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Sample records for adaptive conjoint analysis

  1. Modeling the anti-cyberbullying preferences of university students: Adaptive choice-based conjoint analysis.

    PubMed

    Cunningham, Charles E; Chen, Yvonne; Vaillancourt, Tracy; Rimas, Heather; Deal, Ken; Cunningham, Lesley J; Ratcliffe, Jenna

    2015-01-01

    Adaptive choice-based conjoint analysis was used to study the anti-cyberbullying program preferences of 1,004 university students. More than 60% reported involvement in cyberbullying as witnesses (45.7%), victims (5.7%), perpetrator-victims (4.9%), or perpetrators (4.5%). Men were more likely to report involvement as perpetrators and perpetrator-victims than were women. Students recommended advertisements featuring famous people who emphasized the impact of cyberbullying on victims. They preferred a comprehensive approach teaching skills to prevent cyberbullying, encouraging students to report incidents, enabling anonymous online reporting, and terminating the internet privileges of students involved as perpetrators. Those who cyberbully were least likely, and victims of cyberbullying were most likely, to support an approach combining prevention and consequences. Simulations introducing mandatory reporting, suspensions, or police charges predicted a substantial reduction in the support of uninvolved students, witnesses, victims, and perpetrators.

  2. Integrating sensory evaluation in adaptive conjoint analysis to elaborate the conflicting influence of intrinsic and extrinsic attributes on food choice.

    PubMed

    Hoppert, Karin; Mai, Robert; Zahn, Susann; Hoffmann, Stefan; Rohm, Harald

    2012-12-01

    Sensory properties and packaging information are factors which considerably contribute to food choice. We present a new methodology in which sensory preference testing was integrated in adaptive conjoint analysis. By simultaneous variation of intrinsic and extrinsic attributes on identical levels, this procedure allows assessing the importance of attribute/level combinations on product selection. In a set-up with nine pair-wise comparisons and four subsequent calibration assessments, 101 young consumers evaluated vanilla yoghurt which was varied in fat content (four levels), sugar content (two levels) and flavour intensity (two levels); the same attribute/level combinations were also presented as extrinsic information. The results indicate that the evaluation of a particular attribute may largely diverge in intrinsic and in extrinsic processing. We noticed from our utility values that, for example, the acceptance of yoghurt increases with an increasing level of the actual fat content, whereas acceptance diminishes when a high fat content is labelled on the product. This article further implicates that neglecting these diverging relationships may lead to an over- or underestimation of the importance of an attribute for food choice.

  3. Ranking experts' preferences regarding measures and methods of assessment of welfare in dairy herds using Adaptive Conjoint Analysis.

    PubMed

    Lievaart, J J; Noordhuizen, J P T M

    2011-07-01

    Welfare in dairy herds can be addressed using different concepts. The difficulty is to extract which measures are the most important to practically address welfare at the herd level and the methods to assess traits considered most important. Therefore, the preferences of 24 acknowledged European welfare experts were ranked regarding 70 measures suitable to assess dairy cattle welfare at herd level using the Adaptive Conjoint Analysis (ACA; Sawtooth Software, Inc., Sequim, WA) technique. The experts were selected on the basis of 3 criteria: at least 5 yr experience in animal welfare research; recent scientific publications in the field of animal welfare; and, at the most, 3 animal species including dairy cattle as their field of expertise. The 70 traits were ranked by using the median ACA questionnaire utility scores and the range between the answers of the 24 experts. A high utility score with a low range between the answers of the experts was considered as suitable to assess welfare at farm level. Measures meeting these criteria were prevalence of lameness cases (107.3±11.7), competition for feed and water (96.4±13.9), and number of freestalls per 10 cows (84.8±13.3). Based on the utility score alone, these former measures were replaced by stereotypic behavior (111.7±17.1), prevalence of lameness cases (107.3±11.7), body condition score (108.0±18.9), and hock lesions (104.7±16.1). Subsequently, to demonstrate that the ACA technique can be used to rank either well-known or inconclusive methods of assessment, the methods for the traits lameness cases and the hygiene of the calving pen were ranked using another 2 ACA questionnaires. The results are based on the opinions of selected, internationally acknowledged dairy cattle welfare experts within the European Union. In the future, other parties like dairy farmers and farmers' organization should be included to achieve consensus about the most suitable traits applicable in practice. The currently investigated

  4. Preferences for Training Options: A Conjoint Analysis

    ERIC Educational Resources Information Center

    Gan, Chui Goh; Lee, Julie Anne; Soutar, Geoffrey N.

    2009-01-01

    Singapore is a growing educational hub for the Asia Pacific region. However, no prior research has examined how Singaporean managers trade off attributes of training programs when making executive training decisions. The current study used conjoint analysis to identify the most important attributes of training programs as word of mouth, trainers'…

  5. Strategic marketing applications of conjoint analysis: an HMO perspective.

    PubMed

    Rosko, M D; DeVita, M; McKenna, W F; Walker, L R

    1985-01-01

    The purpose of this article is to demonstrate how data from a conjoint analysis study can be used to help determine the most appropriate marketing mix for an operational HMO which is entering a new market--the geriatric population. Included are two features which are absent in previous articles on health care applications of conjoint analysis: external validation of results, and a demonstration of how conjoint analysis can be used to simulate market responses to changes in the provider's marketing mix.

  6. Choice-Based Conjoint Analysis: Classification vs. Discrete Choice Models

    NASA Astrophysics Data System (ADS)

    Giesen, Joachim; Mueller, Klaus; Taneva, Bilyana; Zolliker, Peter

    Conjoint analysis is a family of techniques that originated in psychology and later became popular in market research. The main objective of conjoint analysis is to measure an individual's or a population's preferences on a class of options that can be described by parameters and their levels. We consider preference data obtained in choice-based conjoint analysis studies, where one observes test persons' choices on small subsets of the options. There are many ways to analyze choice-based conjoint analysis data. Here we discuss the intuition behind a classification based approach, and compare this approach to one based on statistical assumptions (discrete choice models) and to a regression approach. Our comparison on real and synthetic data indicates that the classification approach outperforms the discrete choice models.

  7. Field of Study Choice: Using Conjoint Analysis and Clustering

    ERIC Educational Resources Information Center

    Shtudiner, Ze'ev; Zwilling, Moti; Kantor, Jeffrey

    2017-01-01

    Purpose: The purpose of this paper is to measure student's preferences regarding various attributes that affect their decision process while choosing a higher education area of study. Design/ Methodology/Approach: The paper exhibits two different models which shed light on the perceived value of each examined area of study: conjoint analysis and…

  8. A Conjoint Analysis of Voice Over IP Attributes.

    ERIC Educational Resources Information Center

    Zubey, Michael L.; Wagner, William; Otto, James R.

    2002-01-01

    Managers need to understand the tradeoffs associated with voice over Internet protocol (VoIP) networks as compared to the Public Switched Telephone Network (PSTN). This article measures the preference structures between IP telephony and PSTN services using conjoint analysis. The purpose is to suggest VoIP technology attributes that best meet…

  9. Evaluating alcoholics anonymous sponsor attributes using conjoint analysis.

    PubMed

    Stevens, Edward B; Jason, Leonard A

    2015-12-01

    Alcoholics Anonymous (AA) considers sponsorship an important element of the AA program, especially in early recovery. 225 adult individuals who had experience as either a sponsor, sponsee, or both, participated in a hypothetical sponsor ranking exercise where five attributes were varied across three levels. Conjoint analysis was used to compute part-worth utility of the attributes and their levels for experience, knowledge, availability, confidentiality, and goal-setting. Differences in utilities by attribute were found where confidentiality had the greatest overall possible impact on utility and sponsor knowledge had the least. These findings suggest qualitative differences in sponsors may impact their effectiveness. Future research on AA should continue to investigate sponsor influence on an individual's overall recovery trajectory.

  10. A Conjoint Analysis Framework for Evaluating User Preferences in Machine Translation.

    PubMed

    Kirchhoff, Katrin; Capurro, Daniel; Turner, Anne M

    2014-03-01

    Despite much research on machine translation (MT) evaluation, there is surprisingly little work that directly measures users' intuitive or emotional preferences regarding different types of MT errors. However, the elicitation and modeling of user preferences is an important prerequisite for research on user adaptation and customization of MT engines. In this paper we explore the use of conjoint analysis as a formal quantitative framework to assess users' relative preferences for different types of translation errors. We apply our approach to the analysis of MT output from translating public health documents from English into Spanish. Our results indicate that word order errors are clearly the most dispreferred error type, followed by word sense, morphological, and function word errors. The conjoint analysis-based model is able to predict user preferences more accurately than a baseline model that chooses the translation with the fewest errors overall. Additionally we analyze the effect of using a crowd-sourced respondent population versus a sample of domain experts and observe that main preference effects are remarkably stable across the two samples.

  11. A Conjoint Analysis Framework for Evaluating User Preferences in Machine Translation

    PubMed Central

    Kirchhoff, Katrin; Capurro, Daniel; Turner, Anne M.

    2013-01-01

    Despite much research on machine translation (MT) evaluation, there is surprisingly little work that directly measures users’ intuitive or emotional preferences regarding different types of MT errors. However, the elicitation and modeling of user preferences is an important prerequisite for research on user adaptation and customization of MT engines. In this paper we explore the use of conjoint analysis as a formal quantitative framework to assess users’ relative preferences for different types of translation errors. We apply our approach to the analysis of MT output from translating public health documents from English into Spanish. Our results indicate that word order errors are clearly the most dispreferred error type, followed by word sense, morphological, and function word errors. The conjoint analysis-based model is able to predict user preferences more accurately than a baseline model that chooses the translation with the fewest errors overall. Additionally we analyze the effect of using a crowd-sourced respondent population versus a sample of domain experts and observe that main preference effects are remarkably stable across the two samples. PMID:24683295

  12. Determinants of intravaginal practices among HIV-infected women in Zambia using conjoint analysis.

    PubMed

    Alcaide, Maria L; Cook, Ryan; Chisembele, Maureen; Malupande, Emeria; Jones, Deborah L

    2016-05-01

    Intravaginal practices (IVPs) are associated with an increased risk of bacterial vaginosis and may play a role in HIV transmission. The objective of this study was to identify the importance of factors underlying the decision to engage in IVP using conjoint analysis; a novel statistical technique used to quantify health-related decisions. This study was a cross-sectional study. HIV-infected women in Zambia completed audio computer-administered self-interview questionnaires assessing demographic, risk factors and IVPs. Reasons for engaging in IVPs were explored using conjoint questionnaires. Conjoint analysis was used to identify the relative importance of factors for engaging in IVPs. Results of the conjoint analysis demonstrated that hygiene was the most important reason for engaging in IVPs (mean importance score = 61, SD = 24.3) followed by partner's preference (mean importance score = 20, SD = 14.4) and health (mean importance score = 17, SD = 13.5). When making the decision to engage in IVPs, women rank the importance of hygiene, partner preference and health differently, according to their personal characteristics. The use of conjoint analysis to define the characteristics of women more likely to engage in specific practices should be used to develop tailored rather than standardised IVP interventions, and such interventions should be incorporated into clinical practice and women's health programmes.

  13. The Importance of Take-Out Food Packaging Attributes: Conjoint Analysis and Quality Function Deployment Approach

    NASA Astrophysics Data System (ADS)

    Lestari Widaningrum, Dyah

    2014-03-01

    This research aims to investigate the importance of take-out food packaging attributes, using conjoint analysis and QFD approach among consumers of take-out food products in Jakarta, Indonesia. The conjoint results indicate that perception about packaging material (such as paper, plastic, and polystyrene foam) plays the most important role overall in consumer perception. The clustering results that there is strong segmentation in which take-out food packaging material consumer consider most important. Some consumers are mostly oriented toward the colour of packaging, while another segment of customers concerns on packaging shape and packaging information. Segmentation variables based on packaging response can provide very useful information to maximize image of products through the package's impact. The results of House of Quality development described that Conjoint Analysis - QFD is a useful combination of the two methodologies in product development, market segmentation, and the trade off between customers' requirements in the early stages of HOQ process

  14. Planning and Evaluation of New Academic Library Services by Means of Web-Based Conjoint Analysis

    ERIC Educational Resources Information Center

    Decker, Reinhold; Hermelbracht, Antonia

    2006-01-01

    New product development is an omnipresent challenge to modern libraries in the information age. Therefore, we present the design and selected results of a comprehensive research project aiming at the systematic and user-oriented planning of academic library services by means of conjoint analysis. The applicability of the analytical framework used…

  15. Improving food safety within the dairy chain: an application of conjoint analysis.

    PubMed

    Valeeva, N I; Meuwissen, M P M; Lansink, A G J M Oude; Huirne, R B M

    2005-04-01

    This study determined the relative importance of attributes of food safety improvement in the production chain of fluid pasteurized milk. The chain was divided into 4 blocks: "feed" (compound feed production and its transport), "farm" (dairy farm), "dairy processing" (transport and processing of raw milk, delivery of pasteurized milk), and "consumer" (retailer/catering establishment and pasteurized milk consumption). The concept of food safety improvement focused on 2 main groups of hazards: chemical (antibiotics and dioxin) and microbiological (Salmonella, Escherichia coli, Mycobacterium paratuberculosis, and Staphylococcus aureus). Adaptive conjoint analysis was used to investigate food safety experts' perceptions of the attributes' importance. Preference data from individual experts (n = 24) on 101 attributes along the chain were collected in a computer-interactive mode. Experts perceived the attributes from the "feed" and "farm" blocks as being more vital for controlling the chemical hazards; whereas the attributes from the "farm" and "dairy processing" were considered more vital for controlling the microbiological hazards. For the chemical hazards, "identification of treated cows" and "quality assurance system of compound feed manufacturers" were considered the most important attributes. For the microbiological hazards, these were "manure supply source" and "action in salmonellosis and M. paratuberculosis cases". The rather high importance of attributes relating to quality assurance and traceability systems of the chain participants indicates that participants look for food safety assurance from the preceding participants. This information has substantial decision-making implications for private businesses along the chain and for the government regarding the food safety improvement of fluid pasteurized milk.

  16. Survey of Preferences in Patients Scheduled for Carpal Tunnel Release Using Conjoint Analysis

    PubMed Central

    Kim, Wan Lim; Kim, Jin Sam; Lee, Jun Bum; Kim, Sun Hwa; Min, Dong-Uk

    2017-01-01

    Background This study aimed to investigate the preferences of patients scheduled for carpal tunnel release using conjoint analysis and also introduce an example of how to apply a conjoint analysis to the medical field. The use of conjoint analysis in this study is new to the field of orthopedic surgery. Methods A total of 97 patients scheduled for carpal tunnel release completed the survey. The following four attributes were predefined: board certification status, distance from the patient's residency, medical costs, and waiting time for surgery. Two plausible levels for each attribute were assigned. Based on these attributes and levels, 16 scenarios were generated (2 × 2 × 2 × 2). We employed 8 scenarios using a fractional factorial design (orthogonal plan). Preferences for scenarios were then evaluated by ranking: patients were asked to list the 8 scenarios in their order of preference. Outcomes consisted of two results: the average importance of each attribute and the utility score. Results The most important attribute was the physician's board certificate, followed by distance from the patient's residency to the hospital, waiting time, and costs. Utility estimate findings revealed that patients had a greater preference for a hand specialist than a general orthopedic surgeon. Conclusions Patients considered the physician's expertise as the most important factor when choosing a hospital for carpal tunnel release. This suggests that patients are increasingly seeking safety without complications as interest in medical malpractice has increased. PMID:28261434

  17. Consumer preferences for hearing aid attributes: a comparison of rating and conjoint analysis methods.

    PubMed

    Bridges, John F P; Lataille, Angela T; Buttorff, Christine; White, Sharon; Niparko, John K

    2012-03-01

    Low utilization of hearing aids has drawn increased attention to the study of consumer preferences using both simple ratings (e.g., Likert scale) and conjoint analyses, but these two approaches often produce inconsistent results. The study aims to directly compare Likert scales and conjoint analysis in identifying important attributes associated with hearing aids among those with hearing loss. Seven attributes of hearing aids were identified through qualitative research: performance in quiet settings, comfort, feedback, frequency of battery replacement, purchase price, water and sweat resistance, and performance in noisy settings. The preferences of 75 outpatients with hearing loss were measured with both a 5-point Likert scale and with 8 paired-comparison conjoint tasks (the latter being analyzed using OLS [ordinary least squares] and logistic regression). Results were compared by examining implied willingness-to-pay and Pearson's Rho. A total of 56 respondents (75%) provided complete responses. Two thirds of respondents were male, most had sensorineural hearing loss, and most were older than 50; 44% of respondents had never used a hearing aid. Both methods identified improved performance in noisy settings as the most valued attribute. Respondents were twice as likely to buy a hearing aid with better functionality in noisy environments (p < .001), and willingness to pay for this attribute ranged from US$2674 on the Likert to US$9000 in the conjoint analysis. The authors find a high level of concordance between the methods-a result that is in stark contrast with previous research. The authors conclude that their result stems from constraining the levels on the Likert scale.

  18. Evaluation of Lighting Environment Using Conjoint Analysis (Part 1)—for the Case of Office—

    NASA Astrophysics Data System (ADS)

    Muramatsu, Rikuo; Nakamura, Yoshiki

    In this study, evaluation of the lighting environment in offices, which consists of various attributes that are trade-offs, is conducted using the Conjoint Analysis, common in the field of marketing research. The attributes are illuminance, lighting distribution, glare, design, cost, usage of daylight, and recycling (229 subjects participated.) As a result, preferences of office lighting were quantitatively externalized. In other words, partworth utilities and importance levels of attributes for office lighting displayed general characteristics of all subjects. Moreover, a method of research by grouping the subjects according to the importance levels of attributes or according to their characteristics is proved to be valuable for better understanding the preferences of office lighting.

  19. Drivers of Vaginal Drug Delivery System Acceptability from Internet-Based Conjoint Analysis

    PubMed Central

    Primrose, Rachel J.; Zaveri, Toral; Bakke, Alyssa J.; Ziegler, Gregory R.; Moskowitz, Howard R.; Hayes, John E.

    2016-01-01

    Vaginal microbicides potentially empower women to protect themselves from HIV and other sexually transmitted infections (STIs), especially when culture, religion, or social status may prevent them from negotiating condom use. The open literature contains minimal information on factors that drive user acceptability of women’s health products or vaginal drug delivery systems. By understanding what women find to be most important with regard to sensory properties and product functionality, developers can iteratively formulate a more desirable product. Conjoint analysis is a technique widely used in market research to determine what combination of elements influence a consumer’s willingness to try or use a product. We applied conjoint analysis here to better understand what sexually-active woman want in a microbicide, toward our goal of formulating a product that is highly acceptable to women. Both sensory and non-sensory attributes were tested, including shape, color, wait time, partner awareness, messiness/leakage, duration of protection, and functionality. Heterosexually active women between 18 and 35 years of age in the United States (n = 302) completed an anonymous online conjoint survey using IdeaMap software. Attributes (product elements) were systematically presented in various combinations; women rated these combinations of a 9-point willingness-to-try scale. By coupling systematic combinations and regression modeling, we can estimate the unique appeal of each element. In this population, a multifunctional product (i.e., broad spectrum STI protection, coupled with conception) is far more desirable than a microbicide targeted solely for HIV protection; we also found partner awareness and leakage are potentially strong barriers to use. PMID:26999009

  20. Conjoint Recognition.

    ERIC Educational Resources Information Center

    Brainerd, C. J.; Reyna, V. F.; Mojardin, A. H.

    1999-01-01

    Reviews some limiting properties of the process-dissociation model as it applies to the study of dual-process conceptions of memory. A second-generation model (conjoint recognition) is proposed to address these limitations and supply additional capabilities. Worked applications to data are provided. (Author/GCP)

  1. Using Conjoint Analysis to Elicit GPs’ Preferences for Family Physician Contracts: A Case Study in Iran

    PubMed Central

    Ranjbar Ezatabadi, Mohammad; Rashidian, Arash; Shariati, Mohammad; Rahimi Foroushani, Abbas; Akbari Sari, Ali

    2016-01-01

    Background Family physician plans in Iran face several challenges, one of which is developing attractive and efficient contracts that motivate physicians to participate in the plan. Objectives This study aimed to elicit GPs’ preferences for family physician contracts. Patients and Methods In a cross-sectional study using the conjoint analysis technique, 580 GPs selected from the family physician database in Iran in 2014. Through qualitative and quantitative methods, 18 contract scenarios were developed via orthogonal design i.e., the impact of each attribute is measured independently from changes in other attributes and a questionnaire was developed. Data were collected through this questionnaire and analyzed using the ordered logistic regression (OLR) model. Results The results show that “quotas for admission to specialized courses” is the strongest preference of GPs (β = 1.123). In order of importance, the other preferences are having the right to provide services outside of the specified package (β = 0.962), increased number of covered population (β = 0.814), capitation payment + 15% bonus (β = 0.644), increased catchment area to 5 km (β = 0.349), and increased length of contract to five years (β = 0.345). Conclusions The conjoint analysis results show that GPs concerned about various factors of family physician contracts. These results can be helpful for policy-makers as they complete the process of creating family physician plans, which can help increase the motivation of GPs to participate in the plan. PMID:28191339

  2. Intensive vs. free-range organic beef. A preference study through consumer liking and conjoint analysis.

    PubMed

    García-Torres, S; López-Gajardo, A; Mesías, F J

    2016-04-01

    This paper evaluates consumer liking and preferences towards organic beef from two production systems allowed by EU regulation: i) free-range and ii) intensive (fattened in feed-lot with organic feedstuff) as compared with conventionally produced beef. Data were obtained in April-May 2014 with a sample of 150 regular beef consumers who completed two tasks: firstly a sensory test where consumers tasted and rated the meats and secondly a conjoint analysis to study beef purchasing preferences. Willingness-to-pay for the different meats was also calculated from conjoint results. Results show that consumers preferred organic-from-concentrate beef at sensory level while organic beef from animals fed on grass was preferred when process characteristics (i.e. farming system) or attributes perceived at the point of purchase (i.e. colour) were evaluated. It was also found that the price-premium for organic beef is over 40%, with organic-fed-on grass beef preferred slightly over that fed-on-concentrate.

  3. Personal privacy, public benefits, and biobanks: A conjoint analysis of policy priorities and public perceptions.

    PubMed

    Pullman, Daryl; Etchegary, Holly; Gallagher, Katherine; Hodgkinson, Kathlene; Keough, Montgomery; Morgan, David; Street, Catherine

    2011-09-26

    PURPOSE:: To assess the public's perception of biobank research and the relative importance they place on concerns for privacy and confidentiality, when compared with other key variables when considering participation in biobank research. METHODS:: Conjoint analysis of three key attributes (research focus, research beneficiary, and privacy and confidentiality) under conditions of either blanket or specific consent. RESULTS:: Although the majority of our participants described themselves as private individuals, they consistently ranked privacy and confidentiality as the least important of the variables they considered. The potential beneficiary of proposed research ranked the highest under conditions of both blanket and specific consent. When completing the conjoint task under conditions of blanket consent, participants tended to act more altruistically. CONCLUSION:: The public tend to view biobanks as public goods designed primarily for public benefit. As such they tend to act altruistically with respect to the potential benefits that might accrue from research using biobanked samples. Participants expressed little concern about informational risks (i.e., privacy and confidentiality) should they choose to participate. The manner in which policy priorities are framed could impact participant value preferences with regard to a number of governance issues in biobanking.

  4. Conjoint recognition.

    PubMed

    Brainerd, C J; Reyna, V F; Mojardin, A H

    1999-01-01

    The process-dissociation model has stimulated important advances in the study of dual-process conceptions of memory. The authors review some limiting properties of that model and consider the degree of support for its parent theory (the recollection-familiarity distinction). A 2nd-generation model (conjoint recognition) is proposed that addresses these limitations and supplies additional capabilities, such as goodness-of-fit tests, the ability to measure dual processes for false-memory responses, and statistical procedures for testing within- and between-conditions hypotheses about its parameters. The conjoint-recognition model also implements an alternative theoretical interpretation (the identity-similarity distinction of fuzzy-trace theory). Worked applications to data are provided.

  5. The Use of Multiple Regression Models to Determine if Conjoint Analysis Should Be Conducted on Aggregate Data.

    ERIC Educational Resources Information Center

    Fraas, John W.; Newman, Isadore

    1996-01-01

    In a conjoint-analysis consumer-preference study, researchers must determine whether the product factor estimates, which measure consumer preferences, should be calculated and interpreted for each respondent or collectively. Multiple regression models can determine whether to aggregate data by examining factor-respondent interaction effects. This…

  6. Choosing a University: A Conjoint Analysis of the Impact of Higher Fees on Students Applying for University in 2012

    ERIC Educational Resources Information Center

    Dunnett, Andrew; Moorhouse, Jan; Walsh, Caroline; Barry, Cornelius

    2012-01-01

    In the light of the forthcoming policy shift to full-cost fees for English undergraduates, this study examines the impact of fee changes on how students weigh up their university choices. Conjoint analysis is used to examine the importance that students attach to various attributes of a university. It also explores differences across subsections…

  7. Providing Information to Parents of Children with Mental Health Problems: A Discrete Choice Conjoint Analysis of Professional Preferences

    ERIC Educational Resources Information Center

    Cunningham, Charles E.; Deal, Ken; Rimas, Heather; Chen, Yvonne; Buchanan, Don H.; Sdao-Jarvie, Kathie

    2009-01-01

    We used discrete choice conjoint analysis to model the ways 645 children's mental health (CMH) professionals preferred to provide information to parents seeking CMH services. Participants completed 20 choice tasks presenting experimentally varied combinations of the study's 14 4-level CMH information transfer attributes. Latent class analysis…

  8. Factors influencing korean international students' preferences for mental health professionals: a conjoint analysis.

    PubMed

    Lee, Eun-Jeong; Chan, Fong; Ditchman, Nicole; Feigon, Maia

    2014-01-01

    Asian students comprise over half of all international students in the United States, yet little is known about their help-seeking behaviors and preferences for mental health professionals. The purpose of this study was to use conjoint analysis to examine characteristics of mental health professionals influencing Korean international students' preferences when choosing a mental health professional. Korean international students from three universities in the United States were recruited on a volunteer basis to participate in this study (N = 114). Results indicated that mental health professional characteristics, including ethnicity, age, professional identity, and training institution, were significant factors in students' preference formation; however, gender of the mental health professional was not found to be a significant factor in the present study. Ethnic similarity was the most powerful predictor of preference formation. Implications for promoting help-seeking and mental health service utilization among Asian international students are discussed.

  9. Participant Preferences for Pharmacologic Chronic Pain Treatment Trial Characteristics: An ACTTION Adaptive Choice-Based Conjoint Study.

    PubMed

    Smith, Shannon M; Gewandter, Jennifer S; Kitt, Rachel A; Markman, John D; Vaughan, Janet A; Cowan, Penney; Kopecky, Ernest A; Malamut, Richard; Sadosky, Alesia; Tive, Leslie; Turk, Dennis C; Dworkin, Robert H

    2016-11-01

    Barriers to clinical trial recruitment can delay study completion, potentially resulting in increased costs and an unrepresentative sample. In the current study of 150 participants with chronic pain, we used a computerized adaptive choice-based conjoint survey that included 8 characteristics that may affect enrollment in pharmacologic pain treatment trials (ie, treatment allocation, frequency of pain ratings, treatment administration method, current medications, number of study visits, availability of evening and weekend visits, invasiveness of laboratory procedures, payment). These data were analyzed using Sawtooth Software ver. 8.4.8 (Sawtooth Software, Inc, Orem, UT), which identifies the characteristics that dominate participants' decisions across multiple sets of potential trials. Three characteristics had the largest relative importance in participants' trial preferences: 1) invasiveness of required laboratory procedures (ie, 22%), with no procedures or blood tests preferred over ice-water sensory testing or skin biopsy; 2) ability to continue current pain medications (21%); and 3) payment for study participation (21%), with higher payment preferred. The fourth most important characteristic was number of study visits (13%), with participants preferring fewer in-person visits and more phone contacts. Understanding the preferences of potential participants is an important step toward enhancing enrollment in pain treatment trials.

  10. Forecasting the market for electric vehicles in California using conjoint analysis

    SciTech Connect

    Segal, R.

    1995-12-31

    Beginning in 1998 a percentage of large auto companies` sales in California must include zero-emission vehicles (ZEVs), which at this time are synonymous with electric vehicles. Data on consumer values and the level of consumer acceptance for alternative fuel vehicles are necessary to determine the practicality of the State`s policy. This paper presents the results of a forecast for alternative fuel vehicle purchases in California. This forecast uses conjoint analysis, a multi-attribute utility market forecast methodology developed within the field of marketing research. The forecast yields several types of results, including market simulations of the alternative fuel vehicle market, relative preferences among vehicle attributes, and the identification of market segments most likely to purchase each type of vehicle. The research suggests a market for electric vehicles too small to support California`s ZEV sales mandate, and a very large market for natural gas vehicles. This paper concludes with a discussion of automobile and electric utility industry interests with regard to these forecast market consequences. 47 refs., 1 fig., 6 tabs.

  11. Introducing conjoint analysis method into delayed lotteries studies: its validity and time stability are higher than in adjusting

    PubMed Central

    Białek, Michał; Markiewicz, Łukasz; Sawicki, Przemysław

    2015-01-01

    The delayed lotteries are much more common in everyday life than are pure lotteries. Usually, we need to wait to find out the outcome of the risky decision (e.g., investing in a stock market, engaging in a relationship). However, most research has studied the time discounting and probability discounting in isolation using the methodologies designed specifically to track changes in one parameter. Most commonly used method is adjusting, but its reported validity and time stability in research on discounting are suboptimal. The goal of this study was to introduce the novel method for analyzing delayed lotteries—conjoint analysis—which hypothetically is more suitable for analyzing individual preferences in this area. A set of two studies compared the conjoint analysis with adjusting. The results suggest that individual parameters of discounting strength estimated with conjoint have higher predictive value (Study 1 and 2), and they are more stable over time (Study 2) compared to adjusting. We discuss these findings, despite the exploratory character of reported studies, by suggesting that future research on delayed lotteries should be cross-validated using both methods. PMID:25674069

  12. Conjoint Analysis for Mobile Devices for Ubiquitous Learning in Higher Education: The Korean Case

    ERIC Educational Resources Information Center

    Lee, Hyeongjik

    2013-01-01

    Despite the increasing importance of mobile devices in education, the essential features of these devices for ubiquitous learning have not been empirically addressed. This study empirically investigated the necessary conditions for using mobile devices as an educational tool for ubiquitous learning in higher education by a conjoint method. The…

  13. Degrees of Concern in Components of Waterfront Parks by Conjoint Analysis

    NASA Astrophysics Data System (ADS)

    Shingu, Kiyoshi; Hiratsuka, Kiyotoshi

    The Tokyo Metropolitan Government established “Seaside park plan” (1970) and “Tokyo municipal seaside park ordinance” (1975). The Tokyo Metropolitan Government considers that the conservation of seaside, riverside and urban parks make the creation of places where residents of Tokyo can come in contact with nature. However, it seems that the planning and construction of those parks have been carried out by the administration from one-side view. The waterfront parks are public and have been used by many people. As there have been no data what components of parks are important for users of parks, eight seaside parks called waterfront parks were watched, degrees of satisfactory of eighty two residents who live in metropolitan area about components of parks were surveyed, and degrees of concern about components of the parks have been obtained by conjoint analysis. Those waterfront parks are located at Odaiba near the Tokyo bay. Here, the components of parks are as follows; 1) Hydrophile, 2)Rest space, 3) Public transport and conditions of location, 4) Recreation, 5) Scenery and outlook, 6) Maintenance, 7) Monument, and 8) Openness. The following main results have been obtained from the research.: a) Male and female think scenery and outlook, and hydrophile are important. b) Rest space is less important than other components for the twenties, but important for the thirties, forties and sixties. c) Public transport and location is not much important for teenager, but important for the others. d) The fifties make a point 1) Hydrophile, 3) Public transport and condition of location, and 5) Scenery and outlook.

  14. What patients look for when choosing a plastic surgeon: an assessment of patient preference by conjoint analysis.

    PubMed

    Waltzman, Joshua T; Scholz, Thomas; Evans, Gregory R D

    2011-06-01

    The knowledge of patient preference is crucial for plastic surgeons to determine optimal marketing strategies. Conjoint analysis is a statistical technique whereby research participants make a series of trade-offs. Analysis of these trade-offs reveals the relative importance of component attributes. This study will evaluate the relative importance of attributes that influence the selection and decision-making process when choosing a plastic surgeon. A questionnaire consisting of 18 plastic surgeon profiles was rated by 111 patients. Attributes analyzed were as follows: travel distance, number of years in practice, board certification status, method of referral, office décor, and procedure cost. A traditional full-profile conjoint analysis was performed. Subjects consisted of 10 men and 101 women (n = 111). Median age was 51 years (range, 19-72). The "mean importance" of the attributes are as follows: board certification status, 39.7%; method of referral, 23.5%; distance from home to office, 13.2%; office décor, 9.0%; number of years in practice, 7.5%; and cost of procedure, 7.2%. Internal validity checks showed a high correlation (Pearson ρ = 0.995; P < 0.001). This pilot study demonstrates that conjoint analysis is a very powerful tool for market research in the health care system. The level of importance for each attribute reliably helps plastic surgeons to understand the preferences of their patients, thus being able to improve marketing strategies for private practices and institutions. The present study indicates that the most important attributes were board certification and method of referral.

  15. Designing Products Using Quality Function Deployment and Conjoint Analysis: A Comparison in a Market for Elderly People

    NASA Astrophysics Data System (ADS)

    Abu-Assab, Samah; Baier, Daniel

    In this paper, we compare two product design approaches, quality function deployment (QFD) and conjoint analysis (CA), on the example of mobile phones for elderly people as a target group. Then, we compare between our results and the results from former similar comparisons, e.g., Pullman et al. (J Prod Innov Manage 19(5):354-364, 2002) and Katz (J Innov Manage 21:61-63, 2004). In this work, the same procedures and conditions are taken into consideration as that taken by Pullman et al. in their paper. They viewed the relation between the two methods: QFD and CA as a complementary one in which both should be simultaneously implemented since each provide feedback to the other. They concluded that CA is more efficient in reflecting the end-users’ present preferences for the product attributes, whereas QFD is definitely better in satisfying end-users’ needs from the developers’ point of view. Katz in his response from a practitioner’s point of view agreed with Pullman et al. However, he concluded that the two methods are better used sequentially and that QFD should precede conjoint analysis. We test these results in a market for elderly people.

  16. The Motivating Effect of Antecedent Stimuli on the Web Shop: A Conjoint Analysis of the Impact of Antecedent Stimuli at the Point of Online Purchase

    ERIC Educational Resources Information Center

    Fagerstrom, Asle

    2010-01-01

    This article introduces the concept of motivating operation (MO) to the field of online consumer research. A conjoint analysis was conducted to assess the motivating impact of antecedent stimuli on online purchasing. Stimuli tested were in-stock status, price, other customers' reviews, order confirmation procedures, and donation to charity. The…

  17. Preferences of processing companies for attributes of Swiss milk: a conjoint analysis in a business-to-business market.

    PubMed

    Boesch, I

    2013-04-01

    This study aimed to determine key attributes of milk that drive a processor's supply decisions and possibilities for differentiation based on these product attributes. Feedback-driven exploration was applied to derive product attributes relevant to the buying decision. Conjoint analysis with hierarchical Bayes estimation methods was used to determine the relative importance of attributes. Results show that the technical aspects of milk, as well as the price and country of origin, dominate the buying decision. Potential for differentiation was found for environmental and societal attributes as well as freedom from genetically modified products. Product and supplier criteria also provide the potential to segment the market if the price premium is held within limits.

  18. Weighting of Criteria for Disease Prioritization Using Conjoint Analysis and Based on Health Professional and Student Opinion

    PubMed Central

    Stebler, Nadine; Schuepbach-Regula, Gertraud; Braam, Peter; Falzon, Laura Cristina

    2016-01-01

    Disease prioritization exercises have been used by several organizations to inform surveillance and control measures. Though most methodologies for disease prioritization are based on expert opinion, it is becoming more common to include different stakeholders in the prioritization exercise. This study was performed to compare the weighting of disease criteria, and the consequent prioritization of zoonoses, by both health professionals and students in Switzerland using a Conjoint Analysis questionnaire. The health professionals comprised public health and food safety experts, cantonal physicians and cantonal veterinarians, while the student group comprised first-year veterinary and agronomy students. Eight criteria were selected for this prioritization based on expert elicitation and literature review. These criteria, described on a 3-tiered scale, were evaluated through a choice-based Conjoint Analysis questionnaire with 25 choice tasks. Questionnaire results were analyzed to obtain importance scores (for each criterion) and mean utility values (for each criterion level), and the latter were then used to rank 16 zoonoses. While the most important criterion for both groups was “Severity of the disease in humans”, the second ranked criteria by the health professionals and students were “Economy” and “Treatment in humans”, respectively. Regarding the criterion “Control and Prevention”, health professionals tended to prioritize a disease when the control and preventive measures were described to be 95% effective, while students prioritized a disease if there were almost no control and preventive measures available. Bovine Spongiform Encephalopathy was the top-ranked disease by both groups. Health professionals and students agreed on the weighting of certain criteria such as “Severity” and “Treatment of disease in humans”, but disagreed on others such as “Economy” or “Control and Prevention”. Nonetheless, the overall disease ranking

  19. Hawaiian Residents' Preferences for Miconia Control Program Attributes Using Conjoint Choice Experiment and Latent Class Analysis

    NASA Astrophysics Data System (ADS)

    Chan-Halbrendt, Catherine; Lin, Tun; Yang, Fang; Sisior, Gwendalyn

    2010-02-01

    Invasive species control or eradication is an important issue. On the islands of Hawaii, this problem is exceedingly evident when it comes to Miconia calvescens ( Miconia) . Adequate funding is needed to control or eradicate this invasive plant, but with the limited amount of funding available for the fight against Miconia, it is important to make sure that the fund is being spent in a way that addresses the needs or preferences of the Hawaiian residents. Using the conjoint choice experiment method, we designed a survey that would measure the Hawaiian residents’ willingness to support Miconia control program attributes. The attributes focused on were cost, biodiversity loss, extent of spread and soil erosion. Latent class approach was used to assess the surveyed population to see the different preferences by individual classes. The results show three different classes or groups of individuals with varying preferences for a control program of which cost and erosion were the top preferred attributes among the classes. These groups were defined by their socio-demographics of income, the length of residency and exposure to farming/gardening activities. Even with a preference for lower cost, a group showed willingness to pay more (2.40) for a program that reduces erosion from high to low. Finally, the biodiversity attribute had very low consideration from a majority of the respondents showing the need for educating the public regarding its importance in preserving the unique environment in Hawaii.

  20. Hawaiian residents' preferences for Miconia control program attributes using conjoint choice experiment and latent class analysis.

    PubMed

    Chan-Halbrendt, Catherine; Lin, Tun; Yang, Fang; Sisior, Gwendalyn

    2010-02-01

    Invasive species control or eradication is an important issue. On the islands of Hawaii, this problem is exceedingly evident when it comes to Miconia calvescens (Miconia). Adequate funding is needed to control or eradicate this invasive plant, but with the limited amount of funding available for the fight against Miconia, it is important to make sure that the fund is being spent in a way that addresses the needs or preferences of the Hawaiian residents. Using the conjoint choice experiment method, we designed a survey that would measure the Hawaiian residents' willingness to support Miconia control program attributes. The attributes focused on were cost, biodiversity loss, extent of spread and soil erosion. Latent class approach was used to assess the surveyed population to see the different preferences by individual classes. The results show three different classes or groups of individuals with varying preferences for a control program of which cost and erosion were the top preferred attributes among the classes. These groups were defined by their socio-demographics of income, the length of residency and exposure to farming/gardening activities. Even with a preference for lower cost, a group showed willingness to pay more ($2.40) for a program that reduces erosion from high to low. Finally, the biodiversity attribute had very low consideration from a majority of the respondents showing the need for educating the public regarding its importance in preserving the unique environment in Hawaii.

  1. Use of conjoint analysis to assess HIV vaccine acceptability: feasibility of an innovation in the assessment of consumer health-care preferences.

    PubMed

    Lee, S J; Newman, P A; Comulada, W S; Cunningham, W E; Duan, N

    2012-04-01

    Engaging consumers in prospectively shaping strategies for dissemination of health-care innovations may help to ensure acceptability. We examined the feasibility of using conjoint analysis to assess future HIV vaccine acceptability among three diverse communities: a multiethnic sample in Los Angeles, CA, USA (n = 143); a Thai resident sample in Los Angeles (three groups; n = 27) and an Aboriginal peoples sample in Toronto (n = 13). Efficacy had the greatest impact on acceptability for all three groups, followed by cross-clade protection, side-effects and duration of protection in the Los Angeles sample; side-effects and duration of protection in the Thai-Los Angeles sample; and number of doses and duration of protection in the Aboriginal peoples-Toronto sample. Conjoint analysis provided insights into universal and population-specific preferences among diverse end users of future HIV vaccines, with implications for evidence-informed targeting of dissemination efforts to optimize vaccine uptake.

  2. Use of conjoint analysis to assess HIV vaccine acceptability: feasibility of an innovation in the assessment of consumer health-care preferences

    PubMed Central

    Lee, S J; Newman, P A; Comulada, W S; Cunningham, W E; Duan, N

    2012-01-01

    Summary Engaging consumers in prospectively shaping strategies for dissemination of health-care innovations may help to ensure acceptability. We examined the feasibility of using conjoint analysis to assess future HIV vaccine acceptability among three diverse communities: a multiethnic sample in Los Angeles, CA, USA (n = 143); a Thai resident sample in Los Angeles (three groups; n = 27) and an Aboriginal peoples sample in Toronto (n = 13). Efficacy had the greatest impact on acceptability for all three groups, followed by cross-clade protection, side-effects and duration of protection in the Los Angeles sample; side-effects and duration of protection in the Thai-Los Angeles sample; and number of doses and duration of protection in the Aboriginal peoples-Toronto sample. Conjoint analysis provided insights into universal and population-specific preferences among diverse end users of future HIV vaccines, with implications for evidence-informed targeting of dissemination efforts to optimize vaccine uptake. PMID:22581945

  3. A conjoint analysis of landholder preferences for reward-based land-management contracts in Kapingazi watershed, Eastern Mount Kenya.

    PubMed

    Balana, Bedru Babulo; Yatich, Thomas; Mäkelä, Miika

    2011-10-01

    Unsustainable land-use decisions and agricultural practices have become the key drivers of deteriorating watershed services in developing countries. However, landholders may have little or no incentives to take these impacts into account in their decision-making process. In recent years, reward-based provision of environmental services has emerged as an important market-based incentive for motivating landholders to adopt environmentally friendly land-use changes and agricultural practices. In this regard, for instance, the Pro-Poor Rewards for Environmental Services in Africa (PRESA) project has emerged as a large network to support and facilitate reward mechanisms in Africa. However, in many African rural settings, little is known about landholder attitudes and preferences related to the alternative land-management schemes. Using locally identified sets of six key land-management attributes, this paper applies conjoint methods to evaluate landholder preferences towards alternative land-management schemes aimed at enhancing the provision of watershed services in the River Kapingazi catchment in central Kenya. Data were collected from primary sources through focus groups and a questionnaire based conjoint survey. Three conjoint models were used; a traditional conjoint ratings model, a binary logit model, and an ordered logit model. Results from the focus groups indicated that shortage of water for both domestic use and irrigation was perceived as the most acute environmental problem in the area. Deforestation, poor river bank management and agricultural practices were identified as the major causes of the problem. Results from conjoint models show that the three principal attributes influencing landholder's ratings and probability of adopting the proposed land management options were 'size of land area to be committed', 'length of contract period', and 'granting or prohibiting rights to harvest environmental products from the committed land'. Thus, these attributes

  4. Constructing experimental designs for discrete-choice experiments: report of the ISPOR Conjoint Analysis Experimental Design Good Research Practices Task Force.

    PubMed

    Reed Johnson, F; Lancsar, Emily; Marshall, Deborah; Kilambi, Vikram; Mühlbacher, Axel; Regier, Dean A; Bresnahan, Brian W; Kanninen, Barbara; Bridges, John F P

    2013-01-01

    Stated-preference methods are a class of evaluation techniques for studying the preferences of patients and other stakeholders. While these methods span a variety of techniques, conjoint-analysis methods-and particularly discrete-choice experiments (DCEs)-have become the most frequently applied approach in health care in recent years. Experimental design is an important stage in the development of such methods, but establishing a consensus on standards is hampered by lack of understanding of available techniques and software. This report builds on the previous ISPOR Conjoint Analysis Task Force Report: Conjoint Analysis Applications in Health-A Checklist: A Report of the ISPOR Good Research Practices for Conjoint Analysis Task Force. This report aims to assist researchers specifically in evaluating alternative approaches to experimental design, a difficult and important element of successful DCEs. While this report does not endorse any specific approach, it does provide a guide for choosing an approach that is appropriate for a particular study. In particular, it provides an overview of the role of experimental designs for the successful implementation of the DCE approach in health care studies, and it provides researchers with an introduction to constructing experimental designs on the basis of study objectives and the statistical model researchers have selected for the study. The report outlines the theoretical requirements for designs that identify choice-model preference parameters and summarizes and compares a number of available approaches for constructing experimental designs. The task-force leadership group met via bimonthly teleconferences and in person at ISPOR meetings in the United States and Europe. An international group of experimental-design experts was consulted during this process to discuss existing approaches for experimental design and to review the task force's draft reports. In addition, ISPOR members contributed to developing a consensus

  5. Concurrent vs. Conjoint Marital Therapy.

    ERIC Educational Resources Information Center

    Hefner, Charles W.; Prochaska, James O.

    1984-01-01

    Evaluated couples (N=27) randomly assigned to conjoint or concurrent therapy to compare treatment effectiveness with regard to intrapersonal and interpersonal problems. Results showed no differences between the two treatments on any of the outcome measures. (LLL)

  6. Conjoint Psychotherapy of Marital Pairs

    PubMed Central

    Lundell, F. W.; Mann, Alan M.

    1966-01-01

    Many traditional concepts are being challenged in contemporary psychiatric practice, including the classical “one-to-one” relationship of individual psychotherapy. Where the patient's presenting difficulties include significant inability to function or feel happy in the marital role, the technique of conjoint psychotherapy (having both partners treated simultaneously by the same doctor) may be indicated. Conjoint therapy is envisaged as a continuum, embracing a considerable range of situations where it is sound practice to see husband and wife together. The treatment plan has three stages: complaint, clarification, and compromise, each of which presents specific features and pitfalls. Emphasis is placed on dealing with individual psychopathology of each partner, both per se and in relation to the marital situation. Results to date suggest that conjoint treatment represents a promising therapeutic modality. Even in cases where individual psychopathology cannot fully be resolved, certain plateaus of satisfaction may be attained as communication improves. PMID:5904927

  7. What Does the Shipley-2 Measure for Children and Adolescents? Integrated and Conjoint Confirmatory Factor Analysis With the WISC-IV.

    PubMed

    Reynolds, Matthew R; Hajovsky, Daniel B; Pace, Jesse R; Niileksela, Christopher R

    2016-02-01

    We used integrated and conjoint confirmatory factor analysis of Shipley-2 and Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV) data to investigate constructs measured in the Shipley-2 for children and adolescents. We also estimated Shipley-2 composite reliability at the subtest level rather than the item level. The three Shipley-2 subtests for the most part measured what was described in the manual, although Block Patterns measured visual spatial ability in addition to fluid ability and Abstraction was best considered a measure of psychometric g. The g factors derived from the WISC-IV and Shipley-2 were similar but not identical. Internal reliability estimates for Shipley-2 composites that were based on correlations between the subtests were substantially lower than those based on the items. Last, based on WISC-IV derived g factors, 37% to 53% of the variance in Shipley-2 composites was explained by g. Some of the reliable variance in the Shipley-2 composites was due to something specific that the subtests had in common not explained by psychometric g.

