    2017-07-24

    Gibel carp is an important aquaculture species in China, and a herpesvirus, called as Carassius auratus herpesvirus (CaHV), has hampered the aquaculture development. Diverse gynogenetic clones of gibel carp have been identified or created, and some of them have been used as aquaculture varieties, but their resistances to herpesvirus and the underlying mechanism remain unknown. To reveal their susceptibility differences, we firstly performed herpesvirus challenge experiments in three gynogenetic clones of gibel carp, including the leading variety clone A + , candidate variety clone F and wild clone H. Three clones showed distinct resistances to CaHV. Moreover, 8772, 8679 and 10,982 differentially expressed unigenes (DEUs) were identified from comparative transcriptomes between diseased individuals and control individuals of clone A + , F and H, respectively. Comprehensive analysis of the shared DEUs in all three clones displayed common defense pathways to the herpesvirus infection, activating IFN system and suppressing complements. KEGG pathway analysis of specifically changed DEUs in respective clones revealed distinct immune responses to the herpesvirus infection. The DEU numbers identified from clone H in KEGG immune-related pathways, such as "chemokine signaling pathway", "Toll-like receptor signaling pathway" and others, were remarkably much more than those from clone A + and F. Several IFN-related genes, including Mx1, viperin, PKR and others, showed higher increases in the resistant clone H than that in the others. IFNphi3, IFI44-like and Gig2 displayed the highest expression in clone F and IRF1 uniquely increased in susceptible clone A + . In contrast to strong immune defense in resistant clone H, susceptible clone A + showed remarkable up-regulation of genes related to apoptosis or death, indicating that clone A + failed to resist virus offensive and evidently induced apoptosis or death. Our study is the first attempt to screen distinct resistances and

  6. Doping in Two Elite Athletics Competitions Assessed by Randomized-Response Surveys.

    Science.gov (United States)

    Ulrich, Rolf; Pope, Harrison G; Cléret, Léa; Petróczi, Andrea; Nepusz, Tamás; Schaffer, Jay; Kanayama, Gen; Comstock, R Dawn; Simon, Perikles

    2018-01-01

    Doping in sports compromises fair play and endangers health. To deter doping among elite athletes, the World Anti-Doping Agency (WADA) oversees testing of several hundred thousand athletic blood and urine samples annually, of which 1-2% test positive. Measures using the Athlete Biological Passport suggest a higher mean prevalence of about 14% positive tests. Biological testing, however, likely fails to detect many cutting-edge doping techniques, and thus the true prevalence of doping remains unknown. We surveyed 2167 athletes at two sporting events: the 13th International Association of Athletics Federations Word Championships in Athletics (WCA) in Daegu, South Korea in August 2011 and the 12th Quadrennial Pan-Arab Games (PAG) in Doha, Qatar in December 2011. To estimate the prevalence of doping, we utilized a "randomized response technique," which guarantees anonymity for individuals when answering a sensitive question. We also administered a control question at PAG assessing past-year use of supplements. The estimated prevalence of past-year doping was 43.6% (95% confidence interval 39.4-47.9) at WCA and 57.1% (52.4-61.8) at PAG. The estimated prevalence of past-year supplement use at PAG was 70.1% (65.6-74.7%). Sensitivity analyses, assessing the robustness of these estimates under numerous hypothetical scenarios of intentional or unintentional noncompliance by respondents, suggested that we were unlikely to have overestimated the true prevalence of doping. Doping appears remarkably widespread among elite athletes, and remains largely unchecked despite current biological testing. The survey technique presented here will allow future investigators to generate continued reference estimates of the prevalence of doping.

  7. 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

  8. 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.

  9. Host and Non-Host roots in rice: cellular and molecular approaches reveal differential responses to arbuscular mycorrhizal fungi.

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    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.

  10. Metabolomics reveals metabolic targets and biphasic responses in breast cancer cells treated by curcumin alone and in association with docetaxel.

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    Mathilde Bayet-Robert

    Full Text Available BACKGROUND: Curcumin (CUR has deserved extensive research due to its anti-inflammatory properties, of interest in human diseases including cancer. However, pleiotropic even paradoxical responses of tumor cells have been reported, and the mechanisms of action of CUR remain uncompletely elucidated. METHODOLOGY/PRINCIPAL FINDINGS: (1H-NMR spectroscopy-based metabolomics was applied to get novel insight into responses of MCF7 and MDA-MB-231 breast cancer cells to CUR alone, and MCF7 cells to CUR in cotreatment with docetaxel (DTX. In both cell types, a major target of CUR was glutathione metabolism. Total glutathione (GSx increased at low dose CUR (≤ 10 mg.l(-1-28 µM- (up to +121% in MCF7 cells, P<0.01, and +138% in MDA-MB-231 cells, P<0.01, but decreased at high dose (≥ 25 mg.l(-1 -70 µM- (-49%, in MCF7 cells, P<0.02, and -56% in MDA-MB-231 cells, P<0.025. At high dose, in both cell types, GSx-related metabolites decreased, including homocystein, creatine and taurine (-60 to -80%, all, P<0.05. Together with glutathione-S-transferase actvity, data established that GSx biosynthesis was upregulated at low dose, and GSx consumption activated at high dose. Another major target, in both cell types, was lipid metabolism involving, at high doses, accumulation of polyunsaturated and total free fatty acids (between ×4.5 and ×11, P<0.025, and decrease of glycerophospho-ethanolamine and -choline (about -60%, P<0.025. Multivariate statistical analyses showed a metabolic transition, even a biphasic behavior of some metabolites including GSx, between low and high doses. In addition, CUR at 10 mg.l(-1 in cotreatment with DTX induced modifications in glutathione metabolism, lipid metabolism, and glucose utilization. Some of these changes were biphasic depending on the duration of exposure to CUR. CONCLUSIONS/SIGNIFICANCE: Metabolomics reveals major metabolic targets of CUR in breast cancer cells, and biphasic responses that challenge the widely accepted

  11. Transcriptomic analysis reveals importance of ROS and phytohormones in response to short-term salinity stress in Populus tomentosa

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    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

  12. Ectopic Expression of GsSRK in Medicago sativa Reveals Its Involvement in Plant Architecture and Salt Stress Responses.

    Science.gov (United States)

    Sun, Mingzhe; Qian, Xue; Chen, Chao; Cheng, Shufei; Jia, Bowei; Zhu, Yanming; Sun, Xiaoli

    2018-01-01

    stress responses. In conclusion, results in this research reveal the dual role of GsSRK in regulating both plant architecture and salt stress responses.

  13. Use of SMS-Based Surveys in the Rapid Response to the Ebola Outbreak in Liberia: Opening Community Dialogue.

    Science.gov (United States)

    Berman, Amanda; Figueroa, Maria Elena; Storey, J Douglas

    2017-01-01

    During an emerging health crisis like the 2014 Ebola outbreak in West Africa, communicating with communities to learn from them and to provide timely information can be a challenge. Insight into community thinking, however, is crucial for developing appropriate communication content and strategies and for monitoring the progress of the emergency response. In November 2014, the Health Communication Capacity Collaborative partnered with GeoPoll to implement a Short Message Service (SMS)-based survey that could create a link with affected communities and help guide the communication response to Ebola. The ideation metatheory of communication and behavior change guided the design of the survey questionnaire, which produced critical insights into trusted sources of information, knowledge of transmission modes, and perceived risks-all factors relevant to the design of an effective communication response that further catalyzed ongoing community actions. The use of GeoPoll's infrastructure for data collection proved a crucial source of almost-real-time data. It allowed for rapid data collection and processing under chaotic field conditions. Though not a replacement for standard survey methodologies, SMS surveys can provide quick answers within a larger research process to decide on immediate steps for communication strategies when the demand for speedy emergency response is high. They can also help frame additional research as the response evolves and overall monitor the pulse of the situation at any point in time.

  14. Electric infrastructure failures in Nigeria: a survey-based analysis of the costs and adjustment responses

    International Nuclear Information System (INIS)

    Adenikinju, A.F.

    2003-01-01

    This paper examines the cost of electricity shortages on the Nigerian manufacturing sector. Utilizing the data obtained from a 1998 nationwide survey, the paper details the various costs from power outages and examines the response of manufacturers to the infrastructure problem. The findings of the study confirm that the cost of electricity failures on the Nigerian manufacturing sector is quite high. Firms incur huge costs on the provision of expensive back-up to minimise the expected outage costs. The average costs of this back-up are on the average 3 times the cost of publicly supplied electricity. The marginal cost estimates also indicate that the cost of kWh of unserved electricity in Nigeria is very high. Small-scale firms bear the greater proportion of the cost of the power failure. A situation where firms spend as much as 20-30% of initial investment on the acquisition of facilities to enhance electricity supply reliability has a significant negative impact on costs competitiveness of the manufacturing sector. Thus, the study supports current government efforts to privatise the public monopoly and liberalizes the electricity market. These hopefully will mitigate the burden of poor power supply as well as introduce the needed competition into the electricity market in the country

  15. Transcriptional response of P. pastoris in fed-batch cultivations to Rhizopus oryzae lipase production reveals UPR induction

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    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

  16. Fast, visual specialization for reading in English revealed by the topography of the N170 ERP response

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    McCandliss Bruce D

    2005-08-01

    Full Text Available Abstract Background N170 effects associated with visual words may be related to perceptual expertise effects that have been demonstrated for faces and other extensively studied classes of visual stimuli. Although face and other object expertise effects are typically bilateral or right-lateralized, the spatial topography of reading-related N170 effects are often left-lateralized, providing potential insights into the unique aspects of reading-related perceptual expertise. Methods Extending previous research in German 1, we use a high-density channel array to characterize the N170 topography for reading-related perceptual expertise in English, a language with inconsistent spelling-to-sound mapping. N170 effects related to overall reading-related expertise are defined by contrasting responses to visual words versus novel symbol strings. By contrasting each of these conditions to pseudowords, we examined how this reading-related N170 effect generalizes to well-ordered novel letter strings. Results A sample-by-sample permutation test computed on word versus symbol ERP topographies revealed differences during two time windows corresponding to the N170 and P300 components. Topographic centroid analysis of the word and symbol N170 demonstrated significant differences in both left-right as well as inferior-superior dimensions. Words elicited larger N170 negativities than symbols at inferior occipito-temporal channels, with the maximal effect over left inferior regions often unsampled in conventional electrode montages. Further contrasts produced inferior-superior topographic effects for the pseudoword-symbol comparison and left-lateralized topographic effects for the word-pseudoword comparison. Conclusion Fast specialized perception related to reading experience produces an N170 modulation detectable across different EEG systems and different languages. Characterization of such effects may be improved by sampling with greater spatial frequency recordings

  17. Utility and Cost-Effectiveness of Motivational Messaging to Increase Survey Response in Physicians: A Randomized Controlled Trial

    Science.gov (United States)

    Chan, Randolph C. H.; Mak, Winnie W. S.; Pang, Ingrid H. Y.; Wong, Samuel Y. S.; Tang, Wai Kwong; Lau, Joseph T. F.; Woo, Jean; Lee, Diana T. F.; Cheung, Fanny M.

    2018-01-01

    The present study examined whether, when, and how motivational messaging can boost the response rate of postal surveys for physicians based on Higgin's regulatory focus theory, accounting for its cost-effectiveness. A three-arm, blinded, randomized controlled design was used. A total of 3,270 doctors were randomly selected from the registration…

  18. In vivo phosphoproteome characterization reveals key starch granule-binding phosphoproteins involved in wheat water-deficit response.

    Science.gov (United States)

    Chen, Guan-Xing; Zhen, Shou-Min; Liu, Yan-Lin; Yan, Xing; Zhang, Ming; Yan, Yue-Ming

    2017-10-23

    Drought stress during grain development causes significant yield loss in cereal production. The phosphorylated modification of starch granule-binding proteins (SGBPs) is an important mechanism regulating wheat starch biosynthesis. In this study, we performed the first proteomics and phosphoproteomics analyses of SGBPs in elite Chinese bread wheat (Triticum aestivum L.) cultivar Jingdong 17 under well-watered and water-stress conditions. Water stress treatment caused significant reductions in spike grain numbers and weight, total starch and amylopectin content, and grain yield. Two-dimensional gel electrophoresis revealed that the quantity of SGBPs was reduced significantly by water-deficit treatment. Phosphoproteome characterization of SGBPs under water-deficit treatment demonstrated a reduced level of phosphorylation of main starch synthesis enzymes, particularly for granule-bound starch synthase (GBSS I), starch synthase II-a (SS II-a), and starch synthase III (SS III). Specifically, the Ser34 site of the GBSSI protein, the Tyr358 site of SS II-a, and the Ser837 site of SS III-a exhibited significant less phosphorylation under water-deficit treatment than well-watered treatment. Furthermore, the expression levels of several key genes related with starch biosynthesis detected by qRT-PCR were decreased significantly at 15 days post-anthesis under water-deficit treatment. Immunolocalization showed a clear movement of GBSS I from the periphery to the interior of starch granules during grain development, under both water-deficit and well-watered conditions. Our results demonstrated that the reduction in gene expression or transcription level, protein expression and phosphorylation levels of starch biosynthesis related enzymes under water-deficit conditions is responsible for the significant decrease in total starch content and grain yield.

  19. 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.

  20. African-American esophageal squamous cell carcinoma expression profile reveals dysregulation of stress response and detox networks.

    Science.gov (United States)

    Erkizan, Hayriye Verda; Johnson, Kory; Ghimbovschi, Svetlana; Karkera, Deepa; Trachiotis, Gregory; Adib, Houtan; Hoffman, Eric P; Wadleigh, Robert G

    2017-06-19

    Esophageal carcinoma is the third most common gastrointestinal malignancy worldwide and is largely unresponsive to therapy. African-Americans have an increased risk for esophageal squamous cell carcinoma (ESCC), the subtype that shows marked variation in geographic frequency. The molecular architecture of African-American ESCC is still poorly understood. It is unclear why African-American ESCC is more aggressive and the survival rate in these patients is worse than those of other ethnic groups. To begin to define genetic alterations that occur in African-American ESCC we conducted microarray expression profiling in pairs of esophageal squamous cell tumors and matched control tissues. We found significant dysregulation of genes encoding drug-metabolizing enzymes and stress response components of the NRF2- mediated oxidative damage pathway, potentially representing key genes in African-American esophageal squamous carcinogenesis. Loss of activity of drug metabolizing enzymes would confer increased sensitivity of esophageal cells to xenobiotics, such as alcohol and tobacco smoke, and may account for the high incidence and aggressiveness of ESCC in this ethnic group. To determine whether certain genes are uniquely altered in African-American ESCC we performed a meta-analysis of ESCC expression profiles in our African-American samples and those of several Asian samples. Down-regulation of TP53 pathway components represented the most common feature in ESCC of all ethnic groups. Importantly, this analysis revealed a potential distinctive molecular underpinning of African-American ESCC, that is, a widespread and prominent involvement of the NRF2 pathway. Taken together, these findings highlight the remarkable interplay of genetic and environmental factors in the pathogenesis of African-American ESCC.

  1. Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

    Directory of Open Access Journals (Sweden)

    Sharat K. Pradhan

    2017-04-01

    Full Text Available Rice crop is sensitive to cold stress at seedling stage. A panel of population representing 304 shortlisted germplasm lines was studied for seedling stage chilling tolerance in indica rice. Six phenotypic classes were exposed to six low temperature stress regimes under control phenotyping facility to investigate response pattern. A panel of 66 genotypes representing all phenotypic classes was used for ensuring genetic diversity, population structure and association mapping for the trait using 58 simple sequence repeat (SSR and 2 direct trait linked markers. A moderate level of genetic diversity was detected in the panel population for the trait. Deviation of Hardy-Weinberg's expectation was detected in the studied population using Wright's F statistic. The panel showed 30% variation among population and 70% among individuals. The entire population was categorized into three sub-populations through STRUCTURE analysis. This revealed tolerance for the trait had a common primary ancestor for each sub-population with few admix individuals. The panel population showed the presence of many QTLs for cold stress tolerance in the individuals representing like genome-wide expression of the trait. Nineteen SSR markers were significantly associated at chilling stress of 8°C to 4°C for 7–21 days duration. Thus, the primers linked to the seedling stage cold tolerance QTLs namely qCTS9, qCTS-2, qCTS6.1, qSCT2, qSCT11, qSCT1a, qCTS-3.1, qCTS11.1, qCTS12.1, qCTS-1b, and CTB2 need to be pyramided for development of strongly chilling tolerant variety.

  2. Effect of questionnaire length, personalisation and reminder type on response rate to a complex postal survey: randomised controlled trial

    Science.gov (United States)

    2011-01-01

    Background Minimising participant non-response in postal surveys helps to maximise the generalisability of the inferences made from the data collected. The aim of this study was to examine the effect of questionnaire length, personalisation and reminder type on postal survey response rate and quality and to compare the cost-effectiveness of the alternative survey strategies. Methods In a pilot study for a population study of travel behaviour, physical activity and the environment, 1000 participants sampled from the UK edited electoral register were randomly allocated using a 2 × 2 factorial design to receive one of four survey packs: a personally addressed long (24 page) questionnaire pack, a personally addressed short (15 page) questionnaire pack, a non-personally addressed long questionnaire pack or a non-personally addressed short questionnaire pack. Those who did not return a questionnaire were stratified by initial randomisation group and further randomised to receive either a full reminder pack or a reminder postcard. The effects of the survey design factors on response were examined using multivariate logistic regression. Results An overall response rate of 17% was achieved. Participants who received the short version of the questionnaire were more likely to respond (OR = 1.48, 95% CI 1.06 to 2.07). In those participants who received a reminder, personalisation of the survey pack and reminder also increased the odds of response (OR = 1.44, 95% CI 1.01 to 1.95). Item non-response was relatively low, but was significantly higher in the long questionnaire than the short (9.8% vs 5.8%; p = .04). The cost per additional usable questionnaire returned of issuing the reminder packs was £23.1 compared with £11.3 for the reminder postcards. Conclusions In contrast to some previous studies of shorter questionnaires, this trial found that shortening a relatively lengthy questionnaire significantly increased the response. Researchers should consider the trade off

  3. Consumer responses towards home energy financial incentives: A survey-based study

    International Nuclear Information System (INIS)

    Zhao Tingting; Bell, Lindsey; Horner, Mark W.; Sulik, John; Zhang Jinfeng

    2012-01-01

    Residential energy-efficient and renewable energy (EERE) products play an important role in energy conservation and carbon emissions reduction. Various financial incentive programs have been developed to promote the adoption of these products. However, their effectiveness in attracting consumers is not very well understood. In this study, we investigated impacts of financial incentives on homeowner's decision making towards six EERE products. Two forms of incentives, tax credits and interest-free loans, were examined through a household mailing survey in Florida, the United States. Results showed that, although half of the respondents were interested in EERE products, the high investment cost was a major concern that hindered their purchase activities. Homeowners were attracted to financial incentives and valued tax credits much higher than interest-free loans. The current federal home energy tax credit levels were found to attract only 2–12 percent of homeowners to buy EERE products. The willingness of participation was especially low for the costly products (such as solar panels). The participation rate was also very low for lower income (i.e., annual household income below $50,000) families living in older residences. This study contributes to the understanding of economic and social aspects of consumer decision making on energy efficiency and alternative energy. - Highlights: ► We investigated consumer responses to energy efficiency incentives. ► These included tax credits and interest-free loans for six types of energy products. ► We found that tax credits are more effective than interest-free loans. ► The current tax credit rates are insufficient for expensive products (e.g., solar panels). ► A higher amount of incentives is required for the lower-income (<$50 K/yr) households.