  8. Conjoint analysis to understand preferences of patients with multiple sclerosis for disease-modifying therapy attributes in Spain: a cross-sectional observational study

    PubMed Central

    Arroyo, Rafael; Sempere, Angel P; Ruiz-Beato, Elena; Prefasi, Daniel; Carreño, Agata; Roset, Montse; Maurino, Jorge

    2017-01-01

    Objective To assess patients’ preferences for a range of disease-modifying therapy (DMT) attributes in multiple sclerosis (MS). Design A cross-sectional observational study. Setting The data reported were from 17 MS units throughout Spain. Participants Adult patients with relapsing-remitting MS. Main outcome A conjoint analysis was applied to assess preferences. A total of 221 patients completed a survey with 10 hypothetical DMT profiles developed using an orthogonal design and rating preferences from 1 (most acceptable) to 10 (least acceptable). Medication attributes included preventing relapse, preventing disease progression, side effect risk, route and frequency of administration. Results Patients placed the greatest relative importance on the side effect risk domain (32.9%), followed by route of administration (26.1%), frequency of administration (22.7%), prevention of disease progression (10.0%) and prevention of relapse (8.3%). These results were independent of the Expanded Disability Status Scale score. The importance assigned to side effect risk was highest for patients with a recent diagnosis. Patients who had previously received more than one DMT gave a higher importance to relapse rate reduction than patients receiving their first DMT. Conclusions Patient DMT preferences were mainly driven by risk minimisation, route of administration and treatment schedule. The risk–benefit spectrum of available DMT for MS is becoming increasingly complicated. Understanding which treatment characteristics are meaningful to patients may help to tailor information for them and facilitate shared decision-making in clinical practice. PMID:28274968

  9. Conjoint Retention of Maps and Related Discourse.

    ERIC Educational Resources Information Center

    Kulhavy, Raymond, W.; And Others

    1985-01-01

    Two experiments used fifth grade students to test the hypothesis that conjointly presented verbal/spatial information facilitates retrieval from either stimulus format. Results support the notion of conjoint retention which assumes that related verbal/spatial arrays are stored in a fashion which allows separate use of both formats during…

  10. Conjoint schedules of timeout deletion in pigeons.

    PubMed Central

    Hackenberg, T D

    1992-01-01

    This experiment attempted to bring behavior under joint control of two distinct contingencies, one that provided food and a second that extended the periods during which that food was available. Pigeons' responses on each of two keys were reinforced according to a single random-interval schedule of food presentation except during signaled timeout periods during which the schedule was temporarily disabled. By means of a conjoint schedule, responses on the initially less preferred key not only produced food but also canceled impending timeouts. When behavior came to predominate on this conjoint alternative, the consequences of responding on the two keys were reversed. Responding in 3 of 4 pigeons proved sensitive to the conjoint scheduled consequences, as evidenced by systematic shifts in response rates favoring the conjoint key. In 2 of these 3 pigeons, sensitivity to the conjoint contingency was evident under time-in:timeout ratios of 2:1 (time-in = 120 s, timeout = 60 s) and 1:5 (time-in = 30 s, timeout = 150 s), whereas for the other pigeon preference for the conjoint key was observed only under the latter sequence of conditions. There was only weak evidence of control by the conjoint scheduled consequences in the 4th subject, despite extended training and forced exposure to the conjoint alternative. The overall pattern of results is consistent with studies of timeout avoidance but also shares features in common with positively reinforced behavior. PMID:1402605

  11. Modeling the Bullying Prevention Program Preferences of Educators: A Discrete Choice Conjoint Experiment

    ERIC Educational Resources Information Center

    Cunningham, Charles E.; Vaillancourt, Tracy; Rimas, Heather; Deal, Ken; Cunningham, Lesley; Short, Kathy; Chen, Yvonne

    2009-01-01

    We used discrete choice conjoint analysis to model the bullying prevention program preferences of educators. Using themes from computerized decision support lab focus groups (n = 45 educators), we composed 20 three-level bullying prevention program design attributes. Each of 1,176 educators completed 25 choice tasks presenting experimentally…

  12. Using Maps to Retrieve Text: A Test of Conjoint Retention.

    ERIC Educational Resources Information Center

    Kulhavy, Raymond W.; And Others

    1992-01-01

    Two experiments with 129 college undergraduates tested the conjoint retention model by having subjects learn an intact map and text and then see the map as a retrieval cue in its original or reorganized form. Subjects remember more when cued by the original, supporting the conjoint retention theory. (SLD)

  13. Conjoint bicondylar Hoffa fracture in an adult

    PubMed Central

    Ul Haq, Rehan; Modi, Prashant; Dhammi, IK; Jain, Anil K; Mishra, Puneet

    2013-01-01

    Conjoint bicondylar Hoffa fracture is an extremely rare injury. Only one case has been reported previously in the pediatric age group. We describe this injury in a 17-year-old male who presented following a fall with direct impact on his semiflexed right knee. Plain radiographs were inadequate to define the exact pattern of injury. Computed tomographic (CT) scans demonstrated the coronal fracture involving both the femoral condyles which were joined by a bridge of intact bone. The patient was treated with open reduction and internal fixation using swashbuckler (modified anterior) approach. Union occurred within 3 months and at final followup (at 18 months) the patient had a good clinical outcome. The possible mechanism of injury is discussed. PMID:23798763

  14. Adapting safety requirements analysis to intrusion detection

    NASA Technical Reports Server (NTRS)

    Lutz, R.

    2001-01-01

    Several requirements analysis techniques widely used in safety-critical systems are being adapted to support the analysis of secure systems. Perhaps the most relevant system safety techique for Intrusion Detection Systems is hazard analysis.

  15. Identifying classes of conjoint alcohol and marijuana use in entering freshmen.

    PubMed

    Haas, Amie L; Wickham, Robert; Macia, Kathryn; Shields, Micah; Macher, Rayna; Schulte, Tilman

    2015-09-01

    The current study identified classes of conjoint marijuana and alcohol use in entering college freshmen using latent profile analysis (N = 772; 53% male, 60% White; Mage = 18). Results yielded 4 distinct groups: Class 1 (moderate drinking with recent marijuana use: 22% of sample), Class 2 (moderate drinking with no recent marijuana use: 25%), Class 3 (light drinking with no recent marijuana use: 40%) and Class 4 (heavy drinking with recent marijuana use: 14%). Separate pairwise contrasts examined cross-class differences in demographics and drinking behaviors, comparing differences in drinking when current marijuana use was controlled (Class 1 vs. 4) and differences in marijuana use when drinking was held relatively constant (Class 1 vs. 2). Among moderate drinkers, recent marijuana users were more likely to drink more than intended, drink to get drunk, and had more problems (including higher rates of blackouts, physical injury, and DUI) relative to peers who refrained from marijuana. No cross-class differences were found for alcohol expectancies or behavioral motives. Findings from these analyses show the presence of distinct groups of conjoint users with different drinking behaviors and consequence profiles, and suggest that conjoint alcohol-marijuana use may be more problematic overall than single substance involvement and highlight the need for developing campus prevention and intervention programs that address the increased risk from polysubstance involvement.

  16. Conjoint Forming - Technologies for Simultaneous Forming and Joining

    NASA Astrophysics Data System (ADS)

    Groche, P.; Wohletz, S.; Mann, A.; Krech, M.; Monnerjahn, V.

    2016-03-01

    The market demand for new products optimized for e. g. lightweight applications or smart components leads to new challenges in production engineering. Hybrid structures represent one promising approach. They aim at higher product performance by using a suitable combination of different materials. The developments of hybrid structures stimulate the research on joining of dissimilar materials. Since they allow for joining dissimilar materials without external heating technologies based on joining by plastic deformation seem to be of special attractiveness. The paper at hand discusses the conjoint forming approach. This approach combines forming and joining in one process. Two or more workpieces are joined while at least one workpiece is plastically deformed. After presenting the fundamental joining mechanisms, the conjoint forming approach is discussed comprehensively. Examples of conjoint processes demonstrate the effectiveness and reveal the underlying phenomena.

  17. Conjoint corrosion and wear in titanium alloys.

    PubMed

    Khan, M A; Williams, R L; Williams, D F

    1999-04-01

    When considering titanium alloys for orthopaedic applications it is important to examine the conjoint action of corrosion and wear. In this study we investigate the corrosion and wear behaviour of Ti-6Al-4V, Ti-6Al-7Nb and Ti-13Nb-13Zr in phosphate buffered saline (PBS), bovine albumin solutions in PBS and 10% foetal calf serum solutions in PBS. The tests were performed under four different conditions to evaluate the influence of wear on the corrosion and corrosion on the wear behaviour as follows: corrosion without wear, wear-accelerated corrosion, wear in a non-corrosive environment and wear in a corrosive environment. The corrosion behaviour was investigated using cyclic polarisation studies to measure the ability of the surface to repassivate following breakdown of the passive layer. The properties of the repassivated layer were evaluated by measuring changes in the surface hardness of the alloys. The amount of wear that had occurred was assessed from weight changes and measurement of the depth of the wear scar. It was found that in the presence of wear without corrosion the wear behaviour of Ti-13Nb-13Zr was greater than that of Ti-6Al-7Nb or Ti-6Al-4V and that in the presence of proteins the wear of all three alloys is reduced. In the presence of corrosion without wear Ti-13Nb-13Zr was more corrosion resistant than Ti-6Al-7Nb which was more corrosion resistant than Ti-6Al-4V without proteins whereas in the presence of protein the corrosion resistance of Ti-13Nb-13Zr and Ti-6Al-7Nb was reduced and that of Ti-6Al-4V increased. In the presence of corrosion and wear the corrosion resistance of Ti-13Nb-13Zr is higher than that of Ti-6Al-7Nb or Ti-6Al-4V in PBS but in the presence of proteins the corrosion resistance of Ti-13Nb-13Zr and Ti-6Al-7Nb are very similar but higher than that of Ti-6Al-4V. The wear of Ti-13Nb-13Zr is lower than that of Ti-6Al-7Nb and Ti-6Al-4V with or without the presence of proteins in a corrosive environment. Therefore the overall

  18. Group adaptation, formal darwinism and contextual analysis.

    PubMed

    Okasha, S; Paternotte, C

    2012-06-01

    We consider the question: under what circumstances can the concept of adaptation be applied to groups, rather than individuals? Gardner and Grafen (2009, J. Evol. Biol.22: 659-671) develop a novel approach to this question, building on Grafen's 'formal Darwinism' project, which defines adaptation in terms of links between evolutionary dynamics and optimization. They conclude that only clonal groups, and to a lesser extent groups in which reproductive competition is repressed, can be considered as adaptive units. We re-examine the conditions under which the selection-optimization links hold at the group level. We focus on an important distinction between two ways of understanding the links, which have different implications regarding group adaptationism. We show how the formal Darwinism approach can be reconciled with G.C. Williams' famous analysis of group adaptation, and we consider the relationships between group adaptation, the Price equation approach to multi-level selection, and the alternative approach based on contextual analysis.

  19. Measuring Phantom Recollection in the Simplified Conjoint Recognition Paradigm

    ERIC Educational Resources Information Center

    Stahl, Christoph; Klauer, Karl Christoph

    2009-01-01

    False memories are sometimes strong enough to elicit recollective experiences. This phenomenon has been termed Phantom Recollection (PR). The Conjoint Recognition (CR) paradigm has been used to empirically separate PR from other memory processes. Recently, a simplification of the CR procedure has been proposed. We herein extend the simplified CR…

  20. Conjoint Behavioral Consultation for Children with Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    Garbacz, S. Andrew; McIntyre, Laura Lee

    2016-01-01

    The present study examined the efficacy of Conjoint Behavioral Consultation (CBC) for children with Autism Spectrum Disorder (ASD) in early elementary school. In addition, the parent-teacher relationship, parent and teacher competence in problem solving, and CBC acceptability were examined. Participants included 3 children with ASD in early…

  1. The perforator-based conjoint (chimeric) medial Sural(MEDIAL GASTROCNEMIUS) free flap.

    PubMed

    Sano, Kazufumi; Hallock, Geoffrey G; Hamazaki, Masahiro; Daicyo, Yoshihiro

    2004-12-01

    The prototypical conjoint or so-called "chimeric" free flap heretofore has been composed of several large independent flaps, each supplied by a separate major branch, that ultimately arise from a common source vessel. The perforator-based type of chimeric flap is a relatively new concept, usually involving multiple muscle perforator flaps each based on a solitary musculocutaneous perforator, but still arising from the same "mother" vessel. This principle of split cutaneous perforator flaps has been now successfully adapted to the medial suralMEDIAL GASTROCNEMIUS perforator free flap on 2 separate occasions. As a chimeric flap, there was greater flexibility in insetting, and overall flap width may be larger but still narrow enough to allow primary donor site closure; and yet, by definition, only a single recipient site was needed for any microanastomoses. This is further proof that the perforator-based chimeric free flap may be an option for any muscle perforator flap donor site, so that potential donor territories for conjoint flaps have become virtually unlimited.

  2. ALISA: adaptive learning image and signal analysis

    NASA Astrophysics Data System (ADS)

    Bock, Peter

    1999-01-01

    ALISA (Adaptive Learning Image and Signal Analysis) is an adaptive statistical learning engine that may be used to detect and classify the surfaces and boundaries of objects in images. The engine has been designed, implemented, and tested at both the George Washington University and the Research Institute for Applied Knowledge Processing in Ulm, Germany over the last nine years with major funding from Robert Bosch GmbH and Lockheed-Martin Corporation. The design of ALISA was inspired by the multi-path cortical- column architecture and adaptive functions of the mammalian visual cortex.

  3. Estimating the monetary value of willingness to pay for E-book reader's attributes using partially confounded factorial conjoint choice experiment

    NASA Astrophysics Data System (ADS)

    Yong, Chin-Khian

    2013-09-01

    A partially confounded factorial conjoint choice experiments design was used to examine the monetary value of the willingness to pay for E-book Reader's attributes. Conjoint analysis is an efficient, cost-effective, and most widely used quantitative method in marketing research to understand consumer preferences and value trade-off. Value can be interpreted by customer or consumer as the received of multiple benefits from a price that was paid. The monetary value of willingness to pay for battery life, internal memory, external memory, screen size, text to Speech, touch screen, and converting handwriting to digital text of E-book reader were estimated in this study. Due to the significant interaction effect of the attributes with the price, the monetary values for the seven attributes were found to be different at different values of odds of purchasing versus not purchasing. The significant interactions effects were one of the main contribution of the partially confounded factorial conjoint choice experiment.

  4. Wavefront Analysis of Adaptive Telescope

    NASA Technical Reports Server (NTRS)

    Hadaway, James B.; Hillman, Lloyd

    1997-01-01

    The motivation for this work came from a NASA Headquarters interest in investigating design concepts for a large space telescope employing active optics technology. Current and foreseeable launch vehicles will be limited to carrying around 4-5 meter diameter objects. Thus, if a large, filled-aperture telescope (6-20 meters in diameter) is to be placed in space, it will be required to have a deployable primary mirror. Such a mirror may be an inflatable membrane or a segmented mirror consisting of many smaller pieces. In any case, it is expected that the deployed primary will not be of sufficient quality to achieve diffraction-limited performance for its aperture size. Thus, an active optics system will be needed to correct for initial as well as environmentally-produced primary figure errors. Marshall Space Flight Center has developed considerable expertise in the area of active optics with the PAMELA test-bed. The combination of this experience along with the Marshall optical shop's work in mirror fabrication made MSFC the logical choice to lead NASA's effort to develop active optics technology for large, space-based, astronomical telescopes. Furthermore, UAH's support of MSFC in the areas of optical design, fabrication, and testing of space-based optical systems placed us in a key position to play a major role in the development of this future-generation telescope. A careful study of the active optics components had to be carried out in order to determine control segment size, segment quality, and segment controllability required to achieve diffraction-limited resolution with a given primary mirror. With this in mind, UAH undertook the following effort to provide NASA/MSFC with optical design and analysis support for the large telescope study. All of the work performed under this contract has already been reported, as a team member with MSFC, to NASA Headquarters in a series of presentations given between May and December of 1995. As specified on the delivery

  5. Bounded Linear Stability Margin Analysis of Nonlinear Hybrid Adaptive Control

    NASA Technical Reports Server (NTRS)

    Nguyen, Nhan T.; Boskovic, Jovan D.

    2008-01-01

    This paper presents a bounded linear stability analysis for a hybrid adaptive control that blends both direct and indirect adaptive control. Stability and convergence of nonlinear adaptive control are analyzed using an approximate linear equivalent system. A stability margin analysis shows that a large adaptive gain can lead to a reduced phase margin. This method can enable metrics-driven adaptive control whereby the adaptive gain is adjusted to meet stability margin requirements.

  6. A tutorial introduction to adaptive fractal analysis.

    PubMed

    Riley, Michael A; Bonnette, Scott; Kuznetsov, Nikita; Wallot, Sebastian; Gao, Jianbo

    2012-01-01

    The authors present a tutorial description of adaptive fractal analysis (AFA). AFA utilizes an adaptive detrending algorithm to extract globally smooth trend signals from the data and then analyzes the scaling of the residuals to the fit as a function of the time scale at which the fit is computed. The authors present applications to synthetic mathematical signals to verify the accuracy of AFA and demonstrate the basic steps of the analysis. The authors then present results from applying AFA to time series from a cognitive psychology experiment on repeated estimation of durations of time to illustrate some of the complexities of real-world data. AFA shows promise in dealing with many types of signals, but like any fractal analysis method there are special challenges and considerations to take into account, such as determining the presence of linear scaling regions.

  7. A tutorial introduction to adaptive fractal analysis

    PubMed Central

    Riley, Michael A.; Bonnette, Scott; Kuznetsov, Nikita; Wallot, Sebastian; Gao, Jianbo

    2012-01-01

    The authors present a tutorial description of adaptive fractal analysis (AFA). AFA utilizes an adaptive detrending algorithm to extract globally smooth trend signals from the data and then analyzes the scaling of the residuals to the fit as a function of the time scale at which the fit is computed. The authors present applications to synthetic mathematical signals to verify the accuracy of AFA and demonstrate the basic steps of the analysis. The authors then present results from applying AFA to time series from a cognitive psychology experiment on repeated estimation of durations of time to illustrate some of the complexities of real-world data. AFA shows promise in dealing with many types of signals, but like any fractal analysis method there are special challenges and considerations to take into account, such as determining the presence of linear scaling regions. PMID:23060804

  8. TOWARDS PATIENT-CENTERED CARE FOR DEPRESSION: CONJOINT METHODS TO TAILOR TREATMENT BASED ON PREFERENCES

    PubMed Central

    Wittink, Marsha N.; Cary, Mark; TenHave, Thomas; Baron, Jonathan; Gallo, Joseph J.

    2010-01-01

    Background Although antidepressants and counseling have been shown to be effective in treating patients with depression, non-treatment or under-treatment for depression is common especially among the elderly and minorities. Previous work on patient preferences has focused on medication versus counseling, but less is known about the value patients place on attributes of medication and counseling. Objective Conjoint analysis has been recognized as a valuable means of assessing patient treatment preferences. We examine how conjoint analysis be used to determine the relative importance of various attributes of depression treatment at the group level as well as to determine the range of individual-level relative preference weights for specific depression treatment attributes. In addition we use conjoint analysis to predict what modifications in treatment characteristics are associated with a change in the stated preferred alternative. Study design 86 adults who participated in an internet-based panel responded to an on-line discrete choice task about depression treatment. Participants chose between medication and counseling based on choice sets presented first for a “mild depression” scenario and then for a “severe depression” scenario. Participants were given 18 choice sets which varied for medication based on type of side effect (nausea, dizziness, and sexual dysfunction) and severity of side effect (mild, moderate, and severe); and for counseling based on frequency of counseling sessions (once per week or every other week) and location of the sessions (mental health professional’s office, primary care doctor’s office or office of a spiritual counselor). Results Treatment type (counseling vs. medication) appeared to be more important in driving treatment choice than any specific attribute that was studied. Specifically counseling was preferred by most of the respondents. After treatment type, location of treatment and frequency of treatment were important

  9. Conjoint Monitoring of Symptoms of Premenstrual Syndrome: Impact on Marital Satisfaction.

    ERIC Educational Resources Information Center

    Frank, Beth; And Others

    1993-01-01

    Randomly assigned 30 women with premenstrual syndrome to control group which involved monitoring menstrual cycle symptoms or to conjoint monitoring group which involved both wife and husband in charting cyclic symptoms. Following treatment, Marital Satisfaction Inventory (MSI) scores predicted group membership; conjoint group resulted in…

  10. A Glossy Simultaneous Contrast: Conjoint Measurements of Gloss and Lightness

    PubMed Central

    Mamassian, Pascal

    2017-01-01

    Interactions between the albedo and the gloss on a surface are commonplace. Darker surfaces are perceived glossier (contrast gloss) than lighter surfaces and darker backgrounds can enhance perceived lightness of surfaces. We used maximum likelihood conjoint measurements to simultaneously quantify the strength of those effects. We quantified the extent to which albedo can influence perceived gloss and physical gloss can influence perceived lightness. We modeled the contribution of lightness and gloss and found that increasing lightness reduced perceived gloss by about 32% whereas gloss had a much weaker influence on perceived lightness of about 12%. Moreover, we also investigated how different backgrounds contribute to the perception of lightness and gloss of a surface placed in front. We found that a glossy background reduces slightly perceived lightness of the center and simultaneously enhances its perceived gloss. Lighter backgrounds reduce perceived gloss and perceived lightness. Conjoint measurements lead us to a better understanding of the contextual effects in gloss and lightness perception. Not only do we confirm the importance of contrast in gloss perception and the reduction of the simultaneous contrast with glossy backgrounds, but we also quantify precisely the strength of those effects. PMID:28203352

  11. Adaptive computational methods for aerothermal heating analysis

    NASA Technical Reports Server (NTRS)

    Price, John M.; Oden, J. Tinsley

    1988-01-01

    The development of adaptive gridding techniques for finite-element analysis of fluid dynamics equations is described. The developmental work was done with the Euler equations with concentration on shock and inviscid flow field capturing. Ultimately this methodology is to be applied to a viscous analysis for the purpose of predicting accurate aerothermal loads on complex shapes subjected to high speed flow environments. The development of local error estimate strategies as a basis for refinement strategies is discussed, as well as the refinement strategies themselves. The application of the strategies to triangular elements and a finite-element flux-corrected-transport numerical scheme are presented. The implementation of these strategies in the GIM/PAGE code for 2-D and 3-D applications is documented and demonstrated.

  12. The adaptive safety analysis and monitoring system

    NASA Astrophysics Data System (ADS)

    Tu, Haiying; Allanach, Jeffrey; Singh, Satnam; Pattipati, Krishna R.; Willett, Peter

    2004-09-01

    The Adaptive Safety Analysis and Monitoring (ASAM) system is a hybrid model-based software tool for assisting intelligence analysts to identify terrorist threats, to predict possible evolution of the terrorist activities, and to suggest strategies for countering terrorism. The ASAM system provides a distributed processing structure for gathering, sharing, understanding, and using information to assess and predict terrorist network states. In combination with counter-terrorist network models, it can also suggest feasible actions to inhibit potential terrorist threats. In this paper, we will introduce the architecture of the ASAM system, and discuss the hybrid modeling approach embedded in it, viz., Hidden Markov Models (HMMs) to detect and provide soft evidence on the states of terrorist network nodes based on partial and imperfect observations, and Bayesian networks (BNs) to integrate soft evidence from multiple HMMs. The functionality of the ASAM system is illustrated by way of application to the Indian Airlines Hijacking, as modeled from open sources.

  13. An averaging analysis of discrete-time indirect adaptive control

    NASA Technical Reports Server (NTRS)

    Phillips, Stephen M.; Kosut, Robert L.; Franklin, Gene F.

    1988-01-01

    An averaging analysis of indirect, discrete-time, adaptive control systems is presented. The analysis results in a signal-dependent stability condition and accounts for unmodeled plant dynamics as well as exogenous disturbances. This analysis is applied to two discrete-time adaptive algorithms: an unnormalized gradient algorithm and a recursive least-squares (RLS) algorithm with resetting. Since linearization and averaging are used for the gradient analysis, a local stability result valid for small adaptation gains is found. For RLS with resetting, the assumption is that there is a long time between resets. The results for the two algorithms are virtually identical, emphasizing their similarities in adaptive control.

  14. Speckle-adaptive VISAR fringe analysis technique

    NASA Astrophysics Data System (ADS)

    Erskine, David

    2017-01-01

    A line-VISAR (velocity interferometer) is an important diagnostic in shock physics, simultaneously measuring many fringe histories of adjacent portions of a target splayed along a line on a target, with fringes recorded vs time and space by a streak camera. Due to laser speckle the reflected intensity may be uneven spatially, and due to irregularities in the streak camera electron optics the phase along the slit may be slightly nonlinear. Conventional fringe analysis algorithms which do not properly model these variations can suffer from inferred velocity errors. A speckle-adaptive algorithm has been developed which senses the interferometer and illumination parameters for each individual row (spatial position Y) of the 2d interferogram, so that the interferogram can be compensated for Y-dependent nonfringing intensity, fringe visibility, and nonlinear phase distribution. In numerical simulations and on actual data we have found this individual row-by-row modeling improves the accuracy of the result, compared to a conventional column-by-column analysis approach.

  15. Adaptive path planning: Algorithm and analysis

    SciTech Connect

    Chen, Pang C.

    1993-03-01

    Path planning has to be fast to support real-time robot programming. Unfortunately, current planning techniques are still too slow to be effective, as they often require several minutes, if not hours of computation. To alleviate this problem, we present a learning algorithm that uses past experience to enhance future performance. The algorithm relies on an existing path planner to provide solutions to difficult tasks. From these solutions, an evolving sparse network of useful subgoals is learned to support faster planning. The algorithm is suitable for both stationary and incrementally-changing environments. To analyze our algorithm, we use a previously developed stochastic model that quantifies experience utility. Using this model, we characterize the situations in which the adaptive planner is useful, and provide quantitative bounds to predict its behavior. The results are demonstrated with problems in manipulator planning. Our algorithm and analysis are sufficiently general that they may also be applied to task planning or other planning domains in which experience is useful.

  16. Conjoint representation of texture ensemble and location in the parahippocampal place area.

    PubMed

    Park, Jeongho; Park, Soojin

    2017-04-01

    Texture provides crucial information about the category or identity of a scene. Nonetheless, not much is known about how the texture information in a scene is represented in the brain. Previous studies have shown that the parahippocampal place area (PPA), a scene-selective part of visual cortex, responds to simple patches of texture ensemble. However, in natural scenes textures exist in spatial context within a scene. Here we tested two hypotheses that make different predictions on how textures within a scene context are represented in the PPA. The Texture-Only hypothesis suggests that the PPA represents texture ensemble (i.e., the kind of texture) as is, irrespective of its location in the scene. On the other hand, the Texture and Location hypothesis suggests that the PPA represents texture and its location within a scene (e.g., ceiling or wall) conjointly. We tested these two hypotheses across two experiments, using different but complementary methods. In experiment 1, by using multivoxel pattern analysis (MVPA) and representational similarity analysis, we found that the representational similarity of the PPA activation patterns was significantly explained by the Texture-Only hypothesis but not by the Texture and Location hypothesis. In experiment 2, using a repetition suppression paradigm, we found no repetition suppression for scenes that had the same texture ensemble but differed in location (supporting the Texture and Location hypothesis). On the basis of these results, we propose a framework that reconciles contrasting results from MVPA and repetition suppression and draw conclusions about how texture is represented in the PPA.NEW & NOTEWORTHY This study investigates how the parahippocampal place area (PPA) represents texture information within a scene context. We claim that texture is represented in the PPA at multiple levels: the texture ensemble information at the across-voxel level and the conjoint information of texture and its location at the within

  17. Conjoint Analysis of Values of Reserve Component Attributes

    DTIC Science & Technology

    1977-11-01

    28. 2% of the respsmdisst. uzzsfte euq ~oleyMe provides - supergusmmal incessoft wth ik to amet regular household onpeanes. Others will ase the income...te Li k( 1. 0. Fstintie~ td tcces.-o-’% to lithe prngrnni as crrv’iitly described were tab~ulated htj vikch of 1 2 age -tace g rnup’l atid 1w -ce

  18. Combining Economic and Conjoint Analysis to Determine Optimal Academic Services

    ERIC Educational Resources Information Center

    Howard, Mona Whitley; Sobol, Marion G.

    2004-01-01

    In today's era of global competition, organizations must manage their functions and activities in a manner such that they are responsive to customers' needs and can provide excellence in service to the customer while also being efficient and cost conscious. These issues are extremely common in corporate organizations, but such concerns are equally…

  19. Proteomic analysis of endothelial cold-adaptation

    PubMed Central

    2011-01-01

    Background Understanding how human cells in tissue culture adapt to hypothermia may aid in developing new clinical procedures for improved ischemic and hypothermic protection. Human coronary artery endothelial cells grown to confluence at 37°C and then transferred to 25°C become resistant over time to oxidative stress and injury induced by 0°C storage and rewarming. This protection correlates with an increase in intracellular glutathione at 25°C. To help understand the molecular basis of endothelial cold-adaptation, isolated proteins from cold-adapted (25°C/72 h) and pre-adapted cells were analyzed by quantitative proteomic methods and differentially expressed proteins were categorized using the DAVID Bioinformatics Resource. Results Cells adapted to 25°C expressed changes in the abundance of 219 unique proteins representing a broad range of categories such as translation, glycolysis, biosynthetic (anabolic) processes, NAD, cytoskeletal organization, RNA processing, oxidoreductase activity, response-to-stress and cell redox homeostasis. The number of proteins that decreased significantly with cold-adaptation exceeded the number that increased by 2:1. Almost half of the decreases were associated with protein metabolic processes and a third were related to anabolic processes including protein, DNA and fatty acid synthesis. Changes consistent with the suppression of cytoskeletal dynamics provided further evidence that cold-adapted cells are in an energy conserving state. Among the specific changes were increases in the abundance and activity of redox proteins glutathione S-transferase, thioredoxin and thioredoxin reductase, which correlated with a decrease in oxidative stress, an increase in protein glutathionylation, and a recovery of reduced protein thiols during rewarming from 0°C. Increases in S-adenosylhomocysteine hydrolase and nicotinamide phosphoribosyltransferase implicate a central role for the methionine-cysteine transulfuration pathway in increasing

  20. Modeling the bullying prevention program preferences of educators: a discrete choice conjoint experiment.

    PubMed

    Cunningham, Charles E; Vaillancourt, Tracy; Rimas, Heather; Deal, Ken; Cunningham, Lesley; Short, Kathy; Chen, Yvonne

    2009-10-01

    We used discrete choice conjoint analysis to model the bullying prevention program preferences of educators. Using themes from computerized decision support lab focus groups (n = 45 educators), we composed 20 three-level bullying prevention program design attributes. Each of 1,176 educators completed 25 choice tasks presenting experimentally varied combinations of the study's attribute levels. Latent class analysis yielded three segments with different preferences. Decision Sensitive educators (31%) preferred that individual schools select bullying prevention programs. In contrast, Support Sensitive educators (51%) preferred that local school boards chose bullying prevention programs. This segment preferred more logistical and social support at every stage of the adoption, training, implementation, and long term maintenance processes. Cost Sensitive educators (16%) showed a stronger preference for programs minimizing costs, training, and implementation time demands. They felt prevention programs were less effective and that the time and space in the curriculum for bullying prevention was less adequate. They were less likely to believe that bullying prevention was their responsibility and more likely to agree that prevention was the responsibility of parents. All segments preferred programs supported by the anecdotal reports of colleagues from other schools rather than those based on scientific evidence. To ensure that the bullying prevention options available reflect the complex combination of attributes influencing real world adoption decisions, program developers need to accommodate the differing views of the Decision, Support, and Cost Sensitive segments while maximizing the support of parents and students.

  1. Modeling Mental Health Information Preferences During the Early Adult Years: A Discrete Choice Conjoint Experiment

    PubMed Central

    Cunningham, Charles E.; Walker, John R.; Eastwood, John D.; Westra, Henny; Rimas, Heather; Chen, Yvonne; Marcus, Madalyn; Swinson, Richard P.; Bracken, Keyna

    2013-01-01

    Although most young adults with mood and anxiety disorders do not seek treatment, those who are better informed about mental health problems are more likely to use services. The authors used conjoint analysis to model strategies for providing information about anxiety and depression to young adults. Participants (N = 1,035) completed 17 choice tasks presenting combinations of 15 four-level attributes of a mental health information strategy. Latent class analysis yielded 3 segments. The virtual segment (28.7%) preferred working independently on the Internet to obtain information recommended by young adults who had experienced anxiety or depression. Self-assessment options and links to service providers were more important to this segment. Conventional participants (30.1%) preferred books or pamphlets recommended by a doctor, endorsed by mental health professionals, and used with a doctor's support. They would devote more time to information acquisition but were less likely to use Internet social networking options. Brief sources of information were more important to the low interest segment (41.2%). All segments preferred information about alternative ways to reduce anxiety or depression rather than psychological approaches or medication. Maximizing the use of information requires active and passive approaches delivered through old-media (e.g. books) and new-media (e.g., Internet) channels. PMID:24266450

  2. A Meta-Analysis of Urban Climate Change Adaptation ...

    EPA Pesticide Factsheets

    The concentration of people, infrastructure, and ecosystem services in urban areas make them prime sites for climate change adaptation. While advances have been made in developing frameworks for adaptation planning and identifying both real and potential barriers to action, empirical work evaluating urban adaptation planning processes has been relatively piecemeal. Existing assessments of current experience with urban adaptation provide necessarily broad generalizations based on the available peer-reviewed literature. This paper uses a meta-analysis of U.S. cities’ current experience with urban adaptation planning drawing from 54 sources that include peer-reviewed literature, government reports, white papers, and reports published by non-governmental organizations. The analysis specifically evaluates the institutional support structures being developed for urban climate change adaptation. The results demonstrate that adaptation planning is driven by a desire to reduce vulnerability and often catalyzes new collaborations and coordination mechanisms in urban governance. As a result, building capacity for urban climate change adaptation planning requires a focus not only on city governments themselves but also on the complex horizontal and vertical networks that have arisen around such efforts. Existing adaptation planning often lacks attention to equity issues, social vulnerability, and the influence of non-climatic factors on vulnerability. Engaging city govern

  3. Conjoint IPT for postpartum depression: literature review and overview of a treatment manual.

    PubMed

    Carter, Wendy; Grigoriadis, Sophie; Ravitz, Paula; Ross, Lori E

    2010-01-01

    Distress about the quality of a woman's relationship with her partner has consistently emerged as a risk factor for Postpartum Depression (PPD). In addition to having an increased likelihood of developing PPD, women who are distressed about their relationships, experience more severe depressive symptoms of greater duration, and are more vulnerable to the development of mental health problems. The emotional well-being of partners of depressed mothers is also affected, signalling the need for interventions that incorporate the woman as well as her partner. Few interventions have been designed for women simultaneously experiencing PPD and relationship distress in a conjoint format. This article describes a newly developed Interpersonal Psychotherapy (IPT) conjoint approach to treating PPD in the context of relationship distress. The existing literature on PPD is reviewed, as well as relationship distress and psychotherapy interventions for PPD with couples. This is followed by a description of an IPT conjoint approach to treating PPD with relationship distress.

  4. Clients' relational conceptions of conjoint couple and family therapy quality: a grounded formal theory.

    PubMed

    Chenail, Ronald J; George, Sally St; Wulff, Dan; Duffy, Maureen; Scott, Karen Wilson; Tomm, Karl

    2012-01-01

    Based upon a qualitative metasynthesis of 49 articles centered on clients' experiences of their conjoint couple and family therapy, the investigators constructed a grounded formal theory of Clients' Relational Conceptions of Conjoint Couple and Family Therapy Quality. The theory suggests from pretherapy conceptions to posttherapy reflections, clients' perceptions of conjoint couple and family therapy quality appear to consist of clients' constructed meanings regarding a series of interrelated relationships between clients and their therapists and therapy environments, between clients and themselves, between clients and other family members, and between process and outcome both inside and outside therapy. Within and across these relationships, clients appear to focus on expectations, connections, balance, and change when evaluating the quality of their clinical experiences. Based upon this theory, the investigators recommend that researchers continue to explore this clinical phenomenon and that therapists regularly seek clients' conceptions of quality in therapy.

  5. National Water Infrastructure Adaptation Assessment, Part I: Climate Change Adaptation Readiness Analysis

    EPA Science Inventory

    The report “National Water Infrastructure Adaptation Assessment” is comprised of four parts (Part I to IV), each in an independent volume. The Part I report presented herein describes a preliminary regulatory and technical analysis of water infrastructure and regulations in the ...

  6. The Dependent Poisson Race Model and Modeling Dependence in Conjoint Choice Experiments

    ERIC Educational Resources Information Center

    Ruan, Shiling; MacEachern, Steven N.; Otter, Thomas; Dean, Angela M.

    2008-01-01

    Conjoint choice experiments are used widely in marketing to study consumer preferences amongst alternative products. We develop a class of choice models, belonging to the class of Poisson race models, that describe a "random utility" which lends itself to a process-based description of choice. The models incorporate a dependence structure which…

  7. Does Spatial or Visual Information in Maps Facilitate Text Recall?: Reconsidering the Conjoint Retention Hypothesis

    ERIC Educational Resources Information Center

    Griffin, Marlynn M.; Robinson, Daniel H.; Sarama, Julie

    2005-01-01

    The conjoint retention hypothesis (CRH) claims that students recall more text information when they study geographic maps in addition to text than when they study text alone, because the maps are encoded spatially (Kulhavy, Lee, & Caterino, 1985). This claim was recently challenged by Griffin and Robinson (2000), who found no advantage for maps…

  8. Conjoint Behavioral Consultation: Community-School Collaboration and Behavioral Outcomes Using Multiple Baseline

    ERIC Educational Resources Information Center

    Bellinger, Skylar A.; Lee, Steven W.; Jamison, T. Rene; Reese, R. Matthew

    2016-01-01

    A plethora of literature suggests that collaborative partnerships among families, educators, and outside service providers are necessary and beneficial to address behavior problems, but there continues to be a lack of coordination among these stakeholders. The current study used conjoint behavioral consultation (CBC) to facilitate the development…

  9. Treatment of Selective Mutism: Applications in the Clinic and School through Conjoint Consultation

    ERIC Educational Resources Information Center

    Mitchell, Angela D.; Kratochwill, Thomas R.

    2013-01-01

    The purpose of this study was to evaluate the effectiveness of a psychosocial approach to the treatment of Selective Mutism (SM). Four children with SM along with their parents and teachers participated in the study. A comprehensive assessment was completed; manualized treatment was implemented through a conjoint behavioral consultation approach,…

  10. Impact of Conjoint Trajectories of Body Mass Index and Marijuana Use on Short Sleep Duration

    PubMed Central

    Brook, Judith S.; Lee, Jung Yeon; Balka, Elinor B.; Brook, David W.; Finch, Stephen J.

    2013-01-01

    Background and Objectives We examined the association between the conjoint developmental trajectories of body mass index (BMI) and marijuana use from age 24 to age 32 and short sleep duration. Methods The participants included 158 African American male, 267 African American female, 166 Puerto Rican male, and 225 Puerto Rican female young adults (N=816). Using Mplus, we obtained the conjoint trajectories of BMI and marijuana use. Logistic regression analyses examined the association between the conjoint trajectories and short sleep duration. Results Five conjoint trajectory groups were extracted: normal BMI and no or low marijuana use, obese and no or low marijuana use, morbidly obese and some marijuana use, normal BMI and high marijuana use, and obese and high marijuana use. Those in the obese and no or low marijuana use group, the morbidly obese and some marijuana use group, and the obese and high marijuana use group were more likely to report shorter sleep duration than those with normal BMI and no or low marijuana use group. Conclusions and Scientific Significance This study highlights the significance of examining joint trajectories over several developmental stages. In treating short sleep duration, we propose focusing on treating obesity, and also treating marijuana use if applicable. PMID:25187053

  11. A Personal Projects Analysis: examining adaptation to low back pain.

    PubMed

    Vroman, Kerryellen; Chamberlain, Kerry; Warner, Rebecca

    2009-07-01

    Personal Projects Analysis (PPA) offers an alternative approach to studying adaptation to illnesses. This study investigated adaptation to low back pain using PPA to examine the relationship between participants' perceptions of pain, and their functioning and well-being. Participants appraised their five most important projects on 26 dimensions, such as project value, success and difficulty. Factor analyses of the project ratings yielded five dispositions (Integrity, Personal Agency, Social Visibility, Pain Salience and Stressfulness). In regression analysis all five dispositions significantly predicted Physical and Social Function, Disruption of Roles, and Well-being. ;Pain Salience' was the strongest predictor of functional outcomes, and ;Stressfulness' was the best predictor of well-being.

  12. Convergence Analysis of LMS based Adaptive filter

    NASA Astrophysics Data System (ADS)

    Rai, Amrita; Kohli, Amit Kumar

    2010-11-01

    A standard algorithm for LMS-filter simulation, tested with several convergence criteria is presented in this paper. We analyze the steady-state mean square error (MSE) convergence of the LMS algorithm when random functions are used as reference inputs. In this paper, we make a more precise analysis using the deterministic nature of the reference inputs and their time-variant correlation matrix. Simulations performed under MATLAB show remarkable differences between convergence criteria with various value of the step size.

  13. Modeling the hospital safety partnership preferences of patients and their families: a discrete choice conjoint experiment

    PubMed Central

    Cunningham, Charles E; Hutchings, Tracy; Henderson, Jennifer; Rimas, Heather; Chen, Yvonne

    2016-01-01

    Background Patients and their families play an important role in efforts to improve health service safety. Objective The objective of this study is to understand the safety partnership preferences of patients and their families. Method We used a discrete choice conjoint experiment to model the safety partnership preferences of 1,084 patients or those such as parents acting on their behalf. Participants made choices between hypothetical safety partnerships composed by experimentally varying 15 four-level partnership design attributes. Results Participants preferred an approach to safety based on partnerships between patients and staff rather than a model delegating responsibility for safety to hospital staff. They valued the opportunity to participate in point of service safety partnerships, such as identity and medication double checks, that might afford an immediate risk reduction. Latent class analysis yielded two segments. Actively engaged participants (73.3%) comprised outpatients with higher education, who anticipated more benefits to safety partnerships, were more confident in their ability to contribute, and were more intent on participating. They were more likely to prefer a personal engagement strategy, valued scientific evidence, preferred a more active approach to safety education, and advocated disclosure of errors. The passively engaged segment (26.7%) anticipated fewer benefits, were less confident in their ability to contribute, and were less intent on participating. They were more likely to prefer an engagement strategy based on signage. They preferred that staff explain why they thought patients should help make care safer and decide whether errors were disclosed. Inpatients, those with immigrant backgrounds, and those with less education were more likely to be in this segment. Conclusion Health services need to communicate information regarding risks, ask about partnership preferences, create opportunities respecting individual differences, and

  14. Adaptation.

    PubMed

    Broom, Donald M

    2006-01-01

    The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and

  15. Applications of analysis of dynamic adaptations in parameter trajectories

    PubMed Central

    van Riel, Natal A. W.; Tiemann, Christian A.; Vanlier, Joep; Hilbers, Peter A. J.

    2013-01-01

    Metabolic profiling in combination with pathway-based analyses and computational modelling are becoming increasingly important in clinical and preclinical research. Modelling multi-factorial, progressive diseases requires the integration of molecular data at the metabolome, proteome and transcriptome levels. Also the dynamic interaction of organs and tissues needs to be considered. The processes involved cover time scales that are several orders of magnitude different. We report applications of a computational approach to bridge the scales and different levels of biological detail. Analysis of dynamic adaptations in parameter trajectories (ADAPTs) aims to investigate phenotype transitions during disease development and after a therapeutic intervention. ADAPT is based on a time-dependent evolution of model parameters to describe the dynamics of metabolic adaptations. The progression of metabolic adaptations is predicted by identifying necessary dynamic changes in the model parameters to describe the transition between experimental data obtained during different stages. To get a better understanding of the concept, the ADAPT approach is illustrated in a theoretical study. Its application in research on progressive changes in lipoprotein metabolism is also discussed. PMID:23853705

  16. Modern Sequential Analysis and Its Applications to Computerized Adaptive Testing

    ERIC Educational Resources Information Center

    Bartroff, Jay; Finkelman, Matthew; Lai, Tze Leung

    2008-01-01

    After a brief review of recent advances in sequential analysis involving sequential generalized likelihood ratio tests, we discuss their use in psychometric testing and extend the asymptotic optimality theory of these sequential tests to the case of sequentially generated experiments, of particular interest in computerized adaptive testing. We…

  17. ADAPTIVE DATA ANALYSIS OF COMPLEX FLUCTUATIONS IN PHYSIOLOGIC TIME SERIES

    PubMed Central

    PENG, C.-K.; COSTA, MADALENA; GOLDBERGER, ARY L.

    2009-01-01

    We introduce a generic framework of dynamical complexity to understand and quantify fluctuations of physiologic time series. In particular, we discuss the importance of applying adaptive data analysis techniques, such as the empirical mode decomposition algorithm, to address the challenges of nonlinearity and nonstationarity that are typically exhibited in biological fluctuations. PMID:20041035

  18. Mobility adaptations of older adults: a secondary analysis.

    PubMed

    Rush, Kathy L; Watts, Wilda E; Stanbury, Janice

    2011-02-01

    The purpose of this secondary study was to describe the mobility adaptations of community-living older adults. The primary study, designed to understand weakness and aging from the perspective of older adults, revealed that older adults viewed weakness as a progression from inability to an end point of 'giving up,' which prompted the use of adaptation strategies to preserve mobility and to counter a self-identity of being weak. A qualitative descriptive design guided the primary study of 15 community-living older adults, who participated in in-depth interviews. A systematic secondary analysis using Baltes and Baltes' theory of Selective Optimization with Compensation (SOC) showed that older adults used selection, optimization, and compensation adaptations across a range of mobility behaviors. The SOC model offered a framework for profiling older adults' agency and motivations in meeting mobility challenges as they age and provided the basis for targeted interventions to maximize mobility with aging.

  19. A New Adaptive Mother Wavelet for Electromagnetic Transient Analysis

    NASA Astrophysics Data System (ADS)

    Guillén, Daniel; Idárraga-Ospina, Gina; Cortes, Camilo

    2016-01-01

    Wavelet Transform (WT) is a powerful technique of signal processing, its applications in power systems have been increasing to evaluate power system conditions, such as faults, switching transients, power quality issues, among others. Electromagnetic transients in power systems are due to changes in the network configuration, producing non-periodic signals, which have to be identified to avoid power outages in normal operation or transient conditions. In this paper a methodology to develop a new adaptive mother wavelet for electromagnetic transient analysis is proposed. Classification is carried out with an innovative technique based on adaptive wavelets, where filter bank coefficients will be adapted until a discriminant criterion is optimized. Then, its corresponding filter coefficients will be used to get the new mother wavelet, named wavelet ET, which allowed to identify and to distinguish the high frequency information produced by different electromagnetic transients.

  20. A Decision Analysis Tool for Climate Impacts, Adaptations, and Vulnerabilities

    SciTech Connect

    Omitaomu, Olufemi A; Parish, Esther S; Nugent, Philip J

    2016-01-01

    Climate change related extreme events (such as flooding, storms, and drought) are already impacting millions of people globally at a cost of billions of dollars annually. Hence, there are urgent needs for urban areas to develop adaptation strategies that will alleviate the impacts of these extreme events. However, lack of appropriate decision support tools that match local applications is limiting local planning efforts. In this paper, we present a quantitative analysis and optimization system with customized decision support modules built on geographic information system (GIS) platform to bridge this gap. This platform is called Urban Climate Adaptation Tool (Urban-CAT). For all Urban-CAT models, we divide a city into a grid with tens of thousands of cells; then compute a list of metrics for each cell from the GIS data. These metrics are used as independent variables to predict climate impacts, compute vulnerability score, and evaluate adaptation options. Overall, the Urban-CAT system has three layers: data layer (that contains spatial data, socio-economic and environmental data, and analytic data), middle layer (that handles data processing, model management, and GIS operation), and application layer (that provides climate impacts forecast, adaptation optimization, and site evaluation). The Urban-CAT platform can guide city and county governments in identifying and planning for effective climate change adaptation strategies.

  1. Integrating a consumer orientation into the planning of HMO programs: an application of conjoint segmentation.

    PubMed

    Akaah, I P; Becherer, R C

    1983-01-01

    Despite legislative support and considerable publicity, the predicted boom in health maintenance organizations (HMOs) has not materialized. This has been due, in part, to an absence of marketing-oriented planning in designing such programs. This paper presents a consumer-oriented approach utilizing conjoint segmentation methodology which can be used to develop HMO plans that stand a better chance of consumer acceptance and marketing success.

  2. Adapt

    NASA Astrophysics Data System (ADS)

    Bargatze, L. F.

    2015-12-01

    Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted

  3. Engaging stakeholders for adaptive management using structured decision analysis

    USGS Publications Warehouse

    Irwin, Elise R.; Kathryn, D.; Kennedy, Mickett

    2009-01-01

    Adaptive management is different from other types of management in that it includes all stakeholders (versus only policy makers) in the process, uses resource optimization techniques to evaluate competing objectives, and recognizes and attempts to reduce uncertainty inherent in natural resource systems. Management actions are negotiated by stakeholders, monitored results are compared to predictions of how the system should respond, and management strategies are adjusted in a “monitor-compare-adjust” iterative routine. Many adaptive management projects fail because of the lack of stakeholder identification, engagement, and continued involvement. Primary reasons for this vary but are usually related to either stakeholders not having ownership (or representation) in decision processes or disenfranchisement of stakeholders after adaptive management begins. We present an example in which stakeholders participated fully in adaptive management of a southeastern regulated river. Structured decision analysis was used to define management objectives and stakeholder values and to determine initial flow prescriptions. The process was transparent, and the visual nature of the modeling software allowed stakeholders to see how their interests and values were represented in the decision process. The development of a stakeholder governance structure and communication mechanism has been critical to the success of the project.

  4. A hierarchical structure for automatic meshing and adaptive FEM analysis

    NASA Technical Reports Server (NTRS)

    Kela, Ajay; Saxena, Mukul; Perucchio, Renato

    1987-01-01

    A new algorithm for generating automatically, from solid models of mechanical parts, finite element meshes that are organized as spatially addressable quaternary trees (for 2-D work) or octal trees (for 3-D work) is discussed. Because such meshes are inherently hierarchical as well as spatially addressable, they permit efficient substructuring techniques to be used for both global analysis and incremental remeshing and reanalysis. The global and incremental techniques are summarized and some results from an experimental closed loop 2-D system in which meshing, analysis, error evaluation, and remeshing and reanalysis are done automatically and adaptively are presented. The implementation of 3-D work is briefly discussed.

  5. Adaptive Modeling, Engineering Analysis and Design of Advanced Aerospace Vehicles

    NASA Technical Reports Server (NTRS)

    Mukhopadhyay, Vivek; Hsu, Su-Yuen; Mason, Brian H.; Hicks, Mike D.; Jones, William T.; Sleight, David W.; Chun, Julio; Spangler, Jan L.; Kamhawi, Hilmi; Dahl, Jorgen L.

    2006-01-01

    This paper describes initial progress towards the development and enhancement of a set of software tools for rapid adaptive modeling, and conceptual design of advanced aerospace vehicle concepts. With demanding structural and aerodynamic performance requirements, these high fidelity geometry based modeling tools are essential for rapid and accurate engineering analysis at the early concept development stage. This adaptive modeling tool was used for generating vehicle parametric geometry, outer mold line and detailed internal structural layout of wing, fuselage, skin, spars, ribs, control surfaces, frames, bulkheads, floors, etc., that facilitated rapid finite element analysis, sizing study and weight optimization. The high quality outer mold line enabled rapid aerodynamic analysis in order to provide reliable design data at critical flight conditions. Example application for structural design of a conventional aircraft and a high altitude long endurance vehicle configuration are presented. This work was performed under the Conceptual Design Shop sub-project within the Efficient Aerodynamic Shape and Integration project, under the former Vehicle Systems Program. The project objective was to design and assess unconventional atmospheric vehicle concepts efficiently and confidently. The implementation may also dramatically facilitate physics-based systems analysis for the NASA Fundamental Aeronautics Mission. In addition to providing technology for design and development of unconventional aircraft, the techniques for generation of accurate geometry and internal sub-structure and the automated interface with the high fidelity analysis codes could also be applied towards the design of vehicles for the NASA Exploration and Space Science Mission projects.

  6. Research on PGNAA adaptive analysis method with BP neural network

    NASA Astrophysics Data System (ADS)

    Peng, Ke-Xin; Yang, Jian-Bo; Tuo, Xian-Guo; Du, Hua; Zhang, Rui-Xue

    2016-11-01

    A new approach method to dealing with the puzzle of spectral analysis in prompt gamma neutron activation analysis (PGNAA) is developed and demonstrated. It consists of utilizing BP neural network to PGNAA energy spectrum analysis which is based on Monte Carlo (MC) simulation, the main tasks which we will accomplish as follows: (1) Completing the MC simulation of PGNAA spectrum library, we respectively set mass fractions of element Si, Ca, Fe from 0.00 to 0.45 with a step of 0.05 and each sample is simulated using MCNP. (2) Establishing the BP model of adaptive quantitative analysis of PGNAA energy spectrum, we calculate peak areas of eight characteristic gamma rays that respectively correspond to eight elements in each individual of 1000 samples and that of the standard sample. (3) Verifying the viability of quantitative analysis of the adaptive algorithm where 68 samples were used successively. Results show that the precision when using neural network to calculate the content of each element is significantly higher than the MCLLS.

  7. Adaptive molecular resolution approach in Hamiltonian form: An asymptotic analysis.

    PubMed

    Zhu, Jinglong; Klein, Rupert; Delle Site, Luigi

    2016-10-01

    Adaptive molecular resolution approaches in molecular dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in the way the change of molecular resolution is made in a buffer (transition) region. In particular a central question concerns the possibility of the existence of a global Hamiltonian which, by describing the change of resolution, is at the same time physically consistent, mathematically well defined, and numerically accurate. In this paper we present an asymptotic analysis of the adaptive process complemented by numerical results and show that under certain mathematical conditions a Hamiltonian, which is physically consistent and numerically accurate, may exist. Such conditions show that molecular simulations in the current computational implementation require systems of large size, and thus a Hamiltonian approach such as the one proposed, at this stage, would not be practical from the numerical point of view. However, the Hamiltonian proposed provides the basis for a simplification and generalization of the numerical implementation of adaptive resolution algorithms to other molecular dynamics codes.

  8. Adaptive computational methods for SSME internal flow analysis

    NASA Technical Reports Server (NTRS)

    Oden, J. T.

    1986-01-01

    Adaptive finite element methods for the analysis of classes of problems in compressible and incompressible flow of interest in SSME (space shuttle main engine) analysis and design are described. The general objective of the adaptive methods is to improve and to quantify the quality of numerical solutions to the governing partial differential equations of fluid dynamics in two-dimensional cases. There are several different families of adaptive schemes that can be used to improve the quality of solutions in complex flow simulations. Among these are: (1) r-methods (node-redistribution or moving mesh methods) in which a fixed number of nodal points is allowed to migrate to points in the mesh where high error is detected; (2) h-methods, in which the mesh size h is automatically refined to reduce local error; and (3) p-methods, in which the local degree p of the finite element approximation is increased to reduce local error. Two of the three basic techniques have been studied in this project: an r-method for steady Euler equations in two dimensions and a p-method for transient, laminar, viscous incompressible flow. Numerical results are presented. A brief introduction to residual methods of a-posterior error estimation is also given and some pertinent conclusions of the study are listed.

  9. On-column refolding of denatured lysozyme by the conjoint chromatography composed of SEC and immobilized recombinant DsbA.

    PubMed

    Luo, Man; Guan, Yi-Xin; Yao, Shan-Jing

    2011-10-15

    DsbA (disulfide bond formation protein A) located in the periplasm of Escherichia coli is a disulfide isomerase, which is vital to disulfide bonds formation directly affecting the nascent peptides folding to the correct conformation. In this paper, recombinant DsbA was firstly immobilized onto NHS-activated Sepharose Fast Flow gel. Then Sephadex G-100 gel was sequentially packed on the top of recDsbA Sepharose Fast Flow, and a so-called conjoint chromatography column composed of SEC and immobilized recombinant DsbA was constructed. Denatured lysozyme was applied on the conjoint column. The effect of SEC volume, flow rate, loading amount and volume, pre-equilibrium mode and KCl concentration in the buffer on lysozyme refolding were investigated in detail and the stability of DsbA immobilization was evaluated. Finally the reusability of the conjoint refolding column was also tested. When loading 2.4 mg denatured lysozyme in 0.5 ml solution, the activity recovery reached 92.7% at optimized experimental conditions, and the conjoint column renaturation capacity decreased only 7.7% after six run reuse due to the use of SEC section in the chromatographic refolding process. The conjoint chromatography offers an efficient strategy to refold proteins in vitro with high productivity and column reusability.

  10. A Meta-Analysis of Local Climate Change Adaptation Actions ...

    EPA Pesticide Factsheets

    Local governments are beginning to take steps to address the consequences of climate change, such as sea level rise and heat events. However, we do not have a clear understanding of what local governments are doing -- the extent to which they expect climate change to affect their community, the types of actions they have in place to address climate change, and the resources at their disposal for implementation. Several studies have been conducted by academics, non-governmental organizations, and public agencies to assess the status of local climate change adaptation. This project collates the findings from dozens of such studies to conduct a meta-analysis of local climate change adaptation actions. The studies will be characterized along several dimensions, including (a) methods used, (b) timing and geographic scope, (c) topics covered, (d) types of adaptation actions identified, (e) implementation status, and (f) public engagement and environmental justice dimensions considered. The poster presents the project's rationale and approach and some illustrative findings from early analyses. [Note: The document being reviewed is an abstract in which a poster is being proposed. The poster will enter clearance if the abstract is accepted] The purpose of this poster is to present the research framework and approaches I am developing for my ORISE postdoctoral project, and to get feedback on early analyses.

  11. Modeling the information preferences of parents of children with mental health problems: a discrete choice conjoint experiment.

    PubMed

    Cunningham, Charles E; Deal, Ken; Rimas, Heather; Buchanan, Don H; Gold, Michelle; Sdao-Jarvie, Katherine; Boyle, Michael

    2008-10-01

    Although materials informing parents about children's mental health (CMH) problems can improve outcomes, we know relatively little about the design factors that might influence their utilization of available resources. We used a discrete choice conjoint experiment to model the information preferences of parents seeking mental health services for 6 to 18 year olds. Parents completed 30 choice tasks presenting experimentally varied combinations of 20 four-level CMH information content, transfer process, and outcome attributes. Latent class analysis revealed three segments with different preferences. Parents in the Action segment (43%) chose materials providing step-by-step solutions to behavioral or emotional problems. They preferred weekly meetings with other parents and coaching calls from a therapist. The Information segment (41%) chose materials helping them understand rather than solve their child's problems. These parents were more sensitive to logistical factors such as receiving information in groups, the location where information was available, the modality in which the information was presented, and the time required to obtain and use the information. The Overwhelmed segment (16%) reported more oppositional and conduct problems, felt their children's difficulties exerted a greater adverse impact on family functioning, and reported higher personal depression scores than those in the Action or Information segments. Nonetheless, they did not choose information about, or solutions to, the problems their children presented. Simulations predicted that maximizing utilization and realizing the potential benefits of CMH information would require knowledge transfer strategies consistent with each segment's preferences.

  12. Modeling the bullying prevention program design recommendations of students from grades five to eight: a discrete choice conjoint experiment.

    PubMed

    Cunningham, Charles E; Vaillancourt, Tracy; Cunningham, Lesley J; Chen, Yvonne; Ratcliffe, Jenna

    2011-01-01

    We used a discrete choice conjoint experiment to model the bullying prevention recommendations of 845 students from grades 5 to 8 (aged 9-14). Students made choices between experimentally varied combinations of 14 four-level prevention program attributes. Latent class analysis yielded three segments. The high impact segment (27.1%) recommended uniforms, mandatory recess activities, four playground supervisors, surveillance cameras, and 4-day suspensions when students bully. The moderate impact segment (49.5%) recommended discretionary uniforms and recess activities, four playground supervisors, and 3-day suspensions. Involvement as a bully or bully-victim was associated with membership in a low impact segment (23.4%) that rejected uniforms and surveillance cameras. They recommended fewer anti-bullying activities, discretionary recess activities, fewer playground supervisors, and the 2-day suspensions. Simulations predicted most students would recommend a program maximizing student involvement combining prevention with moderate consequences. The simulated introduction of mandatory uniforms, surveillance cameras, and long suspensions reduced overall support for a comprehensive program, particularly among students involved as bullies or bully-victims.

  13. Expressing Academic Growth on a Conjoint Developmental Scale with General Objectivity

    NASA Astrophysics Data System (ADS)

    Williamson, G. L.

    2016-11-01

    Individual growth curves yield insights about growth that are not available from any other methodology; and, developmental scales based on conjoint measurement models provide unique interpretive advantages for investigations of academic growth. Benefits are demonstrated in three examples. First, a series of fifteen statewide reading growth curves is annotated with historical policy actions related to assessment, accountability and early interventions. Second, a common measurement framework simultaneously addresses five interpretive perspectives—student reading growth; achievement level standards; K-12 text complexity standards; postsecondary reading demands; and, occupational reading demands. Third, incremental velocity norms are introduced for average reading growth based on a parametric mathematical model for individual growth curves.

  14. Latency-aged children with attachment disturbances: a conjoint treatment model.

    PubMed

    Shiller, Virginia M

    2011-01-01

    Psychoanalytic theory and practice has increasingly accepted the importance of attachment relationships in psychic development. However, there have been only very limited efforts to develop psychoanalytically informed interventions for older adopted and foster children who show significant disturbances in attachment. This paper reviews theory and research that lays groundwork for a framework for conceptualizing treatment needs for attachment disordered children. Two cases of conjoint work with parents and their latency age sons are presented. The treatment cases highlight the importance of work to increase parents' reflective functioning capacities and the need to challenge children's defensively excluded early internal working models of self and caregivers.

  15. [Analysis of the stability and adaptability of near infrared spectra qualitative analysis model].

    PubMed

    Cao, Wu; Li, Wei-jun; Wang, Ping; Zhang, Li-ping

    2014-06-01

    The stability and adaptability of model of near infrared spectra qualitative analysis were studied. Method of separate modeling can significantly improve the stability and adaptability of model; but its ability of improving adaptability of model is limited. Method of joint modeling can not only improve the adaptability of the model, but also the stability of model, at the same time, compared to separate modeling, the method can shorten the modeling time, reduce the modeling workload; extend the term of validity of model, and improve the modeling efficiency. The experiment of model adaptability shows that, the correct recognition rate of separate modeling method is relatively low, which can not meet the requirements of application, and joint modeling method can reach the correct recognition rate of 90%, and significantly enhances the recognition effect. The experiment of model stability shows that, the identification results of model by joint modeling are better than the model by separate modeling, and has good application value.

  16. Measuring Children's Perceptions of Parental Involvement in Conjoint Behavioral Consultation: Factor Structure and Reliability of the "Parental Support for Learning Scale"

    ERIC Educational Resources Information Center

    Rogers, Maria; Markel, Clarisa; Midgett, Jonathan D.; Ryan, Bruce A.; Tannock, Rosemary

    2014-01-01

    Practitioners of Conjoint Behavioral Consultation rely on several sources of information to assist in planning and evaluation of consultation efforts. Parental involvement in the home is an important aspect in Conjoint Behavioral Consultation, yet there are few questionnaires available to practitioners to assess this important construct,…

  17. An adaptive gyroscope-based algorithm for temporal gait analysis.

    PubMed

    Greene, Barry R; McGrath, Denise; O'Neill, Ross; O'Donovan, Karol J; Burns, Adrian; Caulfield, Brian

    2010-12-01

    Body-worn kinematic sensors have been widely proposed as the optimal solution for portable, low cost, ambulatory monitoring of gait. This study aims to evaluate an adaptive gyroscope-based algorithm for automated temporal gait analysis using body-worn wireless gyroscopes. Gyroscope data from nine healthy adult subjects performing four walks at four different speeds were then compared against data acquired simultaneously using two force plates and an optical motion capture system. Data from a poliomyelitis patient, exhibiting pathological gait walking with and without the aid of a crutch, were also compared to the force plate. Results show that the mean true error between the adaptive gyroscope algorithm and force plate was -4.5 ± 14.4 ms and 43.4 ± 6.0 ms for IC and TC points, respectively, in healthy subjects. Similarly, the mean true error when data from the polio patient were compared against the force plate was -75.61 ± 27.53 ms and 99.20 ± 46.00 ms for IC and TC points, respectively. A comparison of the present algorithm against temporal gait parameters derived from an optical motion analysis system showed good agreement for nine healthy subjects at four speeds. These results show that the algorithm reported here could constitute the basis of a robust, portable, low-cost system for ambulatory monitoring of gait.

  18. Parameter Estimation Analysis for Hybrid Adaptive Fault Tolerant Control

    NASA Astrophysics Data System (ADS)

    Eshak, Peter B.

    Research efforts have increased in recent years toward the development of intelligent fault tolerant control laws, which are capable of helping the pilot to safely maintain aircraft control at post failure conditions. Researchers at West Virginia University (WVU) have been actively involved in the development of fault tolerant adaptive control laws in all three major categories: direct, indirect, and hybrid. The first implemented design to provide adaptation was a direct adaptive controller, which used artificial neural networks to generate augmentation commands in order to reduce the modeling error. Indirect adaptive laws were implemented in another controller, which utilized online PID to estimate and update the controller parameter. Finally, a new controller design was introduced, which integrated both direct and indirect control laws. This controller is known as hybrid adaptive controller. This last control design outperformed the two earlier designs in terms of less NNs effort and better tracking quality. The performance of online PID has an important role in the quality of the hybrid controller; therefore, the quality of the estimation will be of a great importance. Unfortunately, PID is not perfect and the online estimation process has some inherited issues; the online PID estimates are primarily affected by delays and biases. In order to ensure updating reliable estimates to the controller, the estimator consumes some time to converge. Moreover, the estimator will often converge to a biased value. This thesis conducts a sensitivity analysis for the estimation issues, delay and bias, and their effect on the tracking quality. In addition, the performance of the hybrid controller as compared to direct adaptive controller is explored. In order to serve this purpose, a simulation environment in MATLAB/SIMULINK has been created. The simulation environment is customized to provide the user with the flexibility to add different combinations of biases and delays to

  19. Adaptive approach for nonlinear sensitivity analysis of reaction kinetics.

    PubMed

    Horenko, Illia; Lorenz, Sönke; Schütte, Christof; Huisinga, Wilhelm

    2005-07-15

    We present a unified approach for linear and nonlinear sensitivity analysis for models of reaction kinetics that are stated in terms of systems of ordinary differential equations (ODEs). The approach is based on the reformulation of the ODE problem as a density transport problem described by a Fokker-Planck equation. The resulting multidimensional partial differential equation is herein solved by extending the TRAIL algorithm originally introduced by Horenko and Weiser in the context of molecular dynamics (J. Comp. Chem. 2003, 24, 1921) and discussed it in comparison with Monte Carlo techniques. The extended TRAIL approach is fully adaptive and easily allows to study the influence of nonlinear dynamical effects. We illustrate the scheme in application to an enzyme-substrate model problem for sensitivity analysis w.r.t. to initial concentrations and parameter values.

  20. Prequential Analysis of Complex Data with Adaptive Model Reselection.

    PubMed

    Clarke, Jennifer; Clarke, Bertrand

    2009-11-01

    In Prequential analysis, an inference method is viewed as a forecasting system, and the quality of the inference method is based on the quality of its predictions. This is an alternative approach to more traditional statistical methods that focus on the inference of parameters of the data generating distribution. In this paper, we introduce adaptive combined average predictors (ACAPs) for the Prequential analysis of complex data. That is, we use convex combinations of two different model averages to form a predictor at each time step in a sequence. A novel feature of our strategy is that the models in each average are re-chosen adaptively at each time step. To assess the complexity of a given data set, we introduce measures of data complexity for continuous response data. We validate our measures in several simulated contexts prior to using them in real data examples. The performance of ACAPs is compared with the performances of predictors based on stacking or likelihood weighted averaging in several model classes and in both simulated and real data sets. Our results suggest that ACAPs achieve a better trade off between model list bias and model list variability in cases where the data is very complex. This implies that the choices of model class and averaging method should be guided by a concept of complexity matching, i.e. the analysis of a complex data set may require a more complex model class and averaging strategy than the analysis of a simpler data set. We propose that complexity matching is akin to a bias-variance tradeoff in statistical modeling.

  1. Towards adaptive, streaming analysis of x-ray tomography data

    SciTech Connect

    Thomas, Mathew; Kleese van Dam, Kerstin; Marshall, Matthew J.; Kuprat, Andrew P.; Carson, James P.; Lansing, Carina S.; Guillen, Zoe C.; Miller, Erin A.; Lanekoff, Ingela; Laskin, Julia

    2015-03-04

    Temporal and spatial resolution of chemical imaging methodologies such as x-ray tomography are rapidly increasing, leading to more complex experimental procedures and fast growing data volumes. Automated analysis pipelines and big data analytics are becoming essential to effectively evaluate the results of such experiments. Offering those data techniques in an adaptive, streaming environment can further substantially improve the scientific discovery process, by enabling experimental control and steering based on the evaluation of emerging phenomena as they are observed by the experiment. Pacific Northwest National Laboratory (PNNL)’ Chemical Imaging Initiative (CII - http://imaging.pnnl.gov/ ) has worked since 2011 towards developing a framework that allows users to rapidly compose and customize high throughput experimental analysis pipelines for multiple instrument types. The framework, named ‘Rapid Experimental Analysis’ (REXAN) Framework [1], is based on the idea of reusable component libraries and utilizes the PNNL developed collaborative data management and analysis environment ‘Velo’, to provide a user friendly analysis and data management environment for experimental facilities. This article will, discuss the capabilities established for X-Ray tomography, discuss lessons learned, and provide an overview of our more recent work in the Analysis in Motion Initiative (AIM - http://aim.pnnl.gov/ ) at PNNL to provide REXAN capabilities in a streaming environment.

  2. Adjustment of Adaptive Gain with Bounded Linear Stability Analysis to Improve Time-Delay Margin for Metrics-Driven Adaptive Control

    NASA Technical Reports Server (NTRS)

    Bakhtiari-Nejad, Maryam; Nguyen, Nhan T.; Krishnakumar, Kalmanje Srinvas

    2009-01-01

    This paper presents the application of Bounded Linear Stability Analysis (BLSA) method for metrics driven adaptive control. The bounded linear stability analysis method is used for analyzing stability of adaptive control models, without linearizing the adaptive laws. Metrics-driven adaptive control introduces a notion that adaptation should be driven by some stability metrics to achieve robustness. By the application of bounded linear stability analysis method the adaptive gain is adjusted during the adaptation in order to meet certain phase margin requirements. Analysis of metrics-driven adaptive control is evaluated for a linear damaged twin-engine generic transport model of aircraft. The analysis shows that the system with the adjusted adaptive gain becomes more robust to unmodeled dynamics or time delay.

  3. The conjoint junction of the triceps surae: implications for gastrocnemius tendon lengthening.

    PubMed

    Elson, D W; Whiten, S; Hillman, S J; Johnson, R J; Lo, S S; Robb, J E

    2007-11-01

    Forty embalmed cadaver lower limbs were dissected to identify the morphology of the conjoint junction of the tendons of gastrocnemius and soleus and the location of the gastrocnemius tendon relative to bony landmarks. Five patterns of conjoint junction morphology were found: transverse (25%), oblique passing distally and medially (45%), oblique passing distally and laterally (5%) and arcuate as an inverted U (17.5%) and a U-shape (7.5%). Left-right asymmetry of the junction was observed in 31.6% of 19 paired cadaver legs. On the medial side of the calf the gastrocnemius tendon could be located between 38 and 46% of the proportion of the distance between the upper border of the calcaneus and the fibular head. Corresponding values for the midline and lateral side of the calf were 45-58% and 48-51%. The location of the gastrocnemius tendon relative to bony landmarks may help to guide incision planning for open or endoscopic division of the tendon.

  4. The SMART CLUSTER METHOD - adaptive earthquake cluster analysis and declustering

    NASA Astrophysics Data System (ADS)

    Schaefer, Andreas; Daniell, James; Wenzel, Friedemann

    2016-04-01

    Earthquake declustering is an essential part of almost any statistical analysis of spatial and temporal properties of seismic activity with usual applications comprising of probabilistic seismic hazard assessments (PSHAs) and earthquake prediction methods. The nature of earthquake clusters and subsequent declustering of earthquake catalogues plays a crucial role in determining the magnitude-dependent earthquake return period and its respective spatial variation. Various methods have been developed to address this issue from other researchers. These have differing ranges of complexity ranging from rather simple statistical window methods to complex epidemic models. This study introduces the smart cluster method (SCM), a new methodology to identify earthquake clusters, which uses an adaptive point process for spatio-temporal identification. Hereby, an adaptive search algorithm for data point clusters is adopted. It uses the earthquake density in the spatio-temporal neighbourhood of each event to adjust the search properties. The identified clusters are subsequently analysed to determine directional anisotropy, focussing on a strong correlation along the rupture plane and adjusts its search space with respect to directional properties. In the case of rapid subsequent ruptures like the 1992 Landers sequence or the 2010/2011 Darfield-Christchurch events, an adaptive classification procedure is applied to disassemble subsequent ruptures which may have been grouped into an individual cluster using near-field searches, support vector machines and temporal splitting. The steering parameters of the search behaviour are linked to local earthquake properties like magnitude of completeness, earthquake density and Gutenberg-Richter parameters. The method is capable of identifying and classifying earthquake clusters in space and time. It is tested and validated using earthquake data from California and New Zealand. As a result of the cluster identification process, each event in

  5. Adaptive grid methods for RLV environment assessment and nozzle analysis

    NASA Technical Reports Server (NTRS)

    Thornburg, Hugh J.

    1996-01-01

    Rapid access to highly accurate data about complex configurations is needed for multi-disciplinary optimization and design. In order to efficiently meet these requirements a closer coupling between the analysis algorithms and the discretization process is needed. In some cases, such as free surface, temporally varying geometries, and fluid structure interaction, the need is unavoidable. In other cases the need is to rapidly generate and modify high quality grids. Techniques such as unstructured and/or solution-adaptive methods can be used to speed the grid generation process and to automatically cluster mesh points in regions of interest. Global features of the flow can be significantly affected by isolated regions of inadequately resolved flow. These regions may not exhibit high gradients and can be difficult to detect. Thus excessive resolution in certain regions does not necessarily increase the accuracy of the overall solution. Several approaches have been employed for both structured and unstructured grid adaption. The most widely used involve grid point redistribution, local grid point enrichment/derefinement or local modification of the actual flow solver. However, the success of any one of these methods ultimately depends on the feature detection algorithm used to determine solution domain regions which require a fine mesh for their accurate representation. Typically, weight functions are constructed to mimic the local truncation error and may require substantial user input. Most problems of engineering interest involve multi-block grids and widely disparate length scales. Hence, it is desirable that the adaptive grid feature detection algorithm be developed to recognize flow structures of different type as well as differing intensity, and adequately address scaling and normalization across blocks. These weight functions can then be used to construct blending functions for algebraic redistribution, interpolation functions for unstructured grid generation

  6. Network and adaptive system of systems modeling and analysis.

    SciTech Connect

    Lawton, Craig R.; Campbell, James E. Dr.; Anderson, Dennis James; Eddy, John P.

    2007-05-01

    This report documents the results of an LDRD program entitled ''Network and Adaptive System of Systems Modeling and Analysis'' that was conducted during FY 2005 and FY 2006. The purpose of this study was to determine and implement ways to incorporate network communications modeling into existing System of Systems (SoS) modeling capabilities. Current SoS modeling, particularly for the Future Combat Systems (FCS) program, is conducted under the assumption that communication between the various systems is always possible and occurs instantaneously. A more realistic representation of these communications allows for better, more accurate simulation results. The current approach to meeting this objective has been to use existing capabilities to model network hardware reliability and adding capabilities to use that information to model the impact on the sustainment supply chain and operational availability.

  7. ADGS-2100 Adaptive Display and Guidance System Window Manager Analysis

    NASA Technical Reports Server (NTRS)

    Whalen, Mike W.; Innis, John D.; Miller, Steven P.; Wagner, Lucas G.

    2006-01-01

    Recent advances in modeling languages have made it feasible to formally specify and analyze the behavior of large system components. Synchronous data flow languages, such as Lustre, SCR, and RSML-e are particularly well suited to this task, and commercial versions of these tools such as SCADE and Simulink are growing in popularity among designers of safety critical systems, largely due to their ability to automatically generate code from the models. At the same time, advances in formal analysis tools have made it practical to formally verify important properties of these models to ensure that design defects are identified and corrected early in the lifecycle. This report describes how these tools have been applied to the ADGS-2100 Adaptive Display and Guidance Window Manager being developed by Rockwell Collins Inc. This work demonstrates how formal methods can be easily and cost-efficiently used to remove defects early in the design cycle.

  8. Analysis and design of an adaptive lightweight satellite mirror

    NASA Astrophysics Data System (ADS)

    Duerr, Johannes K.; Honke, Robert; Alberti, Mathias V.; Sippel, Rudolf

    2002-07-01

    Future scientific space missions based on interferometric optical and infrared astronomical instruments are currently under development in the United States as well as in Europe. These instruments require optical path length accuracy in the order of a few nanometers across structural dimensions of several meters. This puts extreme demands on static and dynamic structural stability. It is expected that actively controlled, adaptive structures will increasingly have to be used for these satellite applications to overcome the limits of passive structural accuracy. Based on the evaluation of different piezo-active concepts presented two years ago analysis and design of an adaptive lightweight satellite mirror primarily made of carbon-fiber reinforced plastic with embedded piezoceramic actuators for shape control is being described. Simulation of global mirror performance takes different wavefront-sensors and controls for several cases of loading into account. In addition extensive finite-element optimization of various structural details has been performed. Local material properties of sub-assemblies or geometry effects at the edges of the structure are investigated with respect to their impact on mirror performance. One important result of the analysis was the lay-out of actuator arrays consisting of specifically designed and custom made piezoceramic actuators. Prototype manufacturing and testing of active sub-components is described in detail. The results obtained served as a basis for a final update of finite-element models. The paper concludes with an outline on manufacturing, testing, and space qualification of the prototype demonstrator of an actively controllable lightweight satellite mirror currently under way. The research work presented in this paper is part of the German industrial research project 'ADAPTRONIK'.

  9. Alcoholics Anonymous and Relapse Prevention as Maintenance Strategies After Conjoint Behavioral Alcohol Treatment for Men: 18-Month Outcomes

    ERIC Educational Resources Information Center

    McCrady, Barbara S.; Epstein, Elizabeth E.; Kahler, Christopher W.

    2004-01-01

    Ninety men with alcohol problems and their female partners were randomly assigned to 1 of 3 outpatient conjoint treatments: alcohol behavioral couples therapy (ABCT), ABCT with relapse prevention techniques (RP/ABCT), or ABCT with interventions encouraging Alcoholics Anonymous (AA) involvement (AA/ABCT). Couples were followed for 18 months after…

  10. Supporting the Inclusion of a Student with Asperger Syndrome: A Case Study Using Conjoint Behavioural Consultation and Self-Management

    ERIC Educational Resources Information Center

    Wilkinson, Lee A.

    2005-01-01

    Conjoint behavioural consultation (CBC) is an indirect form of service delivery that combines the resources of home and school to meet the academic, social and behavioural needs of children. The purpose of this paper is to demonstrate the utility of CBC as a service delivery model for supporting the inclusion of a student with Asperger syndrome in…

  11. Conjoint Processing of Time-Compressed Narration in Multimedia Instruction: The Effects on Recall, but Not Recognition

    ERIC Educational Resources Information Center

    Ritzhaupt, Albert D.; Barron, Ann E.; Kealy, William A.

    2011-01-01

    Although previous research shows verbal recall of time-compressed narration is significantly enhanced when it is accompanied by a representational adjunct picture (Ritzhaupt & Barron, 2008), the reason for this increased performance remains unclear. One explanation, explored in the current study, is based on the Conjoint Retention Hypothesis…

  12. Fuzzy Multicriteria Decision Analysis for Adaptive Watershed Management

    NASA Astrophysics Data System (ADS)

    Chang, N.

    2006-12-01

    The dramatic changes of societal complexity due to intensive interactions among agricultural, industrial, and municipal sectors have resulted in acute issues of water resources redistribution and water quality management in many river basins. Given the fact that integrated watershed management is more a political and societal than a technical challenge, there is a need for developing a compelling method leading to justify a water-based land use program in some critical regions. Adaptive watershed management is viewed as an indispensable tool nowadays for providing step-wise constructive decision support that is concerned with all related aspects of the water consumption cycle and those facilities affecting water quality and quantity temporally and spatially. Yet the greatest challenge that decision makers face today is to consider how to leverage ambiguity, paradox, and uncertainty to their competitive advantage of management policy quantitatively. This paper explores a fuzzy multicriteria evaluation method for water resources redistribution and subsequent water quality management with respect to a multipurpose channel-reservoir system--the Tseng- Wen River Basin, South Taiwan. Four fuzzy operators tailored for this fuzzy multicriteria decision analysis depict greater flexibility in representing the complexity of various possible trade-offs among management alternatives constrained by physical, economic, and technical factors essential for adaptive watershed management. The management strategies derived may enable decision makers to integrate a vast number of internal weirs, water intakes, reservoirs, drainage ditches, transfer pipelines, and wastewater treatment facilities within the basin and bring up the permitting issue for transboundary diversion from a neighboring river basin. Experience gained indicates that the use of different types of fuzzy operators is highly instructive, which also provide unique guidance collectively for achieving the overarching goals

  13. Adaptive strategy for the statistical analysis of connectomes.

    PubMed

    Meskaldji, Djalel Eddine; Ottet, Marie-Christine; Cammoun, Leila; Hagmann, Patric; Meuli, Reto; Eliez, Stephan; Thiran, Jean Philippe; Morgenthaler, Stephan

    2011-01-01

    We study an adaptive statistical approach to analyze brain networks represented by brain connection matrices of interregional connectivity (connectomes). Our approach is at a middle level between a global analysis and single connections analysis by considering subnetworks of the global brain network. These subnetworks represent either the inter-connectivity between two brain anatomical regions or by the intra-connectivity within the same brain anatomical region. An appropriate summary statistic, that characterizes a meaningful feature of the subnetwork, is evaluated. Based on this summary statistic, a statistical test is performed to derive the corresponding p-value. The reformulation of the problem in this way reduces the number of statistical tests in an orderly fashion based on our understanding of the problem. Considering the global testing problem, the p-values are corrected to control the rate of false discoveries. Finally, the procedure is followed by a local investigation within the significant subnetworks. We contrast this strategy with the one based on the individual measures in terms of power. We show that this strategy has a great potential, in particular in cases where the subnetworks are well defined and the summary statistics are properly chosen. As an application example, we compare structural brain connection matrices of two groups of subjects with a 22q11.2 deletion syndrome, distinguished by their IQ scores.

  14. Analysis of a Major Electric Grid -- Stability and Adaptive Protection

    NASA Astrophysics Data System (ADS)

    Alanzi, Sultan

    system conditions. This dissertation introduces a combination of quadrilateral and mho characteristics to create a distance relay with a mushroom shape in R-X diagrams. This new relay offers larger protective reach with a lower limitation on loadability. When major disturbances occur, the power balance between load and generation might be disturbed causing the generators to lose synchronism (to be out-of-step) with each other. Out-of-step protection against power swings is essential to provide supervising signals for distance relays to mitigate the effects of the disturbance. A new R-X criterion is proposed to identify out-of-step conditions for large and complex power systems, such as KEG. A proposed Adaptive Out-of-Step Relay (AOSR) will monitor power system conditions and adjust the relay reach accordingly for better power swing classification. When unstable swings are detected, controllable tripping signals are initiated and system separation will create small subsystems or islands of the power system. These smaller systems will be created to achieve a balance of load and available generation. The electric power system chosen to study and to illustrate the criteria for the proposed adaptive relays was that of the country of Kuwait. The small oil-rich country of Kuwait has been dealing with an electric energy crisis that started summer 2006. With a dry dessert climate and intensely hot summers, the 3.6 million residents of Kuwait depend on continuously operated A/C units for living. This is the major reason why the peak load in a summer month reaches almost 11,000 MW while the peak load in a winter month does not exceed 5,000 MW. The Kuwait Electric Grid (KEG) is modelled and analyzed using Power Analytics' software known as PaladinRTM DesignBase(TM). Performance studies produce data to examine distance and out-of-step protection. Power Flow (PF), Short Circuit Analysis (SCA), and Transient Stability Analysis (TSA) are used to verify the model of KEG. These studies

  15. Advanced Diagnostic and Prognostic Testbed (ADAPT) Testability Analysis Report

    NASA Technical Reports Server (NTRS)

    Ossenfort, John

    2008-01-01

    As system designs become more complex, determining the best locations to add sensors and test points for the purpose of testing and monitoring these designs becomes more difficult. Not only must the designer take into consideration all real and potential faults of the system, he or she must also find efficient ways of detecting and isolating those faults. Because sensors and cabling take up valuable space and weight on a system, and given constraints on bandwidth and power, it is even more difficult to add sensors into these complex designs after the design has been completed. As a result, a number of software tools have been developed to assist the system designer in proper placement of these sensors during the system design phase of a project. One of the key functions provided by many of these software programs is a testability analysis of the system essentially an evaluation of how observable the system behavior is using available tests. During the design phase, testability metrics can help guide the designer in improving the inherent testability of the design. This may include adding, removing, or modifying tests; breaking up feedback loops, or changing the system to reduce fault propagation. Given a set of test requirements, the analysis can also help to verify that the system will meet those requirements. Of course, a testability analysis requires that a software model of the physical system is available. For the analysis to be most effective in guiding system design, this model should ideally be constructed in parallel with these efforts. The purpose of this paper is to present the final testability results of the Advanced Diagnostic and Prognostic Testbed (ADAPT) after the system model was completed. The tool chosen to build the model and to perform the testability analysis with is the Testability Engineering and Maintenance System Designer (TEAMS-Designer). The TEAMS toolset is intended to be a solution to span all phases of the system, from design and

  16. The interim service preferences of parents waiting for children's mental health treatment: a discrete choice conjoint experiment.

    PubMed

    Cunningham, Charles E; Chen, Yvonne; Deal, Ken; Rimas, Heather; McGrath, Patrick; Reid, Graham; Lipman, Ellen; Corkum, Penny

    2013-08-01

    Parents seeking help for children with mental health problems are often assigned to a waiting list. We used a discrete choice conjoint experiment to model preferences for interim services that might be used while waiting for the formal assessment and treatment process to begin. A sample of 1,059 parents (92 % mothers) seeking mental health services for 4 to 16 year olds chose between hypothetical interim services composed by experimentally varying combinations of the levels of 13 interim service attributes. Latent Class analysis yielded a four-segment solution. All segments preferred interim options helping them understand how agencies work, enhancing their parenting knowledge and skill, and providing an opportunity to understand or begin dealing with their own difficulties. The Group Contact segment (35.1 %) preferred interim services in meetings with other parents, supported by phone contacts, frequent checkup calls, and wait-time updates. Virtual Contact parents (29.2 %) preferred to meet other parents in small internet chat groups supported by e-mail contact. Membership in this segment was linked to higher education and computer skills. Frequent Contact parents (24.4 %) preferred face-to-face interim services supported by weekly progress checks and wait time updates. Limited Contact parents (11.3 %) were less intent on using interim services. They preferred to pursue interim services alone, with contacts by phone, supported by fewer check-up calls and less frequent wait time updates. All segments were more likely to enroll in interim services involving their child.

  17. Solution-verified reliability analysis and design of bistable MEMS using error estimation and adaptivity.

    SciTech Connect

    Eldred, Michael Scott; Subia, Samuel Ramirez; Neckels, David; Hopkins, Matthew Morgan; Notz, Patrick K.; Adams, Brian M.; Carnes, Brian; Wittwer, Jonathan W.; Bichon, Barron J.; Copps, Kevin D.

    2006-10-01

    This report documents the results for an FY06 ASC Algorithms Level 2 milestone combining error estimation and adaptivity, uncertainty quantification, and probabilistic design capabilities applied to the analysis and design of bistable MEMS. Through the use of error estimation and adaptive mesh refinement, solution verification can be performed in an automated and parameter-adaptive manner. The resulting uncertainty analysis and probabilistic design studies are shown to be more accurate, efficient, reliable, and convenient.

  18. Symmetry Breaking Analysis of Prism Adaptation's Latent Aftereffect

    ERIC Educational Resources Information Center

    Frank, Till D.; Blau, Julia J. C.; Turvey, Michael T.

    2012-01-01

    The effect of prism adaptation on movement is typically reduced when the movement at test (prisms off) differs on some dimension from the movement at training (prisms on). Some adaptation is latent, however, and only revealed through further testing in which the movement at training is fully reinstated. Applying a nonlinear attractor dynamic model…

  19. An adaptive mesh magneto-hydrodynamic analysis of interstellar clouds

    NASA Astrophysics Data System (ADS)

    Kominsky, Paul J.

    Interstellar clouds play a key role in many astrophysical events. The interactions of dense interstellar clouds with shock waves and interstellar wind were investigated using an adaptive three-dimensional Cartesian mesh approach to the magneto-hydrodynamic equations. The mixing of the cloud material with the post-shock material results in complex layers of current density. In both the shock and wind interactions, a tail develops similar to the tail found with comets due to the solar wind. The orientation of this tail structure changes with the direction of the magnetic field, and may be useful to observationally determining the orientation of magnetic fields in the interstellar medium. The octree data structure was analyzed in regard to parallel work units. Larger block sizes have a higher volume to surface ratio and support a higher percentage of computational cells to non-computational cells, but require more cells at the finest grid resolution. Keeping the minimum resolution of the grid fixed, and averaging over all possible grids, the analysis confirms experience that block sizes larger than 8 × 8 × 8 cells do not improve storage efficiency. A novel algorithm was developed to implement rotationally periodic boundary conditions on quadtree and octree data, structures. Astrophysical flows wit h symmetric circulation, such as accretion disks, or periodic instabilities, such supernova remnants, may be able to take advantage of such boundary conditions while maintaining the other benefits of a Cartesian grid.

  20. Development and analysis for core power gamma thermometer adaptation

    SciTech Connect

    Ren-Tai Chiang; Leong, T.

    1996-12-31

    The gamma thermometer (GT) has gained increasing interest to replace the local power range monitor (LPRM) and the traversing in-core probe (TIP) as the core monitoring device in new boiling water reactor (BWR) designs. The number of GTs is designed between the number of LPRMs, 4, and the number of TIPs, 24, per string, but its optimal number is yet to be determined. The authors have modified the BWR core Simulator PANACEA for analyzing the core power GT adaptation and have compared the axial core-averaged relative power distributions and two thermal limits of the GT 8- and 12-point adaptations against those of the TIP 24-point adaptation.

  1. A global analysis of adaptive evolution of operons in cyanobacteria.

    PubMed

    Memon, Danish; Singh, Abhay K; Pakrasi, Himadri B; Wangikar, Pramod P

    2013-02-01

    Operons are an important feature of prokaryotic genomes. Evolution of operons is hypothesized to be adaptive and has contributed significantly towards coordinated optimization of functions. Two conflicting theories, based on (i) in situ formation to achieve co-regulation and (ii) horizontal gene transfer of functionally linked gene clusters, are generally considered to explain why and how operons have evolved. Furthermore, effects of operon evolution on genomic traits such as intergenic spacing, operon size and co-regulation are relatively less explored. Based on the conservation level in a set of diverse prokaryotes, we categorize the operonic gene pair associations and in turn the operons as ancient and recently formed. This allowed us to perform a detailed analysis of operonic structure in cyanobacteria, a morphologically and physiologically diverse group of photoautotrophs. Clustering based on operon conservation showed significant similarity with the 16S rRNA-based phylogeny, which groups the cyanobacterial strains into three clades. Clade C, dominated by strains that are believed to have undergone genome reduction, shows a larger fraction of operonic genes that are tightly packed in larger sized operons. Ancient operons are in general larger, more tightly packed, better optimized for co-regulation and part of key cellular processes. A sub-clade within Clade B, which includes Synechocystis sp. PCC 6803, shows a reverse trend in intergenic spacing. Our results suggest that while in situ formation and vertical descent may be a dominant mechanism of operon evolution in cyanobacteria, optimization of intergenic spacing and co-regulation are part of an ongoing process in the life-cycle of operons.

  2. Land Use Adaptation Strategies Analysis in Landslide Risk Region

    NASA Astrophysics Data System (ADS)

    Lin, Yu-Ching; Chang, Chin-Hsin; Chen, Ying-Tung

    2013-04-01

    In order to respond to the impact of climate and environmental change on Taiwanese mountain region, this study used GTZ (2004) Risk analysis guidelines to assess the landslide risk for 178 Taiwanese mountain towns. This study used 7 indicators to assess landslide risk, which are rainfall distribution, natural environment vulnerability (e.g., rainfall threshold criterion for debris flow, historical disaster frequency, landslide ratio, and road density), physicality vulnerability (e.g., population density) and socio-economic vulnerability (e.g., population with higher education, death rate and income). The landslide risk map can be obtained by multiplying 7 indicators together and ranking the product. The map had 5 risk ranges, and towns within the range of 4 to 5, which are high landslide risk regions, and have high priority in reducing risk. This study collected the regions with high landslide risk regions and analyzed the difference after Typhoon Morakot (2009). The spatial distribution showed that after significant environmental damage high landslide risk regions moved from central to south Taiwan. The changeable pattern of risk regions pointed out the necessity of updating the risk map periodically. Based on the landslide risk map and the land use investigation data which was provided by the National Land Surveying and Mapping Center in 2007, this study calculated the size of the land use area with landslide disaster risk. According to the above results and discussion, this study can be used to suggest appropriate land use adaptation strategies provided for reducing landslide risk under the impact of climate and environmental change.

  3. Adaptive superposition of finite element meshes in linear and nonlinear dynamic analysis

    NASA Astrophysics Data System (ADS)

    Yue, Zhihua

    2005-11-01

    The numerical analysis of transient phenomena in solids, for instance, wave propagation and structural dynamics, is a very important and active area of study in engineering. Despite the current evolutionary state of modern computer hardware, practical analysis of large scale, nonlinear transient problems requires the use of adaptive methods where computational resources are locally allocated according to the interpolation requirements of the solution form. Adaptive analysis of transient problems involves obtaining solutions at many different time steps, each of which requires a sequence of adaptive meshes. Therefore, the execution speed of the adaptive algorithm is of paramount importance. In addition, transient problems require that the solution must be passed from one adaptive mesh to the next adaptive mesh with a bare minimum of solution-transfer error since this form of error compromises the initial conditions used for the next time step. A new adaptive finite element procedure (s-adaptive) is developed in this study for modeling transient phenomena in both linear elastic solids and nonlinear elastic solids caused by progressive damage. The adaptive procedure automatically updates the time step size and the spatial mesh discretization in transient analysis, achieving the accuracy and the efficiency requirements simultaneously. The novel feature of the s-adaptive procedure is the original use of finite element mesh superposition to produce spatial refinement in transient problems. The use of mesh superposition enables the s-adaptive procedure to completely avoid the need for cumbersome multipoint constraint algorithms and mesh generators, which makes the s-adaptive procedure extremely fast. Moreover, the use of mesh superposition enables the s-adaptive procedure to minimize the solution-transfer error. In a series of different solid mechanics problem types including 2-D and 3-D linear elastic quasi-static problems, 2-D material nonlinear quasi-static problems

  4. Pedagogical Content Knowledge of Experienced Teachers in Physical Education: Functional Analysis of Adaptations

    ERIC Educational Resources Information Center

    Ayvazo, Shiri; Ward, Phillip

    2011-01-01

    Pedagogical content knowledge (PCK) is the teacher's ability to pedagogically adapt content to students of diverse abilities. In this study, we investigated how teachers' adaptations of instruction for individual students differed when teaching stronger and weaker instructional units. We used functional analysis (Hanley, Iwata, & McCord, 2003) of…

  5. Multiple Adaptation Types with Mitigation: A Framework for Policy Analysis

    EPA Science Inventory

    Effective climate policy will consist of mitigation and adaptation implemented simultaneously in a policy portfolio to reduce the risks of climate change. The relative share of these responses will vary over time and will be adjusted in response to new information. Furthermore,...

  6. DIF Analysis for Pretest Items in Computer-Adaptive Testing.

    ERIC Educational Resources Information Center

    Zwick, Rebecca; And Others

    A simulation study of methods of assessing differential item functioning (DIF) in computer-adaptive tests (CATs) was conducted by Zwick, Thayer, and Wingersky (in press, 1993). Results showed that modified versions of the Mantel-Haenszel and standardization methods work well with CAT data. DIF methods were also investigated for nonadaptive…

  7. Model-Based Nonrigid Motion Analysis Using Natural Feature Adaptive Mesh

    SciTech Connect

    Zhang, Y.; Goldgof, D.B.; Sarkar, S.; Tsap, L.V.