  4. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. 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.; Eble, Jeffrey A.; DiBattista, Joseph; Rocha, Luiz A.; Randall, John E.; Berumen, Michael L.; Bowen, Brian W.

    2016-01-01

    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.

  6. 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.

  7. Children as respondents in survey research: Cognitive development and response quality

    NARCIS (Netherlands)

    Borgers, N.; Leeuw, E.D. de; Hox, J.J.

    2000-01-01

    Although children are no longer a neglected minority in official statistics and surveys, methodological knowledge on how to survey children is still scarce. Researchers have to rely mainly on ad-hoc knowledge from such diverse fields as child psychiatry and educational testing, or extrapolate

  8. A survey of electric and hybrid vehicles simulation programs. Volume 2: Questionnaire responses

    Science.gov (United States)

    Bevan, J.; Heimburger, D. A.; Metcalfe, M. A.

    1978-01-01

    The data received in a survey conducted within the United States to determine the extent of development and capabilities of automotive performance simulation programs suitable for electric and hybrid vehicle studies are presented. The survey was conducted for the Department of Energy by NASA's Jet Propulsion Laboratory. Volume 1 of this report summarizes and discusses the results contained in Volume 2.

  9. 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…

  10. Comparative transcriptome analysis reveals distinct ethylene-independent regulation of ripening in response to low temperature in kiwifruit.

    Science.gov (United States)

    Asiche, William O; Mitalo, Oscar W; Kasahara, Yuka; Tosa, Yasuaki; Mworia, Eric G; Owino, Willis O; Ushijima, Koichiro; Nakano, Ryohei; Yano, Kentaro; Kubo, Yasutaka

    2018-03-21

    Kiwifruit are classified as climacteric since exogenous ethylene (or its analogue propylene) induces rapid ripening accompanied by ethylene production under positive feedback regulation. However, most of the ripening-associated changes (Phase 1 ripening) in kiwifruit during storage and on-vine occur largely in the absence of any detectable ethylene. This ripening behavior is often attributed to basal levels of system I ethylene, although it is suggested to be modulated by low temperature. To elucidate the mechanisms regulating Phase 1 ripening in kiwifruit, a comparative transcriptome analysis using fruit continuously exposed to propylene (at 20 °C), and during storage at 5 °C and 20 °C was conducted. Propylene exposure induced kiwifruit softening, reduction of titratable acidity (TA), increase in soluble solids content (SSC) and ethylene production within 5 days. During storage, softening and reduction of TA occurred faster in fruit at 5 °C compared to 20 °C although no endogenous ethylene production was detected. Transcriptome analysis revealed 3761 ripening-related differentially expressed genes (DEGs), of which 2742 were up-regulated by propylene while 1058 were up-regulated by low temperature. Propylene exclusively up-regulated 2112 DEGs including those associated with ethylene biosynthesis and ripening such as AcACS1, AcACO2, AcPL1, AcXET1, Acβ-GAL, AcAAT, AcERF6 and AcNAC7. Similarly, low temperature exclusively up-regulated 467 DEGS including AcACO3, AcPL2, AcPMEi, AcADH, Acβ-AMY2, AcGA2ox2, AcNAC5 and AcbZIP2 among others. A considerable number of DEGs such as AcPG, AcEXP1, AcXET2, Acβ-AMY1, AcGA2ox1, AcNAC6, AcMADS1 and AcbZIP1 were up-regulated by either propylene or low temperature. Frequent 1-MCP treatments failed to inhibit the accelerated ripening and up-regulation of associated DEGs by low temperature indicating that the changes were independent of ethylene. On-vine kiwifruit ripening proceeded in the absence of any detectable

  11. cDNA-AFLP analysis reveals the adaptive responses of citrus to long-term boron-toxicity.

    Science.gov (United States)

    Guo, Peng; Qi, Yi-Ping; Yang, Lin-Tong; Ye, Xin; Jiang, Huan-Xin; Huang, Jing-Hao; Chen, Li-Song

    2014-10-28

    Boron (B)-toxicity is an important disorder in agricultural regions across the world. Seedlings of 'Sour pummelo' (Citrus grandis) and 'Xuegan' (Citrus sinensis) were fertigated every other day until drip with 10 μM (control) or 400 μM (B-toxic) H3BO3 in a complete nutrient solution for 15 weeks. The aims of this study were to elucidate the adaptive mechanisms of citrus plants to B-toxicity and to identify B-tolerant genes. B-toxicity-induced changes in seedlings growth, leaf CO2 assimilation, pigments, total soluble protein, malondialdehyde (MDA) and phosphorus were less pronounced in C. sinensis than in C. grandis. B concentration was higher in B-toxic C. sinensis leaves than in B-toxic C. grandis ones. Here we successfully used cDNA-AFLP to isolate 67 up-regulated and 65 down-regulated transcript-derived fragments (TDFs) from B-toxic C. grandis leaves, whilst only 31 up-regulated and 37 down-regulated TDFs from B-toxic C. sinensis ones, demonstrating that gene expression is less affected in B-toxic C. sinensis leaves than in B-toxic C. grandis ones. These differentially expressed TDFs were related to signal transduction, carbohydrate and energy metabolism, nucleic acid metabolism, protein and amino acid metabolism, lipid metabolism, cell wall and cytoskeleton modification, stress responses and cell transport. The higher B-tolerance of C. sinensis might be related to the findings that B-toxic C. sinensis leaves had higher expression levels of genes involved in photosynthesis, which might contribute to the higher photosyntheis and light utilization and less excess light energy, and in reactive oxygen species (ROS) scavenging compared to B-toxic C. grandis leaves, thus preventing them from photo-oxidative damage. In addition, B-toxicity-induced alteration in the expression levels of genes encoding inorganic pyrophosphatase 1, AT4G01850 and methionine synthase differed between the two species, which might play a role in the B-tolerance of C. sinensis. C. sinensis

  12. Differential Gene Expression by Lactobacillus plantarum WCFS1 in Response to Phenolic Compounds Reveals New Genes Involved in Tannin Degradation.

    Science.gov (United States)

    Reverón, Inés; Jiménez, Natalia; Curiel, José Antonio; Peñas, Elena; López de Felipe, Félix; de Las Rivas, Blanca; Muñoz, Rosario

    2017-04-01

    Lactobacillus plantarum is a lactic acid bacterium that can degrade food tannins by the successive action of tannase and gallate decarboxylase enzymes. In the L. plantarum genome, the gene encoding the catalytic subunit of gallate decarboxylase ( lpdC , or lp_2945 ) is only 6.5 kb distant from the gene encoding inducible tannase ( L. plantarum tanB [ tanB Lp ], or lp_2956 ). This genomic context suggests concomitant activity and regulation of both enzymatic activities. Reverse transcription analysis revealed that subunits B ( lpdB , or lp_0271 ) and D ( lpdD , or lp_0272 ) of the gallate decarboxylase are cotranscribed, whereas subunit C ( lpdC , or lp_2945 ) is cotranscribed with a gene encoding a transport protein ( gacP , or lp_2943 ). In contrast, the tannase gene is transcribed as a monocistronic mRNA. Investigation of knockout mutations of genes located in this chromosomal region indicated that only mutants of the gallate decarboxylase (subunits B and C), tannase, GacP transport protein, and TanR transcriptional regulator ( lp_2942 ) genes exhibited altered tannin metabolism. The expression profile of genes involved in tannin metabolism was also analyzed in these mutants in the presence of methyl gallate and gallic acid. It is noteworthy that inactivation of tanR suppresses the induction of all genes overexpressed in the presence of methyl gallate and gallic acid. This transcriptional regulator was also induced in the presence of other phenolic compounds, such as kaempferol and myricetin. This study complements the catalog of L. plantarum expression profiles responsive to phenolic compounds, which enable this bacterium to adapt to a plant food environment. IMPORTANCE Lactobacillus plantarum is a bacterial species frequently found in the fermentation of vegetables when tannins are present. L. plantarum strains degrade tannins to the less-toxic pyrogallol by the successive action of tannase and gallate decarboxylase enzymes. The genes encoding these enzymes are

  13. Possible Factors Promoting Car Evacuation in the 2011 Tohoku Tsunami Revealed by Analysing a Large-Scale Questionnaire Survey in Kesennuma City

    Directory of Open Access Journals (Sweden)

    Fumiyasu Makinoshima

    2017-11-01

    Full Text Available Excessive car evacuation can cause severe traffic jams that can lead to large numbers of casualties during tsunami disasters. Investigating the possible factors that lead to unnecessary car evacuation can ensure smoother tsunami evacuations and mitigate casualty damages in future tsunami events. In this study, we quantitatively investigated the possible factors that promote car evacuation, including both necessary and unnecessary usages, by statistically analysing a large amount of data on actual tsunami evacuation behaviours surveyed in Kesennuma, where devastating damage occurred during the 2011 Tohoku Tsunami. A straightforward statistical analysis revealed a high percentage of car evacuations (approx. 50%; however, this fraction includes a high number of unnecessary usage events that were distinguished based on mode choice reasons. In addition, a binary logistic regression was conducted to quantitatively evaluate the effects of several factors and to identify the dominant factor that affected evacuation mode choice. The regression results suggested that the evacuation distance was the dominant factor for choosing car evacuation relative to other factors, such as age and sex. The cross-validation test of the regression model demonstrated that the considered factors were useful for decision making and the prediction of evacuation mode choice in the target area.

  14. On the influence of a raffle upon responses to an urban transportation survey in New York City.

    Science.gov (United States)

    Morabia, Alfredo; Zheng, Yan

    2009-01-01

    Determine whether raffling off prizes to increase participation in surveys triggers multiple responses from the same participants. All staff, instructors, and students of Queens College, New York, were invited to a 5 minute online survey about commuting in winter 2007. Entry in the raffle to win one of two iPODs was not conditional upon survey completion. Participation was 18.7 %, and 3913 eligible responses. Of the 183 (4.7 %) participants with two answers, responses were consistent, with weighted kappas ranging between 0.48 and 1.00, and Pearson r's between 0.81 and 1.0. Kappa's were lower for opinion than for factual questions. The duplicate responses came from people with characteristics similar to the full sample. Commuting modes included car (46 %), bus but no subway (28 %), and bus and subway (21 %). The median commuting time was 90 minutes round-trip, and was greater than 120 minutes for 1/4 of the respondents. Participation was low despite the raffle. The small percentage of duplicate answers, maybe prompted by the reminding email, had a negligible impact on the results.

  15. Healthcare professionals' perceptions on the emotional impact of having an inadequate response to antidepressant medications: survey and prospective patient audit.

    Science.gov (United States)

    Mago, Rajnish; Fagiolini, Andrea; Weiller, Emmanuelle; Weiss, Catherine

    2018-01-01

    Despite the availability of effective antidepressants, about half of patients with major depressive disorder (MDD) display an inadequate response to their initial treatment. A large patient survey recently reported that 29.8% of MDD patients experiencing an inadequate treatment response felt frustrated about their medication and 19.2% were frustrated with their healthcare provider. This survey and chart audit evaluated healthcare professionals' (HCP) views on the emotional impact of having an inadequate response to antidepressant medication. HCPs who frequently treat patients with MDD completed a survey and chart audit of their MDD patients currently experiencing an inadequate response to antidepressant treatment. 287 HCPs completed 1336 chart audits. HCPs reported that 38% of their patients were trusting/accepting of their MDD medications and 41% of their patients trusted/felt confident with their healthcare provision. Conversely, HCPs reported that 11% of their patients were frustrated with their medication and 5% with their healthcare benefits. HCPs cited impact on daily life (53%) and treatment issues (lack of efficacy and side effects; 50%) as the main drivers for their patients' feelings of frustration. When HCPs recognized patients' feelings of frustration, the top concerns of the HCPs were worsening of symptoms (43%) and non-compliance (41%). This survey and chart audit highlights the emotional burden associated with inadequate responses to MDD treatment in addition to persistent symptoms. Differences between the views of the HCPs and patients are highlighted and suggest that HCPs may underestimate the full impact that having to try numerous medications has on their patients.

  16. 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

    Data collection for economic valuation by using Internet surveys and pre-recruited Internet panels can be associated with severe disadvantages. Problems concerning sample coverage and sample representativeness can be expected. Representation errors may occur since people can choose whether....... 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....

  17. Comprehensive Analysis of CD8+-T-Cell Responses against Hepatitis C Virus Reveals Multiple Unpredicted Specificities

    OpenAIRE

    Lauer, Georg M.; Ouchi, Kei; Chung, Raymond T.; Nguyen, Tam N.; Day, Cheryl L.; Purkis, Deborah R.; Reiser, Markus; Kim, Arthur Y.; Lucas, Michaela; Klenerman, Paul; Walker, Bruce D.

    2002-01-01

    The hepatitis C virus (HCV)-specific CD8+-T-cell response is thought to play a critical role in HCV infection. Studies of these responses have largely relied on the analysis of a small number of previously described or predicted HCV epitopes, mostly restricted by HLA A2. In order to determine the actual breadth and magnitude of CD8+-T-cell responses in the context of diverse HLA class I alleles, we performed a comprehensive analysis of responses to all expressed HCV proteins. By using a panel...

  18. The effect of health, socio-economic position, and mode of data collection on non-response in health interview surveys

    DEFF Research Database (Denmark)

    Ekholm, Ola; Gundgaard, Jens; Rasmussen, Niels K R

    2010-01-01

    AIMS: To investigate the relationship between potential explanatory factors (socio-economic factors and health) and non-response in two general population health interview surveys (face-to-face and telephone), and to compare the effects of the two interview modes on non-response patterns. METHODS...... in health interview surveys, but the non-response rate is higher in lower socio-economic groups. Analyses of non-response should be performed to understand the implications of survey findings.......: Data derives from The Danish Health Interview Survey 2000 (face-to-face interview) and The Funen County Health Survey 2000/2001 (telephone interview). Data on all invited individuals were obtained from administrative registers and linked to survey data at individual level. Multiple logistic regression...

  19. 2004 Workplace and Gender Relations Survey of Reserve Component Members: Tabulations of Responses

    National Research Council Canada - National Science Library

    2005-01-01

    The 2004 Workplace and Gender Relations Survey of Reserve Component Members was designed to both estimate the level of sexual harassment and provide information on a variety of consequences of sexual harassment...

  20. 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

  1. Self-reported responsiveness to direct-to-consumer drug advertising and medication use: results of a national survey.

    Science.gov (United States)

    Dieringer, Nicholas J; Kukkamma, Lisa; Somes, Grant W; Shorr, Ronald I

    2011-09-23

    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 therapeutic

  2. Serological and virological survey of hepatitis E virus (HEV) in animal reservoirs from Uruguay reveals elevated prevalences and a very close phylogenetic relationship between swine and human strains.

    Science.gov (United States)

    Mirazo, Santiago; Gardinali, Noemí R; Cecilia, D'Albora; Verger, Lorenzo; Ottonelli, Florencia; Ramos, Natalia; Castro, Gustavo; Pinto, Marcelo A; Ré, Viviana; Pisano, Belén; Lozano, Alejandra; de Oliveira, Jaqueline Mendes; Arbiza, Juan

    2018-01-01

    Hepatitis E virus (HEV) infection is an issue of public health concern in high-income and non-endemic countries. Increasing evidence supports the hypothesis of a zoonotic route as the main mode of infection in this epidemiological setting, since the transmission of genotypes HEV-3 and HEV-4 from reservoirs to humans has been demonstrated. In America, studies have confirmed the circulation of HEV in pig herds but the zoonotic role of wild boars has never been evaluated. Uruguay has a high burden of HEV- associated acute hepatitis, and a close phylogenetic relationship was observed among human HEV-3 strains and European isolates detected in swine. However in this context, swine herds have never been surveyed. Herein is reported a survey of HEV in swine herds, pigs at slaughter-house and free-living wild boar populations. Two-hundred and twenty sera and 150 liver tissue samples from domestic pigs, and 140 sera from wild boars were tested for HEV by ELISA and PCR-based approaches. All tested swine farms resulted seropositive with an overall rate of 46.8%. In turn, 22.1% of the wild boars had anti-HEV antibodies. HEV RNA was detected in 16.6% and 9.3% of liver samples from slaughter-age pigs and adult wild boars sera, respectively. Three strains from domestic pig were also amplified by nested-PCR approaches. By contrast, none of the positive samples obtained from wild boars could be confirmed by nested-PCR. Phylogenetic analysis revealed a very high nucleotide identity among swine strains and sequences obtained from humans in Uruguay. Results showed that HEV is widely distributed among swine herds in Uruguay. Additionally, this study evidences for the first time in the American continent that wild boar populations are a reservoir for HEV, though its zoonotic role remains to be elucidated. Altogether, data presented here suggest a high zoonotic risk of HEV transmission from swine to humans. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. GLOBAL TRANSCRIPTION PROFILING REVEALS DIFFERENTIAL RESPONSES TO CHRONIC NITROGEN STRESS AND PUTATIVE NITROGEN REGULATORY COMPONENTS IN ARABIDOPSIS

    Science.gov (United States)

    Background: A large quantity of nitrogen (N) fertilizer is used for crop production to achieve high yields at a significant economic and environmental cost. Efforts have been directed to understanding the molecular basis of plant responses to N and to identifying N-responsive gen...

  4. Does an offer for a free on-line continuing medical education (CME) activity increase physician survey response rate? A randomized trial.

    Science.gov (United States)

    Viera, Anthony J; Edwards, Teresa

    2012-03-07

    Achieving a high response rate in a physician survey is challenging. Monetary incentives increase response rates but obviously add cost to a survey project. We wondered whether an offer of a free continuing medical education (CME) activity would be effective in improving survey response rate. As part of a survey of a national sample of physicians, we randomized half to an offer for a free on-line CME activity upon completion of a web-based survey and the other half to no such offer. We compared response rates between the groups. A total of 1214 out of 8477 potentially eligible physicians responded to our survey, for an overall response rate of 14.3%. The response rate among the control group (no offer of CME credit) was 16.6%, while among those offered the CME opportunity, the response rate was 12.0% (p offer for a free on-line CME activity did not improve physician survey response rate. On the contrary, the offer for a free CME activity actually appeared to worsen the response rate. © 2011 Viera et al; licensee BioMed Central Ltd.

  5. 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.

  6. 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

  7. A Systems Vaccinology Approach Reveals Temporal Transcriptomic Changes of Immune Responses to the Yellow Fever 17D Vaccine.

    Science.gov (United States)

    Hou, Jue; Wang, Shuhui; Jia, Manxue; Li, Dan; Liu, Ying; Li, Zhengpeng; Zhu, Hong; Xu, Huifang; Sun, Meiping; Lu, Li; Zhou, Zhinan; Peng, Hong; Zhang, Qichen; Fu, Shihong; Liang, Guodong; Yao, Lena; Yu, Xuesong; Carpp, Lindsay N; Huang, Yunda; McElrath, Julie; Self, Steve; Shao, Yiming

    2017-08-15

    In this study, we used a systems vaccinology approach to identify temporal changes in immune response signatures to the yellow fever (YF)-17D vaccine, with the aim of comprehensively characterizing immune responses associated with protective immunity. We conducted a cohort study in which 21 healthy subjects in China were administered one dose of the YF-17D vaccine; PBMCs were collected at 0 h and then at 4 h and days 1, 2, 3, 5, 7, 14, 28, 84, and 168 postvaccination, and analyzed by transcriptional profiling and immunological assays. At 4 h postvaccination, genes associated with innate cell differentiation and cytokine pathways were dramatically downregulated, whereas receptor genes were upregulated, compared with their baseline levels at 0 h. Immune response pathways were primarily upregulated on days 5 and 7, accompanied by the upregulation of the transcriptional factors JUP, STAT1, and EIF2AK2. We also observed robust activation of innate immunity within 2 d postvaccination and a durable adaptive response, as assessed by transcriptional profiling. Coexpression network analysis indicated that lysosome activity and lymphocyte proliferation were associated with dendritic cell (DC) and CD4 + T cell responses; FGL2, NFAM1, CCR1, and TNFSF13B were involved in these associations. Moreover, individuals who were baseline-seropositive for Abs against another flavivirus exhibited significantly impaired DC, NK cell, and T cell function in response to YF-17D vaccination. Overall, our findings indicate that YF-17D vaccination induces a prompt innate immune response and DC activation, a robust Ag-specific T cell response, and a persistent B cell/memory B cell response. Copyright © 2017 by The American Association of Immunologists, Inc.

  8. The complete genome sequence of Trueperella pyogenes UFV1 reveals a processing system involved in the quorumsensing signal response

    DEFF Research Database (Denmark)

    Duarte, Vinicius da Silva; Treu, Laura; Campanaro, Stefano

    2017-01-01

    We present here the complete genome sequence of Trueperella pyogenes UFV1. The 2.3-Mbp genome contains an extremely interesting AI-2 transporter and processing system related to the quorum-sensing signal response. This specific feature is described in this species for the first time and might be ...... be responsible for a new pathogenic behavior.......We present here the complete genome sequence of Trueperella pyogenes UFV1. The 2.3-Mbp genome contains an extremely interesting AI-2 transporter and processing system related to the quorum-sensing signal response. This specific feature is described in this species for the first time and might...

  9. Sinkholes, subsidence and subrosion on the eastern shore of the Dead Sea as revealed by a close-range photogrammetric survey

    Science.gov (United States)

    Al-Halbouni, Djamil; Holohan, Eoghan P.; Saberi, Leila; Alrshdan, Hussam; Sawarieh, Ali; Closson, Damien; Walter, Thomas R.; Dahm, Torsten

    2017-05-01

    Ground subsidence and sinkhole collapse are phenomena affecting regions of karst geology worldwide. The rapid development of such phenomena around the Dead Sea in the last four decades poses a major geological hazard to the local population, agriculture and industry. Nonetheless many aspects of this hazard are still incompletely described and understood, especially on the eastern Dead Sea shore. In this work, we present a first low altitude (sinkhole area of Ghor Al-Haditha, Jordan. We provide a detailed qualitative and quantitative analysis of a new, high resolution digital surface model (5 cm px-1) and orthophoto of this area (2.1 km2). We also outline the factors affecting the quality and accuracy of this approach. Our analysis reveals a kilometer-scale sinuous depression bound partly by flexure and partly by non-tectonic faults. The estimated minimum volume loss of this subsided zone is 1.83 ṡ 106 m3 with an average subsidence rate of 0.21 m yr-1 over the last 25 years. Sinkholes in the surveyed area are localized mainly within this depression. The sinkholes are commonly elliptically shaped (mean eccentricity 1.31) and clustered (nearest neighbor ratio 0.69). Their morphologies and orientations depend on the type of sediment they form in: in mud, sinkholes have a low depth to diameter ratio (0.14) and a long-axis azimuth of NNE-NE. In alluvium, sinkholes have a higher ratio (0.4) and are orientated NNW-N. From field work, we identify actively evolving artesian springs and channelized, sediment-laden groundwater flows that appear locally in the main depression. Consequently, subrosion, i.e. subsurface mechanical erosion, is identified as a key physical process, in addition to dissolution, behind the subsidence and sinkhole hazard. Furthermore, satellite image analysis links the development of the sinuous depression and sinkhole formation at Ghor Al-Haditha to preferential groundwater flow paths along ancient and current wadi riverbeds.

  10. 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.

  11. An estrogen-responsive plasma protein expression signature in Atlantic cod (Gadus morhua) revealed by SELDI-TOF MS

    DEFF Research Database (Denmark)

    Nielsen, Mari Mæland; Meyer, Sonnich; Larsen, Bodil Katrine

    2011-01-01

    Compound-specific protein expression signatures( PESs) can be revealed by proteomic techniques. The SELDI-TOF MS approach is advantageous due to its simplicity and high-throughput capacity,however, there are concerns regarding the reproducibility of this method. The aim of this study was to define...

  12. Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses

    Directory of Open Access Journals (Sweden)

    Li Chuan

    2012-05-01

    Full Text Available Abstract Background Little is known about the potential of Brachypodium distachyon as a model for low temperature stress responses in Pooideae. The ice recrystallization inhibition protein (IRIP genes, fructosyltransferase (FST genes, and many C-repeat binding factor (CBF genes are Pooideae specific and important in low temperature responses. Here we used comparative analyses to study conservation and evolution of these gene families in B. distachyon to better understand its potential as a model species for agriculturally important temperate grasses. Results Brachypodium distachyon contains cold responsive IRIP genes which have evolved through Brachypodium specific gene family expansions. A large cold responsive CBF3 subfamily was identified in B. distachyon, while CBF4 homologs are absent from the genome. No B. distachyon FST gene homologs encode typical core Pooideae FST-motifs and low temperature induced fructan accumulation was dramatically different in B. distachyon compared to core Pooideae species. Conclusions We conclude that B. distachyon can serve as an interesting model for specific molecular mechanisms involved in low temperature responses in core Pooideae species. However, the evolutionary history of key genes involved in low temperature responses has been different in Brachypodium and core Pooideae species. These differences limit the use of B. distachyon as a model for holistic studies relevant for agricultural core Pooideae species.

  13. "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. ...

  14. Small RNA profiling reveals important roles for miRNAs in Arabidopsis response to Bacillus velezensis FZB42.

    Science.gov (United States)

    Xie, Shanshan; Jiang, Haiyang; Xu, Zhilan; Xu, Qianqian; Cheng, Beijiu

    2017-09-20

    Bacillus velezensis FZB42 (previously classified as Bacillus amyloliquefaciens FZB42) has been confirmed to successfully colonize plant roots and enhance defense response against pathogen infection. This study indicated that FZB42 inoculation enhanced Arabidopsis defense response against Pseudomonas syringae DC3000 through inducing the expression of PR1, PDF1.2 and stomata closure. To further clarify the induced defense response at miRNA level, sRNA libraries from Arabidopsis roots inoculated with FZB42 and control were constructed and sequenced. The reads of 21nt and 24nt in length were the most abundant groups in FZB42-treated library and control library, respectively. 234 known miRNAs and 16 novel miRNAs were identified. Among them, 11 known miRNAs and 4 novel miRNAs were differentially expressed after FZB42 inoculation. Moreover cis-elements (TC-rich repeats, TCA-element and CGTCA-motif) associated with plant defense were also found in the promoters of these miRNAs. Additionally, 141 mRNAs were predicted as potential targets of these differentially expressed miRNAs. GO annotations of the target genes indicated their potential roles in polyamine biosynthetic process and intracellular protein transport biological process, which may contribute to increased defense response. Our findings indicated that Bacillus velezensis FZB42 inoculation altered the expression of Arabidopsis miRNAs and their target genes, which were associated with defense response. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Apple ring rot-responsive putative microRNAs revealed by high-throughput sequencing in Malus × domestica Borkh.

    Science.gov (United States)

    Yu, Xin-Yi; Du, Bei-Bei; Gao, Zhi-Hong; Zhang, Shi-Jie; Tu, Xu-Tong; Chen, Xiao-Yun; Zhang, Zhen; Qu, Shen-Chun

    2014-08-01

    MicroRNAs (miRNAs) are small non-coding RNAs, which silence target mRNA via cleavage or translational inhibition to function in regulating gene expression. MiRNAs act as important regulators of plant development and stress response. For understanding the role of miRNAs responsive to apple ring rot stress, we identified disease-responsive miRNAs using high-throughput sequencing in Malus × domestica Borkh.. Four small RNA libraries were constructed from two control strains in M. domestica, crabapple (CKHu) and Fuji Naga-fu No. 6 (CKFu), and two disease stress strains, crabapple (DSHu) and Fuji Naga-fu No. 6 (DSFu). A total of 59 miRNA families were identified and five miRNAs might be responsive to apple ring rot infection and validated via qRT-PCR. Furthermore, we predicted 76 target genes which were regulated by conserved miRNAs potentially. Our study demonstrated that miRNAs was responsive to apple ring rot infection and may have important implications on apple disease resistance.

  16. Integrative omic analysis reveals distinctive cold responses in leaves and roots of strawberry, Fragaria × ananassa ‘Korona’

    Directory of Open Access Journals (Sweden)

    Gage eKoehler

    2015-10-01

    Full Text Available To assess underlying metabolic processes and regulatory mechanisms during cold exposure of strawberry, integrative omic approaches were applied to Fragaria × ananassa Duch. ‘Korona’. Both root and leaf tissues were examined for responses to the cold acclimation processes. Levels of metabolites, proteins, and transcripts in tissues from plants grown at 18°C were compared to those following 1 to 10 days of cold (2°C exposure. Overall, ‘Korona’ showed a modest increase of protective metabolites such as amino acids (aspartic acid, leucine, isoleucine, and valine, pentoses, phosphorylated and non-phosphorylated hexoses, and distinct compounds of the raffinose pathway (galactinol and raffinose. By 2DE proteomics a total of 845 spots were observed in leaves; 4.6% changed significantly in response to cold.Transcript levels in leaves were determined by microarray, where dozens of cold associated transcripts were quantitatively characterized, and levels of several potential key contributors (e.g., the dehydrin COR47 and GADb to cold tolerance were confirmed by qRT-PCR. Cold responses are placed within the existing knowledge base of low temperature stress change in plants, allowing an evaluation of the uniqueness or generality of Fragaria responses in photosynthetic tissues. Overall, the cold response characteristics of ‘Korona’ are consistent with a moderately cold tolerant plant.

  17. Comparison of response rates and cost-effectiveness for a community-based survey: postal, internet and telephone modes with generic or personalised recruitment approaches

    Science.gov (United States)

    2012-01-01

    Background Epidemiological research often requires collection of data from a representative sample of the community or recruitment of specific groups through broad community approaches. The population coverage of traditional survey methods such as mail-outs to residential addresses, and telephone contact via public directories or random-digit-dialing is declining and survey response rates are falling. There is a need to explore new sampling frames and consider multiple response modes including those offered by changes in telecommunications and internet technology. Methods We evaluated response rates and cost-effectiveness for three modes of survey administration (postal invitation/postal survey, postal invitation/internet survey and postal invitation/telephone survey) and two styles of contact approach (personalised and generic) in a community survey of greywater use. Potential respondents were contacted only once, with no follow up of non-responders. Results The telephone survey produced the highest adjusted response rate (30.2%), followed by the personalised postal survey (10.5%), generic postal survey (7.5%) and then the internet survey (4.7% for the personalised approach and 2.2% for the generic approach). There were some differences in household characteristics and greywater use rates between respondents to different survey modes, and between respondents to personalised and generic approaches. These may be attributable to the differing levels of motivations needed for a response, and varying levels of interest in the survey topic among greywater users and non-users. The generic postal survey had the lowest costs per valid survey received (Australian $22.93), followed by the personalised postal survey ($24.75). Conclusions Our findings suggest that postal surveys currently remain the most economic option for population-based studies, with similar costs for personalised and generic approaches. Internet surveys may be effective for specialised groups where email

  18. Studies of Physcomitrella patens reveal that ethylene-mediated submergence responses arose relatively early in land-plant evolution

    KAUST Repository

    Yasumura, Yuki

    2012-10-18

    Colonization of the land by multicellular green plants was a fundamental step in the evolution of life on earth. Land plants evolved from fresh-water aquatic algae, and the transition to a terrestrial environment required the acquisition of developmental plasticity appropriate to the conditions of water availability, ranging from drought to flood. Here we show that extant bryophytes exhibit submergence-induced developmental plasticity, suggesting that submergence responses evolved relatively early in the evolution of land plants. We also show that a major component of the bryophyte submergence response is controlled by the phytohormone ethylene, using a perception mechanism that has subsequently been conserved throughout the evolution of land plants. Thus a plant environmental response mechanism with major ecological and agricultural importance probably had its origins in the very earliest stages of the colonization of the land. © 2012 Blackwell Publishing Ltd.

  19. 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…

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

    Science.gov (United States)

    2015-01-01

    percent) were more likely than their peers to report engaging in unhealthy lifestyles . However, when the researchers compared the results for 100...Active Duty Military Personnel is a recurring survey that assesses the nature, causes, and consequences of lifestyle health, safety, and substance

  1. 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…

  2. The Northeastern area's objectives and beliefs responses regarding forests and grasslands: 2004 survey results

    Science.gov (United States)

    Lori B. Shelby; Deborah J. Shields; Michael D. Miller; Donna L. Lybecker; Brian M. Kent; Vesna Bashovska

    2009-01-01

    The USDA Forest Service revises its Strategic Plan according to the 1993 Government Performance and Results Act. The goals and objectives included in the Strategic Plan are developed from natural resource trend data (Forest and Rangeland Renewable Planning Act) and from public input such as the results from this telephone survey. The purpose of this report is to...

  3. Adult proxy responses to a survey of children's dermal soil contact activities.

    Science.gov (United States)

    Wong, E Y; Shirai, J H; Garlock, T J; Kissel, J C

    2000-01-01

    Contaminated site cleanup decisions may require estimation of dermal exposures to soil. Telephone surveys represent one means of obtaining relevant activity pattern data. The initial Soil Contact Survey (SCS-I), which primarily gathered information on the activities of adults, was conducted in 1996. Data describing adult behaviors have been previously reported. Results from a second Soil Contact Survey (SCS-II), performed in 1998-1999 and focused on children's activity patterns, are reported here. Telephone surveys were used to query a randomly selected sample of U.S. households. A randomly chosen child, under the age of 18 years, was targeted in each responding household having children. Play activities as well as bathing patterns were investigated to quantify total exposure time, defined as activity time plus delay until washing. Of 680 total survey respondents, 500 (73.5%) reported that their child played outdoors on bare dirt or mixed grass and dirt surfaces. Among these "players," the median reported play frequency was 7 days/week in warm weather and 3 days/week in cold weather. Median play duration was 3 h/day in warm weather and 1 h/day in cold weather. Hand washes were reported to occur a median of 4 times per day in both warm and cold weather months. Bath or shower median frequency was seven times per week in both warm and cold weather. Finally, based on clothing choice data gathered in SCS-I, a median of about 37% of total skin surface is estimated to be exposed during young children's warm weather outdoor play.

  4. Integration of the Pokeweed miRNA and mRNA Transcriptomes Reveals Targeting of Jasmonic Acid-Responsive Genes

    Directory of Open Access Journals (Sweden)

    Kira C. M. Neller

    2018-05-01

    Full Text Available The American pokeweed plant, Phytolacca americana, displays broad-spectrum resistance to plant viruses and is a heavy metal hyperaccumulator. However, little is known about the regulation of biotic and abiotic stress responses in this non-model plant. To investigate the control of miRNAs in gene expression, we sequenced the small RNA transcriptome of pokeweed treated with jasmonic acid (JA, a hormone that mediates pathogen defense and stress tolerance. We predicted 145 miRNAs responsive to JA, most of which were unique to pokeweed. These miRNAs were low in abundance and condition-specific, with discrete expression change. Integration of paired mRNA-Seq expression data enabled us to identify correlated, novel JA-responsive targets that mediate hormone biosynthesis, signal transduction, and pathogen defense. The expression of approximately half the pairs was positively correlated, an uncommon finding that we functionally validated by mRNA cleavage. Importantly, we report that a pokeweed-specific miRNA targets the transcript of OPR3, novel evidence that a miRNA regulates a JA biosynthesis enzyme. This first large-scale small RNA study of a Phytolaccaceae family member shows that miRNA-mediated control is a significant component of the JA response, associated with widespread changes in expression of genes required for stress adaptation.