    2000-04-25

    The success of nonrigid motion analysis using physical finite element model is dependent on the mesh that characterizes the object's geometric structure. We suggest a deformable mesh adapted to the natural features of images. The adaptive mesh requires much fewer number of nodes than the fixed mesh which was used in our previous work. We demonstrate the higher efficiency of the adaptive mesh in the context of estimating burn scar elasticity relative to normal skin elasticity using the observed 2D image sequence. Our results show that the scar assessment method based on the physical model using natural feature adaptive mesh can be applied to images which do not have artificial markers.

  8. Complex adaptive systems and their relevance for nursing: An evolutionary concept analysis.

    PubMed

    Notarnicola, Ippolito; Petrucci, Cristina; De Jesus Barbosa, Maria Rosimar; Giorgi, Fabio; Stievano, Alessandro; Rocco, Gennaro; Lancia, Loreto

    2017-02-08

    This study aimed to analyze the concept of "complex adaptive systems." The construct is still nebulous in the literature, and a further explanation of the idea is needed to have a shared knowledge of it. A concept analysis was conducted utilizing Rodgers evolutionary method. The inclusive years of bibliographic search started from 2005 to 2015. The search was conducted at PubMed©, CINAHL© 2017 John Wiley & Sons Australia, Ltd Nursing is a complex adaptive system, and the nursing profession in practice exhibits complex adaptive system characteristics. Complexity science through complex adaptive systems provides new ways of seeing and understanding the mechanisms that underpin the nursing profession.

  9. Stochastic Game Analysis and Latency Awareness for Self-Adaptation

    DTIC Science & Technology

    2014-01-01

    Tactic: is a primitive action that corresponds to a single step of adaptation, and has an associated: (i) cost/benefit impact on the different quality...dimensions, and (ii) latency, which corresponds to the time it takes since a tactic is started until its effect is observed.2 For instance, in... Gandhi et al. considers the setup time of servers, and is able to deal with unpredictable changes in load by be- ing conservative about removing servers

  10. Analysis and Synthesis of Adaptive Neural Elements and Assemblies.

    DTIC Science & Technology

    2007-11-02

    Form Approved REPORT DOCUMENTATION PAGE OMB No. 0704-0188 u,• thc renortc bsurden 4 ,r this collection of Information s estimated to averav i -our...motivational systems can influence behaviors, in part, by acting on motor systems, such as CPGs. Fourth, motor systems possess cellular mechanisms ...motor behaviors are governed by highly adaptive neural networks and help to explain how systems of nerve cells function to produce and modulate

  11. Adaption of Machine Fluid Analysis for Manufacturing - Final Report

    SciTech Connect

    Pardini, Allan F.

    2005-08-16

    Pacific Northwest National Laboratory (PNNL: Operated by Battelle Memorial Institute for the Department of Energy) is working with the Department of Energy (DOE) to develop technology for the US mining industry. Filtration and lubricant suppliers to the pulp and paper industry had noted the recent accomplishments by PNNL and its industrial partners in the DOE OIT Mining Industry of the Future Program, and asked for assistance in adapting this DOE-funded technology to the pulp and paper industry.

  12. Shielding analysis of the IEM cell offset adapter plate

    SciTech Connect

    Simons, R.L.

    1995-01-13

    The adapter plate for the Interim Examination and Maintenance (IEM) cell ten foot ceiling valve was modified so that the penetration through the valve is offset to the north side of the steel plate. The modifications required that the shielding effectiveness be evaluated for several operating conditions. The highest gamma ray dose rate (51 mrem/hr) occurs when a Core Component Container (CCC) with six high burn-up driver fuel assemblies is transferred into or out of Solid Waste Cask (SWC). The neutron dose rate at the same source location is 2.5 mrem/hr. The total dose rate during the transfer is less than the 200 mrem/hr limit. If the ten foot ceiling valve is closed, the dose rate with twelve DFA in the cell will be less than 0.1 mrem/hr. However, with the ceiling valve open the dose rate will be as high as 12 mrem/hr. The latter condition will require controlled access to the area around the offset adapter plate when the ceiling valve is open. It was found that gaps in the shield block around the SWC floor valve will allow contact dose rates as high as 350 mrem/hr during the transfer of a fully loaded CCC. Although this situation does not pertain to the offset adapter plate, it will require controlled access around the SWC valve during the transfer of a fully loaded CCC.

  13. Adaptive-filter models of the cerebellum: computational analysis.

    PubMed

    Dean, Paul; Porrill, John

    2008-01-01

    Many current models of the cerebellar cortical microcircuit are equivalent to an adaptive filter using the covariance learning rule. The adaptive filter is a development of the original Marr-Albus framework that deals naturally with continuous time-varying signals, thus addressing the issue of 'timing' in cerebellar function, and it can be connected in a variety of ways to other parts of the system, consistent with the microzonal organization of cerebellar cortex. However, its computational capacities are not well understood. Here we summarise the results of recent work that has focused on two of its intrinsic properties. First, an adaptive filter seeks to decorrelate its (mossy fibre) inputs from a (climbing fibre) teaching signal. This procedure can be used both for sensory processing, e.g. removal of interference from sensory signals, and for learning accurate motor commands, by decorrelating an efference copy of those commands from a sensory signal of inaccuracy. As a model of the cerebellum the adaptive filter thus forms a natural link between events at the cellular level, such as forms of synaptic plasticity and the learning rules they embody, and intelligent behaviour at the system level. Secondly, it has been shown that the covariance learning rule enables the filter to handle input and intrinsic noise optimally. Such optimality may underlie the recently described role of the cerebellum in producing accurate smooth pursuit eye movements in the face of sensory noise. Moreover, it has the consequence of driving most input weights to very small values, consistent with experimental data that many parallel-fibre synapses are normally silent. The effectiveness of silent synapses can only be altered by LTP, so learning tasks depending on a reduction of Purkinje cell firing require the synapses to be embedded in a second, inhibitory pathway from parallel fibre to Purkinje cell. This pathway and the appropriate climbing-fibre related plasticity have been described

  14. Adaptive Firefly Algorithm: Parameter Analysis and its Application

    PubMed Central

    Shen, Hong-Bin

    2014-01-01

    As a nature-inspired search algorithm, firefly algorithm (FA) has several control parameters, which may have great effects on its performance. In this study, we investigate the parameter selection and adaptation strategies in a modified firefly algorithm — adaptive firefly algorithm (AdaFa). There are three strategies in AdaFa including (1) a distance-based light absorption coefficient; (2) a gray coefficient enhancing fireflies to share difference information from attractive ones efficiently; and (3) five different dynamic strategies for the randomization parameter. Promising selections of parameters in the strategies are analyzed to guarantee the efficient performance of AdaFa. AdaFa is validated over widely used benchmark functions, and the numerical experiments and statistical tests yield useful conclusions on the strategies and the parameter selections affecting the performance of AdaFa. When applied to the real-world problem — protein tertiary structure prediction, the results demonstrated improved variants can rebuild the tertiary structure with the average root mean square deviation less than 0.4Å and 1.5Å from the native constrains with noise free and 10% Gaussian white noise. PMID:25397812

  15. The Adaptive Analysis of Visual Cognition using Genetic Algorithms

    PubMed Central

    Cook, Robert G.; Qadri, Muhammad A. J.

    2014-01-01

    Two experiments used a novel, open-ended, and adaptive test procedure to examine visual cognition in animals. Using a genetic algorithm, a pigeon was tested repeatedly from a variety of different initial conditions for its solution to an intermediate brightness search task. On each trial, the animal had to accurately locate and peck a target element of intermediate brightness from among a variable number of surrounding darker and lighter distractor elements. Displays were generated from six parametric variables, or genes (distractor number, element size, shape, spacing, target brightness, distractor brightness). Display composition changed over time, or evolved, as a function of the bird’s differential accuracy within the population of values for each gene. Testing three randomized initial conditions and one set of controlled initial conditions, element size and number of distractors were identified as the most important factors controlling search accuracy, with distractor brightness, element shape, and spacing making secondary contributions. The resulting changes in this multidimensional stimulus space suggested the existence of a set of conditions that the bird repeatedly converged upon regardless of initial conditions. This psychological “attractor” represents the cumulative action of the cognitive operations used by the pigeon in solving and performing this search task. The results are discussed regarding their implications for visual cognition in pigeons and the usefulness of adaptive, subject-driven experimentation for investigating human and animal cognition more generally. PMID:24000905

  16. Adaptive firefly algorithm: parameter analysis and its application.

    PubMed

    Cheung, Ngaam J; Ding, Xue-Ming; Shen, Hong-Bin

    2014-01-01

    As a nature-inspired search algorithm, firefly algorithm (FA) has several control parameters, which may have great effects on its performance. In this study, we investigate the parameter selection and adaptation strategies in a modified firefly algorithm - adaptive firefly algorithm (AdaFa). There are three strategies in AdaFa including (1) a distance-based light absorption coefficient; (2) a gray coefficient enhancing fireflies to share difference information from attractive ones efficiently; and (3) five different dynamic strategies for the randomization parameter. Promising selections of parameters in the strategies are analyzed to guarantee the efficient performance of AdaFa. AdaFa is validated over widely used benchmark functions, and the numerical experiments and statistical tests yield useful conclusions on the strategies and the parameter selections affecting the performance of AdaFa. When applied to the real-world problem - protein tertiary structure prediction, the results demonstrated improved variants can rebuild the tertiary structure with the average root mean square deviation less than 0.4Å and 1.5Å from the native constrains with noise free and 10% Gaussian white noise.

  17. Adaptive sequential Monte Carlo for multiple changepoint analysis

    DOE PAGES

    Heard, Nicholas A.; Turcotte, Melissa J. M.

    2016-05-21

    Process monitoring and control requires detection of structural changes in a data stream in real time. This paper introduces an efficient sequential Monte Carlo algorithm designed for learning unknown changepoints in continuous time. The method is intuitively simple: new changepoints for the latest window of data are proposed by conditioning only on data observed since the most recent estimated changepoint, as these observations carry most of the information about the current state of the process. The proposed method shows improved performance over the current state of the art. Another advantage of the proposed algorithm is that it can be mademore » adaptive, varying the number of particles according to the apparent local complexity of the target changepoint probability distribution. This saves valuable computing time when changes in the changepoint distribution are negligible, and enables re-balancing of the importance weights of existing particles when a significant change in the target distribution is encountered. The plain and adaptive versions of the method are illustrated using the canonical continuous time changepoint problem of inferring the intensity of an inhomogeneous Poisson process, although the method is generally applicable to any changepoint problem. Performance is demonstrated using both conjugate and non-conjugate Bayesian models for the intensity. Lastly, appendices to the article are available online, illustrating the method on other models and applications.« less

  18. Adaptive sequential Monte Carlo for multiple changepoint analysis

    SciTech Connect

    Heard, Nicholas A.; Turcotte, Melissa J. M.

    2016-05-21

    Process monitoring and control requires detection of structural changes in a data stream in real time. This paper introduces an efficient sequential Monte Carlo algorithm designed for learning unknown changepoints in continuous time. The method is intuitively simple: new changepoints for the latest window of data are proposed by conditioning only on data observed since the most recent estimated changepoint, as these observations carry most of the information about the current state of the process. The proposed method shows improved performance over the current state of the art. Another advantage of the proposed algorithm is that it can be made adaptive, varying the number of particles according to the apparent local complexity of the target changepoint probability distribution. This saves valuable computing time when changes in the changepoint distribution are negligible, and enables re-balancing of the importance weights of existing particles when a significant change in the target distribution is encountered. The plain and adaptive versions of the method are illustrated using the canonical continuous time changepoint problem of inferring the intensity of an inhomogeneous Poisson process, although the method is generally applicable to any changepoint problem. Performance is demonstrated using both conjugate and non-conjugate Bayesian models for the intensity. Lastly, appendices to the article are available online, illustrating the method on other models and applications.

  19. Analysis of adaptive algorithms for an integrated communication network

    NASA Technical Reports Server (NTRS)

    Reed, Daniel A.; Barr, Matthew; Chong-Kwon, Kim

    1985-01-01

    Techniques were examined that trade communication bandwidth for decreased transmission delays. When the network is lightly used, these schemes attempt to use additional network resources to decrease communication delays. As the network utilization rises, the schemes degrade gracefully, still providing service but with minimal use of the network. Because the schemes use a combination of circuit and packet switching, they should respond to variations in the types and amounts of network traffic. Also, a combination of circuit and packet switching to support the widely varying traffic demands imposed on an integrated network was investigated. The packet switched component is best suited to bursty traffic where some delays in delivery are acceptable. The circuit switched component is reserved for traffic that must meet real time constraints. Selected packet routing algorithms that might be used in an integrated network were simulated. An integrated traffic places widely varying workload demands on a network. Adaptive algorithms were identified, ones that respond to both the transient and evolutionary changes that arise in integrated networks. A new algorithm was developed, hybrid weighted routing, that adapts to workload changes.

  20. Assessing patients' anticoagulation preferences for the treatment of cancer-associated thrombosis using conjoint methodology.

    PubMed

    Noble, Simon; Matzdorff, Axel; Maraveyas, Anthony; Holm, Majbrit V; Pisa, Giovanni

    2015-11-01

    Low molecular weight heparins have demonstrated superiority over coumarins in the extended treatment of cancer-associated thrombosis and are recommended as first-line therapy in clinical guidelines. Non-vitamin K oral antagonists are yet to be evaluated against low molecular weight heparin for this indication. Nevertheless, a perception that patients favor oral anticoagulants over injections may lead to an increased prescribing of warfarin or non-vitamin K oral antagonists despite the evidence gap. There has been no evaluation of cancer patient preferences for anticoagulants and whether such an evidence gap is an acceptable trade-off for patients prescribed orals. We conducted a study to assess what features are most important to CAT patients regarding their choice of anticoagulant. Two modules were applied: Initial in-depth interviews with 9 patients diagnosed with cancer-associated thrombosis, and thereafter quantitative research, where a further 100 patients completed a choice-based-conjoint exercise, where 15 different scenarios were presented to identify the most important attributes of an anticoagulant. Seventy percent of the patients were treated with injected medication (low molecular weight heparin) and 30% with oral medications. Patients most valued an anticoagulant with minimal interference with their cancer treatment (39%), low thrombosis recurrence rate (24%), and low risk of major bleed (19%). Preference for oral administration over injection had moderate importance (13%). The results show that patients prefer an anticoagulant that does not interfere with their cancer treatment, suggesting the primacy of the cancer disease over venous thromboembolism in these patients. Patients also favor efficacy and safety over convenience of route of administration.

  1. The beauty of simple adaptive control and new developments in nonlinear systems stability analysis

    SciTech Connect

    Barkana, Itzhak

    2014-12-10

    Although various adaptive control techniques have been around for a long time and in spite of successful proofs of stability and even successful demonstrations of performance, the eventual use of adaptive control methodologies in practical real world systems has met a rather strong resistance from practitioners and has remained limited. Apparently, it is difficult to guarantee or even understand the conditions that can guarantee stable operations of adaptive control systems under realistic operational environments. Besides, it is difficult to measure the robustness of adaptive control system stability and allow it to be compared with the common and widely used measure of phase margin and gain margin that is utilized by present, mainly LTI, controllers. Furthermore, customary stability analysis methods seem to imply that the mere stability of adaptive systems may be adversely affected by any tiny deviation from the pretty idealistic and assumably required stability conditions. This paper first revisits the fundamental qualities of customary direct adaptive control methodologies, in particular the classical Model Reference Adaptive Control, and shows that some of their basic drawbacks have been addressed and eliminated within the so-called Simple Adaptive Control methodology. Moreover, recent developments in the stability analysis methods of nonlinear systems show that prior conditions that were customarily assumed to be needed for stability are only apparent and can be eliminated. As a result, sufficient conditions that guarantee stability are clearly stated and lead to similarly clear proofs of stability. As many real-world applications show, once robust stability of the adaptive systems can be guaranteed, the added value of using Add-On Adaptive Control along with classical Control design techniques is pushing the desired performance beyond any previous limits.

  2. The beauty of simple adaptive control and new developments in nonlinear systems stability analysis

    NASA Astrophysics Data System (ADS)

    Barkana, Itzhak

    2014-12-01

    Although various adaptive control techniques have been around for a long time and in spite of successful proofs of stability and even successful demonstrations of performance, the eventual use of adaptive control methodologies in practical real world systems has met a rather strong resistance from practitioners and has remained limited. Apparently, it is difficult to guarantee or even understand the conditions that can guarantee stable operations of adaptive control systems under realistic operational environments. Besides, it is difficult to measure the robustness of adaptive control system stability and allow it to be compared with the common and widely used measure of phase margin and gain margin that is utilized by present, mainly LTI, controllers. Furthermore, customary stability analysis methods seem to imply that the mere stability of adaptive systems may be adversely affected by any tiny deviation from the pretty idealistic and assumably required stability conditions. This paper first revisits the fundamental qualities of customary direct adaptive control methodologies, in particular the classical Model Reference Adaptive Control, and shows that some of their basic drawbacks have been addressed and eliminated within the so-called Simple Adaptive Control methodology. Moreover, recent developments in the stability analysis methods of nonlinear systems show that prior conditions that were customarily assumed to be needed for stability are only apparent and can be eliminated. As a result, sufficient conditions that guarantee stability are clearly stated and lead to similarly clear proofs of stability. As many real-world applications show, once robust stability of the adaptive systems can be guaranteed, the added value of using Add-On Adaptive Control along with classical Control design techniques is pushing the desired performance beyond any previous limits.

  3. Adaptively resizing populations: Algorithm, analysis, and first results

    NASA Technical Reports Server (NTRS)

    Smith, Robert E.; Smuda, Ellen

    1993-01-01

    Deciding on an appropriate population size for a given Genetic Algorithm (GA) application can often be critical to the algorithm's success. Too small, and the GA can fall victim to sampling error, affecting the efficacy of its search. Too large, and the GA wastes computational resources. Although advice exists for sizing GA populations, much of this advice involves theoretical aspects that are not accessible to the novice user. An algorithm for adaptively resizing GA populations is suggested. This algorithm is based on recent theoretical developments that relate population size to schema fitness variance. The suggested algorithm is developed theoretically, and simulated with expected value equations. The algorithm is then tested on a problem where population sizing can mislead the GA. The work presented suggests that the population sizing algorithm may be a viable way to eliminate the population sizing decision from the application of GA's.

  4. Adaptive Multi-Rate Compression Effects on Vowel Analysis

    PubMed Central

    Ireland, David; Knuepffer, Christina; McBride, Simon J.

    2015-01-01

    Signal processing on digitally sampled vowel sounds for the detection of pathological voices has been firmly established. This work examines compression artifacts on vowel speech samples that have been compressed using the adaptive multi-rate codec at various bit-rates. Whereas previous work has used the sensitivity of machine learning algorithm to test for accuracy, this work examines the changes in the extracted speech features themselves and thus report new findings on the usefulness of a particular feature. We believe this work will have potential impact for future research on remote monitoring as the identification and exclusion of an ill-defined speech feature that has been hitherto used, will ultimately increase the robustness of the system. PMID:26347863

  5. Adapting Job Analysis Methodology to Improve Evaluation Practice

    ERIC Educational Resources Information Center

    Jenkins, Susan M.; Curtin, Patrick

    2006-01-01

    This article describes how job analysis, a method commonly used in personnel research and organizational psychology, provides a systematic method for documenting program staffing and service delivery that can improve evaluators' knowledge about program operations. Job analysis data can be used to increase evaluators' insight into how staffs…

  6. Multi-channel holographic birfurcative neural network system for real-time adaptive EOS data analysis

    NASA Technical Reports Server (NTRS)

    Liu, Hua-Kuang; Diep, J.; Huang, K.

    1991-01-01

    Viewgraphs on multi-channel holographic bifurcative neural network system for real-time adaptive Earth Observing System (EOS) data analysis are presented. The objective is to research and develop an optical bifurcating neuromorphic pattern recognition system for making optical data array comparisons and to evaluate the use of the system for EOS data classification, reduction, analysis, and other applications.

  7. Analysis of modified SMI method for adaptive array weight control

    NASA Technical Reports Server (NTRS)

    Dilsavor, R. L.; Moses, R. L.

    1989-01-01

    An adaptive array is applied to the problem of receiving a desired signal in the presence of weak interference signals which need to be suppressed. A modification, suggested by Gupta, of the sample matrix inversion (SMI) algorithm controls the array weights. In the modified SMI algorithm, interference suppression is increased by subtracting a fraction F of the noise power from the diagonal elements of the estimated covariance matrix. Given the true covariance matrix and the desired signal direction, the modified algorithm is shown to maximize a well-defined, intuitive output power ratio criterion. Expressions are derived for the expected value and variance of the array weights and output powers as a function of the fraction F and the number of snapshots used in the covariance matrix estimate. These expressions are compared with computer simulation and good agreement is found. A trade-off is found to exist between the desired level of interference suppression and the number of snapshots required in order to achieve that level with some certainty. The removal of noise eigenvectors from the covariance matrix inverse is also discussed with respect to this application. Finally, the type and severity of errors which occur in the covariance matrix estimate are characterized through simulation.

  8. Secretome analysis revealed adaptive and non-adaptive responses of the Staphylococcus carnosus femB mutant.

    PubMed

    Nega, Mulugeta; Dube, Linda; Kull, Melanie; Ziebandt, Anne-Kathrin; Ebner, Patrick; Albrecht, Dirk; Krismer, Bernhard; Rosenstein, Ralf; Hecker, Michael; Götz, Friedrich

    2015-04-01

    FemABX peptidyl transferases are involved in non-ribosomal pentaglycine interpeptide bridge biosynthesis. Here, we characterized the phenotype of a Staphylococcus carnosus femB deletion mutant, which was affected in growth and showed pleiotropic effects such as enhanced methicillin sensitivity, lysostaphin resistance, cell clustering, and decreased peptidoglycan cross-linking. However, comparative secretome analysis revealed a most striking difference in the massive secretion or release of proteins into the culture supernatant in the femB mutant than the wild type. The secreted proteins can be categorized into typical cytosolic proteins and various murein hydrolases. As the transcription of the murein hydrolase genes was up-regulated in the mutant, they most likely represent an adaption response to the life threatening mutation. Even though the transcription of the cytosolic protein genes was unaltered, their high abundance in the supernatant of the mutant is most likely due to membrane leakage triggered by the weakened murein sacculus and enhanced autolysins.

  9. Transcriptome analysis reveals signature of adaptation to landscape fragmentation.

    PubMed

    Somervuo, Panu; Kvist, Jouni; Ikonen, Suvi; Auvinen, Petri; Paulin, Lars; Koskinen, Patrik; Holm, Liisa; Taipale, Minna; Duplouy, Anne; Ruokolainen, Annukka; Saarnio, Suvi; Sirén, Jukka; Kohonen, Jukka; Corander, Jukka; Frilander, Mikko J; Ahola, Virpi; Hanski, Ilkka

    2014-01-01

    We characterize allelic and gene expression variation between populations of the Glanville fritillary butterfly (Melitaea cinxia) from two fragmented and two continuous landscapes in northern Europe. The populations exhibit significant differences in their life history traits, e.g. butterflies from fragmented landscapes have higher flight metabolic rate and dispersal rate in the field, and higher larval growth rate, than butterflies from continuous landscapes. In fragmented landscapes, local populations are small and have a high risk of local extinction, and hence the long-term persistence at the landscape level is based on frequent re-colonization of vacant habitat patches, which is predicted to select for increased dispersal rate. Using RNA-seq data and a common garden experiment, we found that a large number of genes (1,841) were differentially expressed between the landscape types. Hexamerin genes, the expression of which has previously been shown to have high heritability and which correlate strongly with larval development time in the Glanville fritillary, had higher expression in fragmented than continuous landscapes. Genes that were more highly expressed in butterflies from newly-established than old local populations within a fragmented landscape were also more highly expressed, at the landscape level, in fragmented than continuous landscapes. This result suggests that recurrent extinctions and re-colonizations in fragmented landscapes select a for specific expression profile. Genes that were significantly up-regulated following an experimental flight treatment had higher basal expression in fragmented landscapes, indicating that these butterflies are genetically primed for frequent flight. Active flight causes oxidative stress, but butterflies from fragmented landscapes were more tolerant of hypoxia. We conclude that differences in gene expression between the landscape types reflect genomic adaptations to landscape fragmentation.

  10. Application of Avco data analysis and prediction techniques (ADAPT) to prediction of sunspot activity

    NASA Technical Reports Server (NTRS)

    Hunter, H. E.; Amato, R. A.

    1972-01-01

    The results are presented of the application of Avco Data Analysis and Prediction Techniques (ADAPT) to derivation of new algorithms for the prediction of future sunspot activity. The ADAPT derived algorithms show a factor of 2 to 3 reduction in the expected 2-sigma errors in the estimates of the 81-day running average of the Zurich sunspot numbers. The report presents: (1) the best estimates for sunspot cycles 20 and 21, (2) a comparison of the ADAPT performance with conventional techniques, and (3) specific approaches to further reduction in the errors of estimated sunspot activity and to recovery of earlier sunspot historical data. The ADAPT programs are used both to derive regression algorithm for prediction of the entire 11-year sunspot cycle from the preceding two cycles and to derive extrapolation algorithms for extrapolating a given sunspot cycle based on any available portion of the cycle.

  11. Bounded Linear Stability Analysis - A Time Delay Margin Estimation Approach for Adaptive Control

    NASA Technical Reports Server (NTRS)

    Nguyen, Nhan T.; Ishihara, Abraham K.; Krishnakumar, Kalmanje Srinlvas; Bakhtiari-Nejad, Maryam

    2009-01-01

    This paper presents a method for estimating time delay margin for model-reference adaptive control of systems with almost linear structured uncertainty. The bounded linear stability analysis method seeks to represent the conventional model-reference adaptive law by a locally bounded linear approximation within a small time window using the comparison lemma. The locally bounded linear approximation of the combined adaptive system is cast in a form of an input-time-delay differential equation over a small time window. The time delay margin of this system represents a local stability measure and is computed analytically by a matrix measure method, which provides a simple analytical technique for estimating an upper bound of time delay margin. Based on simulation results for a scalar model-reference adaptive control system, both the bounded linear stability method and the matrix measure method are seen to provide a reasonably accurate and yet not too conservative time delay margin estimation.

  12. VALUATION OF VISIBILITY: A CONJOINT ANALYSIS STUDY IN THE WHITE MOUNTAIN NATIONAL FOREST (R825824)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  13. Adaptive unstructured meshing for thermal stress analysis of built-up structures

    NASA Technical Reports Server (NTRS)

    Dechaumphai, Pramote

    1992-01-01

    An adaptive unstructured meshing technique for mechanical and thermal stress analysis of built-up structures has been developed. A triangular membrane finite element and a new plate bending element are evaluated on a panel with a circular cutout and a frame stiffened panel. The adaptive unstructured meshing technique, without a priori knowledge of the solution to the problem, generates clustered elements only where needed. An improved solution accuracy is obtained at a reduced problem size and analysis computational time as compared to the results produced by the standard finite element procedure.

  14. Performance Analysis of Adaptive Volterra Filters in the Finite-Alphabet Input Case

    NASA Astrophysics Data System (ADS)

    Besbes, Hichem; Jaïdane, Mériem; Ezzine, Jelel

    2004-12-01

    This paper deals with the analysis of adaptive Volterra filters, driven by the LMS algorithm, in the finite-alphabet inputs case. A tailored approach for the input context is presented and used to analyze the behavior of this nonlinear adaptive filter. Complete and rigorous mean square analysis is provided without any constraining independence assumption. Exact transient and steady-state performances expressed in terms of critical step size, rate of transient decrease, optimal step size, excess mean square error in stationary mode, and tracking nonstationarities are deduced.

  15. Is adaptation or transformation needed? Active nanomaterials and risk analysis

    NASA Astrophysics Data System (ADS)

    Kuzma, Jennifer; Roberts, John Patrick

    2016-07-01

    Nanotechnology has been a key area of funding and policy for the United States and globally for the past two decades. Since nanotechnology research and development became a focus and nanoproducts began to permeate the market, scholars and scientists have been concerned about how to assess the risks that they may pose to human health and the environment. The newest generation of nanomaterials includes biomolecules that can respond to and influence their environments, and there is a need to explore whether and how existing risk-analysis frameworks are challenged by such novelty. To fill this niche, we used a modified approach of upstream oversight assessment (UOA), a subset of anticipatory governance. We first selected case studies of "active nanomaterials," that are early in research and development and designed for use in multiple sectors, and then considered them under several, key risk-analysis frameworks. We found two ways in which the cases challenge the frameworks. The first category relates to how to assess risk under a narrow framing of the term (direct health and environmental harm), and the second involves the definition of what constitutes a "risk" worthy of assessment and consideration in decision making. In light of these challenges, we propose some changes for risk analysis in the face of active nanostructures in order to improve risk governance.

  16. Design and analysis of closed-loop decoder adaptation algorithms for brain-machine interfaces.

    PubMed

    Dangi, Siddharth; Orsborn, Amy L; Moorman, Helene G; Carmena, Jose M

    2013-07-01

    Closed-loop decoder adaptation (CLDA) is an emerging paradigm for achieving rapid performance improvements in online brain-machine interface (BMI) operation. Designing an effective CLDA algorithm requires making multiple important decisions, including choosing the timescale of adaptation, selecting which decoder parameters to adapt, crafting the corresponding update rules, and designing CLDA parameters. These design choices, combined with the specific settings of CLDA parameters, will directly affect the algorithm's ability to make decoder parameters converge to values that optimize performance. In this article, we present a general framework for the design and analysis of CLDA algorithms and support our results with experimental data of two monkeys performing a BMI task. First, we analyze and compare existing CLDA algorithms to highlight the importance of four critical design elements: the adaptation timescale, selective parameter adaptation, smooth decoder updates, and intuitive CLDA parameters. Second, we introduce mathematical convergence analysis using measures such as mean-squared error and KL divergence as a useful paradigm for evaluating the convergence properties of a prototype CLDA algorithm before experimental testing. By applying these measures to an existing CLDA algorithm, we demonstrate that our convergence analysis is an effective analytical tool that can ultimately inform and improve the design of CLDA algorithms.

  17. Probabilistic Seismic Hazard Analysis: Adaptation for CO2 Sequestration Sites

    NASA Astrophysics Data System (ADS)

    Vasudevan, K.; Eaton, D. W.

    2011-12-01

    Large-scale sequestration of CO2 in depleted oil and gas fields in sedimentary basins such as the Western Canada Sedimentary Basin (WCSB) and in particular, central Alberta, should consider, among other safety and risk issues, a seismic hazard analysis that would include potential ground motions induced by earthquakes. The region is juxtaposed to major tectonically active seismogenic zones such as the Cascadia Subduction Zone, the Queen Charlotte Fault Zone, and the northern Cordillera region. Hazards associated with large-scale storage from strong ground motions caused by large-magnitude earthquakes along the west coast of Canada, and/or medium-to-large magnitude earthquakes triggered by such earthquakes in the neighbourhood of the storage site, must be clearly understood. To this end, stochastic modeling of the accelerograms recorded during large magnitude earthquakes in western Canada has been undertaken. A lack of recorded accelerograms and the absence of a catalogue of ground-motion prediction equations similar to the Next Generation Attenuation (NGA) database, however, hamper such analysis for the WCSB. In order to generate our own database of ground-motions for probabilistic seismic hazard analysis, we employ a site-based stochastic simulation approach. We use it to simulate three-component ground-motion accelerograms recorded during the November 3, 2002 Denali earthquake to mimic the Queen Charlotte Fault earthquakes. To represent a Cascadia megathrust earthquake, we consider three-component strong-motion accelerograms recorded during the March 11, 2011 Tohoku earthquake in Japan. Finally, to simulate an event comparable to the thrust-style Kinbasket Lake earthquake of 1908, we use three-component ground-motion accelerograms recorded during the 1985 Nahanni earthquake and the 2004 Chuetsu earthquake. Here, we develop predictive equations for the stochastic model parameters that describe ground motions in terms of earthquake and site characteristics such as

  18. Finite Element Analysis of Adaptive-Stiffening and Shape-Control SMA Hybrid Composites

    NASA Technical Reports Server (NTRS)

    Gao, Xiujie; Burton, Deborah; Turner, Travis L.; Brinson, Catherine

    2005-01-01

    Shape memory alloy hybrid composites with adaptive-stiffening or morphing functions are simulated using finite element analysis. The composite structure is a laminated fiber-polymer composite beam with embedded SMA ribbons at various positions with respect to the neutral axis of the beam. Adaptive stiffening or morphing is activated via selective resistance heating of the SMA ribbons or uniform thermal loads on the beam. The thermomechanical behavior of these composites was simulated in ABAQUS using user-defined SMA elements. The examples demonstrate the usefulness of the methods for the design and simulation of SMA hybrid composites. Keywords: shape memory alloys, Nitinol, ABAQUS, finite element analysis, post-buckling control, shape control, deflection control, adaptive stiffening, morphing, constitutive modeling, user element

  19. Space-adaptive spectral analysis of hyperspectral imagery

    NASA Astrophysics Data System (ADS)

    Alparone, Luciano; Argenti, Fabrizio; Dionisio, Michele; Facheris, Luca

    2003-03-01

    The aim of this paper is investigating the use of overcomplete bases for the representation of hyperspectral image data. The idea is building an overcomplete basis starting from several orthogonal or non-orthogonal bases and picking up a set of vectors fitting pixel spectra to the largest extent. A common technique to select the most representative elements of a signal is Matching Pursuit (MP). This technique is analogous to the Mixed-Transform Analysis (MTA) and has been successfully used to represent speech and images. The main problems in using MTA for hyperspectral data analysis are: (1) choice of bases that potentially convey the maximum of spectral information; (2) calculation of projections in the non-orthogonal representation. A large variety of bases has been taken into consideration, including several types of wavelets with compact support. An iterative approach is used to find the coefficients of the linear combination of vectors, so that the residual function has minimum energy. The computational cost is extrmeely high when a large set of data is to be processed. To encompass computational constraints, a reduced data set (RDS) is produced by applying the projection pursuit technique to each of the square blocks in which the input hyperspectral iamge is partitioned based on a spatial homogeneity criterion. Then MTA is applied to the RDS to find out a non-orthogonal frame capable to represent such data through waveforms selected to best match spectral features. Experimental results carried out on the hyperspectral data AVIRIS Moffett Field '97 show the joint use of different bases, including wavelet bases, may be preferable to a unique orthogonal basis in terms of energy compaction, was well as of significance of the outcome components.

  20. Adaptive Denoising Technique for Robust Analysis of Functional Magnetic Resonance Imaging Data

    DTIC Science & Technology

    2007-11-02

    or receive while t fMRI o versatil of epoc method ER-fM to the studies comes intra-su functioADAPTIVE DENOISING TECHNIQUE FOR ROBUST ANALYSIS OF...supported in part by the Center for Advanced Software and Biomedical Engineering Consultations (CASBEC), Cairo University, and IBE Technologies , Egypt

  1. Solid rocket booster internal flow analysis by highly accurate adaptive computational methods

    NASA Technical Reports Server (NTRS)

    Huang, C. Y.; Tworzydlo, W.; Oden, J. T.; Bass, J. M.; Cullen, C.; Vadaketh, S.

    1991-01-01

    The primary objective of this project was to develop an adaptive finite element flow solver for simulating internal flows in the solid rocket booster. Described here is a unique flow simulator code for analyzing highly complex flow phenomena in the solid rocket booster. New methodologies and features incorporated into this analysis tool are described.

  2. Adaptive wavelet analysis of optical coherent tomography data: Application in problems of diagnostics

    NASA Astrophysics Data System (ADS)

    Nazimov, A. I.; Pavlov, A. N.; Lychagov, V. V.; Semyachkina-Glushkovskaya, O. V.

    2013-10-01

    A method of adaptive wavelet analysis permitting one to set parameters of the wavelet transform based on principles of the optimization theory is proposed. Applying the method to optical coherent tomography data processing is considered. The efficiency of the proposed method for diagnosing functional disorders in the dynamics of cerebral vessels is illustrated.

  3. Adaptive Spatial Filtering with Principal Component Analysis for Biomedical Photoacoustic Imaging

    NASA Astrophysics Data System (ADS)

    Nagaoka, Ryo; Yamazaki, Rena; Saijo, Yoshifumi

    Photoacoustic (PA) signal is very sensitive to noise generated by peripheral equipment such as power supply, stepping motor or semiconductor laser. Band-pass filter is not effective because the frequency bandwidth of the PA signal also covers the noise frequency. The objective of the present study is to reduce the noise by using an adaptive spatial filter with principal component analysis (PCA).

  4. Adaptive Web-Assisted Learning System for Students with Specific Learning Disabilities: A Needs Analysis Study

    ERIC Educational Resources Information Center

    Polat, Elif; Adiguzel, Tufan; Akgun, Ozcan Erkan

    2012-01-01

    Because there is, currently, no education system for primary school students in grades 1-3 who have specific learning disabilities in Turkey and because such students do not receive sufficient support from face-to-face counseling, a needs analysis was conducted in order to prepare an adaptive, web-assisted learning system according to variables…

  5. Analysis of the Same Subject in Diverse Periodicals: One Method for Teaching Audience Adaptation.

    ERIC Educational Resources Information Center

    Bradford, Annette N.; Whitburn, Merrill D.

    1982-01-01

    Examines two technical writing assignments involving analysis of particular audience adaptive techniques used in five published technical articles from diverse sources on the same limited subject. The first is a discussion exercise involving the entire class, and the second is an individual written exercise. (HTH)

  6. An Exploratory Evaluation of Conjoint Behavioral Consultation to Promote Collaboration among Family, School, and Pediatric Systems: A Role for Pediatric School Psychologists

    ERIC Educational Resources Information Center

    Sheridan, Susan M.; Warnes, Emily D.; Woods, Kathryn E.; Blevins, Carrie A.; Magee, Katie L.; Ellis, Cynthia

    2009-01-01

    Pediatric school psychology is a relatively new subspecialty in the field; however, few specific, prescribed roles have been articulated, and fewer have yielded preliminary efficacy data. In this exploratory study, the acceptability and potential efficacy of conjoint behavioral consultation (CBC) as a model for linking families, schools, and…

  7. Experimental analysis of adaptive optics compensation in free-space coherent laser communications

    NASA Astrophysics Data System (ADS)

    Anzuola, Esdras; Belmonte, Aniceto

    2016-09-01

    In this work we present a practical, experimental analysis of the effects of adaptive optics compensation on the performance of free-space coherent optical receivers. In order to fulfill this objective, we have developed a laboratory test bed for simulating atmospheric turbulence using Kolmogorov statistics; we have implemented a digital-signal-processing-based phase shift keying heterodyne coherent receiver; and we have integrated a compact module operating a low-cost adaptive optics system that applies modal and zonal wavefront correction. We have checked our experimental results against previously reported analytical models describing the performance of coherent receivers using atmospheric compensation techniques.

  8. Analysis of Adaptive Mesh Refinement for IMEX Discontinuous Galerkin Solutions of the Compressible Euler Equations with Application to Atmospheric Simulations

    DTIC Science & Technology

    2013-01-01

    Analysis of Adaptive Mesh Refinement for IMEX Discontinuous Galerkin Solutions of the Compressible Euler Equations with Application to Atmospheric...order discontinuous Galerkin method on quadrilateral grids with non-conforming elements. We perform a detailed analysis of the cost of AMR by comparing...adaptive mesh refinement, discontinuous Galerkin method, non-conforming mesh, IMEX, compressible Euler equations, atmospheric simulations 1. Introduction

  9. Comprehensive Transcriptome Analysis Provides Evidence of Local Thermal Adaptation in Three Loaches (Genus: Misgurnus)

    PubMed Central

    Yi, Shaokui; Wang, Sai; Zhong, Jia; Wang, Weimin

    2016-01-01

    The geographic distribution of three Misgurnus species, M. anguillicaudatus, M. bipartitus, and M. mohoity, displays a specific pattern in China, coincident with temperature zones. In this study, we sequenced the transcriptomes of these three species and used the sequences to investigate the lineage-specific adaptations within the genus Misgurnus. In total, 51 orphan genes (19 in M. anguillicaudatus, 18 in M. bipartitus, and 14 in M. mohoity) that may contribute to the species-specific adaptations were identified. An analysis of 1392 one-to-one orthologous genes revealed significantly higher ratios of nonsynonymous-to-synonymous substitutions in the M. mohoity lineage than in M. anguillicaudatus. The genes displaying signatures of positive selection and rapid evolution in Misgurnus were involved in four function categories, (1) energy metabolism; (2) signal transduction; (3) membrane; and (4) cell proliferation or apoptosis, implying that these candidate genes play critical roles in the thermal adaptation of the fish to their living environments. We also detected more than five positively selected sites in cldn15lb and isca1, which function as important factors in paracellular Na+ transport and Fe/S cluster assembly, respectively. Overall, our study provides valuable insights into the adaptive evolution of loaches from different temperature zones in China and is a foundation for future studies to clarify the genetic basis of temperature adaptation in fishes. PMID:27886141

  10. Analysis of Affordance, Time, and Adaptation in the Assessment of Industrial Control System Cybersecurity Risk.

    PubMed

    Busby, J S; Green, B; Hutchison, D

    2017-01-17

    Industrial control systems increasingly use standard communication protocols and are increasingly connected to public networks-creating substantial cybersecurity risks, especially when used in critical infrastructures such as electricity and water distribution systems. Methods of assessing risk in such systems have recognized for some time the way in which the strategies of potential adversaries and risk managers interact in defining the risk to which such systems are exposed. But it is also important to consider the adaptations of the systems' operators and other legitimate users to risk controls, adaptations that often appear to undermine these controls, or shift the risk from one part of a system to another. Unlike the case with adversarial risk analysis, the adaptations of system users are typically orthogonal to the objective of minimizing or maximizing risk in the system. We argue that this need to analyze potential adaptations to risk controls is true for risk problems more generally, and we develop a framework for incorporating such adaptations into an assessment process. The method is based on the principle of affordances, and we show how this can be incorporated in an iterative procedure based on raising the minimum period of risk materialization above some threshold. We apply the method in a case study of a small European utility provider and discuss the observations arising from this.

  11. The conjoint use of music therapy and reflexology with hospitalized advanced stage cancer patients and their families.

    PubMed

    Magill, Lucanne; Berenson, Susan

    2008-09-01

    Advanced stage cancer patients experience debilitating physical symptoms as well as profound emotional and spiritual struggles. Advanced disease is accompanied by multiple changes and losses for the patient and the family. Palliative care focuses on the relief of overall suffering of patients and families, including symptom control, psychosocial support, and the meeting of spiritual needs. Music therapy and reflexology are complementary therapies that can soothe and provide comfort. When used conjointly, they provide a multifaceted experience that can aid in the reduction of anxiety, pain, and isolation; facilitate communication between patients, family members, and staff; and provide the potential for a more peaceful dying experience for all involved. This article addresses the benefits of the combined use of music therapy and reflexology. Two case studies are presented to illustrate the application and benefits of this dual approach for patients and their families regarding adjustment to the end of life in the presence of anxiety and cognitive impairment.

  12. NAD(P)H: Quinone Oxidoreductase 1 Deficiency Conjoint with Marginal Vitamin C Deficiency Causes Cigarette Smoke Induced Myelodysplastic Syndromes

    PubMed Central

    Das, Archita; Dey, Neekkan; Ghosh, Arunava; Das, Tanusree; Chatterjee, Indu B.

    2011-01-01

    Background The etiology of myelodysplastic syndromes (MDS) is largely unknown. Exposure to cigarette smoke (CS) is reported to be associated with MDS risk. There is inconsistent evidence that deficiency of NAD(P)H-quinone: oxidoreductase 1 (NQO1) increases the risk of MDS. Earlier we had shown that CS induces toxicity only in marginal vitamin C-deficient guinea pigs but not in vitamin C-sufficient ones. We therefore considered that NQO1 deficiency along with marginal vitamin C deficiency might produce MDS in CS-exposed guinea pigs. Methodology and Principal Findings Here we show that CS exposure for 21 days produces MDS in guinea pigs having deficiency of NQO1 (fed 3 mg dicoumarol/day) conjoint with marginal vitamin C deficiency (fed 0.5 mg vitamin C/day). As evidenced by morphology, histology and cytogenetics, MDS produced in the guinea pigs falls in the category of refractory cytopenia with unilineage dysplasia (RCUD): refractory anemia; refractory thrombocytopenia that is associated with ring sideroblasts, micromegakaryocytes, myeloid hyperplasia and aneuploidy. MDS is accompanied by increased CD34(+) cells and oxidative stress as shown by the formation of protein carbonyls and 8-oxodeoxyguanosine. Apoptosis precedes MDS but disappears later with marked decrease in the p53 protein. MDS produced in the guinea pigs are irreversible. MDS and all the aforesaid pathophysiological events do not occur in vitamin C-sufficient guinea pigs. However, after the onset of MDS vitamin C becomes ineffective. Conclusions and Significance CS exposure causes MDS in guinea pigs having deficiency of NQO1 conjoint with marginal vitamin C deficiency. The syndromes are not produced in singular deficiency of NQO1 or marginal vitamin C deficiency. Our results suggest that human smokers having NQO1 deficiency combined with marginal vitamin C deficiency are likely to be at high risk for developing MDS and that intake of a moderately large dose of vitamin C would prevent MDS. PMID:21655231

  13. Effect of conjoint administration of tamoxifen and high-dose radiation on the development of mammary carcinoma

    SciTech Connect

    Kantorowitz, D.A. ); Thompson, H.J. ); Furmanski, P. )

    1993-04-30

    Tamoxifen is currently advocated for post-menopausal breast cancer patients receiving definitive irradiation after limited surgery. The purpose of this study was to assess in an experimental model for breast cancer whether the efficacy of irradiation is altered by conjoint administration of tamoxifen. To this end, rats with small tumors induced by 1-methyl-1-nitrosourea (MNU) were treated with tamoxifen, radiation, or a combination of the two modalities. Female Sprague Dawley rats were injected i.p. with 50 mg MNU/kg body weight at 50 days of age. At 64 days post carcinogen, the majority of the rats had at least one palpable mammary tumor. At that time radiation with or without tamoxifen treatment was initiated and given 5 days per week for 5 weeks. Radiation dose was 4500 cGy delivered as 25, 180 cGy fractions. Tamoxifen, 500 mg/kg body weight, was administered subcutaneously each day during the irradiation interval. The study was terminated 28 weeks after carcinogen treatment. High dose radiation alone induced a reduction in the size of existing tumors, but resulted in a significant increase in the number of tumors that were detected. Treatment with tamoxifen alone also caused a reduction in tumor volume, but had no effect on final incidence or number of mammary tumors. Combined modality treatment resulted in a significant reduction in the volume of existing tumors and suppressed the enhanced occurrence of additional tumors observed when only radiation alone was administered. The findings of this study indicate that in the context of fractionated, high dose radiation treatment of established mammary cancers, tamoxifen may reduce the likelihood of subsequent tumor development and by so doing prove a helpful simultaneous conjoint adjuvant treatment to post-operative irradiation. 35 refs., 1 fig., 2 tabs.

  14. Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis

    PubMed Central

    Cañas, Rafael A.; Canales, Javier; Muñoz-Hernández, Carmen; Granados, Jose M.; Ávila, Concepción; García-Martín, María L.; Cánovas, Francisco M.

    2015-01-01

    Conifers include long-lived evergreen trees of great economic and ecological importance, including pines and spruces. During their long lives conifers must respond to seasonal environmental changes, adapt to unpredictable environmental stresses, and co-ordinate their adaptive adjustments with internal developmental programmes. To gain insights into these responses, we examined metabolite and transcriptomic profiles of needles from naturally growing 25-year-old maritime pine (Pinus pinaster L. Aiton) trees over a year. The effect of environmental parameters such as temperature and rain on needle development were studied. Our results show that seasonal changes in the metabolite profiles were mainly affected by the needles’ age and acclimation for winter, but changes in transcript profiles were mainly dependent on climatic factors. The relative abundance of most transcripts correlated well with temperature, particularly for genes involved in photosynthesis or winter acclimation. Gene network analysis revealed relationships between 14 co-expressed gene modules and development and adaptation to environmental stimuli. Novel Myb transcription factors were identified as candidate regulators during needle development. Our systems-based analysis provides integrated data of the seasonal regulation of maritime pine growth, opening new perspectives for understanding the complex regulatory mechanisms underlying conifers’ adaptive responses. Taken together, our results suggest that the environment regulates the transcriptome for fine tuning of the metabolome during development. PMID:25873654

  15. Adaptive isogeometric analysis based on a combined r-h strategy

    NASA Astrophysics Data System (ADS)

    Basappa, Umesh; Rajagopal, Amirtham; Reddy, J. N.