  5. Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress

    Directory of Open Access Journals (Sweden)

    Close Timothy J

    2009-08-01

    Full Text Available Abstract Background Rice and barley are both members of Poaceae (grass family but have a marked difference in salt tolerance. The molecular mechanism underlying this difference was previously unexplored. This study employs a comparative genomics approach to identify analogous and contrasting gene expression patterns between rice and barley. Results A hierarchical clustering approach identified several interesting expression trajectories among rice and barley genotypes. There were no major conserved expression patterns between the two species in response to salt stress. A wheat salt-stress dataset was queried for comparison with rice and barley. Roughly one-third of the salt-stress responses of barley were conserved with wheat while overlap between wheat and rice was minimal. These results demonstrate that, at transcriptome level, rice is strikingly different compared to the more closely related barley and wheat. This apparent lack of analogous transcriptional programs in response to salt stress is further highlighted through close examination of genes associated with root growth and development. Conclusion The analysis provides support for the hypothesis that conservation of transcriptional signatures in response to environmental cues depends on the genetic similarity among the genotypes within a species, and on the phylogenetic distance between the species.

  6. Studies of Physcomitrella patens reveal that ethylene-mediated submergence responses arose relatively early in land-plant evolution

    KAUST Repository

    Yasumura, Yuki; Pierik, Ronald; Fricker, Mark D.; Voesenek, Laurentius A. C. J.; Harberd, Nicholas P.

    2012-01-01

    in the evolution of land plants. We also show that a major component of the bryophyte submergence response is controlled by the phytohormone ethylene, using a perception mechanism that has subsequently been conserved throughout the evolution of land plants. Thus a

  7. The response of mammalian cells to UV-light reveals Rad54-dependent and independent pathways of homologous recombination

    DEFF Research Database (Denmark)

    Eppink, Berina; Tafel, Agnieszka A; Hanada, Katsuhiro

    2011-01-01

    with lesions in replicating DNA. The core HR protein in mammalian cells is the strand exchange protein RAD51, which is aided by numerous proteins, including RAD54. We used RAD54 as a cellular marker for HR to study the response of mammalian embryonic stem (ES) cells to UV irradiation. In contrast to yeast, ES...

  8. Analysis of Globodera rostochiensis effectors reveals conserved functions of SPRYSEC proteins in suppressing and eliciting plant immune responses

    KAUST Repository

    Ali, Shawkat; Magne, Maxime; Chen, Shiyan; Obradovic, Natasa; Jamshaid, Lubna; Wang, Xiaohong; Bé lair, Guy; Moffett, Peter

    2015-01-01

    in Nicotiana benthamiana and N. tabacum. We have found that all SPRYSEC proteins tested are able to suppress defense responses induced by NB-LRR proteins as well as cell death induced by elicitors, suggesting that defense repression is a common characteristic

  9. Comparative Transcriptomic Analysis Reveals Novel Insights into the Adaptive Response of Skeletonema costatum to Changing Ambient Phosphorus

    Directory of Open Access Journals (Sweden)

    Shu-Feng Zhang

    2016-09-01

    Full Text Available Phosphorus (P is a limiting macronutrient for diatom growth and productivity in the ocean. Much effort has been devoted to the physiological response of marine diatoms to ambient P change, however, the whole-genome molecular mechanisms are poorly understood. Here, we utilized RNA-Seq to compare the global gene expression patterns of a marine diatom Skeletonema costatum grown in inorganic P-replete, P-deficient, and inorganic- and organic-P resupplied conditions. In total 34,942 unique genes were assembled and 20.8% of them altered significantly in abundance under different P conditions. Genes encoding key enzymes/proteins involved in P utilization, nucleotide metabolism, photosynthesis, glycolysis and cell cycle regulation were significantly up-regulated in P-deficient cells. Genes participating in circadian rhythm regulation, such as circadian clock associated 1, were also up-regulated in P-deficient cells. The response of S. costatum to ambient P deficiency shows several similarities to the well-described responses of other marine diatom species, but also has its unique features. S. costatum has evolved the ability to re-program its circadian clock and intracellular biological processes in response to ambient P deficiency. This study provides new insights into the adaptive mechanisms to ambient P deficiency in marine diatoms.

  10. Comparative proteomics of oxidative stress response of Lactobacillus acidophilus NCFM reveals effects on DNA repair and cysteine de novo synthesis

    DEFF Research Database (Denmark)

    Calderini, Elia; Celebioglu, Hasan Ufuk; Villarroel, Julia

    2017-01-01

    acidophilus NCFM to H2O2, simulating an oxidative environment. Bacterial growth was monitored by BioScreen and batch cultures were harvested at exponential phase for protein profiling of stress responses by 2D gel-based comparative proteomics. Proteins identified in 19 of 21 spots changing in abundance due...

  11. RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean.

    Science.gov (United States)

    Horvath, David P; Hansen, Stephanie A; Moriles-Miller, Janet P; Pierik, Ronald; Yan, Changhui; Clay, David E; Scheffler, Brian; Clay, Sharon A

    2015-07-01

    Weeds reduce yield in soybeans (Glycine max) through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate growing seasons. RNASeq data were collected from six biological samples of soybeans growing with or without weeds. Weed species and the methods to maintain weed-free controls varied between years to mitigate treatment effects, and to allow detection of general soybean weed responses. Soybean plants were not visibly nutrient- or water-stressed. We identified 55 consistently downregulated genes in weedy plots. Many of the downregulated genes were heat shock genes. Fourteen genes were consistently upregulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the upregulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in Arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest that the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean. No claim to original US government works New Phytologist © 2015 New Phytologist Trust.

  12. Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance

    Science.gov (United States)

    Roh, Whijae; Chen, Pei-Ling; Reuben, Alexandre; Spencer, Christine N.; Prieto, Peter A.; Miller, John P.; Gopalakrishnan, Vancheswaran; Wang, Feng; Cooper, Zachary A.; Reddy, Sangeetha M.; Gumbs, Curtis; Little, Latasha; Chang, Qing; Chen, Wei-Shen; Wani, Khalida; Petaccia De Macedo, Mariana; Chen, Eveline; Austin-Breneman, Jacob L.; Jiang, Hong; Roszik, Jason; Tetzlaff, Michael T.; Davies, Michael A.; Gershenwald, Jeffrey E.; Tawbi, Hussein; Lazar, Alexander J.; Hwu, Patrick; Hwu, Wen-Jen; Diab, Adi; Glitza, Isabella C.; Patel, Sapna P.; Woodman, Scott E.; Amaria, Rodabe N.; Prieto, Victor G.; Hu, Jianhua; Sharma, Padmanee; Allison, James P.; Chin, Lynda; Zhang, Jianhua; Wargo, Jennifer A.; Futreal, P. Andrew

    2018-01-01

    Immune checkpoint blockade produces clinical benefit in many patients. However better biomarkers of response are still needed, and mechanisms of resistance remain incompletely understood. To address this, we recently studied a cohort of melanoma patients treated with sequential checkpoint blockade against cytotoxic T lymphocyte antigen-4 (CTLA-4) followed by programmed death receptor-1 (PD-1), and identified immune markers of response and resistance. Building on these studies, we performed deep molecular profiling including T-cell receptor sequencing (TCR-seq) and whole exome sequencing (WES) within the same cohort, and demonstrated that a more clonal T cell repertoire was predictive of response to PD-1 but not CTLA-4 blockade. Analysis of copy number alterations identified a higher burden of copy number loss in non-responders to CTLA-4 and PD-1 blockade and found that it was associated with decreased expression of genes in immune-related pathways. The effect of mutational load and burden of copy number loss on response was non-redundant, suggesting the potential utility of a combinatorial biomarker to optimize patient care with checkpoint blockade therapy. PMID:28251903

  13. Objective assessment of chromatic and achromatic pattern adaptation reveals the temporal response properties of different visual pathways.

    Science.gov (United States)

    Robson, Anthony G; Kulikowski, Janus J

    2012-11-01

    The aim was to investigate the temporal response properties of magnocellular, parvocellular, and koniocellular visual pathways using increment/decrement changes in contrast to elicit visual evoked potentials (VEPs). Static achromatic and isoluminant chromatic gratings were generated on a monitor. Chromatic gratings were modulated along red/green (R/G) or subject-specific tritanopic confusion axes, established using a minimum distinct border criterion. Isoluminance was determined using minimum flicker photometry. Achromatic and chromatic VEPs were recorded to contrast increments and decrements of 0.1 or 0.2 superimposed on the static gratings (masking contrast 0-0.6). Achromatic increment/decrement changes in contrast evoked a percept of apparent motion when the spatial frequency was low; VEPs to such stimuli were positive in polarity and largely unaffected by high levels of static contrast, consistent with transient response mechanisms. VEPs to finer achromatic gratings showed marked attenuation as static contrast was increased. Chromatic VEPs to R/G or tritan chromatic contrast increments were of negative polarity and showed progressive attenuation as static contrast was increased, in keeping with increasing desensitization of the sustained responses of the color-opponent visual pathways. Chromatic contrast decrement VEPs were of positive polarity and less sensitive to pattern adaptation. The relative contribution of sustained/transient mechanisms to achromatic processing is spatial frequency dependent. Chromatic contrast increment VEPs reflect the sustained temporal response properties of parvocellular and koniocellular pathways. Cortical VEPs can provide an objective measure of pattern adaptation and can be used to probe the temporal response characteristics of different visual pathways.

  14. Commonfund Study of Responsible Investing: A Survey of Endowments and Their Affiliated Foundations

    Science.gov (United States)

    Commonfund Institute, 2015

    2015-01-01

    The Commonfund Study of Responsible Investing analyzes policies, practices and attitudes with respect to responsible investing among 200 U.S. colleges and universities, constituting 24.0 percent of the 832 institutions that participated in the 2014 National Association of College and University Business Officers (NACUBO)-Commonfund Study of…

  15. Estimating disease prevalence from two-phase surveys with non-response at the second phase

    Science.gov (United States)

    Gao, Sujuan; Hui, Siu L.; Hall, Kathleen S.; Hendrie, Hugh C.

    2010-01-01

    SUMMARY In this paper we compare several methods for estimating population disease prevalence from data collected by two-phase sampling when there is non-response at the second phase. The traditional weighting type estimator requires the missing completely at random assumption and may yield biased estimates if the assumption does not hold. We review two approaches and propose one new approach to adjust for non-response assuming that the non-response depends on a set of covariates collected at the first phase: an adjusted weighting type estimator using estimated response probability from a response model; a modelling type estimator using predicted disease probability from a disease model; and a regression type estimator combining the adjusted weighting type estimator and the modelling type estimator. These estimators are illustrated using data from an Alzheimer’s disease study in two populations. Simulation results are presented to investigate the performances of the proposed estimators under various situations. PMID:10931514

  16. The direction of restructuring of a Korea field epidemiology training program through questionnaire survey among communicable disease response staff in Korea.

    Science.gov (United States)

    Lee, Moo-Sik; Lee, Kwan; Park, Ji-Hyuk; Hong, Jee-Young; Jang, Min Young; Jeon, Byoung-Hak; Cho, Sang Yun; Choi, Sun Ja; Hong, Jeong Ik

    2017-01-01

    We used a survey about the need for an educational training of infectious disease response staff in Korea Centers for Disease Control and Prevention (KCDC) and officer in metropolitan cities and provincial government to conduct field epidemiological investigation. The survey was conducted from January 25 to March 15, 2016. A total of 173 participants were selected from four different groups as follows: 27 clinical specialists, 22 Epidemic Intelligence Service (EIS) officers, 82 KCDC staff, and 42 local health department officials. Results revealed that 83% of KCDC staff and 95% of local health department officials agreed on the need for educational training to strengthen capability of personnel to conduct epidemic research and investigation. The level of their need for training was relatively high, while self-confidence levels of individuals to conduct epidemic research and investigation was low. It was concluded that there was a need to develop training programs to enhance the ability of public health officials, EIS officers, KCDC staff, and local health department personnel to conduct epidemic research and investigation.

  17. Comparison of Community Response to Road Traffic Noise in Japan and SWEDEN—PART i: Outline of Surveys and DOSE-RESPONSE Relationships

    Science.gov (United States)

    SATO, T.; YANO, T.; BJÖRKMAN, M.; RYLANDER, R.

    2002-02-01

    To investigate cross-cultural differences in the community response to road traffic noise, social surveys were conducted in Gothenburg, Sweden, and Kumamoto and Sapporo, Japan, using the same questionnaire and noise measurement method. Typical residential areas with detached houses and apartments were selected as the target areas in each city. The questionnaire comprised 40 questions relating to environmental, housing and personal factors. The key questions concerned annoyance caused by road traffic noise. The total numbers of respondents were 1142 in Gothenburg, 837 in Kumamoto and 780 in Sapporo. The response rates were 68·8, 69·3 and 57·5% respectively. After the questionnaires were completed, noise measurements were made in each area. Community responses were compared on the basis of the dose-response relationships. There were no systematic differences between community responses in Sapporo and Kumamoto, which have the same culture. People living in detached houses in Gothenburg were more annoyed by the same road traffic noise than the people living in Japanese cities. There were no systematic differences among the three cities with regard to activity disturbances indoors, but significant disturbance of activities and resting in gardens or on balconies was noted in Gothenburg. The difference in activity disturbance was due to the differences between lifestyles in the two countries. People living in detached houses were more annoyed by the house vibration caused by road traffic than those living in apartments and people were annoyed by the exhaust from road traffic to the same extent as noise.

  18. Host transcriptomic responses to pneumonic plague reveal that Yersinia pestis inhibits both the initial adaptive and innate immune responses in mice.

    Science.gov (United States)

    Yang, Huiying; Wang, Tong; Tian, Guang; Zhang, Qingwen; Wu, Xiaohong; Xin, Youqian; Yan, Yanfeng; Tan, Yafang; Cao, Shiyang; Liu, Wanbing; Cui, Yujun; Yang, Ruifu; Du, Zongmin

    2017-01-01

    Pneumonic plague is the most deadly form of infection caused by Yersinia pestis and can progress extremely fast. However, our understanding on the host transcriptomic response to pneumonic plague is insufficient. Here, we used RNA-sequencing technology to analyze transcriptomic responses in mice infected with fully virulent strain 201 or EV76, a live attenuated vaccine strain lacking the pigmentation locus. Approximately 600 differentially expressed genes (DEGs) were detected in lungs from both 201- and EV76-infected mice at 12h post-infection (hpi). DEGs in lungs of 201-infected mice exceeded 2000 at 48hpi, accompanied by sustained large numbers of DEGs in the liver and spleen; however, limited numbers of DEGs were detected in those organs of EV-infected mice. Remarkably, DEGs in lungs were significantly enriched in critical immune responses pathways in EV76-infected but not 201-infected mice, including antigen processing and presentation, T cell receptor signaling among others. Pathological and bacterial load analyses confirmed the rapid systemic dissemination of 201-infection and the confined EV76-infection in lungs. Our results suggest that fully virulent Y. pestis inhibits both the innate and adaptive immune responses that are substantially stimulated in a self-limited infection, which update our holistic views on the transcriptomic response to pneumonic plague. Copyright © 2016 Elsevier GmbH. All rights reserved.

  19. Combined chromatin and expression analysis reveals specific regulatory mechanisms within cytokine genes in the macrophage early immune response.

    Directory of Open Access Journals (Sweden)

    Maria Jesus Iglesias

    Full Text Available Macrophages play a critical role in innate immunity, and the expression of early response genes orchestrate much of the initial response of the immune system. Macrophages undergo extensive transcriptional reprogramming in response to inflammatory stimuli such as Lipopolysaccharide (LPS.To identify gene transcription regulation patterns involved in early innate immune responses, we used two genome-wide approaches--gene expression profiling and chromatin immunoprecipitation-sequencing (ChIP-seq analysis. We examined the effect of 2 hrs LPS stimulation on early gene expression and its relation to chromatin remodeling (H3 acetylation; H3Ac and promoter binding of Sp1 and RNA polymerase II phosphorylated at serine 5 (S5P RNAPII, which is a marker for transcriptional initiation. Our results indicate novel and alternative gene regulatory mechanisms for certain proinflammatory genes. We identified two groups of up-regulated inflammatory genes with respect to chromatin modification and promoter features. One group, including highly up-regulated genes such as tumor necrosis factor (TNF, was characterized by H3Ac, high CpG content and lack of TATA boxes. The second group, containing inflammatory mediators (interleukins and CCL chemokines, was up-regulated upon LPS stimulation despite lacking H3Ac in their annotated promoters, which were low in CpG content but did contain TATA boxes. Genome-wide analysis showed that few H3Ac peaks were unique to either +/-LPS condition. However, within these, an unpacking/expansion of already existing H3Ac peaks was observed upon LPS stimulation. In contrast, a significant proportion of S5P RNAPII peaks (approx 40% was unique to either condition. Furthermore, data indicated a large portion of previously unannotated TSSs, particularly in LPS-stimulated macrophages, where only 28% of unique S5P RNAPII peaks overlap annotated promoters. The regulation of the inflammatory response appears to occur in a very specific manner at

  20. In Situ Microscopy Analysis Reveals Local Innate Immune Response Developed around Brucella Infected Cells in Resistant and Susceptible Mice

    Science.gov (United States)

    Copin, Richard; Vitry, Marie-Alice; Hanot Mambres, Delphine; Machelart, Arnaud; De Trez, Carl; Vanderwinden, Jean-Marie; Magez, Stefan; Akira, Shizuo; Ryffel, Bernhard; Carlier, Yves; Letesson, Jean-Jacques; Muraille, Eric

    2012-01-01

    Brucella are facultative intracellular bacteria that chronically infect humans and animals causing brucellosis. Brucella are able to invade and replicate in a broad range of cell lines in vitro, however the cells supporting bacterial growth in vivo are largely unknown. In order to identify these, we used a Brucella melitensis strain stably expressing mCherry fluorescent protein to determine the phenotype of infected cells in spleen and liver, two major sites of B. melitensis growth in mice. In both tissues, the majority of primary infected cells expressed the F4/80 myeloid marker. The peak of infection correlated with granuloma development. These structures were mainly composed of CD11b+ F4/80+ MHC-II+ cells expressing iNOS/NOS2 enzyme. A fraction of these cells also expressed CD11c marker and appeared similar to inflammatory dendritic cells (DCs). Analysis of genetically deficient mice revealed that differentiation of iNOS+ inflammatory DC, granuloma formation and control of bacterial growth were deeply affected by the absence of MyD88, IL-12p35 and IFN-γ molecules. During chronic phase of infection in susceptible mice, we identified a particular subset of DC expressing both CD11c and CD205, serving as a reservoir for the bacteria. Taken together, our results describe the cellular nature of immune effectors involved during Brucella infection and reveal a previously unappreciated role for DC subsets, both as effectors and reservoir cells, in the pathogenesis of brucellosis. PMID:22479178

  1. Polynomial algebra reveals diverging roles of the unfolded protein response in endothelial cells during ischemia-reperfusion injury.