    2016-03-01

    In the present work, an r-h adaptive isogeometric analysis is proposed for plane elasticity problems. For performing the r-adaption, the control net is considered to be a network of springs with the individual spring stiffness values being proportional to the error estimated at the control points. While preserving the boundary control points, relocation of only the interior control points is made by adopting a successive relaxation approach to achieve the equilibrium of spring system. To suit the noninterpolatory nature of the isogeometric approximation, a new point-wise error estimate for the h-refinement is proposed. To evaluate the point-wise error, hierarchical B-spline functions in Sobolev spaces are considered. The proposed adaptive h-refinement strategy is based on using De-Casteljau's algorithm for obtaining the new control points. The subsequent control meshes are thus obtained by using a recursive subdivision of reference control mesh. Such a strategy ensures that the control points lie in the physical domain in subsequent refinements, thus making the physical mesh to exactly interpolate the control mesh and thereby allowing the exact imposition of essential boundary conditions in the classical isogeometric analysis (IGA). The combined r-h adaptive refinement strategy results in better convergence characteristics with reduced errors than r- or h-refinement. Several numerical examples are presented to illustrate the efficiency of the proposed approach.

  16. Adaptive Forward Modeling Method for Analysis and Reconstructions of Orientation Image Map

    SciTech Connect

    Frankie Li, Shiu Fai

    2014-06-01

    IceNine is a MPI-parallel orientation reconstruction and microstructure analysis code. It's primary purpose is to reconstruct a spatially resolved orientation map given a set of diffraction images from a high energy x-ray diffraction microscopy (HEDM) experiment (1). In particular, IceNine implements the adaptive version of the forward modeling method (2, 3). Part of IceNine is a library used to for conbined analysis of the microstructure with the experimentally measured diffraction signal. The libraries is also designed for tapid prototyping of new reconstruction and analysis algorithms. IceNine is also built with a simulator of diffraction images with an input microstructure.

  17. Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

    PubMed Central

    Wang, Hongju; Liu, Siqing; Zhang, Bo

    2016-01-01

    Zika virus (ZIKV) is a mosquito-borne virus (arbovirus) in the family Flaviviridae, and the symptoms caused by ZIKV infection in humans include rash, fever, arthralgia, myalgia, asthenia and conjunctivitis. Codon usage bias analysis can reveal much about the molecular evolution and host adaption of ZIKV. To gain insight into the evolutionary characteristics of ZIKV, we performed a comprehensive analysis on the codon usage pattern in 46 ZIKV strains by calculating the effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and other indicators. The results indicate that the codon usage bias of ZIKV is relatively low. Several lines of evidence support the hypothesis that translational selection plays a role in shaping the codon usage pattern of ZIKV. The results from a correspondence analysis (CA) indicate that other factors, such as base composition, aromaticity, and hydrophobicity may also be involved in shaping the codon usage pattern of ZIKV. Additionally, the results from a comparative analysis of RSCU between ZIKV and its hosts suggest that ZIKV tends to evolve codon usage patterns that are comparable to those of its hosts. Moreover, selection pressure from Homo sapiens on the ZIKV RSCU patterns was found to be dominant compared with that from Aedes aegypti and Aedes albopictus. Taken together, both natural translational selection and mutation pressure are important for shaping the codon usage pattern of ZIKV. Our findings contribute to understanding the evolution of ZIKV and its adaption to its hosts. PMID:27893824

  18. Analysis of adaptive laser scanning optical system with focus-tunable components

    NASA Astrophysics Data System (ADS)

    Pokorný, P.; Mikš, A.; Novák, J.; Novák, P.

    2015-05-01

    This work presents a primary analysis of an adaptive laser scanner based on two-mirror beam-steering device and focustunable components (lenses with tunable focal length). It is proposed an optical scheme of an adaptive laser scanner, which can focus the laser beam in a continuous way to a required spatial position using the lens with tunable focal length. This work focuses on a detailed analysis of the active optical or opto-mechanical components (e.g. focus-tunable lenses) mounted in the optical systems of laser scanners. The algebraic formulas are derived for ray tracing through different configurations of the scanning optical system and one can calculate angles of scanner mirrors and required focal length of the tunable-focus component provided that the position of the focused beam in 3D space is given with a required tolerance. Computer simulations of the proposed system are performed using MATLAB.

  19. Adaptations and Analysis of the AFIT Noise Radar Network for Indoor Navigation

    DTIC Science & Technology

    2013-03-01

    SNR signal-to- noise ratio TDOA time difference of arrival TDR Time-domain reflectometer xv Acronym Definition UHF ultra-high frequency UWB ultra...he estimated via simulation that the phase center moved approximately 7ft in electrical length corresponding to the long TDR distance measured in...ADAPTATIONS AND ANALYSIS OF THE AFIT NOISE RADAR NETWORK FOR INDOOR NAVIGATION THESIS Russell D. Wilson IV, Second Lieutenant, USAF AFIT-ENG-13-M-50

  20. An adaptive-control switching buck regulator - Implementation, analysis, and design

    NASA Technical Reports Server (NTRS)

    Lee, F. C.; Yu, Y.

    1980-01-01

    Describing-function techniques and averaging methods have been employed to characterize a multiloop switching buck regulator by three functional blocks: power stage, analog signal processor, and pulse modulator. The model is employed to explore possible forms of pole-zero cancellation and the adaptive nature of the control to filter parameter changes. Analysis-based design guidelines are provided including a suggested additional RC-compensation loop to optimize regulator performances such as stability, audiosusceptibility, output impedance, and load transient response.

  1. Development of a clinical pathways analysis system with adaptive Bayesian nets and data mining techniques.

    PubMed

    Kopec, D; Shagas, G; Reinharth, D; Tamang, S

    2004-01-01

    The use and development of software in the medical field offers tremendous opportunities for making health care delivery more efficient, more effective, and less error-prone. We discuss and explore the use of clinical pathways analysis with Adaptive Bayesian Networks and Data Mining Techniques to perform such analyses. The computation of "lift" (a measure of completed pathways improvement potential) leads us to optimism regarding the potential for this approach.

  2. Grid and basis adaptive polynomial chaos techniques for sensitivity and uncertainty analysis

    SciTech Connect

    Perkó, Zoltán Gilli, Luca Lathouwers, Danny Kloosterman, Jan Leen

    2014-03-01

    The demand for accurate and computationally affordable sensitivity and uncertainty techniques is constantly on the rise and has become especially pressing in the nuclear field with the shift to Best Estimate Plus Uncertainty methodologies in the licensing of nuclear installations. Besides traditional, already well developed methods – such as first order perturbation theory or Monte Carlo sampling – Polynomial Chaos Expansion (PCE) has been given a growing emphasis in recent years due to its simple application and good performance. This paper presents new developments of the research done at TU Delft on such Polynomial Chaos (PC) techniques. Our work is focused on the Non-Intrusive Spectral Projection (NISP) approach and adaptive methods for building the PCE of responses of interest. Recent efforts resulted in a new adaptive sparse grid algorithm designed for estimating the PC coefficients. The algorithm is based on Gerstner's procedure for calculating multi-dimensional integrals but proves to be computationally significantly cheaper, while at the same it retains a similar accuracy as the original method. More importantly the issue of basis adaptivity has been investigated and two techniques have been implemented for constructing the sparse PCE of quantities of interest. Not using the traditional full PC basis set leads to further reduction in computational time since the high order grids necessary for accurately estimating the near zero expansion coefficients of polynomial basis vectors not needed in the PCE can be excluded from the calculation. Moreover the sparse PC representation of the response is easier to handle when used for sensitivity analysis or uncertainty propagation due to the smaller number of basis vectors. The developed grid and basis adaptive methods have been implemented in Matlab as the Fully Adaptive Non-Intrusive Spectral Projection (FANISP) algorithm and were tested on four analytical problems. These show consistent good performance both

  3. Genome-wide analysis reveals adaptation to high altitudes in Tibetan sheep

    PubMed Central

    Wei, Caihong; Wang, Huihua; Liu, Gang; Zhao, Fuping; Kijas, James W.; Ma, Youji; Lu, Jian; Zhang, Li; Cao, Jiaxue; Wu, Mingming; Wang, Guangkai; Liu, Ruizao; Liu, Zhen; Zhang, Shuzhen; Liu, Chousheng; Du, Lixin

    2016-01-01

    Tibetan sheep have lived on the Tibetan Plateau for thousands of years; however, the process and consequences of adaptation to this extreme environment have not been elucidated for important livestock such as sheep. Here, seven sheep breeds, representing both highland and lowland breeds from different areas of China, were genotyped for a genome-wide collection of single-nucleotide polymorphisms (SNPs). The FST and XP-EHH approaches were used to identify regions harbouring local positive selection between these highland and lowland breeds, and 236 genes were identified. We detected selection events spanning genes involved in angiogenesis, energy production and erythropoiesis. In particular, several candidate genes were associated with high-altitude hypoxia, including EPAS1, CRYAA, LONP1, NF1, DPP4, SOD1, PPARG and SOCS2. EPAS1 plays a crucial role in hypoxia adaption; therefore, we investigated the exon sequences of EPAS1 and identified 12 mutations. Analysis of the relationship between blood-related phenotypes and EPAS1 genotypes in additional highland sheep revealed that a homozygous mutation at a relatively conserved site in the EPAS1 3′ untranslated region was associated with increased mean corpuscular haemoglobin concentration and mean corpuscular volume. Taken together, our results provide evidence of the genetic diversity of highland sheep and indicate potential high-altitude hypoxia adaptation mechanisms, including the role of EPAS1 in adaptation. PMID:27230812

  4. The Applied Behavior Analysis Research Paradigm and Single-Subject Designs in Adapted Physical Activity Research.

    PubMed

    Haegele, Justin A; Hodge, Samuel Russell

    2015-10-01

    There are basic philosophical and paradigmatic assumptions that guide scholarly research endeavors, including the methods used and the types of questions asked. Through this article, kinesiology faculty and students with interests in adapted physical activity are encouraged to understand the basic assumptions of applied behavior analysis (ABA) methodology for conducting, analyzing, and presenting research of high quality in this paradigm. The purposes of this viewpoint paper are to present information fundamental to understanding the assumptions undergirding research methodology in ABA, describe key aspects of single-subject research designs, and discuss common research designs and data-analysis strategies used in single-subject studies.

  5. Envelope analysis with a genetic algorithm-based adaptive filter bank for bearing fault detection.

    PubMed

    Kang, Myeongsu; Kim, Jaeyoung; Choi, Byeong-Keun; Kim, Jong-Myon

    2015-07-01

    This paper proposes a fault detection methodology for bearings using envelope analysis with a genetic algorithm (GA)-based adaptive filter bank. Although a bandpass filter cooperates with envelope analysis for early identification of bearing defects, no general consensus has been reached as to which passband is optimal. This study explores the impact of various passbands specified by the GA in terms of a residual frequency components-to-defect frequency components ratio, which evaluates the degree of defectiveness in bearings and finally outputs an optimal passband for reliable bearing fault detection.

  6. Optimising qualitative longitudinal analysis: Insights from a study of traumatic brain injury recovery and adaptation.

    PubMed

    Fadyl, Joanna K; Channon, Alexis; Theadom, Alice; McPherson, Kathryn M

    2017-04-01

    Knowledge about aspects that influence recovery and adaptation in the postacute phase of disabling health events is key to understanding how best to provide appropriate rehabilitation and health services. Qualitative longitudinal research makes it possible to look for patterns, key time points and critical moments that could be vital for interventions and supports. However, strategies that support robust data management and analysis for longitudinal qualitative research in health-care are not well documented in the literature. This article reviews three challenges encountered in a large longitudinal qualitative descriptive study about experiences of recovery and adaptation after traumatic brain injury in New Zealand, and the strategies and technologies used to address them. These were (i) tracking coding and analysis decisions during an extended analysis period; (ii) navigating interpretations over time and in response to new data; and (iii) exploiting data volume and complexity. Concept mapping during coding review, a considered combination of information technologies, employing both cross-sectional and narrative analysis, and an expectation that subanalyses would be required for key topics helped us manage the study in a way that facilitated useful and novel insights. These strategies could be applied in other qualitative longitudinal studies in healthcare inquiry to optimise data analysis and stimulate important insights.

  7. Genomic and transcriptomic analysis of NDM-1 Klebsiella pneumoniae in spaceflight reveal mechanisms underlying environmental adaptability.

    PubMed

    Li, Jia; Liu, Fei; Wang, Qi; Ge, Pupu; Woo, Patrick C Y; Yan, Jinghua; Zhao, Yanlin; Gao, George F; Liu, Cui Hua; Liu, Changting

    2014-08-28

    The emergence and rapid spread of New Delhi Metallo-beta-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae strains has caused a great concern worldwide. To better understand the mechanisms underlying environmental adaptation of those highly drug-resistant K. pneumoniae strains, we took advantage of the China's Shenzhou 10 spacecraft mission to conduct comparative genomic and transcriptomic analysis of a NDM-1 K. pneumoniae strain (ATCC BAA-2146) being cultivated under different conditions. The samples were recovered from semisolid medium placed on the ground (D strain), in simulated space condition (M strain), or in Shenzhou 10 spacecraft (T strain) for analysis. Our data revealed multiple variations underlying pathogen adaptation into different environments in terms of changes in morphology, H2O2 tolerance and biofilm formation ability, genomic stability and regulation of metabolic pathways. Additionally, we found a few non-coding RNAs to be differentially regulated. The results are helpful for better understanding the adaptive mechanisms of drug-resistant bacterial pathogens.

  8. Genomic and transcriptomic analysis of NDM-1 Klebsiella pneumoniae in spaceflight reveal mechanisms underlying environmental adaptability

    PubMed Central

    Li, Jia; Liu, Fei; Wang, Qi; Ge, Pupu; Woo, Patrick C. Y.; Yan, Jinghua; Zhao, Yanlin; Gao, George F.; Liu, Cui Hua; Liu, Changting

    2014-01-01

    The emergence and rapid spread of New Delhi Metallo-beta-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae strains has caused a great concern worldwide. To better understand the mechanisms underlying environmental adaptation of those highly drug-resistant K. pneumoniae strains, we took advantage of the China's Shenzhou 10 spacecraft mission to conduct comparative genomic and transcriptomic analysis of a NDM-1 K. pneumoniae strain (ATCC BAA-2146) being cultivated under different conditions. The samples were recovered from semisolid medium placed on the ground (D strain), in simulated space condition (M strain), or in Shenzhou 10 spacecraft (T strain) for analysis. Our data revealed multiple variations underlying pathogen adaptation into different environments in terms of changes in morphology, H2O2 tolerance and biofilm formation ability, genomic stability and regulation of metabolic pathways. Additionally, we found a few non-coding RNAs to be differentially regulated. The results are helpful for better understanding the adaptive mechanisms of drug-resistant bacterial pathogens. PMID:25163721

  9. Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species.

    PubMed

    Ronkin, Dana; Seroussi, Eyal; Nitzan, Tali; Doron-Faigenboim, Adi; Cnaani, Avner

    2015-03-01

    Tilapias are a group of freshwater species, which vary in their ability to adapt to high salinity water. Osmotic regulation in fish is conducted mainly in the gills, kidney, and gastrointestinal tract (GIT). The mechanisms involved in ion and water transport through the GIT is not well-characterized, with only a few described complexes. Comparing the transcriptome of the anterior and posterior intestinal sections of a freshwater and saltwater adapted fish by deep-sequencing, we examined the salinity adaptation of two tilapia species: the high salinity-tolerant Oreochromis mossambicus (Mozambique tilapia), and the less salinity-tolerant Oreochromis niloticus (Nile tilapia). This comparative analysis revealed high similarity in gene expression response to salinity change between species in the posterior intestine and large differences in the anterior intestine. Furthermore, in the anterior intestine 68 genes were saltwater up-regulated in one species and down-regulated in the other species (47 genes up-regulated in O. niloticus and down-regulated in O. mossambicus, with 21 genes showing the reverse pattern). Gene ontology (GO) analysis showed a high proportion of transporter and ion channel function among these genes. The results of this study point to a group of genes that differed in their salinity-dependent regulation pattern in the anterior intestine as potentially having a role in the differential salinity tolerance of these two closely related species.

  10. Error Estimation and h-Adaptivity for Optimal Finite Element Analysis

    NASA Technical Reports Server (NTRS)

    Cwik, Tom; Lou, John

    1997-01-01

    The objective of adaptive meshing and automatic error control in finite element analysis is to eliminate the need for the application engineer from re-meshing and re-running design simulations to verify numerical accuracy. The user should only need to enter the component geometry and a coarse finite element mesh. The software will then autonomously and adaptively refine this mesh where needed, reducing the error in the fields to a user prescribed value. The ideal end result of the simulation is a measurable quantity (e.g. scattered field, input impedance), calculated to a prescribed error, in less time and less machine memory than if the user applied typical uniform mesh refinement by hand. It would also allow for the simulation of larger objects since an optimal mesh is created.

  11. Systematic analysis of the kalimantacin assembly line NRPS module using an adapted targeted mutagenesis approach.

    PubMed

    Uytterhoeven, Birgit; Appermans, Kenny; Song, Lijiang; Masschelein, Joleen; Lathouwers, Thomas; Michiels, Chris W; Lavigne, Rob

    2016-04-01

    Kalimantacin is an antimicrobial compound with strong antistaphylococcal activity that is produced by a hybrid trans-acyltransferase polyketide synthase/nonribosomal peptide synthetase system in Pseudomonas fluorescens BCCM_ID9359. We here present a systematic analysis of the substrate specificity of the glycine-incorporating adenylation domain from the kalimantacin biosynthetic assembly line by a targeted mutagenesis approach. The specificity-conferring code was adapted for use in Pseudomonas and mutated adenylation domain active site sequences were introduced in the kalimantacin gene cluster, using a newly adapted ligation independent cloning method. Antimicrobial activity screens and LC-MS analyses revealed that the production of the kalimantacin analogues in the mutated strains was abolished. These results support the idea that further insight in the specificity of downstream domains in nonribosomal peptide synthetases and polyketide synthases is required to efficiently engineer these strains in vivo.

  12. An adaptive singular spectrum analysis approach to murmur detection from heart sounds.

    PubMed

    Sanei, Saeid; Ghodsi, Mansoureh; Hassani, Hossein

    2011-04-01

    Murmur is the result of various heart abnormalities. A new robust approach for separation of murmur from heart sound has been suggested in this article. Singular spectrum analysis (SSA) has been adapted to the changes in the statistical properties of the data and effectively used for detection of murmur from single-channel heart sound (HS) signals. Incorporating a cleverly selected a priori within the SSA reconstruction process, results in an accurate separation of normal HS from the murmur segment. Another contribution of this work is selection of the correct subspace of the desired signal component automatically. In addition, the subspace size can be identified iteratively. A number of HS signals with murmur have been processed using the proposed adaptive SSA (ASSA) technique and the results have been quantified both objectively and subjectively.

  13. Genotypic stability and adaptability in tropical maize based on AMMI and GGE biplot analysis.

    PubMed

    Balestre, M; Von Pinho, R G; Souza, J C; Oliveira, R L

    2009-11-03

    We evaluated the phenotypic and genotypic stability and adaptability of hybrids using the additive main effect and multiplicative interaction (AMMI) and genotype x genotype-environment interaction (GGE) biplot models. Starting with 10 single-cross hybrids, a complete diallel was done, resulting in 45 double-cross hybrids that were appraised in 15 locations in Southeast, Center-West and Northeast Brazil. In most cases, when the effects were considered as random (only G effects or G and GE simultaneously) in AMMI and GGE analysis, the distances between predicted values and observed values were smaller than for AMMI and GGE biplot phenotypic means; the best linear unbiased predictors of G and GE generally showed more accurate predictions in AMMI and GGE analysis. We found the GGE biplot method to be superior to the AMMI 1 graph, due to more retention of GE and G + GE in the graph analysis. However, based on cross-validation results, the GGE biplot was less accurate than the AMMI 1 graph, inferring that the quantity of GE or G + GE retained in the graph analysis alone is not a good parameter for choice of stabilities and adaptabilities when comparing AMMI and GGE analyses.

  14. Singular spectrum analysis and adaptive filtering enhance the functional connectivity analysis of resting state fMRI data.

    PubMed

    Piaggi, Paolo; Menicucci, Danilo; Gentili, Claudio; Handjaras, Giacomo; Gemignani, Angelo; Landi, Alberto

    2014-05-01

    Sources of noise in resting-state fMRI experiments include instrumental and physiological noises, which need to be filtered before a functional connectivity analysis of brain regions is performed. These noisy components show autocorrelated and nonstationary properties that limit the efficacy of standard techniques (i.e. time filtering and general linear model). Herein we describe a novel approach based on the combination of singular spectrum analysis and adaptive filtering, which allows a greater noise reduction and yields better connectivity estimates between regions at rest, providing a new feasible procedure to analyze fMRI data.

  15. An Analysis of a Finite Element Method for Convection-Diffusion Problems. Part II. A Posteriori Error Estimates and Adaptivity.

    DTIC Science & Technology

    1983-03-01

    AN ANALYSIS OF A FINITE ELEMENT METHOD FOR CONVECTION- DIFFUSION PROBLEMS PART II: A POSTERIORI ERROR ESTIMATES AND ADAPTIVITY by W. G. Szymczak Y 6a...PERIOD COVERED AN ANALYSIS OF A FINITE ELEMENT METHOD FOR final life of the contract CONVECTION- DIFFUSION PROBLEM S. Part II: A POSTERIORI ERROR ...Element Method for Convection- Diffusion Problems. Part II: A Posteriori Error Estimates and Adaptivity W. G. Szvmczak and I. Babu~ka# Laboratory for

  16. An analysis of European riverine flood risk and adaptation measures under projected climate change

    NASA Astrophysics Data System (ADS)

    Bouwer, Laurens; Burzel, Andreas; Holz, Friederike; Winsemius, Hessel; de Bruijn, Karind

    2015-04-01

    There is increasing need to assess costs and benefits of adaptation at scales beyond the river basin. In Europe, such estimates are required at the European scale in order to set priorities for action and financing, for instance in the context of the EU Adaptation Strategy. The goal of this work as part of the FP7 BASE project is to develop a flood impact model that can be applied at Pan-European scale and that is able to project changes in flood risk due to climate change and socio-economic developments, and costs of adaptation. For this research, we build upon the global flood hazard estimation method developed by Winsemius et al. (Hydrology and Earth System Sciences, 2013), that produces flood inundation maps at different return period, for present day (EU WATCH) and future climate (IPCC scenarios RCP4.5 and 8.5, for five climate models). These maps are used for the assessment of flood impacts. We developed and tested a model for assessing direct economic flood damages by using large scale land use maps. We characterise vulnerable land use functions, in particular residential, commercial, industrial, infrastructure and agriculture, using depth-damage relationships. Furthermore, we apply up to NUTS3 level information on Gross Domestic Product, which is used as a proxy for relative differences in maximum damage values between different areas. Next, we test two adaptation measures, by adjusting flood protection levels and adjusting damage functions. The results show the projected changes in flood risk in the future. For example, on NUTS2 level, flood risk increases in some regions up to 179% (between the baseline scenario 1960-1999 and time slice 2010-2049). On country level there are increases up to 60% for selected climate models. The conference presentation will show the most relevant improvements in damage modelling on the continental scale, and results of the analysis of adaptation measures. The results will be critically discussed under the aspect of major

  17. The tarsal-metatarsal complex of caviomorph rodents: Anatomy and functional-adaptive analysis.

    PubMed

    Candela, Adriana M; Muñoz, Nahuel A; García-Esponda, César M

    2017-03-27

    Caviomorph rodents represent a major adaptive radiation of Neotropical mammals. They occupy a variety of ecological niches, which is also reflected in their wide array of locomotor behaviors. It is expected that this radiation would be mirrored by an equivalent disparity of tarsal-metatarsal morphology. Here, the tarsal-metatarsal complex of Erethizontidae, Cuniculidae, Dasyproctidae, Caviidae, Chinchillidae, Octodontidae, Ctenomyidae, and Echimyidae was examined, in order to evaluate its anatomical variation and functional-adaptive relevance in relation to locomotor behaviors. A qualitative study in functional morphology and a geometric morphometric analysis were performed. We recognized two distinct tarsal-metatarsal patterns that represent the extremes of anatomical variation in the foot. The first, typically present in arboreal species, is characterized by features that facilitate movements at different levels of the tarsal-metatarsal complex. The second pattern, typically present in cursorial caviomorphs, has a set of features that act to stabilize the joints, improve the interlocking of the tarsal bones, and restrict movements to the parasagittal plane. The morphological disparity recognized in this study seems to result from specific locomotor adaptations to climb, dig, run, jump and swim, as well as phylogenetic effects within and among the groups studies.

  18. Motion artifact removal from photoplethysmographic signals by combining temporally constrained independent component analysis and adaptive filter

    PubMed Central

    2014-01-01

    Background The calculation of arterial oxygen saturation (SpO2) relies heavily on the amplitude information of the high-quality photoplethysmographic (PPG) signals, which could be contaminated by motion artifacts (MA) during monitoring. Methods A new method combining temporally constrained independent component analysis (cICA) and adaptive filters is presented here to extract the clean PPG signals from the MA corrupted PPG signals with the amplitude information reserved. The underlying PPG signal could be extracted from the MA contaminated PPG signals automatically by using cICA algorithm. Then the amplitude information of the PPG signals could be recovered by using adaptive filters. Results Compared with conventional ICA algorithms, the proposed approach is permutation and scale ambiguity-free. Numerical examples with both synthetic datasets and real-world MA corrupted PPG signals demonstrate that the proposed method could remove the MA from MA contaminated PPG signals more effectively than the two existing FFT-LMS and moving average filter (MAF) methods. Conclusions This paper presents a new method which combines the cICA algorithm and adaptive filter to extract the underlying PPG signals from the MA contaminated PPG signals with the amplitude information reserved. The new method could be used in the situations where one wants to extract the interested source automatically from the mixed observed signals with the amplitude information reserved. The results of study demonstrated the efficacy of this proposed method. PMID:24761769

  19. Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles* #

    PubMed Central

    Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-yu; Zhang, Xiao-mei; Song, Da-feng; Zhang, Chen

    2016-01-01

    Objective: In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods: The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). Results: We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Conclusions: Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate. PMID:27487802

  20. A Thematic Analysis of Career Adaptability in Retirees Who Return to Work.

    PubMed

    Luke, Jennifer; McIlveen, Peter; Perera, Harsha N

    2016-01-01

    Retirement can no longer be conceptualized as disengagement, as the end of a person's career, as it is in the life-span, life-space theory. Increasingly, retirees are returning to work, in paid, and unpaid positions, in a part-time or full-time capacity, as an act of re-engagement. Vocational psychology theories are yet to adequately conceptualize the phenomenon of retirees' re-engagement in work. The research reported in this paper is the first attempt to understand re-engagement through the theoretical lens of career construction theory (CCT) and its central construct, career adaptability. The study involved intensive interviews with 22 retirees between the ages of 56 and 78 years (M = 68.24), who had retired no less than 1 year prior to the study. Participants were engaged in a discussion about their reasons for returning to the world of work. Thematic analysis of interview transcripts extracted evidence of the four career adaptability resources: concern, control, curiosity, and confidence. In addition, the influence of family and making a contribution were discerned as important themes. These findings are the first evidence that the CCT and career adaptability provide a new conceptual lens to theorize and conduct research into the phenomenon of retirement.

  1. Transcriptome Analysis of Alkali Shock and Alkali Adaptation in Listeria monocytogenes 10403S

    PubMed Central

    Giotis, Efstathios S.; Muthaiyan, Arunachalam; Natesan, Senthil; Wilkinson, Brian J.; Blair, Ian S.

    2010-01-01

    Abstract Alkali stress is an important means of inactivating undesirable pathogens in a wide range of situations. Unfortunately, Listeria monocytogenes can launch an alkaline tolerance response, significantly increasing persistence of the pathogen in such environments. This study compared transcriptome patterns of alkali and nonalkali-stressed L. monocytogenes 10403S cells, to elucidate the mechanisms by which Listeria adapts and/or grows during short- or long-term alkali stress. Transcription profiles associated with alkali shock (AS) were obtained by DNA microarray analysis of midexponential cells suspended in pH 9 media for 15, 30, or 60 min. Transcription profiles associated with alkali adaptation (AA) were obtained similarly from cells grown to midexponential phase at pH 9. Comparison of AS and AA transcription profiles with control cell profiles identified a high number of differentially regulated open-reading frames in all tested conditions. Rapid (15 min) changes in expression included upregulation of genes encoding for multiple metabolic pathways (including those associated with Na+/H+ antiporters), ATP-binding cassette transporters of functional compatible solutes, motility, and virulence-associated genes as well as the σB controlled stress resistance network. Slower (30 min and more) responses to AS and adaptation during growth in alkaline conditions (AA) involved a different pattern of changes in mRNA concentrations, and genes involved in proton export. PMID:20677981

  2. A Thematic Analysis of Career Adaptability in Retirees Who Return to Work

    PubMed Central

    Luke, Jennifer; McIlveen, Peter; Perera, Harsha N.

    2016-01-01

    Retirement can no longer be conceptualized as disengagement, as the end of a person’s career, as it is in the life-span, life-space theory. Increasingly, retirees are returning to work, in paid, and unpaid positions, in a part-time or full-time capacity, as an act of re-engagement. Vocational psychology theories are yet to adequately conceptualize the phenomenon of retirees’ re-engagement in work. The research reported in this paper is the first attempt to understand re-engagement through the theoretical lens of career construction theory (CCT) and its central construct, career adaptability. The study involved intensive interviews with 22 retirees between the ages of 56 and 78 years (M = 68.24), who had retired no less than 1 year prior to the study. Participants were engaged in a discussion about their reasons for returning to the world of work. Thematic analysis of interview transcripts extracted evidence of the four career adaptability resources: concern, control, curiosity, and confidence. In addition, the influence of family and making a contribution were discerned as important themes. These findings are the first evidence that the CCT and career adaptability provide a new conceptual lens to theorize and conduct research into the phenomenon of retirement. PMID:26925014

  3. Transcriptomic Analysis of Laribacter hongkongensis Reveals Adaptive Response Coupled with Temperature

    PubMed Central

    Kong, Hoi-Kuan; Law, Hon-Wai; Liu, Xuan; Law, Carmen O. K.; Pan, Qing; Gao, Lin; Xiong, Lifeng; Lau, Susanna K. P.; Woo, Patrick C. Y.; Lau, Terrence chi kong

    2017-01-01

    Bacterial adaptation to different hosts requires transcriptomic alteration in response to the environmental conditions. Laribacter hongkongensis is a gram-negative, facultative anaerobic, urease-positive bacillus caused infections in liver cirrhosis patients and community-acquired gastroenteritis. It was also found in intestine from commonly consumed freshwater fishes and drinking water reservoirs. Since L. hongkongensis could survive as either fish or human pathogens, their survival mechanisms in two different habitats should be temperature-regulated and highly complex. Therefore, we performed transcriptomic analysis of L. hongkongensis at body temperatures of fish and human in order to elucidate the versatile adaptation mechanisms coupled with the temperatures. We identified numerous novel temperature-induced pathways involved in host pathogenesis, in addition to the shift of metabolic equilibriums and overexpression of stress-related proteins. Moreover, these pathways form a network that can be activated at a particular temperature, and change the physiology of the bacteria to adapt to the environments. In summary, the dynamic of transcriptomes in L. hongkongensis provides versatile strategies for the bacterial survival at different habitats and this alteration prepares the bacterium for the challenge of host immunity. PMID:28085929

  4. Genome-wide analysis of admixture and adaptation in the Africanized honeybee.

    PubMed

    Nelson, Ronald M; Wallberg, Andreas; Simões, Zilá Luz Paulino; Lawson, Daniel J; Webster, Matthew T

    2017-04-05

    Genetic exchange by hybridization or admixture can make an important contribution to evolution, and introgression of favourable alleles can facilitate adaptation to new environments. A small number of honeybees (Apis mellifera) with African ancestry were introduced to Brazil ~60 years ago, which dispersed and hybridized with existing managed populations of European origin, quickly spreading across much of the Americas in an example of a massive biological invasion. Here we analyse whole genome sequences of 32 Africanized honeybees sampled from throughout Brazil in order to study the effect of this process on genome diversity. By comparison with ancestral populations from Europe and Africa, we infer that these samples have 84% African ancestry, with the remainder from western European populations. However, this proportion varies across the genome and we identify signals of positive selection in regions with high European ancestry proportions. These observations are largely driven by one large gene-rich 1.4-Mbp segment on chromosome 11 where European haplotypes are present at a significantly elevated frequency and likely confer an adaptive advantage in the Africanized honeybee population. This region has previously been implicated in reproductive traits and foraging behaviour in worker bees. Finally, by analysing the distribution of ancestry tract lengths in the context of the known time of the admixture event, we are able to infer an average generation time of 2.0 years. Our analysis highlights the processes by which populations of mixed genetic ancestry form and adapt to new environments. This article is protected by copyright. All rights reserved.

  5. Subjective well-being and adaptation to life events: a meta-analysis.

    PubMed

    Luhmann, Maike; Hofmann, Wilhelm; Eid, Michael; Lucas, Richard E

    2012-03-01

    Previous research has shown that major life events can have short- and long-term effects on subjective well-being (SWB). The present meta-analysis examines (a) whether life events have different effects on affective and cognitive well-being and (b) how the rate of adaptation varies across different life events. Longitudinal data from 188 publications (313 samples, N = 65,911) were integrated to describe the reaction and adaptation to 4 family events (marriage, divorce, bereavement, childbirth) and 4 work events (unemployment, reemployment, retirement, relocation/migration). The findings show that life events have very different effects on affective and cognitive well-being and that for most events the effects of life events on cognitive well-being are stronger and more consistent across samples. Different life events differ in their effects on SWB, but these effects are not a function of the alleged desirability of events. The results are discussed with respect to their theoretical implications, and recommendations for future studies on adaptation are given.

  6. Optimization of an adaptive nonlinear filter for the analysis of nystagmus.

    PubMed

    Engelken, E J; Stevens, K W; Enderle, J D

    1991-01-01

    An adaptive nonlinear digital filter has been designed for the analysis of an eye-movement signal called nystagmus. Nystagmus is a bi-phasic signal consisting of a sequence of tracking eye movements called "slow-phase" interspersed with brief, high-velocity refixation movements called "fast-phase." The objective of the analysis is to separate the nystagmus signal into its fast- and slow-phase components. Specifically, the goal is to produce an evenly sampled estimate of slow-phase velocity (SPV) and an estimate of the peak fast-phase velocity. Classically this has been done using pattern recognition methods that exploit the fact that the fast-phase is a relatively short duration, high-velocity movement compared to the slow-phase. Unfortunately, these velocity and duration differences do not reliably separate the slow- and fast-phases under all conditions, especially when the signal is noisy. We have designed and built an adaptive nonlinear digital filter that easily outperforms the more complex pattern recognition algorithms. This new filter, called an Adaptive Asymmetrically Trimmed-Mean (AATM) filter, works under the assumption that, on the average, the eyes spend more time in slow-phase than in fast-phase. Thus, in any given data segment, most of the data samples are slow-phase samples. By analyzing the amplitude distribution of the data samples in the segment we can determine which of these samples are slow-phase. We used computer generated nystagmus signals contaminated with 3 levels of noise to evaluate the filter. The filter parameters were then optimized using Monte Carlo procedures producing an extremely robust analysis method.

  7. Persian adaptation of Foreign Language Reading Anxiety Scale: a psychometric analysis.

    PubMed

    Baghaei, Purya; Hohensinn, Christine; Kubinger, Klaus D

    2014-04-01

    The validity and psychometric properties of a new Persian adaptation of the Foreign Language Reading Anxiety Scale were investigated. The scale was translated into Persian and administered to 160 undergraduate students (131 women, 29 men; M age = 23.4 yr., SD = 4.3). Rasch model analysis on the scale's original 20 items revealed that the data do not fit the partial credit model. Principal components analysis identified three factors: one related to feelings of anxiety about reading, the second reflected the reverse-worded items, and the third related to general ideas about reading in a foreign language. In a re-analysis, the 12 items that loaded on the first factor showed a good fit with the partial credit model.

  8. Application of an automatic adaptive filter for Heart Rate Variability analysis.

    PubMed

    Dos Santos, Laurita; Barroso, Joaquim J; Macau, Elbert E N; de Godoy, Moacir F

    2013-12-01

    The presence of artifacts and noise effects in temporal series can seriously hinder the analysis of Heart Rate Variability (HRV). The tachograms should be carefully edited to avoid erroneous interpretations. The physician should carefully analyze the tachogram in order to detect points that might be associated with unlikely biophysical behavior and manually eliminate them from the data series. However, this is a time-consuming procedure. To facilitate the pre-analysis of the tachogram, this study uses a method of data filtering based on an adaptive filter which is quickly able to analyze a large amount of data. The method was applied to 229 time series from a database of patients with different clinical conditions: premature newborns, full-term newborns, healthy young adults, adults submitted to a very-low-calorie diet, and adults under preoperative evaluation for coronary artery bypass grafting. This proposed method is compared to the demanding conventional method, wherein the corrections of occasional ectopic beats and artifacts are usually manually executed by a specialist. To confirm the reliability of the results obtained, correlation coefficients were calculated, using both automatic and manual methods of ltering for each HRV index selected. A high correlation between the results was found, with highly significant p values, for all cases, except for some parameters analyzed in the premature newborns group, an issue that is thoroughly discussed. The authors concluded that the proposed adaptive filtering method helps to efficiently handle the task of editing temporal series for HRV analysis.

  9. Adaptive automatic data analysis in full-field fringe-pattern-based optical metrology

    NASA Astrophysics Data System (ADS)

    Trusiak, Maciej; Patorski, Krzysztof; Sluzewski, Lukasz; Pokorski, Krzysztof; Sunderland, Zofia

    2016-12-01

    Fringe pattern processing and analysis is an important task of full-field optical measurement techniques like interferometry, digital holography, structural illumination and moiré. In this contribution we present several adaptive automatic data analysis solutions based on the notion of Hilbert-Huang transform for measurand retrieval via fringe pattern phase and amplitude demodulation. The Hilbert-Huang transform consists of 2D empirical mode decomposition algorithm and Hilbert spiral transform analysis. Empirical mode decomposition adaptively dissects a meaningful number of same-scale subimages from the analyzed pattern - it is a data-driven method. Appropriately managing this set of unique subimages results in a very powerful fringe pre-filtering tool. Phase/amplitude demodulation is performed using Hilbert spiral transform aided by the local fringe orientation estimator. We describe several optical measurement techniques for technical and biological objects characterization basing on the especially tailored Hilbert-Huang algorithm modifications for fringe pattern denoising, detrending and amplitude/phase demodulation.

  10. Time series analysis of Adaptive Optics wave-front sensor telemetry data

    SciTech Connect

    Poyneer, L A; Palmer, D

    2004-03-22

    Time series analysis techniques are applied to wave-front sensor telemetry data from the Lick Adaptive Optics System. For 28 fully-illuminated subapertures, telemetry data of 4096 consecutive slope estimates for each subaperture are available. The primary problem is performance comparison of alternative wave-front sensing algorithms. Using direct comparison of data in open loop and closed-loop trials, we analyze algorithm performance in terms of gain, noise and residual power. We also explore the benefits of multi-input Wiener filtering and analyze the open-loop and closed-loop spatial correlations of the sensor measurements.

  11. Nonlinearities and adaptation of color vision from sequential principal curves analysis.

    PubMed

    Laparra, Valero; Jiménez, Sandra; Camps-Valls, Gustavo; Malo, Jesús

    2012-10-01

    Mechanisms of human color vision are characterized by two phenomenological aspects: the system is nonlinear and adaptive to changing environments. Conventional attempts to derive these features from statistics use separate arguments for each aspect. The few statistical explanations that do consider both phenomena simultaneously follow parametric formulations based on empirical models. Therefore, it may be argued that the behavior does not come directly from the color statistics but from the convenient functional form adopted. In addition, many times the whole statistical analysis is based on simplified databases that disregard relevant physical effects in the input signal, as, for instance, by assuming flat Lambertian surfaces. In this work, we address the simultaneous statistical explanation of the nonlinear behavior of achromatic and chromatic mechanisms in a fixed adaptation state and the change of such behavior (i.e., adaptation) under the change of observation conditions. Both phenomena emerge directly from the samples through a single data-driven method: the sequential principal curves analysis (SPCA) with local metric. SPCA is a new manifold learning technique to derive a set of sensors adapted to the manifold using different optimality criteria. Here sequential refers to the fact that sensors (curvilinear dimensions) are designed one after the other, and not to the particular (eventually iterative) method to draw a single principal curve. Moreover, in order to reproduce the empirical adaptation reported under D65 and A illuminations, a new database of colorimetrically calibrated images of natural objects under these illuminants was gathered, thus overcoming the limitations of available databases. The results obtained by applying SPCA show that the psychophysical behavior on color discrimination thresholds, discount of the illuminant, and corresponding pairs in asymmetric color matching emerge directly from realistic data regularities, assuming no a priori

  12. Transcriptomic and Proteomic Analysis of Oenococcus oeni Adaptation to Wine Stress Conditions

    PubMed Central

    Margalef-Català, Mar; Araque, Isabel; Bordons, Albert; Reguant, Cristina; Bautista-Gallego, Joaquín

    2016-01-01

    Oenococcus oeni, the main lactic acid bacteria responsible for malolactic fermentation in wine, has to adapt to stressful conditions, such as low pH and high ethanol content. In this study, the changes in the transcriptome and the proteome of O. oeni PSU-1 during the adaptation period before MLF start have been studied. DNA microarrays were used for the transcriptomic analysis and two complementary proteomic techniques, 2-D DIGE and iTRAQ labeling were used to analyze the proteomic response. One of the most influenced functions in PSU-1 due to inoculation into wine-like medium (WLM) was translation, showing the over-expression of certain ribosomal genes and the corresponding proteins. Amino acid metabolism and transport was also altered and several peptidases were up regulated both at gene and protein level. Certain proteins involved in glutamine and glutamate metabolism showed an increased abundance revealing the key role of nitrogen uptake under stressful conditions. A strong transcriptional inhibition of carbohydrate metabolism related genes was observed. On the other hand, the transcriptional up-regulation of malate transport and citrate consumption was indicative of the use of L-malate and citrate associated to stress response and as an alternative energy source to sugar metabolism. Regarding the stress mechanisms, our results support the relevance of the thioredoxin and glutathione systems in the adaptation of O. oeni to wine related stress. Genes and proteins related to cell wall showed also significant changes indicating the relevance of the cell envelop as protective barrier to environmental stress. The differences found between transcriptomic and proteomic data suggested the relevance of post-transcriptional mechanisms and the complexity of the stress response in O. oeni adaptation. Further research should deepen into the metabolisms mostly altered due to wine conditions to elucidate the role of each mechanism in the O. oeni ability to develop MLF. PMID

  13. Conjoint occurrence of GABAB receptor antibodies in Lambert-Eaton myasthenic syndrome with antibodies to the voltage gated calcium channel.

    PubMed

    Dogan Onugoren, Müjgan; Rauschka, Helmut; Bien, Christian G

    2014-08-15

    Antibodies (abs) to the GABAB receptor have been recently found to be responsible for immune-mediated encephalitis with dominant seizures. They are in approximately 50% of cases associated with small-cell lung cancer (SCLC). GABAB receptors are mainly located in the hippocampus, thalamus and cerebellum in the presynaptic and postsynaptic regions of synapses. The main function of these receptors is to reduce activity states of neurons. In some instances, GABAB receptor abs in these patients were accompanied by other antibodies, among them VGCC abs (Lancaster et al., 2010, Boronat et al., 2011). VGCC abs cause paraneoplastic Lambert Eaton myasthenic syndrome (LEMS) by reduction of presynaptic VGCCs (Titulaer et al., 2011). In the domain of CNS disease, VGCC abs have been found in association with paraneoplastic cerebellar ataxia (Mason et al., 1997) and rarely and at low titres also in other paraneoplastic encephalopathies together with Hu abs (Lennon et al., 1995). It has been a long-standing debate if abs in paraneoplastic conditions associate rather with the neurological syndrome or the tumour. Here, we describe the conjoint occurrence of abs to the GABAB receptor and to the VGCC in a patient with SCLC presenting only symptoms of the peripheral nervous system giving another example of the latter hypothesis.

  14. Spike-Triggered Covariance Analysis Reveals Phenomenological Diversity of Contrast Adaptation in the Retina

    PubMed Central

    Liu, Jian K.; Gollisch, Tim

    2015-01-01

    When visual contrast changes, retinal ganglion cells adapt by adjusting their sensitivity as well as their temporal filtering characteristics. The latter has classically been described by contrast-induced gain changes that depend on temporal frequency. Here, we explored a new perspective on contrast-induced changes in temporal filtering by using spike-triggered covariance analysis to extract multiple parallel temporal filters for individual ganglion cells. Based on multielectrode-array recordings from ganglion cells in the isolated salamander retina, we found that contrast adaptation of temporal filtering can largely be captured by contrast-invariant sets of filters with contrast-dependent weights. Moreover, differences among the ganglion cells in the filter sets and their contrast-dependent contributions allowed us to phenomenologically distinguish three types of filter changes. The first type is characterized by newly emerging features at higher contrast, which can be reproduced by computational models that contain response-triggered gain-control mechanisms. The second type follows from stronger adaptation in the Off pathway as compared to the On pathway in On-Off-type ganglion cells. Finally, we found that, in a subset of neurons, contrast-induced filter changes are governed by particularly strong spike-timing dynamics, in particular by pronounced stimulus-dependent latency shifts that can be observed in these cells. Together, our results show that the contrast dependence of temporal filtering in retinal ganglion cells has a multifaceted phenomenology and that a multi-filter analysis can provide a useful basis for capturing the underlying signal-processing dynamics. PMID:26230927

  15. Integrated analysis considered mitigation cost, damage cost and adaptation cost in Northeast Asia

    NASA Astrophysics Data System (ADS)

    Park, J. H.; Lee, D. K.; Kim, H. G.; Sung, S.; Jung, T. Y.

    2015-12-01

    Various studies show that raising the temperature as well as storms, cold snap, raining and drought caused by climate change. And variety disasters have had a damage to mankind. The world risk report(2012, The Nature Conservancy) and UNU-EHS (the United Nations University Institute for Environment and Human Security) reported that more and more people are exposed to abnormal weather such as floods, drought, earthquakes, typhoons and hurricanes over the world. In particular, the case of Korea, we influenced by various pollutants which are occurred in Northeast Asian countries, China and Japan, due to geographical meteorological characteristics. These contaminants have had a significant impact on air quality with the pollutants generated in Korea. Recently, around the world continued their effort to reduce greenhouse gas and to improve air quality in conjunction with the national or regional development goals priority. China is also working on various efforts in accordance with the international flows to cope with climate change and air pollution. In the future, effect of climate change and air quality in Korea and Northeast Asia will be change greatly according to China's growth and mitigation policies. The purpose of this study is to minimize the damage caused by climate change on the Korean peninsula through an integrated approach taking into account the mitigation and adaptation plan. This study will suggest a climate change strategy at the national level by means of a comprehensive economic analysis of the impacts and mitigation of climate change. In order to quantify the impact and damage cost caused by climate change scenarios in a regional scale, it should be priority variables selected in accordance with impact assessment of climate change. The sectoral impact assessment was carried out on the basis of selected variables and through this, to derive the methodology how to estimate damage cost and adaptation cost. And then, the methodology was applied in Korea

  16. The conjoint influence of home enriched environment and lead exposure on children's cognition and behaviour in a Mexican lead smelter community.