    Science.gov (United States)

    Le Pape, Sylvain; Dimitrova, Elena; Hannaert, Patrick; Konovalov, Alexander; Volmer, Romain; Ron, David; Thuillier, Raphaël; Hauet, Thierry

    2014-08-25

    The unfolded protein response (UPR)--the endoplasmic reticulum stress response--is found in various pathologies including ischemia-reperfusion injury (IRI). However, its role during IRI is still unclear. Here, by combining two different bioinformatical methods--a method based on ordinary differential equations (Time Series Network Inference) and an algebraic method (probabilistic polynomial dynamical systems)--we identified the IRE1α-XBP1 and the ATF6 pathways as the main UPR effectors involved in cell's adaptation to IRI. We validated these findings experimentally by assessing the impact of their knock-out and knock-down on cell survival during IRI. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  2. Analysis of trophic interactions reveals highly plastic response to climate change in a tri-trophic High-Arctic ecosystem

    DEFF Research Database (Denmark)

    Mortensen, Lars O.; Schmidt, Niels Martin; Hoye, Toke T.

    2016-01-01

    As a response to current climate changes, individual species have changed various biological traits, illustrating an inherent phenotypic plasticity. However, as species are embedded in an ecological network characterised by multiple consumer-resource interactions, ecological mismatches are likely...... to arise when interacting species do not respond homogeneously. The approach of biological networks analysis calls for the use of structural equation modelling (SEM), a multidimensional analytical setup that has proven particularly useful for analysing multiple interactions across trophic levels. Here we...

  3. Metabonomics-based analysis of Brachyspira pilosicoli's response to tiamulin reveals metabolic activity despite significant growth inhibition

    OpenAIRE

    Le Roy, Caroline Ivanne; Passey, Jade Louise; Woodward, Martin John; La Ragione, Roberto Marcello; Claus, Sandrine Paule

    2017-01-01

    Pathogenic anaerobes Brachyspira spp. are responsible for an increasing number of Intestinal Spirochaetosis (IS) cases in livestock against which few approved treatments are available. Tiamulin is used to treat swine dysentery caused by Brachyspira spp. and recently has been used to handle avian intestinal spirochaetosis (AIS). The therapeutic dose used in chickens requires further evaluation since cases of bacterial resistance to tiamulin have been reported. In this study, we evaluated the i...

  4. Analysis of whitefly transcriptional responses to Beauveria bassiana infection reveals new insights into insect-fungus interactions.

    Science.gov (United States)

    Xia, Jun; Zhang, Chang-Rong; Zhang, Shan; Li, Fang-Fang; Feng, Ming-Guang; Wang, Xiao-Wei; Liu, Shu-Sheng

    2013-01-01

    The fungal pathogen, Beauveria bassiana, is an efficient biocontrol agent against a variety of agricultural pests. A thorough understanding of the basic principles of insect-fungus interactions may enable the genetic modification of Beauveria bassiana to enhance its virulence. However, the molecular mechanism of insect response to Beauveria bassiana infection is poorly understood, let alone the identification of fungal virulent factors involved in pathogenesis. Here, next generation sequencing technology was applied to examine the expression of whitefly (Bemisia tabaci) genes in response to the infection of Beauveria bassiana. Results showed that, compared to control, 654 and 1,681genes were differentially expressed at 48 hours and 72 hours post-infected whiteflies, respectively. Functional and enrichment analyses indicated that the DNA damage stimulus response and drug metabolism were important anti-fungi strategies of the whitefly. Mitogen-activated protein kinase (MAPK) pathway was also likely involved in the whitefly defense responses. Furthermore, the notable suppression of general metabolism and ion transport genes observed in 72 hours post-infected B. tabaci might be manipulated by fungal secreted effectors. By mapping the sequencing tags to B. bassiana genome, we also identified a number of differentially expressed fungal genes between the early and late infection stages. These genes are generally associated with fungal cell wall synthesis and energy metabolism. The expression of fungal cell wall protein genes might play an important role in fungal pathogenesis and the dramatically up-regulated enzymes of carbon metabolism indicate the increasing usage of energy during the fungal infection. To our knowledge, this is the first report on the molecular mechanism of fungus-whitefly interactions. Our results provide a road map for future investigations on insect-pathogen interactions and genetically modifying the fungus to enhance its efficiency in whitefly

  5. Multimodal Microvascular Imaging Reveals that Selective Inhibition of Class I PI3K Is Sufficient to Induce an Antivascular Response

    Directory of Open Access Journals (Sweden)

    Deepak Sampath

    2013-07-01

    Full Text Available The phosphatidylinositol 3-kinase (PI3K pathway is a central mediator of vascular endothelial growth factor (VEGF-driven angiogenesis. The discovery of small molecule inhibitors that selectively target PI3K or PI3K and mammalian target of rapamycin (mTOR provides an opportunity to pharmacologically determine the contribution of these key signaling nodes in VEGF-A-driven tumor angiogenesis in vivo. This study used an array of microvascular imaging techniques to monitor the antivascular effects of selective class I PI3K, mTOR, or dual PI3K/ mTOR inhibitors in colorectal and prostate cancer xenograft models. Micro-computed tomography (micro-CT angiography, dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI, vessel size index (VSI MRI, and DCE ultrasound (DCE-U/S were employed to quantitatively evaluate the vascular (structural and physiological response to these inhibitors. GDC-0980, a dual PI3K/mTOR inhibitor, was found to reduce micro-CT angiography vascular density, while VSI MRI demonstrated a significant reduction in vessel density and an increase in mean vessel size, consistent with a loss of small functional vessels and a substantial antivascular response. DCE-MRI showed that GDC-0980 produces a strong functional response by decreasing the vascular permeability/perfusion-related parameter, Ktrans. Interestingly, comparable antivascular effects were observed for both GDC-980 and GNE-490 (a selective class I PI3K inhibitor. In addition, mTOR-selective inhibitors did not affect vascular density, suggesting that PI3K inhibition is sufficient to generate structural changes, characteristic of a robust antivascular response. This study supports the use of noninvasive microvascular imaging techniques (DCE-MRI, VSI MRI, DCE-U/S as pharmacodynamic assays to quantitatively measure the activity of PI3K and dual PI3K/mTOR inhibitors in vivo.

  6. Metabolomics by proton nuclear magnetic resonance spectroscopy of the response to chloroethylnitrosourea reveals drug efficacy and tumor adaptive metabolic pathways.

    Science.gov (United States)

    Morvan, Daniel; Demidem, Aicha

    2007-03-01

    Metabolomics of tumors may allow discovery of tumor biomarkers and metabolic therapeutic targets. Metabolomics by two-dimensional proton high-resolution magic angle spinning nuclear magnetic resonance spectroscopy was applied to investigate metabolite disorders following treatment by chloroethylnitrosourea of murine B16 melanoma (n = 33) and 3LL pulmonary carcinoma (n = 31) in vivo. Treated tumors of both types resumed growth after a delay. Nitrosoureas provoke DNA damage but the metabolic consequences of genotoxic stress are little known yet. Although some differences were observed in the metabolite profile of untreated tumor types, the prominent metabolic features of the response to nitrosourea were common to both. During the growth inhibition phase, there was an accumulation of glucose (more than x10; P < 0.05), glutamine (x3 to 4; P < 0.01), and aspartate (x2 to 5; P < 0.01). This response testified to nucleoside de novo synthesis down-regulation and drug efficacy. However, this phase also involved the increase in alanine (P < 0.001 in B16 melanoma), the decrease in succinate (P < 0.001), and the accumulation of serine-derived metabolites (glycine, phosphoethanolamine, and formate; P < 0.01). This response witnessed the activation of pathways implicated in energy production and resumption of nucleotide de novo synthesis, thus metabolic pathways of DNA repair and adaptation to treatment. During the growth recovery phase, it remained polyunsaturated fatty acid accumulation (x1.5 to 2; P < 0.05) and reduced utilization of glucose compared with glutamine (P < 0.05), a metabolic fingerprint of adaptation. Thus, this study provides the proof of principle that metabolomics of tumor response to an anticancer agent may help discover metabolic pathways of drug efficacy and adaptation to treatment.

  7. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice

    OpenAIRE

    Riaño-Pachón Diego; Gómez-Porras Judith L; Dreyer Ingo; Mayer Jorge E; Mueller-Roeber Bernd

    2007-01-01

    Abstract Background In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with...

  8. UAS in the NAS: Survey Responses by ATC, Manned Aircraft Pilots, and UAS Pilots

    Science.gov (United States)

    Comstock, James R., Jr.; McAdaragh, Raymon; Ghatas, Rania W.; Burdette, Daniel W.; Trujillo, Anna C.

    2014-01-01

    NASA currently is working with industry and the Federal Aviation Administration (FAA) to establish future requirements for Unmanned Aircraft Systems (UAS) flying in the National Airspace System (NAS). To work these issues NASA has established a multi-center "UAS Integration in the NAS" project. In order to establish Ground Control Station requirements for UAS, the perspective of each of the major players in NAS operations was desired. Three on-line surveys were administered that focused on Air Traffic Controllers (ATC), pilots of manned aircraft, and pilots of UAS. Follow-up telephone interviews were conducted with some survey respondents. The survey questions addressed UAS control, navigation, and communications from the perspective of small and large unmanned aircraft. Questions also addressed issues of UAS equipage, especially with regard to sense and avoid capabilities. From the civilian ATC and military ATC perspectives, of particular interest are how mixed operations (manned / UAS) have worked in the past and the role of aircraft equipage. Knowledge gained from this information is expected to assist the NASA UAS Integration in the NAS project in directing research foci thus assisting the FAA in the development of rules, regulations, and policies related to UAS in the NAS.

  9. Analysis of Globodera rostochiensis effectors reveals conserved functions of SPRYSEC proteins in suppressing and eliciting plant immune responses

    Directory of Open Access Journals (Sweden)

    Peter eMoffett

    2015-08-01

    Full Text Available Potato cyst nematodes (PCNs, including Globodera rostochiensis (Woll., are important pests of potato. Plant parasitic nematodes produce multiple effector proteins, secreted from their stylets, to successfully infect their hosts. These include proteins delivered to the apoplast and to the host cytoplasm. A number of effectors from G. rostochiensis predicted to be delivered to the host cytoplasm have been identified, including several belonging to the secreted SPRY domain (SPRYSEC family. SPRYSEC proteins are unique to members of the genera Globodera and have been implicated in both the induction and the repression of host defense responses. We have tested the properties of six different G. rostochiensis SPRYSEC proteins by expressing them in Nicotiana benthamiana and N. tabacum. We have found that all SPRYSEC proteins tested are able to suppress defense responses induced by NB-LRR proteins as well as cell death induced by elicitors, suggesting that defense repression is a common characteristic of members of this effector protein family. At the same time, GrSPRYSEC-15 elicited a defense response in N. tabacum, and tobacco was found to be resistant to a virus expressing GrSPRYSEC-15. These results suggest that SPRYSEC proteins may possess characteristics that allow them to be recognized by the plant immune system.

  10. Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings.

    Science.gov (United States)

    Zhu, Fu-Yuan; Chen, Mo-Xian; Ye, Neng-Hui; Shi, Lu; Ma, Kai-Long; Yang, Jing-Fang; Cao, Yun-Ying; Zhang, Youjun; Yoshida, Takuya; Fernie, Alisdair R; Fan, Guang-Yi; Wen, Bo; Zhou, Ruo; Liu, Tie-Yuan; Fan, Tao; Gao, Bei; Zhang, Di; Hao, Ge-Fei; Xiao, Shi; Liu, Ying-Gao; Zhang, Jianhua

    2017-08-01

    In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron-containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non-conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  11. An immunoproteomic approach revealing peptides from Sporothrix brasiliensis that induce a cellular immune response in subcutaneous sporotrichosis.

    Science.gov (United States)

    de Almeida, José Roberto Fogaça; Jannuzzi, Grasielle Pereira; Kaihami, Gilberto Hideo; Breda, Leandro Carvalho Dantas; Ferreira, Karen Spadari; de Almeida, Sandro Rogério

    2018-03-08

    Sporothrix brasiliensis is the most virulent fungus of the Sporothrix complex and is the main species recovered in the sporotrichosis zoonotic hyperendemic area in Rio de Janeiro. A vaccine against S. brasiliensis could improve the current sporotrichosis situation. Here, we show 3 peptides from S. brasiliensis immunogenic proteins that have a higher likelihood for engaging MHC-class II molecules. We investigated the efficiency of the peptides as vaccines for preventing subcutaneous sporotrichosis. In this study, we observed a decrease in lesion diameters in peptide-immunized mice, showing that the peptides could induce a protective immune response against subcutaneous sporotrichosis. ZR8 peptide is from the GP70 protein, the main antigen of the Sporothrix complex, and was the best potential vaccine candidate by increasing CD4 + T cells and higher levels of IFN-γ, IL-17A and IL-1β characterizing a strong cellular immune response. This immune environment induced a higher number of neutrophils in lesions that are associated with fungus clearance. These results indicated that the ZR8 peptide induces a protective immune response against subcutaneous sporotrichosis and is a vaccine candidate against S. brasiliensis infection.

  12. Bayesian Diallel Analysis Reveals Mx1-Dependent and Mx1-Independent Effects on Response to Influenza A Virus in Mice

    Directory of Open Access Journals (Sweden)

    Paul L. Maurizio

    2018-02-01

    Full Text Available Influenza A virus (IAV is a respiratory pathogen that causes substantial morbidity and mortality during both seasonal and pandemic outbreaks. Infection outcomes in unexposed populations are affected by host genetics, but the host genetic architecture is not well understood. Here, we obtain a broad view of how heritable factors affect a mouse model of response to IAV infection using an 8 × 8 diallel of the eight inbred founder strains of the Collaborative Cross (CC. Expanding on a prior statistical framework for modeling treatment response in diallels, we explore how a range of heritable effects modify acute host response to IAV through 4 d postinfection. Heritable effects in aggregate explained ∼57% of the variance in IAV-induced weight loss. Much of this was attributable to a pattern of additive effects that became more prominent through day 4 postinfection and was consistent with previous reports of antiinfluenza myxovirus resistance 1 (Mx1 polymorphisms segregating between these strains; these additive effects largely recapitulated haplotype effects observed at the Mx1 locus in a previous study of the incipient CC, and are also replicated here in a CC recombinant intercross population. Genetic dominance of protective Mx1 haplotypes was observed to differ by subspecies of origin: relative to the domesticus null Mx1 allele, musculus acts dominantly whereas castaneus acts additively. After controlling for Mx1, heritable effects, though less distinct, accounted for ∼34% of the phenotypic variance. Implications for future mapping studies are discussed.

  13. Comparative proteomic analyses reveal the proteome response to short-term drought in Italian ryegrass (Lolium multiflorum.

    Directory of Open Access Journals (Sweden)

    Ling Pan

    Full Text Available Drought is a major abiotic stress that impairs growth and productivity of Italian ryegrass. Comparative analysis of drought responsive proteins will provide insight into molecular mechanism in Lolium multiflorum drought tolerance. Using the iTRAQ-based approach, proteomic changes in tolerant and susceptible lines were examined in response to drought condition. A total of 950 differentially accumulated proteins was found to be involved in carbohydrate metabolism, amino acid metabolism, biosynthesis of secondary metabolites, and signal transduction pathway, such as β-D-xylosidase, β-D-glucan glucohydrolase, glycerate dehydrogenase, Cobalamin-independent methionine synthase, glutamine synthetase 1a, Farnesyl pyrophosphate synthase, diacylglycerol, and inositol 1, 4, 5-trisphosphate, which might contributed to enhance drought tolerance or adaption in Lolium multiflorum. Interestingly, the two specific metabolic pathways, arachidonic acid and inositol phosphate metabolism including differentially accumulated proteins, were observed only in the tolerant lines. Cysteine protease cathepsin B, Cysteine proteinase, lipid transfer protein and Aquaporin were observed as drought-regulated proteins participating in hydrolysis and transmembrane transport. The activities of phospholipid hydroperoxide glutathione peroxidase, peroxiredoxin, dehydroascorbate reductase, peroxisomal ascorbate peroxidase and monodehydroascorbate reductase associated with alleviating the accumulation of reactive oxygen species in stress inducing environments. Our results showed that drought-responsive proteins were closely related to metabolic processes including signal transduction, antioxidant defenses, hydrolysis, and transmembrane transport.

  14. A meta-analysis of responses of canopy photosynthetic conversion efficiency to environmental factors reveals major causes of yield gap

    Science.gov (United States)

    Slattery, Rebecca A.; Ainsworth, Elizabeth A.; Ort, Donald R.

    2013-01-01

    Improving plant energy conversion efficiency (εc) is crucial for increasing food and bioenergy crop production and yields. Using a meta-analysis, the effects of greenhouse gases, weather-related stresses projected to intensify due to climate change, and management practices including inputs, shading, and intercropping on εc were statistically quantified from 140 published studies to identify where improvements would have the largest impact on closing yield gaps. Variation in the response of εc to treatment type and dosage, plant characteristics, and growth conditions were also examined. Significant mean increases in εc were caused by elevated [CO2] (20%), shade (18%), and intercropping (15%). εc increased curvilinearly up to 55% with nitrogen additions whereas phosphorus application was most beneficial at low levels. Significant decreases in εc of –8.4% due to elevated [O3], –16.8% due to water stress, and –6.5% due to foliar damage were found. A non-significant decrease in εc of –17.3% was caused by temperature stress. These results identify the need to engineer greater stress tolerance and enhanced responses to positive factors such as [CO2] and nitrogen to improve average yields and yield potential. Optimizing management strategies will also enhance the benefits possible with intercropping, shade, and pest resilience. To determine optimal practices for εc improvement, further studies should be conducted in the field since several responses were exaggerated by non-field experimental conditions. PMID:23873996

  15. Analysis of Globodera rostochiensis effectors reveals conserved functions of SPRYSEC proteins in suppressing and eliciting plant immune responses

    KAUST Repository

    Ali, Shawkat

    2015-08-11

    Potato cyst nematodes (PCNs), including Globodera rostochiensis (Woll.), are important pests of potato. Plant parasitic nematodes produce multiple effector proteins, secreted from their stylets, to successfully infect their hosts. These include proteins delivered to the apoplast and to the host cytoplasm. A number of effectors from G. rostochiensis predicted to be delivered to the host cytoplasm have been identified, including several belonging to the secreted SPRY domain (SPRYSEC) family. SPRYSEC proteins are unique to members of the genus Globodera and have been implicated in both the induction and the repression of host defense responses. We have tested the properties of six different G. rostochiensis SPRYSEC proteins by expressing them in Nicotiana benthamiana and N. tabacum. We have found that all SPRYSEC proteins tested are able to suppress defense responses induced by NB-LRR proteins as well as cell death induced by elicitors, suggesting that defense repression is a common characteristic of members of this effector protein family. At the same time, GrSPRYSEC-15 elicited a defense responses in N. tabacum, which was found to be resistant to a virus expressing GrSPRYSEC-15. These results suggest that SPRYSEC proteins may possess characteristics that allow them to be recognized by the plant immune system.

  16. Meta-analysis reveals complex marine biological responses to the interactive effects of ocean acidification and warming

    Science.gov (United States)

    Harvey, Ben P; Gwynn-Jones, Dylan; Moore, Pippa J

    2013-01-01

    Ocean acidification and warming are considered two of the greatest threats to marine biodiversity, yet the combined effect of these stressors on marine organisms remains largely unclear. Using a meta-analytical approach, we assessed the biological responses of marine organisms to the effects of ocean acidification and warming in isolation and combination. As expected biological responses varied across taxonomic groups, life-history stages, and trophic levels, but importantly, combining stressors generally exhibited a stronger biological (either positive or negative) effect. Using a subset of orthogonal studies, we show that four of five of the biological responses measured (calcification, photosynthesis, reproduction, and survival, but not growth) interacted synergistically when warming and acidification were combined. The observed synergisms between interacting stressors suggest that care must be made in making inferences from single-stressor studies. Our findings clearly have implications for the development of adaptive management strategies particularly given that the frequency of stressors interacting in marine systems will be likely to intensify in the future. There is now an urgent need to move toward more robust, holistic, and ecologically realistic climate change experiments that incorporate interactions. Without them accurate predictions about the likely deleterious impacts to marine biodiversity and ecosystem functioning over the next century will not be possible. PMID:23610641

  17. Protein Profiles Reveal Diverse Responsive Signaling Pathways in Kernels of Two Maize Inbred Lines with Contrasting Drought Sensitivity

    Directory of Open Access Journals (Sweden)

    Liming Yang

    2014-10-01

    Full Text Available Drought stress is a major factor that contributes to disease susceptibility and yield loss in agricultural crops. To identify drought responsive proteins and explore metabolic pathways involved in maize tolerance to drought stress, two maize lines (B73 and Lo964 with contrasting drought sensitivity were examined. The treatments of drought and well water were applied at 14 days after pollination (DAP, and protein profiles were investigated in developing kernels (35 DAP using iTRAQ (isobaric tags for relative and absolute quantitation. Proteomic analysis showed that 70 and 36 proteins were significantly altered in their expression under drought treatments in B73 and Lo964, respectively. The numbers and levels of differentially expressed proteins were generally higher in the sensitive genotype, B73, implying an increased sensitivity to drought given the function of the observed differentially expressed proteins, such as redox homeostasis, cell rescue/defense, hormone regulation and protein biosynthesis and degradation. Lo964 possessed a more stable status with fewer differentially expressed proteins. However, B73 seems to rapidly initiate signaling pathways in response to drought through adjusting diverse defense pathways. These changes in protein expression allow for the production of a drought stress-responsive network in maize kernels.

  18. Proteomic analysis of the intestinal adaptation response reveals altered expression of fatty acid binding proteins following massive small bowel resection.

    Science.gov (United States)

    Stephens, Andrew N; Pereira-Fantini, Prue M; Wilson, Guineva; Taylor, Russell G; Rainczuk, Adam; Meehan, Katie L; Sourial, Magdy; Fuller, Peter J; Stanton, Peter G; Robertson, David M; Bines, Julie E

    2010-03-05

    Intestinal adaptation in response to the loss of the small intestine is essential to restore enteral autonomy in patients who have undergone massive small bowel resection (MSBR). In a proportion of patients, intestinal function is not restored, resulting in chronic intestinal failure (IF). Early referral of such patients for transplant provides the best prognosis; however, the molecular mechanisms underlying intestinal adaptation remain elusive and there is currently no convenient marker to predict whether patients will develop IF. We have investigated the adaptation response in a well-characterized porcine model of intestinal adaptation. 2D DIGE analysis of ileal epithelium from piglets recovering from massive small bowel resection (MSBR) identified over 60 proteins that changed specifically in MSBR animals relative to nonoperational or sham-operated controls. Three fatty acid binding proteins (L-FABP, FABP-6, and I-FABP) showed changes in MSBR animals. The expression changes and localization of each FABP were validated by immunoblotting and immunohistochemical analysis. FABP expression changes in MSBR animals occurred concurrently with altered triglyceride and bile acid metabolism as well as weight gain. The observed FABP expression changes in the ileal epithelium occur as part of the intestinal adaptation response and could provide a clinically useful marker to evaluate adaptation following MSBR.

  19. Comparative Physiological and Proteomic Analysis Reveals the Leaf Response to Cadmium-Induced Stress in Poplar (Populus yunnanensis.

    Directory of Open Access Journals (Sweden)

    Yunqiang Yang

    Full Text Available Excess amounts of heavy metals are important environmental pollutants with significant ecological and nutritional effects. Cdmium (Cd is of particular concern because of its widespread occurrence and high toxicity. We conducted physiological and proteomic analyses to improve our understanding of the responses of Populus yunnanensis to Cd stress. The plantlets experienced two apparent stages in their response to Cd stress. During the first stage, transiently induced defense-response molecules, photosynthesis- and energy-associated proteins, antioxidant enzymes and heat shock proteins (HSPs accumulated to enhance protein stability and establish a new cellular homeostasis. This activity explains why plant photosynthetic capability during this period barely changed. During the second stage, a decline of ribulose-1, 5-bisphosphate carboxylase (RuBisCO and HSP levels led to imbalance of the plant photosynthetic system. Additionally, the expression of Mitogen-activated protein kinase 3 (MPK3, Mitogen-activated protein kinase 6 (MPK6 and a homeobox-leucine zipper protein was higher in the second stage. Higher expression of caffeoyl-CoA O-methyltransferase (CCoAOMT may regulate plant cell wall synthesis for greater Cd storage. These genes may be candidates for further research and use in genetic manipulation of poplar tolerance to Cd stress.

  20. A Dualistic Conformational Response to Substrate Binding in the Human Serotonin Transporter Reveals a High Affinity State for Serotonin*

    Science.gov (United States)

    Bjerregaard, Henriette; Severinsen, Kasper; Said, Saida; Wiborg, Ove; Sinning, Steffen

    2015-01-01

    Serotonergic neurotransmission is modulated by the membrane-embedded serotonin transporter (SERT). SERT mediates the reuptake of serotonin into the presynaptic neurons. Conformational changes in SERT occur upon binding of ions and substrate and are crucial for translocation of serotonin across the membrane. Our understanding of these conformational changes is mainly based on crystal structures of a bacterial homolog in various conformations, derived homology models of eukaryotic neurotransmitter transporters, and substituted cysteine accessibility method of SERT. However, the dynamic changes that occur in the human SERT upon binding of ions, the translocation of substrate, and the role of cholesterol in this interplay are not fully elucidated. Here we show that serotonin induces a dualistic conformational response in SERT. We exploited the substituted cysteine scanning method under conditions that were sensitized to detect a more outward-facing conformation of SERT. We found a novel high affinity outward-facing conformational state of the human SERT induced by serotonin. The ionic requirements for this new conformational response to serotonin mirror the ionic requirements for translocation. Furthermore, we found that membrane cholesterol plays a role in the dualistic conformational response in SERT induced by serotonin. Our results indicate the existence of a subpopulation of SERT responding differently to serotonin binding than hitherto believed and that membrane cholesterol plays a role in this subpopulation of SERT. PMID:25614630

  1. Responses of high-elevation herbaceous plant assemblages to low glacial CO₂ concentrations revealed by fossil marmot (Marmota) teeth.

    Science.gov (United States)

    McLean, Bryan S; Ward, Joy K; Polito, Michael J; Emslie, Steven D

    2014-08-01

    Atmospheric CO2 cycles of the Quaternary likely imposed major constraints on the physiology and growth of C3 plants worldwide. However, the measured record of this remains both geographically and taxonomically sparse. We present the first reconstruction of physiological responses in a late Quaternary high-elevation herbaceous plant community from the Southern Rocky Mountains, USA. We used a novel proxy-fossilized tooth enamel of yellow-bellied marmots (Marmota flaviventris)-which we developed using detailed isotopic analysis of modern individuals. Calculated C isotopic discrimination (Δ) of alpine plants was nearly 2 ‰ lower prior to the Last Glacial Maximum than at present, a response almost identical to that of nonherbaceous taxa from lower elevations. However, initial shifts in Δ aligned most closely with the onset of the late Pleistocene bipolar temperature "seesaw" rather than CO2 increase, indicating unique limitations on glacial-age high-elevation plants may have existed due to both low temperatures and low CO2. Further development of system-specific faunal proxies can help to clarify this and other plant- and ecosystem-level responses to past environmental change.

  2. Ocular-following responses to white noise stimuli in humans reveal a novel nonlinearity that results from temporal sampling.

    Science.gov (United States)

    Sheliga, Boris M; Quaia, Christian; FitzGibbon, Edmond J; Cumming, Bruce G

    2016-01-01

    White noise stimuli are frequently used to study the visual processing of broadband images in the laboratory. A common goal is to describe how responses are derived from Fourier components in the image. We investigated this issue by recording the ocular-following responses (OFRs) to white noise stimuli in human subjects. For a given speed we compared OFRs to unfiltered white noise with those to noise filtered with band-pass filters and notch filters. Removing components with low spatial frequency (SF) reduced OFR magnitudes, and the SF associated with the greatest reduction matched the SF that produced the maximal response when presented alone. This reduction declined rapidly with SF, compatible with a winner-take-all operation. Removing higher SF components increased OFR magnitudes. For higher speeds this effect became larger and propagated toward lower SFs. All of these effects were quantitatively well described by a model that combined two factors: (a) an excitatory drive that reflected the OFRs to individual Fourier components and (b) a suppression by higher SF channels where the temporal sampling of the display led to flicker. This nonlinear interaction has an important practical implication: Even with high refresh rates (150 Hz), the temporal sampling introduced by visual displays has a significant impact on visual processing. For instance, we show that this distorts speed tuning curves, shifting the peak to lower speeds. Careful attention to spectral content, in the light of this nonlinearity, is necessary to minimize the resulting artifact when using white noise patterns undergoing apparent motion.

  3. A Study of General Education Astronomy Students' Understandings of Cosmology. Part III. Evaluating Four Conceptual Cosmology Surveys: An Item Response Theory Approach

    Science.gov (United States)

    Wallace, Colin S.; Prather, Edward E.; Duncan, Douglas K.

    2012-01-01

    This is the third of five papers detailing our national study of general education astronomy students' conceptual and reasoning difficulties with cosmology. In this paper, we use item response theory to analyze students' responses to three out of the four conceptual cosmology surveys we developed. The specific item response theory model we use is…

  4. A survey of antiepileptic drug responses identifies drugs with potential efficacy for seizure control in Wolf-Hirschhorn syndrome.

    Science.gov (United States)

    Ho, Karen S; Markham, Leah M; Twede, Hope; Lortz, Amanda; Olson, Lenora M; Sheng, Xiaoming; Weng, Cindy; Wassman, E Robert; Newcomb, Tara; Wassman, E Robert; Carey, John C; Battaglia, Agatino

    2018-04-01

    Seizures are present in over 90% of infants and children with Wolf-Hirschhorn syndrome (WHS). When present, they significantly affect quality of life. The goal of this study was to use caregiver reports to describe the comparative efficacies of commonly used antiepileptic medications in a large population of individuals with WHS. A web-based, confidential caregiver survey was developed to capture seizure semiology and a chronologic record of seizure treatments as well as responses to each treatment. Adverse events for each drug were also cataloged. We received 141 complete survey responses (47% response rate) describing the seizures of individuals ranging in age from 4months to 61years (90 females: 51 males). Using the Early Childhood Epilepsy Severity Scale (E-Chess), WHS-associated seizures are demonstrably severe regardless of deletion size. The best-performing antiepileptic drugs (AEDs) for controlling seizures in this cohort were broad spectrum drugs clobazam, levetiracetam, and lamotrigine; whereas, the three commonly used carboxamide class drugs: carbamazepine, phenytoin, and oxcarbazepine, were reported to have little effect on, or even exacerbate, seizures. The carboxamide class drugs, along with phenobarbital and topiramate, were also associated with the highest rate of intolerance due to cooccurrence of adverse events. Levetiracetam, clobazam, and clonazepam demonstrated higher tolerability and comparatively less severe adverse events (Wilcoxon rank sum comparison between performance of levetiracetam and carboxamide class drugs gives a psyndromes which may have complex seizure etiologies. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Optogenetic activation of CA1 pyramidal neurons at the dorsal and ventral hippocampus evokes distinct brain-wide responses revealed by mouse fMRI.

    Directory of Open Access Journals (Sweden)

    Norio Takata

    Full Text Available The dorsal and ventral hippocampal regions (dHP and vHP are proposed to have distinct functions. Electrophysiological studies have revealed intra-hippocampal variances along the dorsoventral axis. Nevertheless, the extra-hippocampal influences of dHP and vHP activities remain unclear. In this study, we compared the spatial distribution of brain-wide responses upon dHP or vHP activation and further estimate connection strengths between the dHP and the vHP with corresponding extra-hippocampal areas. To achieve this, we first investigated responses of local field potential (LFP and multi unit activities (MUA upon light stimulation in the hippocampus of an anesthetized transgenic mouse, whose CA1 pyramidal neurons expressed a step-function opsin variant of channelrhodopsin-2 (ChR2. Optogenetic stimulation increased hippocampal LFP power at theta, gamma, and ultra-fast frequency bands, and augmented MUA, indicating light-induced activation of CA1 pyramidal neurons. Brain-wide responses examined using fMRI revealed that optogenetic activation at the dHP or vHP caused blood oxygenation level-dependent (BOLD fMRI signals in situ. Although activation at the dHP induced BOLD responses at the vHP, the opposite was not observed. Outside the hippocampal formation, activation at the dHP, but not the vHP, evoked BOLD responses at the retrosplenial cortex (RSP, which is in line with anatomical evidence. In contrast, BOLD responses at the lateral septum (LS were induced only upon vHP activation, even though both dHP and vHP send axonal fibers to the LS. Our findings suggest that the primary targets of dHP and vHP activation are distinct, which concurs with attributed functions of the dHP and RSP in spatial memory, as well as of the vHP and LS in emotional responses.

  6. 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 rate to the telephone survey. The majority of respondents (77%) said that they had experienced consultations with refugees and asylum seekers in which language assistance was required. Despite this, general practitioners in the majority of cases managed without an interpreter or used informal methods of interpretation. In fact, when given a choice general practitioners would more often choose informal over professional methods of interpretation despite the fact that confidentiality was a significant concern. CONCLUSION: The need for language assistance in consultations with refugees and asylum seekers in Irish general practice is high. General practitioners rely on informal responses. It is necessary to improve knowledge about the organisational contexts that shape general practitioners responses. We also recommend dialogue between general practitioners, patients and interpreters about the relative merits of informal and professional methods of interpretation so that general practitioners\\' choices are responsive to the needs of patients with limited English.

  7. Survey and online discussion groups to develop a patient-rated outcome measure on acceptability of treatment response in vitiligo

    Science.gov (United States)

    2014-01-01

    Background 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. Method 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. Results 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. Conclusions 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

  8. Metabolomics reveals differences in postprandial responses to breads and fasting metabolic characteristics associated with postprandial insulin demand in postmenopausal women.

    Science.gov (United States)

    Moazzami, Ali A; Shrestha, Aahana; Morrison, David A; Poutanen, Kaisa; Mykkänen, Hannu

    2014-06-01

    Changes in serum metabolic profile after the intake of different food products (e.g., bread) can provide insight into their interaction with human metabolism. Postprandial metabolic responses were compared after the intake of refined wheat (RWB), whole-meal rye (WRB), and refined rye (RRB) breads. In addition, associations between the metabolic profile in fasting serum and the postprandial concentration of insulin in response to different breads were investigated. Nineteen postmenopausal women with normal fasting glucose and normal glucose tolerance participated in a randomized, controlled, crossover meal study. The test breads, RWB (control), RRB, and WRB, providing 50 g of available carbohydrate, were each served as a single meal. The postprandial metabolic profile was measured using nuclear magnetic resonance and targeted LC-mass spectrometry and was compared between different breads using ANOVA and multivariate models. Eight amino acids had a significant treatment effect (P insulin. Women with higher fasting concentrations of leucine and isoleucine and lower fasting concentrations of sphingomyelins and phosphatidylcholines had higher insulin responses despite similar glucose concentration after all kinds of bread (cross-validated ANOVA, P = 0.048). High blood concentration of branched-chain amino acids, i.e., leucine and isoleucine, has been associated with the increased risk of diabetes, which suggests that additional consideration should be given to bread proteins in understanding the beneficial health effects of different kinds of breads. The present study suggests that the fasting metabolic profile can be used to characterize the postprandial insulin demand in individuals with normal glucose metabolism that can be used for establishing strategies for the stratification of individuals in personalized nutrition. © 2014 American Society for Nutrition.