    PubMed

    Moodie, Sue; Ialongo, Nick; López, Patricia; Rosado, Jorge; García-Vargas, Gonzalo; Ronquillo, Dolores; Kordas, Katarzyna

    2013-01-01

    A range of studies has been conducted on the detrimental effects of lead in mining and smelting communities. The neurocognitive and behavioural health effects of lead on children are well known. This research characterized the conjoint influence of lead exposure and home enriched environment on neurocognitive function and behaviour for first-grade children living in a Mexican lead smelter community. Structural equation models were used for this analysis with latent outcome variables, Cognition and Behaviour, constructed based on a battery of assessments administered to the first-grade children, their parents, and teachers. Structural equation modelling was used to describe complex relationships of exposure and health outcomes in a manner that permitted partition of both direct and indirect effects of the factors being measured. Home Environment (a latent variable constructed from information on mother's education and support of school work and extracurricular activities), and child blood lead concentration each had a main significant effect on cognition and behaviour. However, there were no statistically significant moderation relationships between lead and Home Environment on these latent outcomes. Home Environment had a significant indirect mediation effect between lead and both Cognition and Behaviour (p-value<0.001). The mediation model had a good fit with Root Mean Square Error of Approximation <0.0001 and a Weighted Root Mean Square Residual of 0.895. These results were highly significant and suggest that Home Environment has a moderate mediation effect with respect to lead effects on Behaviour (β=0.305) and a lower mediation effect on Cognition (β=0.184). The extent of home enrichment in this study was most highly related to the mother's support of schoolwork and slightly less by the mother's support of extracurricular activities or mother's education. Further research may be able to develop approaches to support families to make changes within their home

  17. Tooth form and function: insights into adaptation through the analysis of dental microwear.

    PubMed

    Ungar, Peter S

    2009-01-01

    Mammalian molar form is clearly adapted to fracture foods with specific material properties. Studies of dental functional morphology can therefore offer important clues about the diets of fossil taxa. That said, analyses of tooth form provide insights into ability to fracture resistant foods rather than the food preferences of individuals. Recent work suggests that specialized occlusal morphology can relate to either preferred foods, or to occasionally eaten fallback items critical for survival. This paper reviews dental microwear texture analysis, a new approach that can be used to infer fracture properties of foods eaten in life. High-resolution 3D point clouds of microwear surfaces are collected and analyzed using scale-sensitive fractal analyses. Resulting data are free from operator measurement error, and allow the characterization and comparison of within-species variation in microwear texture attributes. Examples given here include four extant primate species (two folivores and two hard object fallback feeders), and two fossil hominin taxa. All groups show at least some individuals with simple microwear surfaces that suggest a lack of consumption of hard and brittle abrasive foods during the last few meals. On the other hand, some hard object fallback specimens have very complex surfaces consistent with consumption of hard, brittle foods. The latter pattern is also found in one hominin species. These results suggest that dental microwear texture analysis can help us determine whether craniodental specializations in fossil species are adaptations to preferred foods, or to less often but still critical fallback items.

  18. Regression-based adaptive sparse polynomial dimensional decomposition for sensitivity analysis

    NASA Astrophysics Data System (ADS)

    Tang, Kunkun; Congedo, Pietro; Abgrall, Remi

    2014-11-01

    Polynomial dimensional decomposition (PDD) is employed in this work for global sensitivity analysis and uncertainty quantification of stochastic systems subject to a large number of random input variables. Due to the intimate structure between PDD and Analysis-of-Variance, PDD is able to provide simpler and more direct evaluation of the Sobol' sensitivity indices, when compared to polynomial chaos (PC). Unfortunately, the number of PDD terms grows exponentially with respect to the size of the input random vector, which makes the computational cost of the standard method unaffordable for real engineering applications. In order to address this problem of curse of dimensionality, this work proposes a variance-based adaptive strategy aiming to build a cheap meta-model by sparse-PDD with PDD coefficients computed by regression. During this adaptive procedure, the model representation by PDD only contains few terms, so that the cost to resolve repeatedly the linear system of the least-square regression problem is negligible. The size of the final sparse-PDD representation is much smaller than the full PDD, since only significant terms are eventually retained. Consequently, a much less number of calls to the deterministic model is required to compute the final PDD coefficients.

  19. The adaptation of GDL motion recognition system to sport and rehabilitation techniques analysis.

    PubMed

    Hachaj, Tomasz; Ogiela, Marek R

    2016-06-01

    The main novelty of this paper is presenting the adaptation of Gesture Description Language (GDL) methodology to sport and rehabilitation data analysis and classification. In this paper we showed that Lua language can be successfully used for adaptation of the GDL classifier to those tasks. The newly applied scripting language allows easily extension and integration of classifier with other software technologies and applications. The obtained execution speed allows using the methodology in the real-time motion capture data processing where capturing frequency differs from 100 Hz to even 500 Hz depending on number of features or classes to be calculated and recognized. Due to this fact the proposed methodology can be used to the high-end motion capture system. We anticipate that using novel, efficient and effective method will highly help both sport trainers and physiotherapist in they practice. The proposed approach can be directly applied to motion capture data kinematics analysis (evaluation of motion without regard to the forces that cause that motion). The ability to apply pattern recognition methods for GDL description can be utilized in virtual reality environment and used for sport training or rehabilitation treatment.

  20. Robust motion tracking based on adaptive speckle decorrelation analysis of OCT signal.

    PubMed

    Wang, Yuewen; Wang, Yahui; Akansu, Ali; Belfield, Kevin D; Hubbi, Basil; Liu, Xuan

    2015-11-01

    Speckle decorrelation analysis of optical coherence tomography (OCT) signal has been used in motion tracking. In our previous study, we demonstrated that cross-correlation coefficient (XCC) between Ascans had an explicit functional dependency on the magnitude of lateral displacement (δx). In this study, we evaluated the sensitivity of speckle motion tracking using the derivative of function XCC(δx) on variable δx. We demonstrated the magnitude of the derivative can be maximized. In other words, the sensitivity of OCT speckle tracking can be optimized by using signals with appropriate amount of decorrelation for XCC calculation. Based on this finding, we developed an adaptive speckle decorrelation analysis strategy to achieve motion tracking with optimized sensitivity. Briefly, we used subsequently acquired Ascans and Ascans obtained with larger time intervals to obtain multiple values of XCC and chose the XCC value that maximized motion tracking sensitivity for displacement calculation. Instantaneous motion speed can be calculated by dividing the obtained displacement with time interval between Ascans involved in XCC calculation. We implemented the above-described algorithm in real-time using graphic processing unit (GPU) and demonstrated its effectiveness in reconstructing distortion-free OCT images using data obtained from a manually scanned OCT probe. The adaptive speckle tracking method was validated in manually scanned OCT imaging, on phantom as well as in vivo skin tissue.

  1. Continuous digital ECG analysis over accurate R-peak detection using adaptive wavelet technique.

    PubMed

    Gopalakrishnan Nair, T R; Geetha, A P; Asharani, M

    2013-10-01

    Worldwide, health care segment is under a severe challenge to achieve more accurate and intelligent biomedical systems in order to assist healthcare professionals with more accurate and consistent data as well as reliability. The role of ECG in healthcare is one of the paramount importances and it has got a multitude of abnormal relations and anomalies which characterizes intricate cardiovascular performance image. Until the recent past, ECG instruments and analysis played the role of providing the PQRST signal as raw observational output either on paper or on a console or in a file having many diagnostic clues embedded in the signal left to the expert cardiologist to look out for characteristic intervals and to detect the cardiovascular abnormality. Methods and practises are required more and more, to automate this process of cardiac expertise using knowledge engineering and an intelligent systems approach. This paper presents one of the challenging R-peak detections to classify diagnosis and estimate cardio disorders in a fully automated signal processing sequence. This study used an adaptive wavelet approach to generate an appropriate wavelet for R-signal identification under noise, baseband wandering and temporal variations of R-positions. This study designed an adaptive wavelet and successfully detected R- peak variations under various ECG signal conditions. The result and analysis of this method and the ways to use it for further purposes are presented here.

  2. Adapting Human Reliability Analysis from Nuclear Power to Oil and Gas Applications

    SciTech Connect

    Boring, Ronald Laurids

    2015-09-01

    ABSTRACT: Human reliability analysis (HRA), as currently used in risk assessments, largely derives its methods and guidance from application in the nuclear energy domain. While there are many similarities be-tween nuclear energy and other safety critical domains such as oil and gas, there remain clear differences. This paper provides an overview of HRA state of the practice in nuclear energy and then describes areas where refinements to the methods may be necessary to capture the operational context of oil and gas. Many key distinctions important to nuclear energy HRA such as Level 1 vs. Level 2 analysis may prove insignifi-cant for oil and gas applications. On the other hand, existing HRA methods may not be sensitive enough to factors like the extensive use of digital controls in oil and gas. This paper provides an overview of these con-siderations to assist in the adaptation of existing nuclear-centered HRA methods to the petroleum sector.

  3. Pairwise Classifier Ensemble with Adaptive Sub-Classifiers for fMRI Pattern Analysis.

    PubMed

    Kim, Eunwoo; Park, HyunWook

    2017-02-01

    The multi-voxel pattern analysis technique is applied to fMRI data for classification of high-level brain functions using pattern information distributed over multiple voxels. In this paper, we propose a classifier ensemble for multiclass classification in fMRI analysis, exploiting the fact that specific neighboring voxels can contain spatial pattern information. The proposed method converts the multiclass classification to a pairwise classifier ensemble, and each pairwise classifier consists of multiple sub-classifiers using an adaptive feature set for each class-pair. Simulated and real fMRI data were used to verify the proposed method. Intra- and inter-subject analyses were performed to compare the proposed method with several well-known classifiers, including single and ensemble classifiers. The comparison results showed that the proposed method can be generally applied to multiclass classification in both simulations and real fMRI analyses.

  4. Quantitative analysis of terahertz spectra for illicit drugs using adaptive-range micro-genetic algorithm

    NASA Astrophysics Data System (ADS)

    Chen, Yi; Ma, Yong; Lu, Zheng; Peng, Bei; Chen, Qin

    2011-08-01

    In the field of anti-illicit drug applications, many suspicious mixture samples might consist of various drug components—for example, a mixture of methamphetamine, heroin, and amoxicillin—which makes spectral identification very difficult. A terahertz spectroscopic quantitative analysis method using an adaptive range micro-genetic algorithm with a variable internal population (ARVIPɛμGA) has been proposed. Five mixture cases are discussed using ARVIPɛμGA driven quantitative terahertz spectroscopic analysis in this paper. The devised simulation results show agreement with the previous experimental results, which suggested that the proposed technique has potential applications for terahertz spectral identifications of drug mixture components. The results show agreement with the results obtained using other experimental and numerical techniques.

  5. Global Megacities Differing Adaptation Responses to Climate Change: an Analysis of Annual Spend of Ten Major cities on the adaptation economy

    NASA Astrophysics Data System (ADS)

    Maslin, M. A.; Georgeson, L.

    2015-12-01

    Urban areas are increasingly at risk from climate change with negative impacts predicted for human health, the economy and ecosystems. These risks require responses from cities, to improve the resilience of their infrastructure, economy and environment to climate change. Policymakers need to understand what is already being spent on adaptation so that they can make more effective and comprehensive adaptation plans. Through the measurement of spend in the newly defined 'Adaptation Economy' we analysis the current efforts of 10 global megacities in adapting to climate change. These cities were chosen based on their size, geographical location and their developmental status. The cities are London, Paris, New York, Mexico City, Sao Paulo, Beijing, Mumbai, Jakarta, Lagos and Addis Ababa. It is important to study a range of cities in different regions of the world, with different climates and at different states of socio-economic development. While in economic terms, disaster losses from weather, climate and geophysical events are greater in developed countries, fatalities and economic losses as a proportion of GDP are higher in developing countries. In all cities examined the Adaptation Economy is still a small part of the overall economy accounting for a maximum of 0.3% of the Cities total GDP (GDPc). The differences in total spend are significant between cities in developed and rapidly emerging countries, compared to those in developing countries with a spend ranging from £16 million to £1,500 million. Comparing key sub sectors, we demonstrate that there are distinctive adaptation profiles with developing cities having a higher relative spend on health, while developed cities have a higher spend on disaster preparedness, ICT and professional services. Comparing spend per capita and as a percentage of GDPc demonstrates even more clearly disparities between the cities in the study; developing country cities spend half as much as a proportion of GPCc in some cases, and

  6. Facilitating Joint Chaos and Fractal Analysis of Biosignals through Nonlinear Adaptive Filtering

    PubMed Central

    Gao, Jianbo; Hu, Jing; Tung, Wen-wen

    2011-01-01

    Background Chaos and random fractal theories are among the most important for fully characterizing nonlinear dynamics of complicated multiscale biosignals. Chaos analysis requires that signals be relatively noise-free and stationary, while fractal analysis demands signals to be non-rhythmic and scale-free. Methodology/Principal Findings To facilitate joint chaos and fractal analysis of biosignals, we present an adaptive algorithm, which: (1) can readily remove nonstationarities from the signal, (2) can more effectively reduce noise in the signals than linear filters, wavelet denoising, and chaos-based noise reduction techniques; (3) can readily decompose a multiscale biosignal into a series of intrinsically bandlimited functions; and (4) offers a new formulation of fractal and multifractal analysis that is better than existing methods when a biosignal contains a strong oscillatory component. Conclusions The presented approach is a valuable, versatile tool for the analysis of various types of biological signals. Its effectiveness is demonstrated by offering new important insights into brainwave dynamics and the very high accuracy in automatically detecting epileptic seizures from EEG signals. PMID:21915312

  7. Adaptive elastic-net sparse principal component analysis for pathway association testing.

    PubMed

    Chen, Xi

    2011-10-24

    Pathway or gene set analysis has become an increasingly popular approach for analyzing high-throughput biological experiments such as microarray gene expression studies. The purpose of pathway analysis is to identify differentially expressed pathways associated with outcomes. Important challenges in pathway analysis are selecting a subset of genes contributing most to association with clinical phenotypes and conducting statistical tests of association for the pathways efficiently. We propose a two-stage analysis strategy: (1) extract latent variables representing activities within each pathway using a dimension reduction approach based on adaptive elastic-net sparse principal component analysis; (2) integrate the latent variables with the regression modeling framework to analyze studies with different types of outcomes such as binary, continuous or survival outcomes. Our proposed approach is computationally efficient. For each pathway, because the latent variables are estimated in an unsupervised fashion without using disease outcome information, in the sample label permutation testing procedure, the latent variables only need to be calculated once rather than for each permutation resample. Using both simulated and real datasets, we show our approach performed favorably when compared with five other currently available pathway testing methods.

  8. Adaptive Elastic-Net Sparse Principal Component Analysis for Pathway Association Testing

    PubMed Central

    Chen, Xi

    2011-01-01

    Pathway or gene set analysis has become an increasingly popular approach for analyzing high-throughput biological experiments such as microarray gene expression studies. The purpose of pathway analysis is to identify differentially expressed pathways associated with outcomes. Important challenges in pathway analysis are selecting a subset of genes contributing most to association with clinical phenotypes and conducting statistical tests of association for the pathways efficiently. We propose a two-stage analysis strategy: (1) extract latent variables representing activities within each pathway using a dimension reduction approach based on adaptive elastic-net sparse principal component analysis; (2) integrate the latent variables with the regression modeling framework to analyze studies with different types of outcomes such as binary, continuous or survival outcomes. Our proposed approach is computationally efficient. For each pathway, because the latent variables are estimated in an unsupervised fashion without using disease outcome information, in the sample label permutation testing procedure, the latent variables only need to be calculated once rather than for each permutation resample. Using both simulated and real datasets, we show our approach performed favorably when compared with five other currently available pathway testing methods. PMID:23089825

  9. Adaptation and Evaluation of a Multi-Criteria Decision Analysis Model for Lyme Disease Prevention.

    PubMed

    Aenishaenslin, Cécile; Gern, Lise; Michel, Pascal; Ravel, André; Hongoh, Valérie; Waaub, Jean-Philippe; Milord, François; Bélanger, Denise

    2015-01-01

    Designing preventive programs relevant to vector-borne diseases such as Lyme disease (LD) can be complex given the need to include multiple issues and perspectives into prioritizing public health actions. A multi-criteria decision aid (MCDA) model was previously used to rank interventions for LD prevention in Quebec, Canada, where the disease is emerging. The aim of the current study was to adapt and evaluate the decision model constructed in Quebec under a different epidemiological context, in Switzerland, where LD has been endemic for the last thirty years. The model adaptation was undertaken with a group of Swiss stakeholders using a participatory approach. The PROMETHEE method was used for multi-criteria analysis. Key elements and results of the MCDA model are described and contrasted with the Quebec model. All criteria and most interventions of the MCDA model developed for LD prevention in Quebec were directly transferable to the Swiss context. Four new decision criteria were added, and the list of proposed interventions was modified. Based on the overall group ranking, interventions targeting human populations were prioritized in the Swiss model, with the top ranked action being the implementation of a large communication campaign. The addition of criteria did not significantly alter the intervention rankings, but increased the capacity of the model to discriminate between highest and lowest ranked interventions. The current study suggests that beyond the specificity of the MCDA models developed for Quebec and Switzerland, their general structure captures the fundamental and common issues that characterize the complexity of vector-borne disease prevention. These results should encourage public health organizations to adapt, use and share MCDA models as an effective and functional approach to enable the integration of multiple perspectives and considerations in the prevention and control of complex public health issues such as Lyme disease or other vector

  10. Adaptation and Evaluation of a Multi-Criteria Decision Analysis Model for Lyme Disease Prevention

    PubMed Central

    Aenishaenslin, Cécile; Gern, Lise; Michel, Pascal; Ravel, André; Hongoh, Valérie; Waaub, Jean-Philippe; Milord, François; Bélanger, Denise

    2015-01-01

    Designing preventive programs relevant to vector-borne diseases such as Lyme disease (LD) can be complex given the need to include multiple issues and perspectives into prioritizing public health actions. A multi-criteria decision aid (MCDA) model was previously used to rank interventions for LD prevention in Quebec, Canada, where the disease is emerging. The aim of the current study was to adapt and evaluate the decision model constructed in Quebec under a different epidemiological context, in Switzerland, where LD has been endemic for the last thirty years. The model adaptation was undertaken with a group of Swiss stakeholders using a participatory approach. The PROMETHEE method was used for multi-criteria analysis. Key elements and results of the MCDA model are described and contrasted with the Quebec model. All criteria and most interventions of the MCDA model developed for LD prevention in Quebec were directly transferable to the Swiss context. Four new decision criteria were added, and the list of proposed interventions was modified. Based on the overall group ranking, interventions targeting human populations were prioritized in the Swiss model, with the top ranked action being the implementation of a large communication campaign. The addition of criteria did not significantly alter the intervention rankings, but increased the capacity of the model to discriminate between highest and lowest ranked interventions. The current study suggests that beyond the specificity of the MCDA models developed for Quebec and Switzerland, their general structure captures the fundamental and common issues that characterize the complexity of vector-borne disease prevention. These results should encourage public health organizations to adapt, use and share MCDA models as an effective and functional approach to enable the integration of multiple perspectives and considerations in the prevention and control of complex public health issues such as Lyme disease or other vector

  11. Muscular adaptations in low- versus high-load resistance training: A meta-analysis.

    PubMed

    Schoenfeld, Brad J; Wilson, Jacob M; Lowery, Ryan P; Krieger, James W

    2016-01-01

    There has been much debate as to optimal loading strategies for maximising the adaptive response to resistance exercise. The purpose of this paper therefore was to conduct a meta-analysis of randomised controlled trials to compare the effects of low-load (≤60% 1 repetition maximum [RM]) versus high-load (≥65% 1 RM) training in enhancing post-exercise muscular adaptations. The strength analysis comprised 251 subjects and 32 effect sizes (ESs), nested within 20 treatment groups and 9 studies. The hypertrophy analysis comprised 191 subjects and 34 ESs, nested with 17 treatment groups and 8 studies. There was a trend for strength outcomes to be greater with high loads compared to low loads (difference = 1.07 ± 0.60; CI: -0.18, 2.32; p = 0.09). The mean ES for low loads was 1.23 ± 0.43 (CI: 0.32, 2.13). The mean ES for high loads was 2.30 ± 0.43 (CI: 1.41, 3.19). There was a trend for hypertrophy outcomes to be greater with high loads compared to low loads (difference = 0.43 ± 0.24; CI: -0.05, 0.92; p = 0.076). The mean ES for low loads was 0.39 ± 0.17 (CI: 0.05, 0.73). The mean ES for high loads was 0.82 ± 0.17 (CI: 0.49, 1.16). In conclusion, training with loads ≤50% 1 RM was found to promote substantial increases in muscle strength and hypertrophy in untrained individuals, but a trend was noted for superiority of heavy loading with respect to these outcome measures with null findings likely attributed to a relatively small number of studies on the topic.

  12. Analysis of Anoxybacillus Genomes from the Aspects of Lifestyle Adaptations, Prophage Diversity, and Carbohydrate Metabolism

    PubMed Central

    Goh, Kian Mau; Gan, Han Ming; Chan, Kok-Gan; Chan, Giek Far; Shahar, Saleha; Chong, Chun Shiong; Kahar, Ummirul Mukminin; Chai, Kian Piaw

    2014-01-01

    Species of Anoxybacillus are widespread in geothermal springs, manure, and milk-processing plants. The genus is composed of 22 species and two subspecies, but the relationship between its lifestyle and genome is little understood. In this study, two high-quality draft genomes were generated from Anoxybacillus spp. SK3-4 and DT3-1, isolated from Malaysian hot springs. De novo assembly and annotation were performed, followed by comparative genome analysis with the complete genome of Anoxybacillus flavithermus WK1 and two additional draft genomes, of A. flavithermus TNO-09.006 and A. kamchatkensis G10. The genomes of Anoxybacillus spp. are among the smaller of the family Bacillaceae. Despite having smaller genomes, their essential genes related to lifestyle adaptations at elevated temperature, extreme pH, and protection against ultraviolet are complete. Due to the presence of various competence proteins, Anoxybacillus spp. SK3-4 and DT3-1 are able to take up foreign DNA fragments, and some of these transferred genes are important for the survival of the cells. The analysis of intact putative prophage genomes shows that they are highly diversified. Based on the genome analysis using SEED, many of the annotated sequences are involved in carbohydrate metabolism. The presence of glycosyl hydrolases among the Anoxybacillus spp. was compared, and the potential applications of these unexplored enzymes are suggested here. This is the first study that compares Anoxybacillus genomes from the aspect of lifestyle adaptations, the capacity for horizontal gene transfer, and carbohydrate metabolism. PMID:24603481

  13. An Empirical Bayes Enhancement of Mantel-Haenszel DIF Analysis for Computer-Adaptive Tests. LSAC Research Report Series.

    ERIC Educational Resources Information Center

    Zwick, Rebecca; Thayer, Dorothy T.

    This study investigated the applicability to computerized adaptive testing (CAT) data of a differential item functioning (DIF) analysis that involves an empirical Bayes (EB) enhancement of the popular Mantel Haenszel (MH) DIF analysis method. The computerized Law School Admission Test (LSAT) assumed for this study was similar to that currently…

  14. Application of an Empirical Bayes Enhancement of Mantel-Haenszel Differential Item Functioning Analysis to a Computerized Adaptive Test.

    ERIC Educational Resources Information Center

    Zwick, Rebecca; Thayer, Dorothy T.

    2002-01-01

    Used a simulation to investigate the applicability to computerized adaptive test data of a differential item functioning (DIF) analysis method. Results show the performance of this empirical Bayes enhancement of the Mantel Haenszel DIF analysis method to be quite promising. (SLD)

  15. Analysis of the FGF gene family provides insights into aquatic adaptation in cetaceans

    PubMed Central

    Nam, Kiwoong; Lee, Kyeong Won; Chung, Oksung; Yim, Hyung-Soon; Cha, Sun-Shin; Lee, Sae-Won; Jun, JeHoon; Cho, Yun Sung; Bhak, Jong; Magalhães, João Pedro de; Lee, Jung-Hyun; Jeong, Jae-Yeon

    2017-01-01

    Cetacean body structure and physiology exhibit dramatic adaptations to their aquatic environment. Fibroblast growth factors (FGFs) are a family of essential factors that regulate animal development and physiology; however, their role in cetacean evolution is not clearly understood. Here, we sequenced the fin whale genome and analysed FGFs from 8 cetaceans. FGF22, a hair follicle-enriched gene, exhibited pseudogenization, indicating that the function of this gene is no longer necessary in cetaceans that have lost most of their body hair. An evolutionary analysis revealed signatures of positive selection for FGF3 and FGF11, genes related to ear and tooth development and hypoxia, respectively. We found a D203G substitution in cetacean FGF9, which was predicted to affect FGF9 homodimerization, suggesting that this gene plays a role in the acquisition of rigid flippers for efficient manoeuvring. Cetaceans utilize low bone density as a buoyancy control mechanism, but the underlying genes are not known. We found that the expression of FGF23, a gene associated with reduced bone density, is greatly increased in the cetacean liver under hypoxic conditions, thus implicating FGF23 in low bone density in cetaceans. Altogether, our results provide novel insights into the roles of FGFs in cetacean adaptation to the aquatic environment. PMID:28074842

  16. Hierarchical adaptation scheme for multiagent data fusion and resource management in situation analysis

    NASA Astrophysics Data System (ADS)

    Benaskeur, Abder R.; Roy, Jean

    2001-08-01

    Sensor Management (SM) has to do with how to best manage, coordinate and organize the use of sensing resources in a manner that synergistically improves the process of data fusion. Based on the contextual information, SM develops options for collecting further information, allocates and directs the sensors towards the achievement of the mission goals and/or tunes the parameters for the realtime improvement of the effectiveness of the sensing process. Conscious of the important role that SM has to play in modern data fusion systems, we are currently studying advanced SM Concepts that would help increase the survivability of the current Halifax and Iroquois Class ships, as well as their possible future upgrades. For this purpose, a hierarchical scheme has been proposed for data fusion and resource management adaptation, based on the control theory and within the process refinement paradigm of the JDL data fusion model, and taking into account the multi-agent model put forward by the SASS Group for the situation analysis process. The novelty of this work lies in the unified framework that has been defined for tackling the adaptation of both the fusion process and the sensor/weapon management.

  17. A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool

    PubMed Central

    Mazandu, Gaston K.; Chimusa, Emile R.; Mbiyavanga, Mamana; Mulder, Nicola J.

    2016-01-01

    Summary: Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biological information contained in the GO structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable Gene Ontology semantic similarity-based Functional analysis). It is a portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures. A-DaGO-Fun has the advantage not only of handling datasets from the current high-throughput genome-wide applications, but also allowing users to choose the most relevant semantic similarity approach for their biological applications and to adapt a given module to their needs. Availability and implementation: A-DaGO-Fun is freely available to the research community at http://web.cbio.uct.ac.za/ITGOM/adagofun. It is implemented in Linux using Python under free software (GNU General Public Licence). Contact: gmazandu@cbio.uct.ac.za or Nicola.Mulder@uct.ac.za Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26476781

  18. Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes

    PubMed Central

    Fang, Xiaodong; Seim, Inge; Huang, Zhiyong; Gerashchenko, Maxim V.; Xiong, Zhiqiang; Turanov, Anton A.; Zhu, Yabing; Lobanov, Alexei V.; Fan, Dingding; Yim, Sun Hee; Yao, Xiaoming; Ma, Siming; Yang, Lan; Lee, Sang-Goo; Kim, Eun Bae; Bronson, Roderick T.; Šumbera, Radim; Buffenstein, Rochelle; Zhou, Xin; Krogh, Anders; Park, Thomas J.; Zhang, Guojie; Wang, Jun; Gladyshev, Vadim N.

    2014-01-01

    SUMMARY Subterranean mammals spend their lives in dark, unventilated environments rich in carbon dioxide and ammonia, and low in oxygen. Many of these animals are also long-lived and exhibit reduced aging-associated diseases, such as neurodegenerative disorders and cancer. We sequenced the genome of the Damaraland mole rat (DMR, Fukomys damarensis) and improved the genome assembly of the naked mole rat (NMR, Heterocephalus glaber). Comparative genome analysis, along with transcriptomes of related subterranean rodents, reveal candidate molecular adaptations for subterranean life and longevity, including a divergent insulin peptide, expression of oxygen-carrying globins in the brain, prevention of high CO2-induced pain perception, and enhanced ammonia detoxification. Juxtaposition of the genomes of DMR and other more conventional animals with the genome of NMR revealed several truly exceptional NMR features: unusual thermogenesis, aberrant melatonin system, pain insensitivity, and novel processing of 28S rRNA. Together, the new genomes and transcriptomes extend our understanding of subterranean adaptations, stress resistance and longevity. PMID:25176646

  19. Comparative transcriptomic analysis of salt adaptation in roots of contrasting Medicago truncatula genotypes.

    PubMed

    Zahaf, Ons; Blanchet, Sandrine; de Zélicourt, Axel; Alunni, Benoît; Plet, Julie; Laffont, Carole; de Lorenzo, Laura; Imbeaud, Sandrine; Ichanté, Jean-Laurent; Diet, Anouck; Badri, Mounawer; Zabalza, Ana; González, Esther M; Delacroix, Hervé; Gruber, Véronique; Frugier, Florian; Crespi, Martin

    2012-09-01

    Evolutionary diversity can be driven by the interaction of plants with different environments. Molecular bases involved in ecological adaptations to abiotic constraints can be explored using genomic tools. Legumes are major crops worldwide and soil salinity is a main stress affecting yield in these plants. We analyzed in the Medicago truncatula legume the root transcriptome of two genotypes having contrasting responses to salt stress: TN1.11, sampled in a salty Tunisian soil, and the reference Jemalong A17 genotype. TN1.11 plants show increased root growth under salt stress as well as a differential accumulation of sodium ions when compared to A17. Transcriptomic analysis revealed specific gene clusters preferentially regulated by salt in root apices of TN1.11, notably those related to the auxin pathway and to changes in histone variant isoforms. Many genes encoding transcription factors (TFs) were also differentially regulated between the two genotypes in response to salt. Among those selected for functional studies, overexpression in roots of the A17 genotype of the bHLH-type TF most differentially regulated between genotypes improved significantly root growth under salt stress. Despite the global complexity of the differential transcriptional responses, we propose that an increase in this bHLH TF expression may be linked to the adaptation of M. truncatula to saline soil environments.

  20. Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations.

    PubMed

    Förster, Frank; Beisser, Daniela; Grohme, Markus A; Liang, Chunguang; Mali, Brahim; Siegl, Alexander Matthias; Engelmann, Julia C; Shkumatov, Alexander V; Schokraie, Elham; Müller, Tobias; Schnölzer, Martina; Schill, Ralph O; Frohme, Marcus; Dandekar, Thomas

    2012-01-01

    Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.

  1. Adaptive Tensor-Based Principal Component Analysis for Low-Dose CT Image Denoising.

    PubMed

    Ai, Danni; Yang, Jian; Fan, Jingfan; Cong, Weijian; Wang, Yongtian

    2015-01-01

    Computed tomography (CT) has a revolutionized diagnostic radiology but involves large radiation doses that directly impact image quality. In this paper, we propose adaptive tensor-based principal component analysis (AT-PCA) algorithm for low-dose CT image denoising. Pixels in the image are presented by their nearby neighbors, and are modeled as a patch. Adaptive searching windows are calculated to find similar patches as training groups for further processing. Tensor-based PCA is used to obtain transformation matrices, and coefficients are sequentially shrunk by the linear minimum mean square error. Reconstructed patches are obtained, and a denoised image is finally achieved by aggregating all of these patches. The experimental results of the standard test image show that the best results are obtained with two denoising rounds according to six quantitative measures. For the experiment on the clinical images, the proposed AT-PCA method can suppress the noise, enhance the edge, and improve the image quality more effectively than NLM and KSVD denoising methods.

  2. Real-Time Adaptive EEG Source Separation Using Online Recursive Independent Component Analysis.

    PubMed

    Hsu, Sheng-Hsiou; Mullen, Tim R; Jung, Tzyy-Ping; Cauwenberghs, Gert

    2016-03-01

    Independent component analysis (ICA) has been widely applied to electroencephalographic (EEG) biosignal processing and brain-computer interfaces. The practical use of ICA, however, is limited by its computational complexity, data requirements for convergence, and assumption of data stationarity, especially for high-density data. Here we study and validate an optimized online recursive ICA algorithm (ORICA) with online recursive least squares (RLS) whitening for blind source separation of high-density EEG data, which offers instantaneous incremental convergence upon presentation of new data. Empirical results of this study demonstrate the algorithm's: 1) suitability for accurate and efficient source identification in high-density (64-channel) realistically-simulated EEG data; 2) capability to detect and adapt to nonstationarity in 64-ch simulated EEG data; and 3) utility for rapidly extracting principal brain and artifact sources in real 61-channel EEG data recorded by a dry and wearable EEG system in a cognitive experiment. ORICA was implemented as functions in BCILAB and EEGLAB and was integrated in an open-source Real-time EEG Source-mapping Toolbox (REST), supporting applications in ICA-based online artifact rejection, feature extraction for real-time biosignal monitoring in clinical environments, and adaptable classifications in brain-computer interfaces.

  3. Real-time Adaptive EEG Source Separation using Online Recursive Independent Component Analysis

    PubMed Central

    Hsu, Sheng-Hsiou; Mullen, Tim; Jung, Tzyy-Ping; Cauwenberghs, Gert

    2016-01-01

    Independent Component Analysis (ICA) has been widely applied to electroencephalographic (EEG) biosignal processing and brain-computer interfaces. The practical use of ICA, however, is limited by its computational complexity, data requirements for convergence, and assumption of data stationarity, especially for high-density data. Here we study and validate an optimized online recursive ICA algorithm (ORICA) with online recursive least squares (RLS) whitening for blind source separation of high-density EEG data, which offers instantaneous incremental convergence upon presentation of new data. Empirical results of this study demonstrate the algorithm's: (a) suitability for accurate and efficient source identification in high-density (64-channel) realistically-simulated EEG data; (b) capability to detect and adapt to non-stationarity in 64-ch simulated EEG data; and (c) utility for rapidly extracting principal brain and artifact sources in real 61-channel EEG data recorded by a dry and wearable EEG system in a cognitive experiment. ORICA was implemented as functions in BCILAB and EEGLAB and was integrated in an open-source Real-time EEG Source-mapping Toolbox (REST), supporting applications in ICA-based online artifact rejection, feature extraction for real-time biosignal monitoring in clinical environments, and adaptable classifications in brain-computer interfaces. PMID:26685257

  4. Adaptive Tensor-Based Principal Component Analysis for Low-Dose CT Image Denoising

    PubMed Central

    Ai, Danni; Yang, Jian; Fan, Jingfan; Cong, Weijian; Wang, Yongtian

    2015-01-01

    Computed tomography (CT) has a revolutionized diagnostic radiology but involves large radiation doses that directly impact image quality. In this paper, we propose adaptive tensor-based principal component analysis (AT-PCA) algorithm for low-dose CT image denoising. Pixels in the image are presented by their nearby neighbors, and are modeled as a patch. Adaptive searching windows are calculated to find similar patches as training groups for further processing. Tensor-based PCA is used to obtain transformation matrices, and coefficients are sequentially shrunk by the linear minimum mean square error. Reconstructed patches are obtained, and a denoised image is finally achieved by aggregating all of these patches. The experimental results of the standard test image show that the best results are obtained with two denoising rounds according to six quantitative measures. For the experiment on the clinical images, the proposed AT-PCA method can suppress the noise, enhance the edge, and improve the image quality more effectively than NLM and KSVD denoising methods. PMID:25993566

  5. Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations

    PubMed Central

    Förster, Frank; Beisser, Daniela; Grohme, Markus A.; Liang, Chunguang; Mali, Brahim; Siegl, Alexander Matthias; Engelmann, Julia C.; Shkumatov, Alexander V.; Schokraie, Elham; Müller, Tobias; Schnölzer, Martina; Schill, Ralph O.; Frohme, Marcus; Dandekar, Thomas

    2012-01-01

    Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant. PMID:22563243

  6. Measuring the economic value of alternative clam fishing management practices in the Venice Lagoon: results from a conjoint valuation application

    NASA Astrophysics Data System (ADS)

    Nunes, Paulo A. L. D.; Rossetto, Luca; de Blaeij, Arianne

    2004-11-01

    This article focuses on the economic valuation of alternative clam management practices in the Venice Lagoon. The proposed valuation method is characterized by the design of a survey questionnaire applied to the fishermen population. In each questionnaire, two fishing alternatives are described. The respondent is asked to choose one of them. This valuation method, referred in the article as conjoint valuation, gives sufficient flexibility to set, alter, and combine the valuation of different clam management practices. Furthermore, this approach presents an important advantage to the well-known contingent valuation method since it makes the monetary valuation of each management attribute possible. Estimation results show that all three attributes used in the questionnaire to describe and value different clam management practices—price of the annual permit and fishing technological system—are statistically robust, indicating that fishermen bear a utility change whenever these attributes change. In particular, fishermen's willingness to pay for a larger clam fishing area ranges between 568 and 811 € per year. In addition, an individual's willingness to pay for a fishing practice exclusively based on the vibrant rake system ranges between 1005 and 2456 €. Finally, the adoption of a clam fish management practice in the Venice Lagoon that is exclusively based on the use of manual rakes, which is associated with the lowest damage to the lagoon ecosystem, will represent a welfare loss of 5904 € per fisherman per year. Combining such a value estimate with the total number of fishermen currently operating in the Lagoon of Venice, the welfare loss associated with the adoption of this type of clam management policy amounts to 11.8 € million per year. This figure can be regarded as an upper bound to the cost of implementation of a clam fishing system anchored in the use of manual, ecosystem friendly rakes.

  7. Fractal behavior of traffic volume on urban expressway through adaptive fractal analysis

    NASA Astrophysics Data System (ADS)

    He, Hong-di; Wang, Jun-li; Wei, Hai-rui; Ye, Cheng; Ding, Yi

    2016-02-01

    In this paper, we investigate the fractal behavior of traffic volume in urban expressway based on a newly developed adaptive fractal analysis (AFA), which has a number of advantages over traditional method of detrended fluctuation analysis (DFA). Before fractal analysis, autocorrelation function was first adopted on traffic volume data and the long-range correlation behavior was found to be existed in both on-ramp and off-ramp situations. Then AFA as well as DFA was applied to further examine the fractal behavior. The results showed that the multifractality and the long-range anti-persistent behavior existed on both on-ramp and off-ramp. Additionally, multifractal analysis on weekdays and weekends are performed respectively and the results show that the degree of multifractality on weekdays is higher than that on weekends, implying that long-range correlation behaviors were more obvious on weekdays. Finally, the source of multifractality is examined with randomly shuffled and the surrogated series. Long-range correlation behaviors are identified in both on-ramp and off-ramp situations and fat-tail distributions were found to make little in the contributions of multifractality.

  8. Evaluation of Load Analysis Methods for NASAs GIII Adaptive Compliant Trailing Edge Project

    NASA Technical Reports Server (NTRS)

    Cruz, Josue; Miller, Eric J.

    2016-01-01

    The Air Force Research Laboratory (AFRL), NASA Armstrong Flight Research Center (AFRC), and FlexSys Inc. (Ann Arbor, Michigan) have collaborated to flight test the Adaptive Compliant Trailing Edge (ACTE) flaps. These flaps were installed on a Gulfstream Aerospace Corporation (GAC) GIII aircraft and tested at AFRC at various deflection angles over a range of flight conditions. External aerodynamic and inertial load analyses were conducted with the intention to ensure that the change in wing loads due to the deployed ACTE flap did not overload the existing baseline GIII wing box structure. The objective of this paper was to substantiate the analysis tools used for predicting wing loads at AFRC. Computational fluid dynamics (CFD) models and distributed mass inertial models were developed for predicting the loads on the wing. The analysis tools included TRANAIR (full potential) and CMARC (panel) models. Aerodynamic pressure data from the analysis codes were validated against static pressure port data collected in-flight. Combined results from the CFD predictions and the inertial load analysis were used to predict the normal force, bending moment, and torque loads on the wing. Wing loads obtained from calibrated strain gages installed on the wing were used for substantiation of the load prediction tools. The load predictions exhibited good agreement compared to the flight load results obtained from calibrated strain gage measurements.

  9. Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis

    PubMed Central

    Whitlock, Raj

    2014-01-01

    Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These

  10. A Meta-Analysis of Urban Climate Change Adaptation Planning in the U.S.

    EPA Science Inventory

    The concentration of people, infrastructure, and ecosystem services in urban areas make them prime sites for climate change adaptation. While advances have been made in developing frameworks for adaptation planning and identifying both real and potential barriers to action, empir...

  11. Multi-layer holographic bifurcative neural network system for real-time adaptive EOS data analysis

    NASA Technical Reports Server (NTRS)

    Liu, Hua-Kuang; Huang, K. S.; Diep, J.

    1993-01-01

    Optical data processing techniques have the inherent advantage of high data throughout, low weight and low power requirements. These features are particularly desirable for onboard spacecraft in-situ real-time data analysis and data compression applications. the proposed multi-layer optical holographic neural net pattern recognition technique will utilize the nonlinear photorefractive devices for real-time adaptive learning to classify input data content and recognize unexpected features. Information can be stored either in analog or digital form in a nonlinear photofractive device. The recording can be accomplished in time scales ranging from milliseconds to microseconds. When a system consisting of these devices is organized in a multi-layer structure, a feedforward neural net with bifurcating data classification capability is formed. The interdisciplinary research will involve the collaboration with top digital computer architecture experts at the University of Southern California.

  12. Multi-layer holographic bifurcative neural network system for real-time adaptive EOS data analysis

    NASA Technical Reports Server (NTRS)

    Liu, Hua-Kuang; Huang, K.; Diep, J.

    1992-01-01

    Optical data processing techniques have the inherent advantage of high data throughout, low weight and low power requirements. These features are particularly desirable for onboard spacecraft in-situ real-time data analysis and data compression applications. The proposed multi-layer optical holographic neural net pattern recognition technique will utilize the nonlinear photorefractive devices for real-time adaptive learning to classify input data content and recognize unexpected features. Information can be stored either in analog or digital form in a nonlinear photorefractive device. The recording can be accomplished in time scales ranging from milliseconds to microseconds. When a system consisting of these devices is organized in a multi-layer structure, a feed forward neural net with bifurcating data classification capability is formed. The interdisciplinary research will involve the collaboration with top digital computer architecture experts at the University of Southern California.

  13. [An adaptive ultrasound sound speed optimization based on image contrast analysis].

    PubMed

    Li, Xiaoying; Liu, Dongquan

    2011-12-01

    In order to get real time ultrasound images with clear structure and improved contrast, an adaptive ultrasound sound speed optimization method based on image contrast analysis was investigated. It firstly introduced the dynamic beamforming of ultrasound system, as well as the definition of assumed system's sound speed and the true sound speed propagated in tissues the degrade image quality due to their mismatch was also discussed. After given the pixel gray level value based ultrasound image contrast ratio, the basic idea to precisely estimate the true sound speed for real time system sound speed was proposed. Algorithms have been verified both in tissue-mimicking phantoms with known sound speeds and in vivo ultrasound images, compared with other existing method. The testing results showed that this new method not only produced accurate sound speed for ultrasound image optimization, but also finely met the critical computation requirement for real time applications.

  14. Regenerated phase-shifted sinusoids assisted EMD for adaptive analysis of fringe patterns

    NASA Astrophysics Data System (ADS)

    Wang, Chenxing; Kemao, Qian; Da, Feipeng

    2016-12-01

    Fringe patterns are often produced from optical metrology. It is important yet challenging to reduce noise and remove a complicated background in a fringe pattern, for which empirical mode decomposition based methods have been proven useful. However, the mode-mixing problem and the difficulty in automatic mode classification limit the application of these methods. In this paper, a newly developed method named regenerated phase-shifted sinusoids assisted empirical mode decomposition is introduced to decompose a fringe pattern, and subsequently, a new noise-signal-background classification strategy is proposed. The former avoids the mode-mixing problem appearing during the decomposition, while the latter adaptively classifies the decomposition results to remove the noise and background. The proposed method is testified by both simulation and real experiments, which shows effective and robust for fringe pattern analysis under different noise, fringe modulation, and defects.

  15. Cyclone preparedness and response: an analysis of lessons identified using an adapted military planning framework.

    PubMed

    Tatham, Peter; Oloruntoba, Richard; Spens, Karen

    2012-01-01

    The United Kingdom uses the Defence Lines of Development (DLOD) framework to analyse and understand the key components and costs of a military capability. Rooted in the Resource Based View (RBV) of a firm, an adapted DLOD approach is employed to explore, analyse and discuss the preparedness, planning and response strategies of two markedly different countries (Australia and Bangladesh) when faced with a major cyclone event of a comparable size. Given the numerous similarities in the challenges facing military forces in a complex emergency and humanitarian agencies in a natural disaster, the paper demonstrates the applicability of the DLOD framework as an analysis and planning tool in the cyclone preparedness planning and response phases, and more broadly within the disaster management area. In addition, the paper highlights the benefit to disaster managers, policymakers and researchers of exploiting comparative cross-learning opportunities from disaster events, drawn from different sectors and countries.

  16. Analysis of spatial lamellar distribution from adaptive-optics second harmonic generation corneal images.

    PubMed

    Bueno, Juan M; Palacios, Raquel; Chessey, Mary K; Ginis, Harilaos

    2013-07-01

    The spatial organization of stromal collagen of ex-vivo corneas has been quantified in adaptive-optics second harmonic generation (SHG) images by means of an optimized Fourier transform (FT) based analysis. At a particular depth location, adjacent lamellae often present similar orientations and run parallel to the corneal surface. However this pattern might be combined with interweaved collagen bundles leading to crosshatched structures with different orientations. The procedure here reported provides us with both principal and crosshatched angles. This is also able to automatically distinguish a random distribution from a cross-shaped one, since it uses the ratio of the axes lengths of the best-fitted ellipse of the FT data as an auxiliary parameter. The technique has successfully been applied to SHG images of healthy corneas (both stroma and Bowman's layer) of different species and to corneas undergoing cross-linking treatment.

  17. Regularized least-squares migration of simultaneous-source seismic data with adaptive singular spectrum analysis.

    PubMed

    Li, Chuang; Huang, Jian-Ping; Li, Zhen-Chun; Wang, Rong-Rong

    2017-01-01

    Simultaneous-source acquisition has been recognized as an economic and efficient acquisition method, but the direct imaging of the simultaneous-source data produces migration artifacts because of the interference of adjacent sources. To overcome this problem, we propose the regularized least-squares reverse time migration method (RLSRTM) using the singular spectrum analysis technique that imposes sparseness constraints on the inverted model. Additionally, the difference spectrum theory of singular values is presented so that RLSRTM can be implemented adaptively to eliminate the migration artifacts. With numerical tests on a flat layer model and a Marmousi model, we validate the superior imaging quality, efficiency and convergence of RLSRTM compared with LSRTM when dealing with simultaneous-source data, incomplete data and noisy data.

  18. Calculation of intravascular signal in dynamic contrast enhanced-MRI using adaptive complex independent component analysis.

    PubMed

    Mehrabian, Hatef; Chopra, Rajiv; Martel, Anne L

    2013-04-01

    Assessing tumor response to therapy is a crucial step in personalized treatments. Pharmacokinetic (PK) modeling provides quantitative information about tumor perfusion and vascular permeability that are associated with prognostic factors. A fundamental step in most PK analyses is calculating the signal that is generated in the tumor vasculature. This signal is usually inseparable from the extravascular extracellular signal. It was shown previously using in vivo and phantom experiments that independent component analysis (ICA) is capable of calculating the intravascular time-intensity curve in dynamic contrast enhanced (DCE)-MRI. A novel adaptive complex independent component analysis (AC-ICA) technique is developed in this study to calculate the intravascular time-intensity curve and separate this signal from the DCE-MR images of tumors. The use of the complex-valued DCE-MRI images rather than the commonly used magnitude images satisfied the fundamental assumption of ICA, i.e., linear mixing of the sources. Using an adaptive cost function in ICA through estimating the probability distribution of the tumor vasculature at each iteration resulted in a more robust and accurate separation algorithm. The AC-ICA algorithm provided a better estimate for the intravascular time-intensity curve than the previous ICA-based method. A simulation study was also developed in this study to realistically simulate DCE-MRI data of a leaky tissue mimicking phantom. The passage of the MR contrast agent through the leaky phantom was modeled with finite element analysis using a diffusion model. Once the distribution of the contrast agent in the imaging field of view was calculated, DCE-MRI data was generated by solving the Bloch equation for each voxel at each time point. The intravascular time-intensity curve calculation results were compared to the previously proposed ICA-based intravascular time-intensity curve calculation method that applied ICA to the magnitude of the DCE-MRI data

  19. Experimental Design and Primary Data Analysis Methods for Comparing Adaptive Interventions

    ERIC Educational Resources Information Center

    Nahum-Shani, Inbal; Qian, Min; Almirall, Daniel; Pelham, William E.; Gnagy, Beth; Fabiano, Gregory A.; Waxmonsky, James G.; Yu, Jihnhee; Murphy, Susan A.