  9. Dynamic Maize Responses to Aphid Feeding Are Revealed by a Time Series of Transcriptomic and Metabolomic Assays1[OPEN

    Science.gov (United States)

    Tzin, Vered; Fernandez-Pozo, Noe; Richter, Annett; Schmelz, Eric A.; Schoettner, Matthias; Schäfer, Martin; Ahern, Kevin R.; Meihls, Lisa N.; Kaur, Harleen; Huffaker, Alisa; Mori, Naoki; Degenhardt, Joerg; Mueller, Lukas A.; Jander, Georg

    2015-01-01

    As a response to insect attack, maize (Zea mays) has inducible defenses that involve large changes in gene expression and metabolism. Piercing/sucking insects such as corn leaf aphid (Rhopalosiphum maidis) cause direct damage by acquiring phloem nutrients as well as indirect damage through the transmission of plant viruses. To elucidate the metabolic processes and gene expression changes involved in maize responses to aphid attack, leaves of inbred line B73 were infested with corn leaf aphids for 2 to 96 h. Analysis of infested maize leaves showed two distinct response phases, with the most significant transcriptional and metabolic changes occurring in the first few hours after the initiation of aphid feeding. After 4 d, both gene expression and metabolite profiles of aphid-infested maize reverted to being more similar to those of control plants. Although there was a predominant effect of salicylic acid regulation, gene expression changes also indicated prolonged induction of oxylipins, although not necessarily jasmonic acid, in aphid-infested maize. The role of specific metabolic pathways was confirmed using Dissociator transposon insertions in maize inbred line W22. Mutations in three benzoxazinoid biosynthesis genes, Bx1, Bx2, and Bx6, increased aphid reproduction. In contrast, progeny production was greatly decreased by a transposon insertion in the single W22 homolog of the previously uncharacterized B73 terpene synthases TPS2 and TPS3. Together, these results show that maize leaves shift to implementation of physical and chemical defenses within hours after the initiation of aphid feeding and that the production of specific metabolites can have major effects in maize-aphid interactions. PMID:26378100

  10. Transcriptome analysis reveals the host response to Schmallenberg virus in bovine cells and antagonistic effects of the NSs protein.

    Science.gov (United States)

    Blomström, Anne-Lie; Gu, Quan; Barry, Gerald; Wilkie, Gavin; Skelton, Jessica K; Baird, Margaret; McFarlane, Melanie; Schnettler, Esther; Elliott, Richard M; Palmarini, Massimo; Kohl, Alain

    2015-04-19

    Schmallenberg virus (SBV) is a member of the Orthobunyavirus genus (Bunyaviridae family) causing malformations and abortions in ruminants. Although, as for other members of this family/genus, the non-structural protein NSs has been shown to be an interferon antagonist, very little is known regarding the overall inhibitory effects and targets of orthobunyavirus NSs proteins on host gene expression during infection. Therefore, using RNA-seq this study describes changes to the transcriptome of primary bovine cells following infection with Schmallenberg virus (SBV) or with a mutant lacking the non-structural protein NSs (SBVdelNSs) providing a detailed comparison of the effect of NSs expression on the host cell. The sequence reads from all samples (uninfected cells, SBV and SBVdelNSs) assembled well to the bovine host reference genome (on average 87.43% of the reads). During infection with SBVdelNSs, 649 genes were differentially expressed compared to uninfected cells (78.7% upregulated) and many of these were known antiviral and IFN-stimulated genes. On the other hand, only nine genes were differentially expressed in SBV infected cells compared to uninfected control cells, demonstrating the strong inhibitory effect of NSs on cellular gene expression. However, the majority of the genes that were expressed during SBV infection are involved in restriction of viral replication and spread indicating that SBV does not completely manage to shutdown the host antiviral response. In this study we show the effects of SBV NSs on the transcriptome of infected cells as well as the cellular response to wild type SBV. Although NSs is very efficient in shutting down genes of the host innate response, a number of possible antiviral factors were identified. Thus the data from this study can serve as a base for more detailed mechanistic studies of SBV and other orthobunyaviruses.

  11. Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection

    Science.gov (United States)

    Pandey, Rajesh; Bhattacharya, Aniket; Bhardwaj, Vivek; Jha, Vineet; Mandal, Amit K.; Mukerji, Mitali

    2016-09-01

    Primate-specific Alus harbor different regulatory features, including miRNA targets. In this study, we provide evidence for miRNA-mediated modulation of transcript isoform levels during heat-shock response through exaptation of Alu-miRNA sites in mature mRNA. We performed genome-wide expression profiling coupled with functional validation of miRNA target sites within exonized Alus, and analyzed conservation of these targets across primates. We observed that two miRNAs (miR-15a-3p and miR-302d-3p) elevated in stress response, target RAD1, GTSE1, NR2C1, FKBP9 and UBE2I exclusively within Alu. These genes map onto the p53 regulatory network. Ectopic overexpression of miR-15a-3p downregulates GTSE1 and RAD1 at the protein level and enhances cell survival. This Alu-mediated fine-tuning seems to be unique to humans as evident from the absence of orthologous sites in other primate lineages. We further analyzed signatures of selection on Alu-miRNA targets in the genome, using 1000 Genomes Phase-I data. We found that 198 out of 3177 Alu-exonized genes exhibit signatures of selection within Alu-miRNA sites, with 60 of them containing SNPs supported by multiple evidences (global-FST > 0.3, pair-wise-FST > 0.5, Fay-Wu’s H  2.0, high ΔDAF) and implicated in p53 network. We propose that by affecting multiple genes, Alu-miRNA interactions have the potential to facilitate population-level adaptations in response to environmental challenges.

  12. Anterograde transneuronal viral tract tracing reveals central sensory circuits from brown fat and sensory denervation alters its thermogenic responses.

    Science.gov (United States)

    Vaughan, Cheryl H; Bartness, Timothy J

    2012-05-01

    Brown adipose tissue (BAT) thermogenic activity and growth are controlled by its sympathetic nervous system (SNS) innervation, but nerve fibers containing sensory-associated neuropeptides [substance P, calcitonin gene-related peptide (CGRP)] also suggest sensory innervation. The central nervous system (CNS) projections of BAT afferents are unknown. Therefore, we used the H129 strain of the herpes simplex virus-1 (HSV-1), an anterograde transneuronal viral tract tracer used to delineate sensory nerve circuits, to define these projections. HSV-1 was injected into interscapular BAT (IBAT) of Siberian hamsters and HSV-1 immunoreactivity (ir) was assessed 24, 48, 72, 96, and 114 h postinjection. The 96- and 114-h groups had the most HSV-1-ir neurons with marked infections in the hypothalamic paraventricular nucleus, periaqueductal gray, olivary areas, parabrachial nuclei, raphe nuclei, and reticular areas. These sites also are involved in sympathetic outflow to BAT suggesting possible BAT sensory-SNS thermogenesis feedback circuits. We tested the functional contribution of IBAT sensory innervation on thermogenic responses to an acute (24 h) cold exposure test by injecting the specific sensory nerve toxin capsaicin directly into IBAT pads and then measuring core (T(c)) and IBAT (T(IBAT)) temperature responses. CGRP content was significantly decreased in capsaicin-treated IBAT demonstrating successful sensory nerve destruction. T(IBAT) and T(c) were significantly decreased in capsaicin-treated hamsters compared with the saline controls at 2 h of cold exposure. Thus the central sensory circuits from IBAT have been delineated for the first time, and impairment of sensory feedback from BAT appears necessary for the appropriate, initial thermogenic response to acute cold exposure.

  13. Quantitative proteomics reveals divergent responses in Apis mellifera worker and drone pupae to parasitization by Varroa destructor.

    Science.gov (United States)

    Surlis, Carla; Carolan, James C; Coffey, Mary; Kavanagh, Kevin

    Varroa destructor is a haemophagous ectoparasite of honeybees and is considered a major causal agent of colony losses in Europe and North America. Although originating in Eastern Asia where it parasitizes Apis cerana, it has shifted hosts to the western honeybee Apis mellifera on which it has a greater deleterious effect on the individual and colony level. To investigate this important host-parasite interaction and to determine whether Varroa causes different effects on different castes we conducted a label free quantitative proteomic analysis of Varroa-parasitized and non-parasitized drone and worker Apis mellifera pupae. 1195 proteins were identified in total, of which 202 and 250 were differentially abundant in parasitized drone and worker pupae, respectively. Both parasitized drone and worker pupae displayed reduced abundance in proteins associated with the cuticle, lipid transport and innate immunity. Proteins involved in metabolic processes were more abundant in both parasitized castes although the response in workers was more pronounced. A number of caste specific responses were observed including differential abundance of numerous cytoskeletal and muscle proteins, which were of higher abundance in parasitized drones in comparison to parasitized workers. Proteins involved in fatty acid and carbohydrate metabolism were more abundant in parasitized workers as were a large number of ribosomal proteins highlighting either potentially divergent responses to Varroa or a different strategy by the mite when parasitizing the different castes. This data improves our understanding of this interaction and may provide a basis for future studies into improvements to therapy and control of Varroasis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Cloning the uteroglobin gene promoter from the relic volcano rabbit (Romerolagus diazi) reveals an ancient estrogen-response element.

    Science.gov (United States)

    Acosta-MontesdeOca, Adriana; Zariñán, Teresa; Macías, Héctor; Pérez-Solís, Marco A; Ulloa-Aguirre, Alfredo; Gutiérrez-Sagal, Rubén

    2012-05-01

    To gain further insight on the estrogen-dependent transcriptional regulation of the uteroglobin (UG) gene, we cloned the 5'-flanking region of the UG gene from the phylogenetically ancient volcano rabbit (Romerolagus diazi; Rd). The cloned region spans 812 base pairs (bp; -812/-1) and contains a noncanonical TATA box (TACA). The translation start site is 48 bp downstream from the putative transcription initiation site (AGA), and is preceded by a consensus Kozak box. Comparison of the Rd-UG gene with that previously isolated from rabbits (Oryctolagus cuniculus) showed 93% in sequence identity as well as a number of conserved cis-acting elements, including the estrogen-response element (ERE; -265/-251), which differs from the consensus by two nucleotides. In MCF-7 cells, 17β-estradiol (E(2)) induced transcription of a luciferase reporter driven by the Rd-UG promoter in a similar manner as in an equivalent rabbit UG reporter; the Rd-UG promoter was 30% more responsive to E(2) than the rabbit promoter. Mutagenesis studies on the Rd-ERE confirmed this cis-element as a target of E(2) as two luciferase mutant reporters of the Rd-promoter, one with the rabbit and the other with the consensus ERE, were more responsive to the hormone than the wild-type reporter. Gel shift and super-shift assays showed that estrogen receptor-α indeed binds to the imperfect palindromic sequence of the Rd-ERE. Copyright © 2012 Wiley Periodicals, Inc.

  15. Mammary gene expression profiles during an intramammary challenge reveal potential mechanisms linking negative energy balance with impaired immune response

    DEFF Research Database (Denmark)

    Moyes, Kasey; Drackley, J K; Morin, D E

    2010-01-01

    Our objective was to compare mammary tissue gene expression profiles during a Streptococcus uberis (S. uberis) mastitis challenge between lactating cows subjected to dietary-induced negative energy balance (NEB; n = 5) and cows fed ad libitum to maintain positive energy balance (PEB; n = 5...... 0.05), with 86 DEG up-regulated and 201 DEG down-regulated. Canonical pathways most affected by NEB were IL-8 Signaling (10 genes), Glucocorticoid Receptor Signaling (13), and NRF2-mediated Oxidative Stress Response (10). Among genes differentially expressed by NEB, Cell Growth and Proliferation (48...

  16. Proteomic responses reveal the differential effects induced by cadmium in mussels Mytilus galloprovincialis at early life stages.

    Science.gov (United States)

    Xu, Lanlan; Peng, Xiao; Yu, Deliang; Ji, Chenglong; Zhao, Jianmin; Wu, Huifeng

    2016-08-01

    Cadmium (Cd) has become an important metal contaminant and posed severe risk on the organisms in the coastal environments of the Bohai Sea. Marine mussel Mytilus galloprovincialis is widely distributed along the Bohai coast and consumed as seafood by local residents. Evidences indicate that the early stages of marine organisms are more sensitive to metal contaminants. In this study, we applied two-dimensional electrophoresis-based proteomics to characterize the biological effects of Cd (50 μg L(-1)) in the early life stages (D-shape larval and juvenile) of mussels. The different proteomic responses demonstrated the differential responsive mechanisms to Cd exposure in these two early life stages of mussels. In details, results indicated that Cd mainly induced immune and oxidative stresses in both D-shape larval and juvenile mussels via different pathways. In addition, the significant up-regulation of triosephosphate isomerase and metallothionein confirmed the enhanced energy demand and mobilized detoxification mechanism in D-shape larval mussels exposed to Cd. In juvenile mussels, Cd exposure also induced clear apoptosis. Overall, this work suggests that Cd is a potential immune toxicant to mussel M. galloprovincialis at early life stages. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. A new approach for determining phase response curves reveals that Purkinje cells can act as perfect integrators.

    Directory of Open Access Journals (Sweden)

    Elena Phoka

    2010-04-01

    Full Text Available Cerebellar Purkinje cells display complex intrinsic dynamics. They fire spontaneously, exhibit bistability, and via mutual network interactions are involved in the generation of high frequency oscillations and travelling waves of activity. To probe the dynamical properties of Purkinje cells we measured their phase response curves (PRCs. PRCs quantify the change in spike phase caused by a stimulus as a function of its temporal position within the interspike interval, and are widely used to predict neuronal responses to more complex stimulus patterns. Significant variability in the interspike interval during spontaneous firing can lead to PRCs with a low signal-to-noise ratio, requiring averaging over thousands of trials. We show using electrophysiological experiments and simulations that the PRC calculated in the traditional way by sampling the interspike interval with brief current pulses is biased. We introduce a corrected approach for calculating PRCs which eliminates this bias. Using our new approach, we show that Purkinje cell PRCs change qualitatively depending on the firing frequency of the cell. At high firing rates, Purkinje cells exhibit single-peaked, or monophasic PRCs. Surprisingly, at low firing rates, Purkinje cell PRCs are largely independent of phase, resembling PRCs of ideal non-leaky integrate-and-fire neurons. These results indicate that Purkinje cells can act as perfect integrators at low firing rates, and that the integration mode of Purkinje cells depends on their firing rate.

  18. TaWRKY68 responses to biotic stresses are revealed by the orthologous genes from major cereals

    Directory of Open Access Journals (Sweden)

    Bo Ding

    2014-01-01

    Full Text Available WRKY transcription factors have been extensively characterized in the past 20 years, but in wheat, studies onWRKY genes and their function are lagging behind many other species. To explore the function of wheat WRKY genes, we identified a TaWRKY68 gene from a common wheat cultivar. It encodes a protein comprising 313 amino acids which harbors 19 conserved motifs or active sites. Gene expression patterns were determined by analyzing microarray data of TaWRKY68 in wheat and of orthologous genes from maize, rice and barley using Genevestigator. TaWRKY68 orthologs were identified and clustered using DELTA-BLAST and COBALT programs available at NCBI. The results showed that these genes, which are expressed in all tissues tested, had relatively higher levels in the roots and were up-regulated in response to biotic stresses. Bioinformatics results were confirmed by RT-PCR experiments using wheat plants infected by Agrobacterium tumefaciens and Blumeria graminis, or treated with Deoxynivalenol, a Fusarium graminearum-induced mycotoxin in wheat or barley. In summary,TaWRKY68 functions differ during plant developmental stages and might be representing a hub gene function in wheat responses to various biotic stresses. It was also found that including data from major cereal genes in the bioinformatics analysis gave more accurate and comprehensive predictions of wheat gene functions.

  19. Identification and expression analyses of WRKY genes reveal their involvement in growth and abiotic stress response in watermelon (Citrullus lanatus).

    Science.gov (United States)

    Yang, Xiaozhen; Li, Hao; Yang, Yongchao; Wang, Yongqi; Mo, Yanling; Zhang, Ruimin; Zhang, Yong; Ma, Jianxiang; Wei, Chunhua; Zhang, Xian

    2018-01-01

    Despite identification of WRKY family genes in numerous plant species, a little is known about WRKY genes in watermelon, one of the most economically important fruit crops around the world. Here, we identified a total of 63 putative WRKY genes in watermelon and classified them into three major groups (I-III) and five subgroups (IIa-IIe) in group II. The structure analysis indicated that ClWRKYs with different WRKY domains or motifs may play different roles by regulating respective target genes. The expressions of ClWRKYs in different tissues indicate that they are involved in various tissue growth and development. Furthermore, the diverse responses of ClWRKYs to drought, salt, or cold stress suggest that they positively or negatively affect plant tolerance to various abiotic stresses. In addition, the altered expression patterns of ClWRKYs in response to phytohormones such as, ABA, SA, MeJA, and ETH, imply the occurrence of complex cross-talks between ClWRKYs and plant hormone signals in regulating plant physiological and biological processes. Taken together, our findings provide valuable clues to further explore the function and regulatory mechanisms of ClWRKY genes in watermelon growth, development, and adaption to environmental stresses.

  20. Identification and expression analyses of WRKY genes reveal their involvement in growth and abiotic stress response in watermelon (Citrullus lanatus.

    Directory of Open Access Journals (Sweden)

    Xiaozhen Yang

    Full Text Available Despite identification of WRKY family genes in numerous plant species, a little is known about WRKY genes in watermelon, one of the most economically important fruit crops around the world. Here, we identified a total of 63 putative WRKY genes in watermelon and classified them into three major groups (I-III and five subgroups (IIa-IIe in group II. The structure analysis indicated that ClWRKYs with different WRKY domains or motifs may play different roles by regulating respective target genes. The expressions of ClWRKYs in different tissues indicate that they are involved in various tissue growth and development. Furthermore, the diverse responses of ClWRKYs to drought, salt, or cold stress suggest that they positively or negatively affect plant tolerance to various abiotic stresses. In addition, the altered expression patterns of ClWRKYs in response to phytohormones such as, ABA, SA, MeJA, and ETH, imply the occurrence of complex cross-talks between ClWRKYs and plant hormone signals in regulating plant physiological and biological processes. Taken together, our findings provide valuable clues to further explore the function and regulatory mechanisms of ClWRKY genes in watermelon growth, development, and adaption to environmental stresses.