    2012-01-01

    In recent years, research in the area of intervention development has been shifting from the traditional fixed-intervention approach to "adaptive interventions," which allow greater individualization and adaptation of intervention options (i.e., intervention type and/or dosage) over time. Adaptive interventions are operationalized via a sequence…

  20. Early-Emerging Social Adaptive Skills in Toddlers with Autism Spectrum Disorders: An Item Analysis

    ERIC Educational Resources Information Center

    Ventola, Pamela; Saulnier, Celine A.; Steinberg, Elizabeth; Chawarska, Katarzyna; Klin, Ami

    2014-01-01

    Individuals with ASD have significant impairments in adaptive skills, particularly adaptive socialization skills. The present study examined the extent to which 20 items from the Vineland Adaptive Behavior Scales-Socialization Domain differentiated between ASD and developmentally delayed (DD) groups. Participants included 108 toddlers with ASD or…

  1. Q-Learning: A Data Analysis Method for Constructing Adaptive Interventions

    ERIC Educational Resources Information Center

    Nahum-Shani, Inbal; Qian, Min; Almirall, Daniel; Pelham, William E.; Gnagy, Beth; Fabiano, Gregory A.; Waxmonsky, James G.; Yu, Jihnhee; Murphy, Susan A.

    2012-01-01

    Increasing interest in individualizing and adapting intervention services over time has led to the development of adaptive interventions. Adaptive interventions operationalize the individualization of a sequence of intervention options over time via the use of decision rules that input participant information and output intervention…

  2. Adaptive data analysis for characterizing the temporal variability of the solar resource

    NASA Astrophysics Data System (ADS)

    Bengulescu, Marc; Blanc, Philippe; Wald, Lucien

    2016-04-01

    One of the key challenges associated with the large-scale penetration of solar power is the inherent spatio-temporal variability of the solar radiation impinging on the surface. Particular methods are currently employed to measure, estimate or forecast the extent and availability of the solar resource depending on the effective spatial and temporal scales of interest, such as numerical weather prediction models, satellite-based estimates, sky-imagers or in-situ ground measurements. Here we present a method for characterizing the intrinsic time-scales of the solar resource variability. The study deals with decennial time-series of daily values of the surface solar irradiance (SSI) issued from high-quality BSRN ground measurement stations. Geophysical signals, such as the SSI time-series under scrutiny, are often the result of non-linear interactions of physical processes that are also often under natural or anthropogenic non-stationary forcings. Therefore, an adaptive data analysis technique is employed that makes no beforehand assumptions about the data: neither linearity, nor stationarity of the signal is assumed. The method, called the Hilbert-Huang transform, first extracts all the embedded oscillations that have a similar time-scale, to which it then applies Hilbert spectral analysis. A time-frequency-energy representation of the signal is thus constructed, which reveals the time-varying character of the intrinsic temporal scales of variability (frequency modulation), along with any fluctuations in the intensity of the signal at the corresponding scale (amplitude modulation). In order to test whether the features extracted from the data are the expression of deterministic physical processes, as opposed to being stochastic realizations of various background processes (i.e. noise), a novel, adaptive null-hypothesis based on the statistical properties of noise is employed. It is shown that the data, irrespective of the geographical conditions, shares common time

  3. Adaptive evolution of anti-predator ability promotes the diversity of prey species: critical function analysis.

    PubMed

    Zu, Jian; Takeuchi, Yasuhiro

    2012-08-01

    In this paper, with the method of adaptive dynamics and critical function analysis, we investigate the evolutionary diversification of prey species. We assume that prey species can evolve safer strategies such that it can reduce the predation risk, but this has a cost in terms of its reproduction. First, by using the method of critical function analysis, we identify the general properties of trade-off functions that allow for continuously stable strategy and evolutionary branching in the prey strategy. It is found that if the trade-off curve is globally concave, then the evolutionarily singular strategy is continuously stable. However, if the trade-off curve is concave-convex-concave and the prey's sensitivity to crowding is not strong, then the evolutionarily singular strategy may be an evolutionary branching point, near which the resident and mutant prey can coexist and diverge in their strategies. Second, we find that after branching has occurred in the prey strategy, if the trade-off curve is concave-convex-concave, the prey population will eventually evolve into two different types, which can coexist on the long-term evolutionary timescale. The algebraical analysis reveals that an attractive dimorphism will always be evolutionarily stable and that no further branching is possible for the concave-convex-concave trade-off relationship.

  4. The Accuracy of Computerized Adaptive Testing in Heterogeneous Populations: A Mixture Item-Response Theory Analysis

    PubMed Central

    Kopec, Jacek A.; Wu, Amery D.; Zumbo, Bruno D.

    2016-01-01

    Background Computerized adaptive testing (CAT) utilizes latent variable measurement model parameters that are typically assumed to be equivalently applicable to all people. Biased latent variable scores may be obtained in samples that are heterogeneous with respect to a specified measurement model. We examined the implications of sample heterogeneity with respect to CAT-predicted patient-reported outcomes (PRO) scores for the measurement of pain. Methods A latent variable mixture modeling (LVMM) analysis was conducted using data collected from a heterogeneous sample of people in British Columbia, Canada, who were administered the 36 pain domain items of the CAT-5D-QOL. The fitted LVMM was then used to produce data for a simulation analysis. We evaluated bias by comparing the referent PRO scores of the LVMM with PRO scores predicted by a “conventional” CAT (ignoring heterogeneity) and a LVMM-based “mixture” CAT (accommodating heterogeneity). Results The LVMM analysis indicated support for three latent classes with class proportions of 0.25, 0.30 and 0.45, which suggests that the sample was heterogeneous. The simulation analyses revealed differences between the referent PRO scores and the PRO scores produced by the “conventional” CAT. The “mixture” CAT produced PRO scores that were nearly equivalent to the referent scores. Conclusion Bias in PRO scores based on latent variable models may result when population heterogeneity is ignored. Improved accuracy could be obtained by using CATs that are parameterized using LVMM. PMID:26930348

  5. Analysis of the early adaptive response of endothelial cells to hypoxia via a long serial analysis of gene expression

    SciTech Connect

    Liang, Guang-Ping; Su, Yong-Yue; Chen, Jian; Yang, Zong-Cheng; Liu, You-Sheng; Luo, Xiang-Dong

    2009-07-10

    Activation of endothelial cells in humans is an early event in the response to hypoxia that may contribute to the endothelium's endogenous capacity to reduce tissue injury. To better understand the mechanism underlying this process, we utilized Long Serial Analysis of Gene Expression to study the transcriptome of human vein umbilical endothelial cells (EA.hy926) shortly after the induction of hypoxia. Of over 13,000 genes detected in each pool, 112 showed obvious differences in expression. Metabolic processes such as protein biosynthesis and proteolysis, aminoglycan metabolism, ribonucleotide biosynthesis, adenosine salvage, and lipid metabolism were reinforced. Pro-proliferation and pro-apoptotic states suggest the co-existence of pro- and anti-injury forces in endothelium shortly after the induction of hypoxia. Other adaptive responses include reinforced angiogenesis and vasodilation. Additionally, gene transcription in the endothelium shortly after the induction of hypoxia was regulated independently of HIF-1{alpha}. Our efforts to elucidate the adaptive response at an early post-hypoxia stage should contribute to further investigation of the protective processes that occur in the endothelium and has potential clinical implications.

  6. Adaptive Photothermal Emission Analysis Techniques for Robust Thermal Property Measurements of Thermal Barrier Coatings

    NASA Astrophysics Data System (ADS)

    Valdes, Raymond

    The characterization of thermal barrier coating (TBC) systems is increasingly important because they enable gas turbine engines to operate at high temperatures and efficiency. Phase of photothermal emission analysis (PopTea) has been developed to analyze the thermal behavior of the ceramic top-coat of TBCs, as a nondestructive and noncontact method for measuring thermal diffusivity and thermal conductivity. Most TBC allocations are on actively-cooled high temperature turbine blades, which makes it difficult to precisely model heat transfer in the metallic subsystem. This reduces the ability of rote thermal modeling to reflect the actual physical conditions of the system and can lead to higher uncertainty in measured thermal properties. This dissertation investigates fundamental issues underpinning robust thermal property measurements that are adaptive to non-specific, complex, and evolving system characteristics using the PopTea method. A generic and adaptive subsystem PopTea thermal model was developed to account for complex geometry beyond a well-defined coating and substrate system. Without a priori knowledge of the subsystem characteristics, two different measurement techniques were implemented using the subsystem model. In the first technique, the properties of the subsystem were resolved as part of the PopTea parameter estimation algorithm; and, the second technique independently resolved the subsystem properties using a differential "bare" subsystem. The confidence in thermal properties measured using the generic subsystem model is similar to that from a standard PopTea measurement on a "well-defined" TBC system. Non-systematic bias-error on experimental observations in PopTea measurements due to generic thermal model discrepancies was also mitigated using a regression-based sensitivity analysis. The sensitivity analysis reported measurement uncertainty and was developed into a data reduction method to filter out these "erroneous" observations. It was found

  7. A design and analysis approach for drag reduction on aircraft with adaptive lifting surfaces

    NASA Astrophysics Data System (ADS)

    Cusher, Aaron Anthony

    Adaptive lifting surfaces, which can be tailored for different flight conditions, have been shown to be beneficial for drag reduction when compared with conventional non-adaptive surfaces. Applying multiple trailing-edge flaps along the wing span allows for the redistribution of lift to suit different flight conditions. The current approach uses the trailing-edge flap distribution to reduce both induced- and profile- components of drag with a trim constraint. Induced drag is reduced by optimally redistributing the lift between the lifting surfaces and along the span of each surface. Profile drag is reduced through the use of natural laminar flow airfoils, which maintain distinct low-drag-ranges (drag buckets) surrounding design lift values. The low-drag-ranges can be extended to include off-design values through small flap deflections, similar to cruise flaps. Trim is constrained for a given static margin by considering longitudinal pitching moment contributions from changes in airfoil section due to individual flap deflections, and from the redistribution of fore-and-aft lift due to combination of flap deflections. The approach uses the concept of basic and additional lift to linearlize the problem, which allows for standard constrained-minimization theory to be employed for determining optimal flap-angle solutions. The resulting expressions for optimal flap-angle solutions are presented as simple matrix equations. This work presents a design and analysis approach which is used to produce flap-angle solutions that independently reduce induced, profile, and total drag. Total drag is defined to be the sum of the induced- and profile-components of drag. The general drag reduction approach is adapted for each specific situation to develop specific drag reduction schemes that are applied to single- and multiple-surface configurations. Successful results show that, for the application of the induced drag reduction schemes on a tailless aircraft, near-elliptical lift

  8. Biomimetic evolutionary analysis: testing the adaptive value of vertebrate tail stiffness in autonomous swimming robots.

    PubMed

    Long, J H; Koob, T J; Irving, K; Combie, K; Engel, V; Livingston, N; Lammert, A; Schumacher, J

    2006-12-01

    For early vertebrates, a long-standing hypothesis is that vertebrae evolved as a locomotor adaptation, stiffening the body axis and enhancing swimming performance. While supported by biomechanical data, this hypothesis has not been tested using an evolutionary approach. We did so by extending biomimetic evolutionary analysis (BEA), which builds physical simulations of extinct systems, to include use of autonomous robots as proxies of early vertebrates competing in a forage navigation task. Modeled after free-swimming larvae of sea squirts (Chordata, Urochordata), three robotic tadpoles (;Tadros'), each with a propulsive tail bearing a biomimetic notochord of variable spring stiffness, k (N m(-1)), searched for, oriented to, and orbited in two dimensions around a light source. Within each of ten generations, we selected for increased swimming speed, U (m s(-1)) and decreased time to the light source, t (s), average distance from the source, R (m) and wobble maneuvering, W (rad s(-2)). In software simulation, we coded two quantitative trait loci (QTL) that determine k: bending modulus, E (Nm(-2)) and length, L (m). Both QTL were mutated during replication, independently assorted during meiosis and, as haploid gametes, entered into the gene pool in proportion to parental fitness. After random mating created three new diploid genotypes, we fabricated three new offspring tails. In the presence of both selection and chance events (mutation, genetic drift), the phenotypic means of this small population evolved. The classic hypothesis was supported in that k was positively correlated (r(2)=0.40) with navigational prowess, NP, the dimensionless ratio of U to the product of R, t and W. However, the plausible adaptive scenario, even in this simplified system, is more complex, since the remaining variance in NP was correlated with the residuals of R and U taken with respect to k, suggesting that changes in k alone are insufficient to explain the evolution of NP.

  9. Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma

    PubMed Central

    Capaldo, Brian J.; Roller, Devin; Axelrod, Mark J.; Koeppel, Alex F.; Petricoin, Emanuel F.; Slingluff, Craig L.; Weber, Michael J.; Mackey, Aaron J.; Gioeli, Daniel; Bekiranov, Stefan

    2015-01-01

    Fifty percent of cutaneous melanomas are driven by activated BRAFV600E, but tumors treated with RAF inhibitors, even when they respond dramatically, rapidly adapt and develop resistance. Thus, there is a pressing need to identify the major mechanisms of intrinsic and adaptive resistance and develop drug combinations that target these resistance mechanisms. In a combinatorial drug screen on a panel of 12 treatment-naïve BRAFV600E mutant melanoma cell lines of varying levels of resistance to mitogen-activated protein kinase (MAPK) pathway inhibition, we identified the combination of PLX4720, a targeted inhibitor of mutated BRaf, and lapatinib, an inhibitor of the ErbB family of receptor tyrosine kinases, as synergistically cytotoxic in the subset of cell lines that displayed the most resistance to PLX4720. To identify potential mechanisms of resistance to PLX4720 treatment and synergy with lapatinib treatment, we performed a multi-platform functional genomics analysis to profile the genome as well as the transcriptional and proteomic responses of these cell lines to treatment with PLX4720. We found modest levels of resistance correlated with the zygosity of the BRAF V600E allele and receptor tyrosine kinase (RTK) mutational status. Layered over base-line resistance was substantial upregulation of many ErbB pathway genes in response to BRaf inhibition, thus generating the vulnerability to combination with lapatinib. The transcriptional responses of ErbB pathway genes are associated with a number of transcription factors, including ETS2 and its associated cofactors that represent a convergent regulatory mechanism conferring synergistic drug susceptibility in the context of diverse mutational landscapes. PMID:26405815

  10. Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes.

    PubMed

    Wang, Ying; Yang, Liandong; Wu, Bo; Song, Zhaobin; He, Shunping

    2015-07-10

    Triplophysa dalaica, endemic species of Qinghai-Tibetan Plateau, is informative for understanding the genetic basis of adaptation to hypoxic conditions of high altitude habitats. Here, a comprehensive gene repertoire for this plateau fish was generated using the Illumina deep paired-end high-throughput sequencing technology. De novo assembly yielded 145, 256 unigenes with an average length of 1632 bp. Blast searches against GenBank non-redundant database annotated 74,594 (51.4%) unigenes encoding for 30,047 gene descriptions in T. dalaica. Functional annotation and classification of assembled sequences were performed using Gene Ontology (GO), clusters of euKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. After comparison with other fish transcriptomes, including silver carp (Hypophthalmichthys molitrix) and mud loach (Misgurnus anguillicaudatus), 2621 high-quality orthologous gene alignments were constructed among these species. 61 (2.3%) of the genes were identified as having undergone positive selection in the T. dalaica lineage. Within the positively selected genes, 13 genes were involved in hypoxia response, of which 11 were listed in HypoxiaDB. Furthermore, duplicated hif-α (hif-1αA/B and hif-2αA/B), EGLN1 and PPARA candidate genes involved in adaptation to hypoxia were identified in T. dalaica transcriptome. Branch-site model in PAML validated that hif-1αB and hif-2αA genes have undergone positive selection in T.dalaica. Finally, 37,501 simple sequence repeats (SSRs) and 19,497 high-quality single nucleotide polymorphisms (SNPs) were identified in T. dalaica. The identified SSR and SNP markers will facilitate the genetic structure, population geography and ecological studies of Triplophysa fishes.

  11. Adaptation of a Bioinformatics Microarray Analysis Workflow for a Toxicogenomic Study in Rainbow Trout

    PubMed Central

    Depiereux, Sophie; De Meulder, Bertrand; Bareke, Eric; Berger, Fabrice; Le Gac, Florence; Depiereux, Eric; Kestemont, Patrick

    2015-01-01

    Sex steroids play a key role in triggering sex differentiation in fish, the use of exogenous hormone treatment leading to partial or complete sex reversal. This phenomenon has attracted attention since the discovery that even low environmental doses of exogenous steroids can adversely affect gonad morphology (ovotestis development) and induce reproductive failure. Modern genomic-based technologies have enhanced opportunities to find out mechanisms of actions (MOA) and identify biomarkers related to the toxic action of a compound. However, high throughput data interpretation relies on statistical analysis, species genomic resources, and bioinformatics tools. The goals of this study are to improve the knowledge of feminisation in fish, by the analysis of molecular responses in the gonads of rainbow trout fry after chronic exposure to several doses (0.01, 0.1, 1 and 10 μg/L) of ethynylestradiol (EE2) and to offer target genes as potential biomarkers of ovotestis development. We successfully adapted a bioinformatics microarray analysis workflow elaborated on human data to a toxicogenomic study using rainbow trout, a fish species lacking accurate functional annotation and genomic resources. The workflow allowed to obtain lists of genes supposed to be enriched in true positive differentially expressed genes (DEGs), which were subjected to over-representation analysis methods (ORA). Several pathways and ontologies, mostly related to cell division and metabolism, sexual reproduction and steroid production, were found significantly enriched in our analyses. Moreover, two sets of potential ovotestis biomarkers were selected using several criteria. The first group displayed specific potential biomarkers belonging to pathways/ontologies highlighted in the experiment. Among them, the early ovarian differentiation gene foxl2a was overexpressed. The second group, which was highly sensitive but not specific, included the DEGs presenting the highest fold change and lowest p

  12. Simulation and analysis of laser guide star adaptive optics systems for the eight to ten meter class telescopes

    SciTech Connect

    Gavel, D.T.; Olivier, S.S.

    1994-03-01

    This paper discusses the design and analysis of laser-guided adaptive optic systems for the large, 8--10 meter class telescopes. We describe a technique for calculating the expected modulation transfer function and the point spread function for a closed loop adaptive optics system, parameterized by the degree of correction and the seeing conditions. The results agree closely with simulations and experimental data, and validate well known scaling law models even at low order correction. Scaling law.model analysis of a proposed adaptive optics system at the Keck telescope leads to the conclusion that a single laser guide star beacon will be adequate for diffraction limited imaging at wavelengths between 1 and 3 am with reasonable coverage of the sky. Cone anisoplanatism will dominate wavefront correction error at the visible wavelengths unless multiple laser guide stars are used.

  13. Finite element analysis of low-cost membrane deformable mirrors for high-order adaptive optics

    NASA Astrophysics Data System (ADS)

    Winsor, Robert S.; Sivaramakrishnan, Anand; Makidon, Russell B.

    1999-10-01

    We demonstrate the feasibility of glass membrane deformable mirror (DM) support structures intended for very high order low-stroke adaptive optics systems. We investigated commercially available piezoelectric ceramics. Piezoelectric tubes were determined to offer the largest amount of stroke for a given amount of space on the mirror surface that each actuator controls. We estimated the minimum spacing and the maximum expected stroke of such actuators. We developed a quantitative understanding of the response of a membrane mirror surface by performing a Finite Element Analysis (FEA) study. The results of the FEA analysis were used to develop a design and fabrication process for membrane deformable mirrors of 200 - 500 micron thicknesses. Several different values for glass thickness and actuator spacing were analyzed to determine the best combination of actuator stoke and surface deformation quality. We considered two deformable mirror configurations. The first configuration uses a vacuum membrane attachment system where the actuator tubes' central holes connect to an evacuated plenum, and atmospheric pressure holds the membrane against the actuators. This configuration allows the membrane to be removed from the actuators, facilitating easy replacement of the glass. The other configuration uses precision bearing balls epoxied to the ends of the actuator tubes, with the glass membrane epoxied to the ends of the ball bearings. While this kind of DM is not serviceable, it allows actuator spacings of 4 mm, in addition to large stroke. Fabrication of a prototype of the latter kind of DM was started.

  14. Adaptive Filter-bank Approach to Restoration and Spectral Analysis of Gapped Data

    NASA Astrophysics Data System (ADS)

    Stoica, Petre; Larsson, Erik G.; Li, Jian

    2000-10-01

    The main topic of this paper is the nonparametric estimation of complex (both amplitude and phase) spectra from gapped data, as well as the restoration of such data. The focus is on the extension of the APES (amplitude and phase estimation) approach to data sequences with gaps. APES, which is one of the most successful existing nonparametric approaches to the spectral analysis of full data sequences, uses a bank of narrowband adaptive (both frequency and data dependent) filters to estimate the spectrum. A recent interpretation of this approach showed that the filterbank used by APES and the resulting spectrum minimize a least-squares (LS) fitting criterion between the filtered sequence and its spectral decomposition. The extended approach, which is called GAPES for somewhat obvious reasons, capitalizes on the aforementioned interpretation: it minimizes the APES-LS fitting criterion with respect to the missing data as well. This should be a sensible thing to do whenever the full data sequence is stationary, and hence the missing data have the same spectral content as the available data. We use both simulated and real data examples to show that GAPES estimated spectra and interpolated data sequences have excellent accuracy. We also show the performance gain achieved by GAPES over two of the most commonly used approaches for gapped-data spectral analysis, viz., the periodogram and the parametric CLEAN method. This work was partly supported by the Swedish Foundation for Strategic Research.

  15. Adaptive online monitoring for ICU patients by combining just-in-time learning and principal component analysis.

    PubMed

    Li, Xuejian; Wang, Youqing

    2016-12-01

    Offline general-type models are widely used for patients' monitoring in intensive care units (ICUs), which are developed by using past collected datasets consisting of thousands of patients. However, these models may fail to adapt to the changing states of ICU patients. Thus, to be more robust and effective, the monitoring models should be adaptable to individual patients. A novel combination of just-in-time learning (JITL) and principal component analysis (PCA), referred to learning-type PCA (L-PCA), was proposed for adaptive online monitoring of patients in ICUs. JITL was used to gather the most relevant data samples for adaptive modeling of complex physiological processes. PCA was used to build an online individual-type model and calculate monitoring statistics, and then to judge whether the patient's status is normal or not. The adaptability of L-PCA lies in the usage of individual data and the continuous updating of the training dataset. Twelve subjects were selected from the Physiobank's Multi-parameter Intelligent Monitoring for Intensive Care II (MIMIC II) database, and five vital signs of each subject were chosen. The proposed method was compared with the traditional PCA and fast moving-window PCA (Fast MWPCA). The experimental results demonstrated that the fault detection rates respectively increased by 20 % and 47 % compared with PCA and Fast MWPCA. L-PCA is first introduced into ICU patients monitoring and achieves the best monitoring performance in terms of adaptability to changes in patient status and sensitivity for abnormality detection.

  16. Jumeaux conjoints au niveau d’une omphalocèle commune avec extrophie cloacale et ambigüité sexuelle

    PubMed Central

    Boujoual, Majdouline; Madani, Hamid; Benhaddou, Housain; Belahcen, Mohamed

    2014-01-01

    Les jumeaux conjoints sont considérés comme étant une complication rare et grave des grossesses monozygotes. Le diagnostic anténatal permet de définir avec précision les structures communes, de rechercher une anomalie congénitale associée, d'organiser l´accouchement et la prise en charge néonatale. Nous présentons un cas rare de jumeaux conjoints dont la fusion se situait au niveau d'une omphalocèle commune associée à une extrophie cloacale, ambiguïté sexuelle et pieds bots. Le diagnostic a été méconnu pendant la grossesse, ce qui a engendré une dystocie lors de l'accouchement. L'issue a été fatale malgré une tentative de séparation et des mesures de réanimation. Ce cas illustre la difficulté liée d'une part à la méconnaissance du diagnostic, d'autre part au caractère urgent de la césarienne et de la séparation chirurgicale. PMID:25170387

  17. Integrated System Design: Promoting the Capacity of Sociotechnical Systems for Adaptation through Extensions of Cognitive Work Analysis.

    PubMed

    Naikar, Neelam; Elix, Ben

    2016-01-01

    This paper proposes an approach for integrated system design, which has the intent of facilitating high levels of effectiveness in sociotechnical systems by promoting their capacity for adaptation. Building on earlier ideas and empirical observations, this approach recognizes that to create adaptive systems it is necessary to integrate the design of all of the system elements, including the interfaces, teams, training, and automation, such that workers are supported in adapting their behavior as well as their structure, or organization, in a coherent manner. Current approaches for work analysis and design are limited in regard to this fundamental objective, especially in cases when workers are confronted with unforeseen events. A suitable starting point is offered by cognitive work analysis (CWA), but while this framework can support actors in adapting their behavior, it does not necessarily accommodate adaptations in their structure. Moreover, associated design approaches generally focus on individual system elements, and those that consider multiple elements appear limited in their ability to facilitate integration, especially in the manner intended here. The proposed approach puts forward the set of possibilities for work organization in a system as the central mechanism for binding the design of its various elements, so that actors can adapt their structure as well as their behavior-in a unified fashion-to handle both familiar and novel conditions. Accordingly, this paper demonstrates how the set of possibilities for work organization in a system may be demarcated independently of the situation, through extensions of CWA, and how it may be utilized in design. This lynchpin, conceptualized in the form of a diagram of work organization possibilities (WOP), is important for preserving a system's inherent capacity for adaptation. Future research should focus on validating these concepts and establishing the feasibility of implementing them in industrial contexts.

  18. Integrated System Design: Promoting the Capacity of Sociotechnical Systems for Adaptation through Extensions of Cognitive Work Analysis

    PubMed Central

    Naikar, Neelam; Elix, Ben

    2016-01-01

    This paper proposes an approach for integrated system design, which has the intent of facilitating high levels of effectiveness in sociotechnical systems by promoting their capacity for adaptation. Building on earlier ideas and empirical observations, this approach recognizes that to create adaptive systems it is necessary to integrate the design of all of the system elements, including the interfaces, teams, training, and automation, such that workers are supported in adapting their behavior as well as their structure, or organization, in a coherent manner. Current approaches for work analysis and design are limited in regard to this fundamental objective, especially in cases when workers are confronted with unforeseen events. A suitable starting point is offered by cognitive work analysis (CWA), but while this framework can support actors in adapting their behavior, it does not necessarily accommodate adaptations in their structure. Moreover, associated design approaches generally focus on individual system elements, and those that consider multiple elements appear limited in their ability to facilitate integration, especially in the manner intended here. The proposed approach puts forward the set of possibilities for work organization in a system as the central mechanism for binding the design of its various elements, so that actors can adapt their structure as well as their behavior—in a unified fashion—to handle both familiar and novel conditions. Accordingly, this paper demonstrates how the set of possibilities for work organization in a system may be demarcated independently of the situation, through extensions of CWA, and how it may be utilized in design. This lynchpin, conceptualized in the form of a diagram of work organization possibilities (WOP), is important for preserving a system's inherent capacity for adaptation. Future research should focus on validating these concepts and establishing the feasibility of implementing them in industrial

  19. Real time on-chip sequential adaptive principal component analysis for data feature extraction and image compression

    NASA Technical Reports Server (NTRS)

    Duong, T. A.

    2004-01-01

    In this paper, we present a new, simple, and optimized hardware architecture sequential learning technique for adaptive Principle Component Analysis (PCA) which will help optimize the hardware implementation in VLSI and to overcome the difficulties of the traditional gradient descent in learning convergence and hardware implementation.

  20. Adaptation of Flanders' Interaction Analysis to Assist in Developing Communication Skills in Final-Year Pharmacy Students

    ERIC Educational Resources Information Center

    Walker, James K.

    1976-01-01

    Flanders' Interaction Analysis was adapted to assess the communication process of an interview more accurately, and with more inter-student consistency. Experimental results indicate that students can learn the major elements of interview technique by the traditional lecture method and with a minimum of media support. (LBH)

  1. Adaptive L₁/₂ shooting regularization method for survival analysis using gene expression data.

    PubMed

    Liu, Xiao-Ying; Liang, Yong; Xu, Zong-Ben; Zhang, Hai; Leung, Kwong-Sak

    2013-01-01

    A new adaptive L₁/₂ shooting regularization method for variable selection based on the Cox's proportional hazards mode being proposed. This adaptive L₁/₂ shooting algorithm can be easily obtained by the optimization of a reweighed iterative series of L₁ penalties and a shooting strategy of L₁/₂ penalty. Simulation results based on high dimensional artificial data show that the adaptive L₁/₂ shooting regularization method can be more accurate for variable selection than Lasso and adaptive Lasso methods. The results from real gene expression dataset (DLBCL) also indicate that the L₁/₂ regularization method performs competitively.

  2. Real-time feature extraction of P300 component using adaptive nonlinear principal component analysis

    PubMed Central

    2011-01-01

    Background The electroencephalography (EEG) signals are known to involve the firings of neurons in the brain. The P300 wave is a high potential caused by an event-related stimulus. The detection of P300s included in the measured EEG signals is widely investigated. The difficulties in detecting them are that they are mixed with other signals generated over a large brain area and their amplitudes are very small due to the distance and resistivity differences in their transmittance. Methods A novel real-time feature extraction method for detecting P300 waves by combining an adaptive nonlinear principal component analysis (ANPCA) and a multilayer neural network is proposed. The measured EEG signals are first filtered using a sixth-order band-pass filter with cut-off frequencies of 1 Hz and 12 Hz. The proposed ANPCA scheme consists of four steps: pre-separation, whitening, separation, and estimation. In the experiment, four different inter-stimulus intervals (ISIs) are utilized: 325 ms, 350 ms, 375 ms, and 400 ms. Results The developed multi-stage principal component analysis method applied at the pre-separation step has reduced the external noises and artifacts significantly. The introduced adaptive law in the whitening step has made the subsequent algorithm in the separation step to converge fast. The separation performance index has varied from -20 dB to -33 dB due to randomness of source signals. The robustness of the ANPCA against background noises has been evaluated by comparing the separation performance indices of the ANPCA with four algorithms (NPCA, NSS-JD, JADE, and SOBI), in which the ANPCA algorithm demonstrated the shortest iteration time with performance index about 0.03. Upon this, it is asserted that the ANPCA algorithm successfully separates mixed source signals. Conclusions The independent components produced from the observed data using the proposed method illustrated that the extracted signals were clearly the P300 components elicited by task

  3. Image segmentation for uranium isotopic analysis by SIMS: Combined adaptive thresholding and marker controlled watershed approach

    SciTech Connect

    Willingham, David G.; Naes, Benjamin E.; Heasler, Patrick G.; Zimmer, Mindy M.; Barrett, Christopher A.; Addleman, Raymond S.

    2016-05-31

    A novel approach to particle identification and particle isotope ratio determination has been developed for nuclear safeguard applications. This particle search approach combines an adaptive thresholding algorithm and marker-controlled watershed segmentation (MCWS) transform, which improves the secondary ion mass spectrometry (SIMS) isotopic analysis of uranium containing particle populations for nuclear safeguards applications. The Niblack assisted MCWS approach (a.k.a. SEEKER) developed for this work has improved the identification of isotopically unique uranium particles under conditions that have historically presented significant challenges for SIMS image data processing techniques. Particles obtained from five NIST uranium certified reference materials (CRM U129A, U015, U150, U500 and U850) were successfully identified in regions of SIMS image data 1) where a high variability in image intensity existed, 2) where particles were touching or were in close proximity to one another and/or 3) where the magnitude of ion signal for a given region was count limited. Analysis of the isotopic distributions of uranium containing particles identified by SEEKER showed four distinct, accurately identified 235U enrichment distributions, corresponding to the NIST certified 235U/238U isotope ratios for CRM U129A/U015 (not statistically differentiated), U150, U500 and U850. Additionally, comparison of the minor uranium isotope (234U, 235U and 236U) atom percent values verified that, even in the absence of high precision isotope ratio measurements, SEEKER could be used to segment isotopically unique uranium particles from SIMS image data. Although demonstrated specifically for SIMS analysis of uranium containing particles for nuclear safeguards, SEEKER has application in addressing a broad set of image processing challenges.

  4. A Review: Development of a Microdose Model for Analysis of Adaptive Response and Bystander Dose Response Behavior

    PubMed Central

    Leonard, Bobby E.

    2008-01-01

    Prior work has provided incremental phases to a microdosimetry modeling program to describe the dose response behavior of the radio-protective adaptive response effect. We have here consolidated these prior works (Leonard 2000, 2005, 2007a, 2007b, 2007c) to provide a composite, comprehensive Microdose Model that is also herein modified to include the bystander effect. The nomenclature for the model is also standardized for the benefit of the experimental cellular radio-biologist. It extends the prior work to explicitly encompass separately the analysis of experimental data that is 1.) only dose dependent and reflecting only adaptive response radio-protection, 2.) both dose and dose-rate dependent data and reflecting only adaptive response radio-protection for spontaneous and challenge dose damage, 3.) only dose dependent data and reflecting both bystander deleterious damage and adaptive response radio-protection (AR-BE model). The Appendix cites the various applications of the model. Here we have used the Microdose Model to analyze the, much more human risk significant, Elmore et al (2006) data for the dose and dose rate influence on the adaptive response radio-protective behavior of HeLa x Skin cells for naturally occurring, spontaneous chromosome damage from a Brachytherapy type 125I photon radiation source. We have also applied the AR-BE Microdose Model to the Chromosome inversion data of Hooker et al (2004) reflecting both low LET bystander and adaptive response effects. The micro-beam facility data of Miller et al (1999), Nagasawa and Little (1999) and Zhou et al (2003) is also examined. For the Zhou et al (2003) data, we use the AR-BE model to estimate the threshold for adaptive response reduction of the bystander effect. The mammogram and diagnostic X-ray induction of AR and protective BE are observed. We show that bystander damage is reduced in the similar manner as spontaneous and challenge dose damage as shown by the Azzam et al (1996) data. We cite

  5. Detrended fluctuation analysis and adaptive fractal analysis of stride time data in Parkinson's disease: stitching together short gait trials.

    PubMed

    Kirchner, Marietta; Schubert, Patric; Liebherr, Magnus; Haas, Christian T

    2014-01-01

    Variability indicates motor control disturbances and is suitable to identify gait pathologies. It can be quantified by linear parameters (amplitude estimators) and more sophisticated nonlinear methods (structural information). Detrended Fluctuation Analysis (DFA) is one method to measure structural information, e.g., from stride time series. Recently, an improved method, Adaptive Fractal Analysis (AFA), has been proposed. This method has not been applied to gait data before. Fractal scaling methods (FS) require long stride-to-stride data to obtain valid results. However, in clinical studies, it is not usual to measure a large number of strides (e.g., [Formula: see text][Formula: see text] strides). Amongst others, clinical gait analysis is limited due to short walkways, thus, FS seem to be inapplicable. The purpose of the present study was to evaluate FS under clinical conditions. Stride time data of five self-paced walking trials ([Formula: see text] strides each) of subjects with PD and a healthy control group (CG) was measured. To generate longer time series, stride time sequences were stitched together. The coefficient of variation (CV), fractal scaling exponents [Formula: see text] (DFA) and [Formula: see text] (AFA) were calculated. Two surrogate tests were performed: A) the whole time series was randomly shuffled; B) the single trials were randomly shuffled separately and afterwards stitched together. CV did not discriminate between PD and CG. However, significant differences between PD and CG were found concerning [Formula: see text] and [Formula: see text]. Surrogate version B yielded a higher mean squared error and empirical quantiles than version A. Hence, we conclude that the stitching procedure creates an artificial structure resulting in an overestimation of true [Formula: see text]. The method of stitching together sections of gait seems to be appropriate in order to distinguish between PD and CG with FS. It provides an approach to integrate FS as

  6. Detrended Fluctuation Analysis and Adaptive Fractal Analysis of Stride Time Data in Parkinson's Disease: Stitching Together Short Gait Trials

    PubMed Central

    Liebherr, Magnus; Haas, Christian T.

    2014-01-01

    Variability indicates motor control disturbances and is suitable to identify gait pathologies. It can be quantified by linear parameters (amplitude estimators) and more sophisticated nonlinear methods (structural information). Detrended Fluctuation Analysis (DFA) is one method to measure structural information, e.g., from stride time series. Recently, an improved method, Adaptive Fractal Analysis (AFA), has been proposed. This method has not been applied to gait data before. Fractal scaling methods (FS) require long stride-to-stride data to obtain valid results. However, in clinical studies, it is not usual to measure a large number of strides (e.g., strides). Amongst others, clinical gait analysis is limited due to short walkways, thus, FS seem to be inapplicable. The purpose of the present study was to evaluate FS under clinical conditions. Stride time data of five self-paced walking trials ( strides each) of subjects with PD and a healthy control group (CG) was measured. To generate longer time series, stride time sequences were stitched together. The coefficient of variation (CV), fractal scaling exponents (DFA) and (AFA) were calculated. Two surrogate tests were performed: A) the whole time series was randomly shuffled; B) the single trials were randomly shuffled separately and afterwards stitched together. CV did not discriminate between PD and CG. However, significant differences between PD and CG were found concerning and . Surrogate version B yielded a higher mean squared error and empirical quantiles than version A. Hence, we conclude that the stitching procedure creates an artificial structure resulting in an overestimation of true . The method of stitching together sections of gait seems to be appropriate in order to distinguish between PD and CG with FS. It provides an approach to integrate FS as standard in clinical gait analysis and to overcome limitations such as short walkways. PMID:24465708

  7. Factors Influencing Students' Adaptability in School: A Production Function Model and Multilevel Analysis

    ERIC Educational Resources Information Center

    Du, Ping

    2008-01-01

    This study used sampling survey data from rural elementary schools in western China to analyze school adaptability, which is the representative noncognitive development of rural elementary students. It also investigated factors influencing the school adaptability of elementary school students at an individual and school level by using production…

  8. Culturally Adapted Psychotherapy and the Legitimacy of Myth: A Multilevel Model, Direct Comparison Meta-Analysis

    ERIC Educational Resources Information Center

    Benish, Steven G.

    2010-01-01

    Culturally adapted psychotherapy has potential to improve psychotherapy outcomes for ethnic and racial minorities and solve a decades-long conundrum that alteration of specific ingredients does not improve psychotherapy outcomes. Adaptation of the cultural explanation of illness, known as the anthropological Myth in universal healing practices…

  9. Analysis of adaptive walks on NK fitness landscapes with different interaction schemes

    NASA Astrophysics Data System (ADS)

    Nowak, Stefan; Krug, Joachim

    2015-06-01

    Fitness landscapes are genotype to fitness mappings commonly used in evolutionary biology and computer science which are closely related to spin glass models. In this paper, we study the NK model for fitness landscapes where the interaction scheme between genes can be explicitly defined. The focus is on how this scheme influences the overall shape of the landscape. Our main tool for the analysis are adaptive walks, an idealized dynamics by which the population moves uphill in fitness and terminates at a local fitness maximum. We use three different types of walks and investigate how their length (the number of steps required to reach a local peak) and height (the fitness at the endpoint of the walk) depend on the dimensionality and structure of the landscape. We find that the distribution of local maxima over the landscape is particularly sensitive to the choice of interaction pattern. Most quantities that we measure are simply correlated to the rank of the scheme, which is equal to the number of nonzero coefficients in the expansion of the fitness landscape in terms of Walsh functions.

  10. Movement Analysis of Flexion and Extension of Honeybee Abdomen Based on an Adaptive Segmented Structure.

    PubMed

    Zhao, Jieliang; Wu, Jianing; Yan, Shaoze

    2015-01-01

    Honeybees (Apis mellifera) curl their abdomens for daily rhythmic activities. Prior to determining this fact, people have concluded that honeybees could curl their abdomen casually. However, an intriguing but less studied feature is the possible unidirectional abdominal deformation in free-flying honeybees. A high-speed video camera was used to capture the curling and to analyze the changes in the arc length of the honeybee abdomen not only in free-flying mode but also in the fixed sample. Frozen sections and environment scanning electron microscope were used to investigate the microstructure and motion principle of honeybee abdomen and to explore the physical structure restricting its curling. An adaptive segmented structure, especially the folded intersegmental membrane (FIM), plays a dominant role in the flexion and extension of the abdomen. The structural features of FIM were utilized to mimic and exhibit movement restriction on honeybee abdomen. Combining experimental analysis and theoretical demonstration, a unidirectional bending mechanism of honeybee abdomen was revealed. Through this finding, a new perspective for aerospace vehicle design can be imitated.

  11. Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass

    PubMed Central

    D'haeseleer, Patrik; Gladden, John M.; Allgaier, Martin; Chain, Patrik S. G.; Tringe, Susannah G.; Malfatti, Stephanie A.; Aldrich, Joshua T.; Nicora, Carrie D.; Robinson, Errol W.; Paša-Tolić, Ljiljana; Hugenholtz, Philip; Simmons, Blake A.; Singer, Steven W.

    2013-01-01

    Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the little-studied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify >3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction. PMID:23894306

  12. Adaptive Quantification and Longitudinal Analysis of Pulmonary Emphysema with a Hidden Markov Measure Field Model

    PubMed Central

    Häme, Yrjö; Angelini, Elsa D.; Hoffman, Eric A.; Barr, R. Graham; Laine, Andrew F.

    2014-01-01

    The extent of pulmonary emphysema is commonly estimated from CT images by computing the proportional area of voxels below a predefined attenuation threshold. However, the reliability of this approach is limited by several factors that affect the CT intensity distributions in the lung. This work presents a novel method for emphysema quantification, based on parametric modeling of intensity distributions in the lung and a hidden Markov measure field model to segment emphysematous regions. The framework adapts to the characteristics of an image to ensure a robust quantification of emphysema under varying CT imaging protocols and differences in parenchymal intensity distributions due to factors such as inspiration level. Compared to standard approaches, the present model involves a larger number of parameters, most of which can be estimated from data, to handle the variability encountered in lung CT scans. The method was used to quantify emphysema on a cohort of 87 subjects, with repeated CT scans acquired over a time period of 8 years using different imaging protocols. The scans were acquired approximately annually, and the data set included a total of 365 scans. The results show that the emphysema estimates produced by the proposed method have very high intra-subject correlation values. By reducing sensitivity to changes in imaging protocol, the method provides a more robust estimate than standard approaches. In addition, the generated emphysema delineations promise great advantages for regional analysis of emphysema extent and progression, possibly advancing disease subtyping. PMID:24759984

  13. Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis.

    PubMed

    Davies, Kalina T J; Bennett, Nigel C; Tsagkogeorga, Georgia; Rossiter, Stephen J; Faulkes, Christopher G

    2015-12-01

    During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subterranean niche, African mole-rats are one of the most successful. Much of their ecological success can be attributed to a diet of plant storage organs, which has allowed them to colonize climatically varied habitats across sub-Saharan Africa, and has probably contributed to the evolution of their diverse social systems. Yet despite their many remarkable phenotypic specializations, little is known about molecular adaptations underlying these traits. To address this, we sequenced the transcriptomes of seven mole-rat taxa, including three solitary species, and combined new sequences with existing genomic data sets. Alignments of more than 13,000 protein-coding genes encompassed, for the first time, all six genera and the full spectrum of ecological and social variation in the clade. We detected positive selection within the mole-rat clade and along ancestral branches in approximately 700 genes including loci associated with tumorigenesis, aging, morphological development, and sociality. By combining these results with gene ontology annotation and protein-protein networks, we identified several clusters of functionally related genes. This family wide analysis of molecular evolution in mole-rats has identified a suite of positively selected genes, deepening our understanding of the extreme phenotypic traits exhibited by this group.

  14. Molecular Genetic Analysis of Orf Virus: A Poxvirus That Has Adapted to Skin

    PubMed Central

    Fleming, Stephen B.; Wise, Lyn M.; Mercer, Andrew A.

    2015-01-01

    Orf virus is the type species of the Parapoxvirus genus of the family Poxviridae. It induces acute pustular skin lesions in sheep and goats and is transmissible to humans. The genome is G+C rich, 138 kbp and encodes 132 genes. It shares many essential genes with vaccinia virus that are required for survival but encodes a number of unique factors that allow it to replicate in the highly specific immune environment of skin. Phylogenetic analysis suggests that both viral interleukin-10 and vascular endothelial growth factor genes have been “captured” from their host during the evolution of the parapoxviruses. Genes such as a chemokine binding protein and a protein that binds granulocyte-macrophage colony-stimulating factor and interleukin-2 appear to have evolved from a common poxvirus ancestral gene while three parapoxvirus nuclear factor (NF)-κB signalling pathway inhibitors have no homology to other known NF-κB inhibitors. A homologue of an anaphase-promoting complex subunit that is believed to manipulate the cell cycle and enhance viral DNA synthesis appears to be a specific adaptation for viral-replication in keratinocytes. The review focuses on the unique genes of orf virus, discusses their evolutionary origins and their role in allowing viral-replication in the skin epidermis. PMID:25807056

  15. Adaptive quantification and longitudinal analysis of pulmonary emphysema with a hidden Markov measure field model.

    PubMed

    Hame, Yrjo; Angelini, Elsa D; Hoffman, Eric A; Barr, R Graham; Laine, Andrew F

    2014-07-01

    The extent of pulmonary emphysema is commonly estimated from CT scans by computing the proportional area of voxels below a predefined attenuation threshold. However, the reliability of this approach is limited by several factors that affect the CT intensity distributions in the lung. This work presents a novel method for emphysema quantification, based on parametric modeling of intensity distributions and a hidden Markov measure field model to segment emphysematous regions. The framework adapts to the characteristics of an image to ensure a robust quantification of emphysema under varying CT imaging protocols, and differences in parenchymal intensity distributions due to factors such as inspiration level. Compared to standard approaches, the presented model involves a larger number of parameters, most of which can be estimated from data, to handle the variability encountered in lung CT scans. The method was applied on a longitudinal data set with 87 subjects and a total of 365 scans acquired with varying imaging protocols. The resulting emphysema estimates had very high intra-subject correlation values. By reducing sensitivity to changes in imaging protocol, the method provides a more robust estimate than standard approaches. The generated emphysema delineations promise advantages for regional analysis of emphysema extent and progression.

  16. Movement Analysis of Flexion and Extension of Honeybee Abdomen Based on an Adaptive Segmented Structure

    PubMed Central

    Zhao, Jieliang; Wu, Jianing; Yan, Shaoze

    2015-01-01

    Honeybees (Apis mellifera) curl their abdomens for daily rhythmic activities. Prior to determining this fact, people have concluded that honeybees could curl their abdomen casually. However, an intriguing but less studied feature is the possible unidirectional abdominal deformation in free-flying honeybees. A high-speed video camera was used to capture the curling and to analyze the changes in the arc length of the honeybee abdomen not only in free-flying mode but also in the fixed sample. Frozen sections and environment scanning electron microscope were used to investigate the microstructure and motion principle of honeybee abdomen and to explore the physical structure restricting its curling. An adaptive segmented structure, especially the folded intersegmental membrane (FIM), plays a dominant role in the flexion and extension of the abdomen. The structural features of FIM were utilized to mimic and exhibit movement restriction on honeybee abdomen. Combining experimental analysis and theoretical demonstration, a unidirectional bending mechanism of honeybee abdomen was revealed. Through this finding, a new perspective for aerospace vehicle design can be imitated. PMID:26223946

  17. An Adaptive Fisher’s Combination Method for Joint Analysis of Multiple Phenotypes in Association Studies

    PubMed Central

    Liang, Xiaoyu; Wang, Zhenchuan; Sha, Qiuying; Zhang, Shuanglin

    2016-01-01

    Currently, the analyses of most genome-wide association studies (GWAS) have been performed on a single phenotype. There is increasing evidence showing that pleiotropy is a widespread phenomenon in complex diseases. Therefore, using only one single phenotype may lose statistical power to identify the underlying genetic mechanism. There is an increasing need to develop and apply powerful statistical tests to detect association between multiple phenotypes and a genetic variant. In this paper, we develop an Adaptive Fisher’s Combination (AFC) method for joint analysis of multiple phenotypes in association studies. The AFC method combines p-values obtained in standard univariate GWAS by using the optimal number of p-values which is determined by the data. We perform extensive simulations to evaluate the performance of the AFC method and compare the power of our method with the powers of TATES, Tippett’s method, Fisher’s combination test, MANOVA, MultiPhen, and SUMSCORE. Our simulation studies show that the proposed method has correct type I error rates and is either the most powerful test or comparable with the most powerful test. Finally, we illustrate our proposed methodology by analyzing whole-genome genotyping data from a lung function study. PMID:27694844

  18. Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass

    SciTech Connect

    D'haeseleer, Patrik; Gladden, John M.; Allgaier, Martin; Chain, Patrick; Tringe, Susannah G.; Malfatti, Stephanie; Aldrich, Joshua T.; Nicora, Carrie D.; Robinson, Errol W.; Pasa-Tolic, Ljiljana; Hugenholtz, Philip; Simmons, Blake A.; Singer, Steven W.

    2013-07-19

    Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the littlestudied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify .3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.