  1. A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens.

    Directory of Open Access Journals (Sweden)

    Guillermo Rodrigo

    Full Text Available Understanding the mechanisms by which plants trigger host defenses in response to viruses has been a challenging problem owing to the multiplicity of factors and complexity of interactions involved. The advent of genomic techniques, however, has opened the possibility to grasp a global picture of the interaction. Here, we used Arabidopsis thaliana to identify and compare genes that are differentially regulated upon infection with seven distinct (+ssRNA and one ssDNA plant viruses. In the first approach, we established lists of genes differentially affected by each virus and compared their involvement in biological functions and metabolic processes. We found that phylogenetically related viruses significantly alter the expression of similar genes and that viruses naturally infecting Brassicaceae display a greater overlap in the plant response. In the second approach, virus-regulated genes were contextualized using models of transcriptional and protein-protein interaction networks of A. thaliana. Our results confirm that host cells undergo significant reprogramming of their transcriptome during infection, which is possibly a central requirement for the mounting of host defenses. We uncovered a general mode of action in which perturbations preferentially affect genes that are highly connected, central and organized in modules.

  2. Comparative proteomic analysis reveals molecular mechanism of seedling roots of different salt tolerant soybean genotypes in responses to salinity stress

    Directory of Open Access Journals (Sweden)

    Hongyu Ma

    2014-09-01

    Full Text Available Salinity stress is one of the major abiotic stresses that limit agricultural yield. To understand salt-responsive protein networks in soybean seedling, the extracted proteins from seedling roots of two different genotypes (Lee 68 and Jackson were analyzed under salt stress by two-dimensional polyacrylamide gel electrophoresis. Sixty-eight differentially expressed proteins were detected and identified. The identified proteins were involved in 13 metabolic pathways and cellular processes. Proteins correlated to brassinosteroid and gilbberellin signalings were significantly increased only in the genotype Lee 68 under salt stress; abscisic acid content was positively correlated with this genotype; proteins that can be correlated to Ca2+ signaling were more strongly enhanced by salt stress in the seedling roots of genotype Lee 68 than in those of genotype Jackson; moreover, genotype Lee 68 had stronger capability of reactive oxygen species scavenging and cell K+/Na+ homeostasis maintaining in seedling roots than genotype Jackson under salt stress. Since the genotype Lee 68 has been described in literature as being tolerant and Jackson as sensitive, we hypothesize that these major differences in the genotype Lee 68 might contribute to salt tolerance. Combined with our previous comparative proteomics analysis on seedling leaves, the similarities and differences between the salt-responsive protein networks found in the seedling leaves and roots of both the genotypes were discussed. Such a result will be helpful in breeding of salt-tolerant soybean cultivars.

  3. Proteome analysis reveals distinct uranium stress response in two strains of Cyanobacteria native to Indian paddy fields

    International Nuclear Information System (INIS)

    Panda, Bandita; Basu, Bhakti; Acharya, Celin; Rajaram, Hema; Apte, Shree Kumar

    2017-01-01

    Uranium present in phosphate fertilizer contaminates agricultural land. Uranium exerts chemical toxicity to the resident biota as it induces oxidative stress by generating free radicals. Two strains of nitrogen fixing cyanobacteria viz., Anabaena PCC 7120 and L-31 native to Indian paddy, regularly experience oxidative stress induced by different stresses and heavy metals. The present study investigated their response to uranium exposure at proteomic level. LD_5_0 dose for Anabaena 7120 and Anabaena L-31 was determined to be 75 μM and 200 μM uranyl carbonate exposure for 3 h. A total of 79 proteins from Anabaena 7120 and 64 proteins from Anabaena L-31 were identified by MALDI mass spectrometry, of which levels of 45 and 27 proteins respectively were found to be differentially modulated in the two strains in response to uranium exposure. The differentially expressed proteins belonged to the major functional categories of photosynthesis, carbon metabolism and oxidative stress alleviation, commensurate with their uranium tolerance. Better oxidative stress management, and maintenance of metabolic and energy homeostasis lead to superior uranium tolerance in Anabaena L-31 as compared to Anabaena PCC 7120

  4. Metabonomics-based analysis of Brachyspira pilosicoli's response to tiamulin reveals metabolic activity despite significant growth inhibition.

    Science.gov (United States)

    Le Roy, Caroline Ivanne; Passey, Jade Louise; Woodward, Martin John; La Ragione, Roberto Marcello; Claus, Sandrine Paule

    2017-06-01

    Pathogenic anaerobes Brachyspira spp. are responsible for an increasing number of Intestinal Spirochaetosis (IS) cases in livestock against which few approved treatments are available. Tiamulin is used to treat swine dysentery caused by Brachyspira spp. and recently has been used to handle avian intestinal spirochaetosis (AIS). The therapeutic dose used in chickens requires further evaluation since cases of bacterial resistance to tiamulin have been reported. In this study, we evaluated the impact of tiamulin at varying concentrations on the metabolism of B. pilosicoli using a 1 H-NMR-based metabonomics approach allowing the capture of the overall bacterial metabolic response to antibiotic treatment. Based on growth curve studies, tiamulin impacted bacterial growth even at very low concentration (0.008 μg/mL) although its metabolic activity was barely affected 72 h post exposure to antibiotic treatment. Only the highest dose of tiamulin tested (0.250 μg/mL) caused a major metabolic shift. Results showed that below this concentration, bacteria could maintain a normal metabolic trajectory despite significant growth inhibition by the antibiotic, which may contribute to disease reemergence post antibiotic treatment. Indeed, we confirmed that B. pilosicoli remained viable even after exposition to the highest antibiotic dose. This paper stresses the need to ensure new evaluation of bacterial viability post bacteriostatic exposure such as tiamulin to guarantee treatment efficacy and decrease antibiotic resistance development. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Neonatal maternal deprivation response and developmental changes in gene expression revealed by hypothalamic gene expression profiling in mice.

    Directory of Open Access Journals (Sweden)

    Feng Ding

    Full Text Available Neonatal feeding problems are observed in several genetic diseases including Prader-Willi syndrome (PWS. Later in life, individuals with PWS develop hyperphagia and obesity due to lack of appetite control. We hypothesized that failure to thrive in infancy and later-onset hyperphagia are related and could be due to a defect in the hypothalamus. In this study, we performed gene expression microarray analysis of the hypothalamic response to maternal deprivation in neonatal wild-type and Snord116del mice, a mouse model for PWS in which a cluster of imprinted C/D box snoRNAs is deleted. The neonatal starvation response in both strains was dramatically different from that reported in adult rodents. Genes that are affected by adult starvation showed no expression change in the hypothalamus of 5 day-old pups after 6 hours of maternal deprivation. Unlike in adult rodents, expression levels of Nanos2 and Pdk4 were increased, and those of Pgpep1, Ndp, Brms1l, Mett10d, and Snx1 were decreased after neonatal deprivation. In addition, we compared hypothalamic gene expression profiles at postnatal days 5 and 13 and observed significant developmental changes. Notably, the gene expression profiles of Snord116del deletion mice and wild-type littermates were very similar at all time points and conditions, arguing against a role of Snord116 in feeding regulation in the neonatal period.

  6. X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture1[OPEN

    Science.gov (United States)

    Rogers, Eric D.; Monaenkova, Daria; Mijar, Medhavinee; Goldman, Daniel I.

    2016-01-01

    Root system architecture (RSA) impacts plant fitness and crop yield by facilitating efficient nutrient and water uptake from the soil. A better understanding of the effects of soil on RSA could improve crop productivity by matching roots to their soil environment. We used x-ray computed tomography to perform a detailed three-dimensional quantification of changes in rice (Oryza sativa) RSA in response to the physical properties of a granular substrate. We characterized the RSA of eight rice cultivars in five different growth substrates and determined that RSA is the result of interactions between genotype and growth environment. We identified cultivar-specific changes in RSA in response to changing growth substrate texture. The cultivar Azucena exhibited low RSA plasticity in all growth substrates, whereas cultivar Bala root depth was a function of soil hardness. Our imaging techniques provide a framework to study RSA in different growth environments, the results of which can be used to improve root traits with agronomic potential. PMID:27208237

  7. Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Moschen, Sebastián; Di Rienzo, Julio A; Higgins, Janet; Tohge, Takayuki; Watanabe, Mutsumi; González, Sergio; Rivarola, Máximo; García-García, Francisco; Dopazo, Joaquin; Hopp, H Esteban; Hoefgen, Rainer; Fernie, Alisdair R; Paniego, Norma; Fernández, Paula; Heinz, Ruth A

    2017-07-01

    By integration of transcriptional and metabolic profiles we identified pathways and hubs transcription factors regulated during drought conditions in sunflower, useful for applications in molecular and/or biotechnological breeding. Drought is one of the most important environmental stresses that effects crop productivity in many agricultural regions. Sunflower is tolerant to drought conditions but the mechanisms involved in this tolerance remain unclear at the molecular level. The aim of this study was to characterize and integrate transcriptional and metabolic pathways related to drought stress in sunflower plants, by using a system biology approach. Our results showed a delay in plant senescence with an increase in the expression level of photosynthesis related genes as well as higher levels of sugars, osmoprotectant amino acids and ionic nutrients under drought conditions. In addition, we identified transcription factors that were upregulated during drought conditions and that may act as hubs in the transcriptional network. Many of these transcription factors belong to families implicated in the drought response in model species. The integration of transcriptomic and metabolomic data in this study, together with physiological measurements, has improved our understanding of the biological responses during droughts and contributes to elucidate the molecular mechanisms involved under this environmental condition. These findings will provide useful biotechnological tools to improve stress tolerance while maintaining crop yield under restricted water availability.

  8. Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation.

    Science.gov (United States)

    Deng, Ye; Zhang, Ping; Qin, Yujia; Tu, Qichao; Yang, Yunfeng; He, Zhili; Schadt, Christopher Warren; Zhou, Jizhong

    2016-01-01

    Discerning network interactions among different species/populations in microbial communities has evoked substantial interests in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. Here, we modified the random matrix theory-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the network interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140-269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. Particularly, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  9. Multi-omics analysis of thermal stress response in a zooxanthellate cnidarian reveals the importance of associating with thermotolerant symbionts

    KAUST Repository

    Cziesielski, Maha J.

    2018-04-18

    Corals and their endosymbiotic dinoflagellates of the genus Symbiodinium have a fragile relationship that breaks down under heat stress, an event known as bleaching. However, many coral species have adapted to high temperature environments such as the Red Sea (RS). To investigate mechanisms underlying temperature adaptation in zooxanthellate cnidarians we compared transcriptome- and proteome-wide heat stress response (24 h at 32°C) of three strains of the model organism Aiptasia pallida from regions with differing temperature profiles; North Carolina (CC7), Hawaii (H2) and the RS. Correlations between transcript and protein levels were generally low but inter-strain comparisons highlighted a common core cnidarian response to heat stress, including protein folding and oxidative stress pathways. RS anemones showed the strongest increase in antioxidant gene expression and exhibited significantly lower reactive oxygen species (ROS) levels in hospite However, comparisons of antioxidant gene and protein expression between strains did not show strong differences, indicating similar antioxidant capacity across the strains. Subsequent analysis of ROS production in isolated symbionts confirmed that the observed differences of ROS levels in hospite were symbiont-driven. Our findings indicate that RS anemones do not show increased antioxidant capacity but may have adapted to higher temperatures through association with more thermally tolerant symbionts.

  10. Multi-omics analysis of thermal stress response in a zooxanthellate cnidarian reveals the importance of associating with thermotolerant symbionts

    KAUST Repository

    Cziesielski, Maha J.; Liew, Yi Jin; Cui, Guoxin; Schmidt-Roach, Sebastian; Campana, Sara; Marondedze, Claudius; Aranda, Manuel

    2018-01-01

    Corals and their endosymbiotic dinoflagellates of the genus Symbiodinium have a fragile relationship that breaks down under heat stress, an event known as bleaching. However, many coral species have adapted to high temperature environments such as the Red Sea (RS). To investigate mechanisms underlying temperature adaptation in zooxanthellate cnidarians we compared transcriptome- and proteome-wide heat stress response (24 h at 32°C) of three strains of the model organism Aiptasia pallida from regions with differing temperature profiles; North Carolina (CC7), Hawaii (H2) and the RS. Correlations between transcript and protein levels were generally low but inter-strain comparisons highlighted a common core cnidarian response to heat stress, including protein folding and oxidative stress pathways. RS anemones showed the strongest increase in antioxidant gene expression and exhibited significantly lower reactive oxygen species (ROS) levels in hospite However, comparisons of antioxidant gene and protein expression between strains did not show strong differences, indicating similar antioxidant capacity across the strains. Subsequent analysis of ROS production in isolated symbionts confirmed that the observed differences of ROS levels in hospite were symbiont-driven. Our findings indicate that RS anemones do not show increased antioxidant capacity but may have adapted to higher temperatures through association with more thermally tolerant symbionts.

  11. A comparative study of ethylene growth response kinetics in eudicots and monocots reveals a role for gibberellin in growth inhibition and recovery.

    Science.gov (United States)

    Kim, Joonyup; Wilson, Rebecca L; Case, J Brett; Binder, Brad M

    2012-11-01

    Time-lapse imaging of dark-grown Arabidopsis (Arabidopsis thaliana) hypocotyls has revealed new aspects about ethylene signaling. This study expands upon these results by examining ethylene growth response kinetics of seedlings of several plant species. Although the response kinetics varied between the eudicots studied, all had prolonged growth inhibition for as long as ethylene was present. In contrast, with continued application of ethylene, white millet (Panicum miliaceum) seedlings had a rapid and transient growth inhibition response, rice (Oryza sativa 'Nipponbare') seedlings had a slow onset of growth stimulation, and barley (Hordeum vulgare) had a transient growth inhibition response followed, after a delay, by a prolonged inhibition response. Growth stimulation in rice correlated with a decrease in the levels of rice ETHYLENE INSENSTIVE3-LIKE2 (OsEIL2) and an increase in rice F-BOX DOMAIN AND LRR CONTAINING PROTEIN7 transcripts. The gibberellin (GA) biosynthesis inhibitor paclobutrazol caused millet seedlings to have a prolonged growth inhibition response when ethylene was applied. A transient ethylene growth inhibition response has previously been reported for Arabidopsis ethylene insensitive3-1 (ein3-1) eil1-1 double mutants. Paclobutrazol caused these mutants to have a prolonged response to ethylene, whereas constitutive GA signaling in this background eliminated ethylene responses. Sensitivity to paclobutrazol inversely correlated with the levels of EIN3 in Arabidopsis. Wild-type Arabidopsis seedlings treated with paclobutrazol and mutants deficient in GA levels or signaling had a delayed growth recovery after ethylene removal. It is interesting to note that ethylene caused alterations in gene expression that are predicted to increase GA levels in the ein3-1 eil1-1 seedlings. These results indicate that ethylene affects GA levels leading to modulation of ethylene growth inhibition kinetics.

  12. A Comparative Study of Ethylene Growth Response Kinetics in Eudicots and Monocots Reveals a Role for Gibberellin in Growth Inhibition and Recovery1[W][OA

    Science.gov (United States)

    Kim, Joonyup; Wilson, Rebecca L.; Case, J. Brett; Binder, Brad M.

    2012-01-01

    Time-lapse imaging of dark-grown Arabidopsis (Arabidopsis thaliana) hypocotyls has revealed new aspects about ethylene signaling. This study expands upon these results by examining ethylene growth response kinetics of seedlings of several plant species. Although the response kinetics varied between the eudicots studied, all had prolonged growth inhibition for as long as ethylene was present. In contrast, with continued application of ethylene, white millet (Panicum miliaceum) seedlings had a rapid and transient growth inhibition response, rice (Oryza sativa ‘Nipponbare’) seedlings had a slow onset of growth stimulation, and barley (Hordeum vulgare) had a transient growth inhibition response followed, after a delay, by a prolonged inhibition response. Growth stimulation in rice correlated with a decrease in the levels of rice ETHYLENE INSENSTIVE3-LIKE2 (OsEIL2) and an increase in rice F-BOX DOMAIN AND LRR CONTAINING PROTEIN7 transcripts. The gibberellin (GA) biosynthesis inhibitor paclobutrazol caused millet seedlings to have a prolonged growth inhibition response when ethylene was applied. A transient ethylene growth inhibition response has previously been reported for Arabidopsis ethylene insensitive3-1 (ein3-1) eil1-1 double mutants. Paclobutrazol caused these mutants to have a prolonged response to ethylene, whereas constitutive GA signaling in this background eliminated ethylene responses. Sensitivity to paclobutrazol inversely correlated with the levels of EIN3 in Arabidopsis. Wild-type Arabidopsis seedlings treated with paclobutrazol and mutants deficient in GA levels or signaling had a delayed growth recovery after ethylene removal. It is interesting to note that ethylene caused alterations in gene expression that are predicted to increase GA levels in the ein3-1 eil1-1 seedlings. These results indicate that ethylene affects GA levels leading to modulation of ethylene growth inhibition kinetics. PMID:22977279

  13. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  14. Adrenaline modulates the global transcriptional profile of Salmonella revealing a role in the antimicrobial peptide and oxidative stress resistance responses

    Directory of Open Access Journals (Sweden)

    Williams P

    2008-10-01

    Full Text Available Abstract Background The successful interaction of bacterial pathogens with host tissues requires the sensing of specific chemical and physical cues. The human gut contains a huge number of neurons involved in the secretion and sensing of a class of neuroendocrine hormones called catecholamines. Recently, in Escherichia coli O157:H7, the catecholamines adrenaline and noradrenaline were shown to act synergistically with a bacterial quorum sensing molecule, autoinducer 3 (AI-3, to affect bacterial virulence and motility. We wished to investigate the impact of adrenaline on the biology of Salmonella spp. Results We have determined the effect of adrenaline on the transcriptome of the gut pathogen Salmonella enterica serovar Typhimurium. Addition of adrenaline led to an induction of key metal transport systems within 30 minutes of treatment. The oxidative stress responses employing manganese internalisation were also elicited. Cells lacking the key oxidative stress regulator OxyR showed reduced survival in the presence of adrenaline and complete restoration of growth upon addition of manganese. A significant reduction in the expression of the pmrHFIJKLM antimicrobial peptide resistance operon reduced the ability of Salmonella to survive polymyxin B following addition of adrenaline. Notably, both phenotypes were reversed by the addition of the β-adrenergic blocker propranolol. Our data suggest that the BasSR two component signal transduction system is the likely adrenaline sensor mediating the antimicrobial p