  19. Adaptive Signal Recovery on Graphs via Harmonic Analysis for Experimental Design in Neuroimaging

    PubMed Central

    Kim, Won Hwa; Hwang, Seong Jae; Adluru, Nagesh; Johnson, Sterling C.; Singh, Vikas

    2016-01-01

    Consider an experimental design of a neuroimaging study, where we need to obtain p measurements for each participant in a setting where p′ (< p) are cheaper and easier to acquire while the remaining (p – p′) are expensive. For example, the p′ measurements may include demographics, cognitive scores or routinely offered imaging scans while the (p – p′) measurements may correspond to more expensive types of brain image scans with a higher participant burden. In this scenario, it seems reasonable to seek an “adaptive” design for data acquisition so as to minimize the cost of the study without compromising statistical power. We show how this problem can be solved via harmonic analysis of a band-limited graph whose vertices correspond to participants and our goal is to fully recover a multi-variate signal on the nodes, given the full set of cheaper features and a partial set of more expensive measurements. This is accomplished using an adaptive query strategy derived from probing the properties of the graph in the frequency space. To demonstrate the benefits that this framework can provide, we present experimental evaluations on two independent neuroimaging studies and show that our proposed method can reliably recover the true signal with only partial observations directly yielding substantial financial savings. PMID:27807594

  20. Design and analysis of an adaptive lens that mimics the performance of the crystalline lens in the human eye

    NASA Astrophysics Data System (ADS)

    Santiago-Alvarado, Agustin; Cruz-Félix, Angel S.; Iturbide-Jiménez, F.; Martínez-López, M.; Ramírez-Como, M.; Armengol-Cruz, V.; Vásquez-Báez, I.

    2014-09-01

    Tunable lenses are optical systems that have attracted much attention due to their potential applications in such areas like ophthalmology, machine vision, microscopy and laser processing. In recent years we have been working in the analysis and performance of a liquid-filled variable focal length lens, this is a lens that can modify its focal length by changing the amount of water within it. Nowadays we extend our study to a particular adaptive lens known as solid elastic lens (SEL) that it is formed by an elastic main body made of Polydimethylsiloxane (PDMS Sylgard 184). In this work, we present the design, simulation and analysis of an adaptive solid elastic lens that in principle imitates the accommodation process of the crystalline lens in the human eye. For this work, we have adopted the parameters of the schematic eye model developed in 1985 by Navarro et al.; this model represents the anatomy of the eye as close as possible to reality by predicting an acceptable and accurate quantity of spherical and chromatic aberrations without any shape fitting. An opto-mechanical analysis of the accommodation process of the adaptive lens is presented, by simulating a certain amount of radial force applied onto the SEL using the finite element method with the commercial software SolidWorks®. We also present ray-trace diagrams of the simulated compression process of the adaptive lens using the commercial software OSLO®.

  1. In Silico and Biochemical Analysis of Physcomitrella patens Photosynthetic Antenna: Identification of Subunits which Evolved upon Land Adaptation

    PubMed Central

    Alboresi, Alessandro; Caffarri, Stefano; Nogue, Fabien; Bassi, Roberto; Morosinotto, Tomas

    2008-01-01

    Background In eukaryotes the photosynthetic antenna system is composed of subunits encoded by the light harvesting complex (Lhc) multigene family. These proteins play a key role in photosynthesis and are involved in both light harvesting and photoprotection. The moss Physcomitrella patens is a member of a lineage that diverged from seed plants early after land colonization and therefore by studying this organism, we may gain insight into adaptations to the aerial environment. Principal Findings In this study, we characterized the antenna protein multigene family in Physcomitrella patens, by sequence analysis as well as biochemical and functional investigations. Sequence identification and analysis showed that some antenna polypeptides, such as Lhcb3 and Lhcb6, are present only in land organisms, suggesting they play a role in adaptation to the sub-aerial environment. Our functional analysis which showed that photo-protective mechanisms in Physcomitrella patens are very similar to those in seed plants fits with this hypothesis. In particular, Physcomitrella patens also activates Non Photochemical Quenching upon illumination, consistent with the detection of an ortholog of the PsbS protein. As a further adaptation to terrestrial conditions, the content of Photosystem I low energy absorbing chlorophylls also increased, as demonstrated by differences in Lhca3 and Lhca4 polypeptide sequences, in vitro reconstitution experiments and low temperature fluorescence spectra. Conclusions This study highlights the role of Lhc family members in environmental adaptation and allowed proteins associated with mechanisms of stress resistance to be identified within this large family. PMID:18446222

  2. Adaptive Thresholds

    SciTech Connect

    Bremer, P. -T.

    2014-08-26

    ADAPT is a topological analysis code that allow to compute local threshold, in particular relevance based thresholds for features defined in scalar fields. The initial target application is vortex detection but the software is more generally applicable to all threshold based feature definitions.

  3. Projective analysis of staple food crop productivity in adaptation to future climate change in China

    NASA Astrophysics Data System (ADS)

    Zhang, Qing; Zhang, Wen; Li, Tingting; Sun, Wenjuan; Yu, Yongqiang; Wang, Guocheng

    2017-02-01

    Climate change continually affects our capabilities to feed the increasing population. Rising temperatures have the potential to shorten the crop growth duration and therefore reduce crop yields. In the past decades, China has successfully improved crop cultivars to stabilize, and even lengthen, the crop growth duration to make use of increasing heat resources. However, because of the complex cropping systems in the different regions of China, the possibility and the effectiveness of regulating crop growth duration to reduce the negative impacts of future climate change remain questionable. Here, we performed a projective analysis of the staple food crop productivity in double-rice, wheat-rice, wheat-maize, single-rice, and single-maize cropping systems in China using modeling approaches. The results indicated that from the present to the 2040s, the warming climate would shorten the growth duration of the current rice, wheat, and maize cultivars by 2-24, 11-13, and 9-29 days, respectively. The most significant shortening of the crop growth duration would be in Northeast China, where single-rice and single-maize cropping dominates the croplands. The shortened crop growth duration would consequently reduce crop productivity. The most significant decreases would be 27-31, 6-20, and 7-22% for the late crop in the double-rice rotation, wheat in the winter wheat-rice rotation, and single maize, respectively. However, our projection analysis also showed that the negative effects of the warming climate could be compensated for by stabilizing the growth duration of the crops via improvement in crop cultivars. In this case, the productivity of rice, wheat, and maize in the 2040s would increase by 4-16, 31-38, and 11-12%, respectively. Our modeling results implied that the possibility of securing future food production exists by adopting proper adaptation options in China.

  4. Comparative Genomic Analysis of the Endosymbionts of Herbivorous Insects Reveals Eco-Environmental Adaptations: Biotechnology Applications

    PubMed Central

    Shi, Weibing; Xie, Shangxian; Chen, Xueyan; Sun, Su; Zhou, Xin; Liu, Lantao; Gao, Peng; Kyrpides, Nikos C.; No, En-Gyu; Yuan, Joshua S.

    2013-01-01

    Metagenome analysis of the gut symbionts of three different insects was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts. A second goal was the discovery of novel biocatalysts for biorefinery applications. Grasshopper and cutworm gut symbionts were sequenced and compared with the previously identified metagenome of termite gut microbiota. These insect hosts represent three different insect orders and specialize on different food types. The comparative analysis revealed dramatic differences among the three insect species in the abundance and taxonomic composition of the symbiont populations present in the gut. The composition and abundance of symbionts was correlated with their previously identified capacity to degrade and utilize the different types of food consumed by their hosts. The metabolic reconstruction revealed that the gut metabolome of cutworms and grasshoppers was more enriched for genes involved in carbohydrate metabolism and transport than wood-feeding termite, whereas the termite gut metabolome was enriched for glycosyl hydrolase (GH) enzymes relevant to lignocellulosic biomass degradation. Moreover, termite gut metabolome was more enriched with nitrogen fixation genes than those of grasshopper and cutworm gut, presumably due to the termite's adaptation to the high fiber and less nutritious food types. In order to evaluate and exploit the insect symbionts for biotechnology applications, we cloned and further characterized four biomass-degrading enzymes including one endoglucanase and one xylanase from both the grasshopper and cutworm gut symbionts. The results indicated that the grasshopper symbiont enzymes were generally more efficient in biomass degradation than the homologous enzymes from cutworm symbionts. Together, these results demonstrated a correlation between the composition and putative metabolic functionality of the gut microbiome and host diet, and suggested

  5. The smart cluster method - Adaptive earthquake cluster identification and analysis in strong seismic regions

    NASA Astrophysics Data System (ADS)

    Schaefer, Andreas M.; Daniell, James E.; Wenzel, Friedemann

    2017-03-01

    Earthquake clustering is an essential part of almost any statistical analysis of spatial and temporal properties of seismic activity. The nature of earthquake clusters and subsequent declustering of earthquake catalogues plays a crucial role in determining the magnitude-dependent earthquake return period and its respective spatial variation for probabilistic seismic hazard assessment. This study introduces the Smart Cluster Method (SCM), a new methodology to identify earthquake clusters, which uses an adaptive point process for spatio-temporal cluster identification. It utilises the magnitude-dependent spatio-temporal earthquake density to adjust the search properties, subsequently analyses the identified clusters to determine directional variation and adjusts its search space with respect to directional properties. In the case of rapid subsequent ruptures like the 1992 Landers sequence or the 2010-2011 Darfield-Christchurch sequence, a reclassification procedure is applied to disassemble subsequent ruptures using near-field searches, nearest neighbour classification and temporal splitting. The method is capable of identifying and classifying earthquake clusters in space and time. It has been tested and validated using earthquake data from California and New Zealand. A total of more than 1500 clusters have been found in both regions since 1980 with M m i n = 2.0. Utilising the knowledge of cluster classification, the method has been adjusted to provide an earthquake declustering algorithm, which has been compared to existing methods. Its performance is comparable to established methodologies. The analysis of earthquake clustering statistics lead to various new and updated correlation functions, e.g. for ratios between mainshock and strongest aftershock and general aftershock activity metrics.

  6. Goodness-of-Fit Tests and Nonparametric Adaptive Estimation for Spike Train Analysis

    PubMed Central

    2014-01-01

    When dealing with classical spike train analysis, the practitioner often performs goodness-of-fit tests to test whether the observed process is a Poisson process, for instance, or if it obeys another type of probabilistic model (Yana et al. in Biophys. J. 46(3):323–330, 1984; Brown et al. in Neural Comput. 14(2):325–346, 2002; Pouzat and Chaffiol in Technical report, http://arxiv.org/abs/arXiv:0909.2785, 2009). In doing so, there is a fundamental plug-in step, where the parameters of the supposed underlying model are estimated. The aim of this article is to show that plug-in has sometimes very undesirable effects. We propose a new method based on subsampling to deal with those plug-in issues in the case of the Kolmogorov–Smirnov test of uniformity. The method relies on the plug-in of good estimates of the underlying model that have to be consistent with a controlled rate of convergence. Some nonparametric estimates satisfying those constraints in the Poisson or in the Hawkes framework are highlighted. Moreover, they share adaptive properties that are useful from a practical point of view. We show the performance of those methods on simulated data. We also provide a complete analysis with these tools on single unit activity recorded on a monkey during a sensory-motor task. Electronic Supplementary Material The online version of this article (doi:10.1186/2190-8567-4-3) contains supplementary material. PMID:24742008

  7. Goodness-of-Fit Tests and Nonparametric Adaptive Estimation for Spike Train Analysis.

    PubMed

    Reynaud-Bouret, Patricia; Rivoirard, Vincent; Grammont, Franck; Tuleau-Malot, Christine

    2014-04-17

    When dealing with classical spike train analysis, the practitioner often performs goodness-of-fit tests to test whether the observed process is a Poisson process, for instance, or if it obeys another type of probabilistic model (Yana et al. in Biophys. J. 46(3):323-330, 1984; Brown et al. in Neural Comput. 14(2):325-346, 2002; Pouzat and Chaffiol in Technical report, http://arxiv.org/abs/arXiv:0909.2785, 2009). In doing so, there is a fundamental plug-in step, where the parameters of the supposed underlying model are estimated. The aim of this article is to show that plug-in has sometimes very undesirable effects. We propose a new method based on subsampling to deal with those plug-in issues in the case of the Kolmogorov-Smirnov test of uniformity. The method relies on the plug-in of good estimates of the underlying model that have to be consistent with a controlled rate of convergence. Some nonparametric estimates satisfying those constraints in the Poisson or in the Hawkes framework are highlighted. Moreover, they share adaptive properties that are useful from a practical point of view. We show the performance of those methods on simulated data. We also provide a complete analysis with these tools on single unit activity recorded on a monkey during a sensory-motor task.Electronic Supplementary MaterialThe online version of this article (doi:10.1186/2190-8567-4-3) contains supplementary material.

  8. Projective analysis of staple food crop productivity in adaptation to future climate change in China.

    PubMed

    Zhang, Qing; Zhang, Wen; Li, Tingting; Sun, Wenjuan; Yu, Yongqiang; Wang, Guocheng

    2017-02-28

    Climate change continually affects our capabilities to feed the increasing population. Rising temperatures have the potential to shorten the crop growth duration and therefore reduce crop yields. In the past decades, China has successfully improved crop cultivars to stabilize, and even lengthen, the crop growth duration to make use of increasing heat resources. However, because of the complex cropping systems in the different regions of China, the possibility and the effectiveness of regulating crop growth duration to reduce the negative impacts of future climate change remain questionable. Here, we performed a projective analysis of the staple food crop productivity in double-rice, wheat-rice, wheat-maize, single-rice, and single-maize cropping systems in China using modeling approaches. The results indicated that from the present to the 2040s, the warming climate would shorten the growth duration of the current rice, wheat, and maize cultivars by 2-24, 11-13, and 9-29 days, respectively. The most significant shortening of the crop growth duration would be in Northeast China, where single-rice and single-maize cropping dominates the croplands. The shortened crop growth duration would consequently reduce crop productivity. The most significant decreases would be 27-31, 6-20, and 7-22% for the late crop in the double-rice rotation, wheat in the winter wheat-rice rotation, and single maize, respectively. However, our projection analysis also showed that the negative effects of the warming climate could be compensated for by stabilizing the growth duration of the crops via improvement in crop cultivars. In this case, the productivity of rice, wheat, and maize in the 2040s would increase by 4-16, 31-38, and 11-12%, respectively. Our modeling results implied that the possibility of securing future food production exists by adopting proper adaptation options in China.

  9. Data-adaptive wavelets and multi-scale singular-spectrum analysis

    NASA Astrophysics Data System (ADS)

    Yiou, Pascal; Sornette, Didier; Ghil, Michael

    2000-08-01

    Using multi-scale ideas from wavelet analysis, we extend singular-spectrum analysis (SSA) to the study of nonstationary time series, including the case where intermittency gives rise to the divergence of their variance. The wavelet transform resembles a local Fourier transform within a finite moving window whose width W, proportional to the major period of interest, is varied to explore a broad range of such periods. SSA, on the other hand, relies on the construction of the lag-correlation matrix C on M lagged copies of the time series over a fixed window width W to detect the regular part of the variability in that window in terms of the minimal number of oscillatory components; here W= MΔ t with Δ t as the time step. The proposed multi-scale SSA is a local SSA analysis within a moving window of width M≤ W≤ N, where N is the length of the time series. Multi-scale SSA varies W, while keeping a fixed W/ M ratio, and uses the eigenvectors of the corresponding lag-correlation matrix C(M) as data-adaptive wavelets; successive eigenvectors of C(M) correspond approximately to successive derivatives of the first mother wavelet in standard wavelet analysis. Multi-scale SSA thus solves objectively the delicate problem of optimizing the analyzing wavelet in the time-frequency domain by a suitable localization of the signal’s correlation matrix. We present several examples of application to synthetic signals with fractal or power-law behavior which mimic selected features of certain climatic or geophysical time series. The method is applied next to the monthly values of the Southern Oscillation Index (SOI) for 1933-1996; the SOI time series is widely believed to capture major features of the El Niño/Southern Oscillation (ENSO) in the Tropical Pacific. Our methodology highlights an abrupt periodicity shift in the SOI near 1960. This abrupt shift between 5 and 3 years supports the Devil’s staircase scenario for the ENSO phenomenon (preliminary results of this study

  10. Climate change impact and adaptation research requires integrated assessment and farming systems analysis: a case study in the Netherlands

    NASA Astrophysics Data System (ADS)

    Reidsma, Pytrik; Wolf, Joost; Kanellopoulos, Argyris; Schaap, Ben F.; Mandryk, Maryia; Verhagen, Jan; van Ittersum, Martin K.

    2015-04-01

    Rather than on crop modelling only, climate change impact assessments in agriculture need to be based on integrated assessment and farming systems analysis, and account for adaptation at different levels. With a case study for Flevoland, the Netherlands, we illustrate that (1) crop models cannot account for all relevant climate change impacts and adaptation options, and (2) changes in technology, policy and prices have had and are likely to have larger impacts on farms than climate change. While crop modelling indicates positive impacts of climate change on yields of major crops in 2050, a semi-quantitative and participatory method assessing impacts of extreme events shows that there are nevertheless several climate risks. A range of adaptation measures are, however, available to reduce possible negative effects at crop level. In addition, at farm level farmers can change cropping patterns, and adjust inputs and outputs. Also farm structural change will influence impacts and adaptation. While the 5th IPCC report is more negative regarding impacts of climate change on agriculture compared to the previous report, also for temperate regions, our results show that when putting climate change in context of other drivers, and when explicitly accounting for adaptation at crop and farm level, impacts may be less negative in some regions and opportunities are revealed. These results refer to a temperate region, but an integrated assessment may also change perspectives on climate change for other parts of the world.

  11. Gene Co-Expression Network Analysis Unraveling Transcriptional Regulation of High-Altitude Adaptation of Tibetan Pig

    PubMed Central

    Koltes, James E.; Gou, Xiao; Yang, Shuli; Yan, Dawei; Lu, Shaoxiong

    2016-01-01

    Tibetan pigs have survived at high altitude for millennia and they have a suite of adaptive features to tolerate the hypoxic environment. However, the molecular mechanisms underlying the regulation of hypoxia-adaptive phenotypes have not been completely elucidated. In this study, we analyzed differentially expressed genes (DEGs), biological pathways and constructed co-expression regulation networks using whole-transcriptome microarrays from lung tissues of Tibetan and Duroc pigs both at high and low altitude. A total of 3,066 DEGs were identified and this list was over-represented for the ontology terms including metabolic process, catalytic activity, and KEGG pathway including metabolic pathway and PI3K-Akt signaling pathway. The regulatory (RIF) and phenotypic (PIF) impact factor analysis identified several known and several potentially novel regulators of hypoxia adaption, including: IKBKG, KLF6 and RBPJ (RIF1), SF3B1, EFEMP1, HOXB6 and ATF6 (RIF2). These findings provide new details of the regulatory architecture of hypoxia-adaptive genes and also insight into which genes may undergo epigenetic modification for further study in the high-altitude adaptation. PMID:27936142

  12. Integrating Conjoint Analysis with TOPSIS Algorithm to the Visual Effect of Icon Design Based on Multiple Users' Image Perceptions

    ERIC Educational Resources Information Center

    Tung, Ting-Chun; Chen, Hung-Yuan

    2017-01-01

    With the advance of mobile computing and wireless technology, a user's intent to interact with the interface of a mobile device is motivated not only by its intuitional operation, but also by the emotional perception induced by its aesthetic appeal. A graphical interface employing icons with suitable visual effect based on the users' emotional…

  13. Experimental study on monitoring CO2 sequestration by conjoint analysis of the P-wave velocity and amplitude.

    PubMed

    Chen, Hao; Yang, Shenglai; Huan, Kangning; Li, Fangfang; Huang, Wei; Zheng, Aiai; Zhang, Xing

    2013-09-03

    CO2 sequestration has been considered to be one of the most straightforward carbon management strategies for industrial CO2 emission. Monitoring of the CO2 injection process is one of the best ways to make sure the safety storage but is also a major challenge in CO2 geological sequestration. Previous field and laboratory researches have shown that seismic methods are among the most promising monitoring methods because of the obvious reduction in P-wave velocities caused by CO2 injection. However, as CO2 injection continues, the P-wave velocity becomes increasingly insensitive according to the pilot projects when CO2 saturation is higher than 20-40%. Therefore, the conventional seismic method needs improvement or replacement to solve its limitations. In this study, P-wave velocity and amplitude responses to supercritical CO2 injection in brine-saturated core samples from Jilin oilfield were tested using core displacement and an ultrasonic detection integrated system. Results showed that neither the P-wave velocity nor amplitude could simply be used to monitor the CO2 injection process because of the insensitive or nonmonotonous response. Consequently, a new index was established by synthetically considering these two parameters to invert and monitor the CO2 process, which can be thought of as a newer and more effective assessment criterion for the seismic method.

  14. Identification of conjoint genomic regions for multiple traits using RIL populations through meta-QTL analysis in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In recent years, several quantitative trait locus (QTL) studies have been conducted for tolerance to drought, resistance to foliar diseases and yield-related traits in peanut. Number as well as position of the identified QTLs for a given trait, however, differed in different studies mainly because o...

  15. An Examination through Conjoint Analysis of the Preferences of Students Concerning Online Learning Environments According to Their Learning Styles

    ERIC Educational Resources Information Center

    Daghan, Gökhan; Akkoyunlu, Buket

    2012-01-01

    This study examines learning styles of students receiving education via online learning environments, and their preferences concerning the online learning environment. Maggie McVay Lynch Learning Style Inventory was used to determine learning styles of the students. The preferences of students concerning online learning environments were detected…

  16. Conjoint Membership in Orthodontics examination of the Royal College of Surgeons of Edinburgh and the College of Dental Surgeons of Hong Kong 2007 Gold Medal -- report of two cases.

    PubMed

    Lee, Wilson; Wong, Ricky; Rabie, Bakr

    2011-06-01

    This article describes the treatment of two orthodontic patients by the recipient of the Gold Medal for the Conjoint Membership in Orthodontics of the Royal College of Surgeons of Edinburgh and the College of Dental Surgeons of Hong Kong in November 2007.

  17. A Fast, Locally Adaptive, Interactive Retrieval Algorithm for the Analysis of DIAL Measurements

    NASA Astrophysics Data System (ADS)

    Samarov, D. V.; Rogers, R.; Hair, J. W.; Douglass, K. O.; Plusquellic, D.

    2010-12-01

    Differential absorption light detection and ranging (DIAL) is a laser-based tool which is used for remote, range-resolved measurement of particular gases in the atmosphere, such as carbon-dioxide and methane. In many instances it is of interest to study how these gases are distributed over a region such as a landfill, factory, or farm. While a single DIAL measurement only tells us about the distribution of a gas along a single path, a sequence of consecutive measurements provides us with information on how that gas is distributed over a region, making DIAL a natural choice for such studies. DIAL measurements present a number of interesting challenges; first, in order to convert the raw data to concentration it is necessary to estimate the derivative along the path of the measurement. Second, as the distribution of gases across a region can be highly heterogeneous it is important that the spatial nature of the measurements be taken into account. Finally, since it is common for the set of collected measurements to be quite large it is important for the method to be computationally efficient. Existing work based on Local Polynomial Regression (LPR) has been developed which addresses the first two issues, but the issue of computational speed remains an open problem. In addition to the latter, another desirable property is to allow user input into the algorithm. In this talk we present a novel method based on LPR which utilizes a variant of the RODEO algorithm to provide a fast, locally adaptive and interactive approach to the analysis of DIAL measurements. This methodology is motivated by and applied to several simulated examples and a study out of NASA Langley Research Center (LaRC) looking at the estimation of aerosol extinction in the atmosphere. A comparison study of our method against several other algorithms is also presented. References Chaudhuri, P., Marron, J.S., Scale-space view of curve estimation, Annals of Statistics 28 (2000) 408-428. Duong, T., Cowling

  18. Adopting public values and climate change adaptation strategies in urban forest management: A review and analysis of the relevant literature.

    PubMed

    Ordóñez Barona, Camilo

    2015-12-01

    Urban trees are a dominant natural element in cities; they provide important ecosystem services to urban citizens and help urban areas adapt to climate change. Many rationales have been proposed to provide a purpose for urban forest management, some of which have been ineffective in addressing important ecological and social management themes. Among these rationales we find a values-based perspective, which sees management as a process where the desires of urban dwellers are met. Another perspective is climate change adaptation, which sees management as a process where urban forest vulnerability to climate change is reduced and resilience enhanced. Both these rationales have the advantage of complementing, enhancing, and broadening urban forest management objectives. A critical analysis of the literature on public values related to urban forests and climate change adaptation in the context of urban forests is undertaken to discuss what it means to adopt these two issues in urban forest management. The analysis suggests that by seeing urban forest management as a process by which public values are satisfied and urban-forest vulnerabilities to climate change are reduced, we can place issues such as naturalization, adaptive management, and engaging people in management at the centre of urban forest management. Focusing urban forest management on these issues may help ensure the success of programs focused on planting more trees and increasing citizen participation in urban forest management.

  19. The Jakobsonian One-Stem Analysis of the Russian Verb: Adaptations and Pedagogical Strategies.

    ERIC Educational Resources Information Center

    Gaines, Billie D.

    1982-01-01

    The evolution of one-stem verb theory since Roman Jakobson's 1948 study of Russian conjugation is outlined, and adaptations of his one-stem conjugation methodology for current classroom use are discussed and compared. (MSE)

  20. The contribution of transcriptomic and proteomic analysis in elucidating stress adaptation responses of Listeria monocytogenes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The foodborne transmission of Listeria monocytogenes requires physiological adaptation to various conditions, including the cold, osmotic, heat, acid, alkaline, and oxidative stresses, associated with food hygiene, processing, and preservation measures. We review the current knowledge on the molecul...

  1. Metagenomic analysis of Atriplex microbiomes: Investigating Plant-microbe interactions that enhance adaptation to extreme habitats

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cryptic symbiotic microbes influence host adaptation by improving nutrient uptake or stress tolerance. Current technologies for increasing plant productivity, whether for food and fuel production or for restoration and remediation, often utilize approaches that bypass, rather than leverage, microb...

  2. A Critical Analysis of the Behavioral Adaptation Explanation of the Probing Effect.

    ERIC Educational Resources Information Center

    Levine, Timothy R.; McCornack, Steven A.

    1996-01-01

    Documents three problems with the behavioral adaption explanation (BAE) that, taken together, suggest that it cannot account for the probing effect, i.e., the finding that sources interrogatively probed appear more honest to message recipients than nonprobed sources. (TB)

  3. Comparative Genome Analysis Reveals Metabolic Versatility and Environmental Adaptations of Sulfobacillus thermosulfidooxidans Strain ST

    PubMed Central

    Guo, Xue; Yin, Huaqun; Liang, Yili; Hu, Qi; Zhou, Xishu; Xiao, Yunhua; Ma, Liyuan; Zhang, Xian; Qiu, Guanzhou; Liu, Xueduan

    2014-01-01

    The genus Sulfobacillus is a cohort of mildly thermophilic or thermotolerant acidophiles within the phylum Firmicutes and requires extremely acidic environments and hypersalinity for optimal growth. However, our understanding of them is still preliminary partly because few genome sequences are available. Here, the draft genome of Sulfobacillus thermosulfidooxidans strain ST was deciphered to obtain a comprehensive insight into the genetic content and to understand the cellular mechanisms necessary for its survival. Furthermore, the expressions of key genes related with iron and sulfur oxidation were verified by semi-quantitative RT-PCR analysis. The draft genome sequence of Sulfobacillus thermosulfidooxidans strain ST, which encodes 3225 predicted coding genes on a total length of 3,333,554 bp and a 48.35% G+C, revealed the high degree of heterogeneity with other Sulfobacillus species. The presence of numerous transposases, genomic islands and complete CRISPR/Cas defence systems testifies to its dynamic evolution consistent with the genome heterogeneity. As expected, S. thermosulfidooxidans encodes a suit of conserved enzymes required for the oxidation of inorganic sulfur compounds (ISCs). The model of sulfur oxidation in S. thermosulfidooxidans was proposed, which showed some different characteristics from the sulfur oxidation of Gram-negative A. ferrooxidans. Sulfur oxygenase reductase and heterodisulfide reductase were suggested to play important roles in the sulfur oxidation. Although the iron oxidation ability was observed, some key proteins cannot be identified in S. thermosulfidooxidans. Unexpectedly, a predicted sulfocyanin is proposed to transfer electrons in the iron oxidation. Furthermore, its carbon metabolism is rather flexible, can perform the transformation of pentose through the oxidative and non-oxidative pentose phosphate pathways and has the ability to take up small organic compounds. It encodes a multitude of heavy metal resistance systems to

  4. Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis

    PubMed Central

    Davies, Kalina T.J.; Bennett, Nigel C.; Tsagkogeorga, Georgia; Rossiter, Stephen J.; Faulkes, Christopher G.

    2015-01-01

    During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subterranean niche, African mole-rats are one of the most successful. Much of their ecological success can be attributed to a diet of plant storage organs, which has allowed them to colonize climatically varied habitats across sub-Saharan Africa, and has probably contributed to the evolution of their diverse social systems. Yet despite their many remarkable phenotypic specializations, little is known about molecular adaptations underlying these traits. To address this, we sequenced the transcriptomes of seven mole-rat taxa, including three solitary species, and combined new sequences with existing genomic data sets. Alignments of more than 13,000 protein-coding genes encompassed, for the first time, all six genera and the full spectrum of ecological and social variation in the clade. We detected positive selection within the mole-rat clade and along ancestral branches in approximately 700 genes including loci associated with tumorigenesis, aging, morphological development, and sociality. By combining these results with gene ontology annotation and protein–protein networks, we identified several clusters of functionally related genes. This family wide analysis of molecular evolution in mole-rats has identified a suite of positively selected genes, deepening our understanding of the extreme phenotypic traits exhibited by this group. PMID:26318402

  5. Comparative genome analysis reveals metabolic versatility and environmental adaptations of Sulfobacillus thermosulfidooxidans strain ST.

    PubMed

    Guo, Xue; Yin, Huaqun; Liang, Yili; Hu, Qi; Zhou, Xishu; Xiao, Yunhua; Ma, Liyuan; Zhang, Xian; Qiu, Guanzhou; Liu, Xueduan

    2014-01-01

    The genus Sulfobacillus is a cohort of mildly thermophilic or thermotolerant acidophiles within the phylum Firmicutes and requires extremely acidic environments and hypersalinity for optimal growth. However, our understanding of them is still preliminary partly because few genome sequences are available. Here, the draft genome of Sulfobacillus thermosulfidooxidans strain ST was deciphered to obtain a comprehensive insight into the genetic content and to understand the cellular mechanisms necessary for its survival. Furthermore, the expressions of key genes related with iron and sulfur oxidation were verified by semi-quantitative RT-PCR analysis. The draft genome sequence of Sulfobacillus thermosulfidooxidans strain ST, which encodes 3225 predicted coding genes on a total length of 3,333,554 bp and a 48.35% G+C, revealed the high degree of heterogeneity with other Sulfobacillus species. The presence of numerous transposases, genomic islands and complete CRISPR/Cas defence systems testifies to its dynamic evolution consistent with the genome heterogeneity. As expected, S. thermosulfidooxidans encodes a suit of conserved enzymes required for the oxidation of inorganic sulfur compounds (ISCs). The model of sulfur oxidation in S. thermosulfidooxidans was proposed, which showed some different characteristics from the sulfur oxidation of Gram-negative A. ferrooxidans. Sulfur oxygenase reductase and heterodisulfide reductase were suggested to play important roles in the sulfur oxidation. Although the iron oxidation ability was observed, some key proteins cannot be identified in S. thermosulfidooxidans. Unexpectedly, a predicted sulfocyanin is proposed to transfer electrons in the iron oxidation. Furthermore, its carbon metabolism is rather flexible, can perform the transformation of pentose through the oxidative and non-oxidative pentose phosphate pathways and has the ability to take up small organic compounds. It encodes a multitude of heavy metal resistance systems to

  6. Motion Analysis of 100 Mediastinal Lymph Nodes: Potential Pitfalls in Treatment Planning and Adaptive Strategies

    SciTech Connect

    Pantarotto, Jason R.; Piet, Anna H.M.; Vincent, Andrew; Soernsen de Koste, John R. van; Senan, Suresh

    2009-07-15

    Purpose: The motion of mediastinal lymph nodes may undermine local control with involved-field radiotherapy. We studied patterns of nodal and tumor motion in 41 patients with lung cancer. Methods and Materials: Four-dimensional (4D) computed tomography planning scans were retrospectively evaluated to identify patients with clearly visible mediastinal lymph nodes. One hundred nodes from 14 patients with Stage I and 27 patients with Stage III were manually contoured in all 4D computed tomography respiratory phases. Motion was derived from changes in the nodal center-of-mass position. Primary tumors were also delineated in all phases for 16 patients with Stage III disease. Statistical analysis included a multivariate mixed-effects model of grouped data. Results: Average 3D nodal motion during quiet breathing was 0.68 cm (range, 0.17-1.64 cm); 77% moved greater than 0.5 cm, and 10% moved greater than 1.0 cm. Motion was greatest in the lower mediastinum (p = 0.002), and nodes measuring 2 cm or greater in diameter showed motion similar to that in smaller nodes. In 11 of 16 patients studied, at least one node moved more than the corresponding primary tumor. No association between 3D primary tumor motion and nodal motion was observed. For mobile primary tumors, phase offsets between the primary tumor and nodes of two or more and three or more phases were observed for 33% and 12% of nodes, respectively. Conclusions: Mediastinal nodal motion is common, with phase offsets seen between the primary tumor and different nodes in the same patient. Patient-specific information is needed to ensure geometric coverage, and adaptive strategies based solely on the primary tumor may be misleading.

  7. Analysis of differential immune responses induced by innate and adaptive immunity following transplantation

    PubMed Central

    He, Hongzhen; Stone, James R; Perkins, David L

    2003-01-01

    The roles of innate and adaptive immunity in allograft rejection remain incompletely understood. Previous studies analysing lymphocyte deficient or syngeneic graft recipients have identified subsets of inflammatory chemokines and cytokines induced by antigen independent mechanisms. In the current study, we analysed a panel of 60 inflammatory parameters including serum cytokines, intragraft chemokines and cytokines, receptors, and cellular markers. Our results confirmed the up-regulation of a subset of markers by innate mechanisms and also identified a subset of parameters up-regulated only in the context of an adaptive response. Thus, we successfully differentiated markers of the innate and adaptive phases of rejection. Current paradigms emphasize that innate signals can promote a subsequent adaptive response. Interestingly, in our studies, expression of the markers induced by innate mechanisms was markedly amplified in the allogeneic, but not syngeneic or lymphocyte deficient, recipients. These results suggest that inflammatory mediators can have functional overlap between the innate and adaptive responses, and that the adaptive component of the rejection process amplifies the innate response by positive feedback regulation. PMID:12757613

  8. Analysis and design of a high power laser adaptive phased array transmitter

    NASA Technical Reports Server (NTRS)

    Mevers, G. E.; Soohoo, J. F.; Winocur, J.; Massie, N. A.; Southwell, W. H.; Brandewie, R. A.; Hayes, C. L.

    1977-01-01

    The feasibility of delivering substantial quantities of optical power to a satellite in low earth orbit from a ground based high energy laser (HEL) coupled to an adaptive antenna was investigated. Diffraction effects, atmospheric transmission efficiency, adaptive compensation for atmospheric turbulence effects, including the servo bandwidth requirements for this correction, and the adaptive compensation for thermal blooming were examined. To evaluate possible HEL sources, atmospheric investigations were performed for the CO2, (C-12)(O-18)2 isotope, CO and DF wavelengths using output antenna locations of both sea level and mountain top. Results indicate that both excellent atmospheric and adaption efficiency can be obtained for mountain top operation with a micron isotope laser operating at 9.1 um, or a CO laser operating single line (P10) at about 5.0 (C-12)(O-18)2um, which was a close second in the evaluation. Four adaptive power transmitter system concepts were generated and evaluated, based on overall system efficiency, reliability, size and weight, advanced technology requirements and potential cost. A multiple source phased array was selected for detailed conceptual design. The system uses a unique adaption technique of phase locking independent laser oscillators which allows it to be both relatively inexpensive and most reliable with a predicted overall power transfer efficiency of 53%.

  9. Comparative analysis of field-isolate and monkey-adapted Plasmodium vivax genomes.

    PubMed

    Chan, Ernest R; Barnwell, John W; Zimmerman, Peter A; Serre, David

    2015-03-01

    Significant insights into the biology of Plasmodium vivax have been gained from the ability to successfully adapt human infections to non-human primates. P. vivax strains grown in monkeys serve as a renewable source of parasites for in vitro and ex vivo experimental studies and functional assays, or for studying in vivo the relapse characteristics, mosquito species compatibilities, drug susceptibility profiles or immune responses towards potential vaccine candidates. Despite the importance of these studies, little is known as to how adaptation to a different host species may influence the genome of P. vivax. In addition, it is unclear whether these monkey-adapted strains consist of a single clonal population of parasites or if they retain the multiclonal complexity commonly observed in field isolates. Here we compare the genome sequences of seven P. vivax strains adapted to New World monkeys with those of six human clinical isolates collected directly in the field. We show that the adaptation of P. vivax parasites to monkey hosts, and their subsequent propagation, did not result in significant modifications of their genome sequence and that these monkey-adapted strains recapitulate the genomic diversity of field isolates. Our analyses also reveal that these strains are not always genetically homogeneous and should be analyzed cautiously. Overall, our study provides a framework to better leverage this important research material and fully utilize this resource for improving our understanding of P. vivax biology.

  10. Convergence and low temperature adaptability analysis of the high temperature series expansion of the free energy.

    PubMed

    Zhou, Shiqi

    2013-09-28

    By appealing to the coupling parameter series expansion to calculate the first seven perturbation coefficients of the high temperature series expansion (HTSE) of the free energy, analysis of convergence and low temperature adaptability of the HTSE in calculating fluid thermodynamic properties is performed for the first time; the fluid thermodynamic properties considered include critical parameters, vapor-liquid coexistence curve, thermodynamic characteristic functions, chemical potential, pressure, and constant volume excess heat capacity. To proceed with the analysis, a well known square well model is used as sample; the well widths considered range over a wide interval, and the relevant temperatures amenable to simulation calculations (used as "exact" results to analyze the HTSE) can be both very high and very low. The main discoveries reached are summarized as follows: (1) The HTSE usually converges at the 4th-order truncation, but with decrease of the temperature considered, the lowest truncation order, which makes the HTSE to converge, tends to rise. As a conservative estimate, it is considered that the HTSE always converges for reduced temperature T* higher than 0.25, whereas for T* < 0.25 there appear signs indicating that the HTSE may diverge from the 7th-order truncation. (2) Within the temperature interval with T* ≥ 0.5, the HTSE converges approximately to the correct solution, and the HTSE can be reliably used to calculate the fluid thermodynamic properties, and within this temperature interval, the 4th-order truncation is enough; whereas for T* < 0.5, such as within the temperature interval with 0.275 ≤ T* ≤ 0.355, although the HTSE does converge, it does not converge to the correct solution, and the deviations between the HTSE calculations and MC simulations become an ever-prominent issue with the rising of the density, and the slopes of the thermodynamic properties over density are not satisfactorily represented. As a result, the HTSE is not

  11. Cognitive-Behavioral Conjoint Therapy for PTSD Improves Various PTSD Symptoms and Trauma-related Cognitions: Results from a Randomized Controlled Trial

    PubMed Central

    Macdonald, Alexandra; Pukay-Martin, Nicole D.; Wagner, Anne C.; Fredman, Steffany J.; Monson, Candice M.

    2015-01-01

    Numerous studies document an association between posttraumatic stress disorder (PTSD) and impairments in intimate relationship functioning, and there is evidence that PTSD symptoms and associated impairments are improved by cognitive-behavioral conjoint therapy for PTSD (CBCT for PTSD; Monson & Fredman, 2012). The present study investigated changes across treatment in clinician-rated PTSD symptom clusters and patient-rated trauma-related cognitions in a randomized controlled trial comparing CBCT for PTSD with waitlist in a sample of 40 individuals with PTSD and their partners (N = 40) (REDACTED). Compared with waitlist, patients who received CBCT for PTSD immediately demonstrated greater improvements in all PTSD symptom clusters, trauma-related beliefs, and guilt cognitions (Hedge's gs -.33 to -1.51). Results suggest that CBCT for PTSD improves all PTSD symptom clusters and trauma-related cognitions among individuals with PTSD and further supports the value of utilizing a couple-based approach to the treatment of PTSD. PMID:26651352

  12. Analysis of adaptive mesh refinement for IMEX discontinuous Galerkin solutions of the compressible Euler equations with application to atmospheric simulations

    NASA Astrophysics Data System (ADS)

    Kopera, Michal A.; Giraldo, Francis X.

    2014-10-01

    The resolutions of interests in atmospheric simulations require prohibitively large computational resources. Adaptive mesh refinement (AMR) tries to mitigate this problem by putting high resolution in crucial areas of the domain. We investigate the performance of a tree-based AMR algorithm for the high order discontinuous Galerkin method on quadrilateral grids with non-conforming elements. We perform a detailed analysis of the cost of AMR by comparing this to uniform reference simulations of two standard atmospheric test cases: density current and rising thermal bubble. The analysis shows up to 15 times speed-up of the AMR simulations with the cost of mesh adaptation below 1% of the total runtime. We pay particular attention to the implicit-explicit (IMEX) time integration methods and show that the ARK2 method is more robust with respect to dynamically adapting meshes than BDF2. Preliminary analysis of preconditioning reveals that it can be an important factor in the AMR overhead. The compiler optimizations provide significant runtime reduction and positively affect the effectiveness of AMR allowing for speed-ups greater than it would follow from the simple performance model.

  13. Flexible adaptive paradigms for fMRI using a novel software package 'Brain Analysis in Real-Time' (BART).

    PubMed

    Hellrung, Lydia; Hollmann, Maurice; Zscheyge, Oliver; Schlumm, Torsten; Kalberlah, Christian; Roggenhofer, Elisabeth; Okon-Singer, Hadas; Villringer, Arno; Horstmann, Annette

    2015-01-01

    In this work we present a new open source software package offering a unified framework for the real-time adaptation of fMRI stimulation procedures. The software provides a straightforward setup and highly flexible approach to adapt fMRI paradigms while the experiment is running. The general framework comprises the inclusion of parameters from subject's compliance, such as directing gaze to visually presented stimuli and physiological fluctuations, like blood pressure or pulse. Additionally, this approach yields possibilities to investigate complex scientific questions, for example the influence of EEG rhythms or fMRI signals results themselves. To prove the concept of this approach, we used our software in a usability example for an fMRI experiment where the presentation of emotional pictures was dependent on the subject's gaze position. This can have a significant impact on the results. So far, if this is taken into account during fMRI data analysis, it is commonly done by the post-hoc removal of erroneous trials. Here, we propose an a priori adaptation of the paradigm during the experiment's runtime. Our fMRI findings clearly show the benefits of an adapted paradigm in terms of statistical power and higher effect sizes in emotion-related brain regions. This can be of special interest for all experiments with low statistical power due to a limited number of subjects, a limited amount of time, costs or available data to analyze, as is the case with real-time fMRI.

  14. Design and analysis on thermal adaptive clamping device for PPMgLN crystal used in solid state laser

    NASA Astrophysics Data System (ADS)

    Yan, Conglin; Chen, Yongliang; Zhang, Wei

    2015-02-01

    The quality of clamping device for PPMgLN crystal has a vital influence on the optical property of solid-state laser. It has highly requirements of work stability and environmental adaptation ability, especially the thermal adaptation under high temperature differences. To achieve thermal adaptation, structural stiffness will be unavoidably weakened. How to keep both enough stiffness and thermal adaptation as far as possible is the key design point and also difficult point. In this paper, a kind of flexible thermal release unit which can work permanent under 130+/-10°C is studied. Thermal compensation principle and flexible thermal release theory are applied. Analysis results indicate that this device can effectively decreased the thermal stress of the crystal from 85MPa to 0.66MPa. The results of the vibration resistance test on the optical axis direction of the crystal indicate that the device can provide at least 5.62N to resistant 57.2g impact vibration and 18.5g impact vibration in the side direction, well satisfied the requirements of ability to resistant 6g impact vibration.

  15. Analysis of trait mean and variability versus temperature in trematode cercariae: is there scope for adaptation to global warming?

    PubMed

    Studer, A; Poulin, R

    2014-05-01

    The potential of species for evolutionary adaptation in the context of global climate change has recently come under scrutiny. Estimates of phenotypic variation in biological traits may prove valuable for identifying species, or groups of species, with greater or lower potential for evolutionary adaptation, as this variation, when heritable, represents the basis for natural selection. Assuming that measures of trait variability reflect the evolutionary potential of these traits, we conducted an analysis across trematode species to determine the potential of these parasites as a group to adapt to increasing temperatures. Firstly, we assessed how the mean number of infective stages (cercariae) emerging from infected snail hosts as well as the survival and infectivity of cercariae are related to temperature. Secondly and importantly in the context of evolutionary potential, we assessed how coefficients of variation for these traits are related to temperature, in both cases controlling for other factors such as habitat, acclimatisation, latitude and type of target host. With increasing temperature, an optimum curve was found for mean output and mean infectivity, and a linear decrease for survival of cercariae. For coefficients of variation, temperature was only an important predictor in the case of cercarial output, where results indicated that there is, however, no evidence for limited trait variation at the higher temperature range. No directional trend was found for either variation of survival or infectivity. These results, characterising general patterns among trematodes, suggest that all three traits considered may have potential to change through adaptive evolution.

  16. The Andean Adaptive Toolkit to Counteract High Altitude Maladaptation: Genome-Wide and Phenotypic Analysis of the Collas

    PubMed Central

    Eichstaedt, Christina A.; Antão, Tiago; Pagani, Luca; Cardona, Alexia; Kivisild, Toomas; Mormina, Maru

    2014-01-01

    During their migrations out of Africa, humans successfully colonised and adapted to a wide range of habitats, including extreme high altitude environments, where reduced atmospheric oxygen (hypoxia) imposes a number of physiological challenges. This study evaluates genetic and phenotypic variation in the Colla population living in the Argentinean Andes above 3500 m and compares it to the nearby lowland Wichí group in an attempt to pinpoint evolutionary mechanisms underlying adaptation to high altitude hypoxia. We genotyped 730,525 SNPs in 25 individuals from each population. In genome-wide scans of extended haplotype homozygosity Collas showed the strongest signal around VEGFB, which plays an essential role in the ischemic heart, and ELTD1, another gene crucial for heart development and prevention of cardiac hypertrophy. Moreover, pathway enrichment analysis showed an overrepresentation of pathways associated with cardiac morphology. Taken together, these findings suggest that Colla highlanders may have evolved a toolkit of adaptative mechanisms resulting in cardiac reinforcement, most likely to counteract the adverse effects of the permanently increased haematocrit and associated shear forces that characterise the Andean response to hypoxia. Regulation of cerebral vascular flow also appears to be part of the adaptive response in Collas. These findings are not only relevant to understand the evolution of hypoxia protection in high altitude populations but may also suggest new avenues for medical research into conditions where hypoxia constitutes a detrimental factor. PMID:24686296

  17. Empirical Analysis of EEG and ERPs for Psychophysiological Adaptive Task Allocation

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence J., III; Pope, Alan T.; Freeman, Frederick G.; Scerbo, Mark W.; Mikulka, Peter J.

    2001-01-01

    The present study was designed to test the efficacy of using Electroencephalogram (EEG) and Event-Related Potentials (ERPs) for making task allocation decisions. Thirty-six participants were randomly assigned to an experimental, yoked, or control group condition. Under the experimental condition, a tracking task was switched between task modes based upon the participant's EEG. The results showed that the use of adaptive aiding improved performance and lowered subjective workload under negative feedback as predicted. Additionally, participants in the adaptive group had significantly lower RMSE and NASA-TLX ratings than participants in either the yoked or control group conditions. Furthermore, the amplitudes of the N1 and P3 ERP components were significantly larger under the experimental group condition than under either the yoked or control group conditions. These results are discussed in terms of the implications for adaptive automation design.

  18. Serial identification of EEG patterns using adaptive wavelet-based analysis

    NASA Astrophysics Data System (ADS)

    Nazimov, A. I.; Pavlov, A. N.; Nazimova, A. A.; Grubov, V. V.; Koronovskii, A. A.; Sitnikova, E.; Hramov, A. E.

    2013-10-01

    A problem of recognition specific oscillatory patterns in the electroencephalograms with the continuous wavelet-transform is discussed. Aiming to improve abilities of the wavelet-based tools we propose a serial adaptive method for sequential identification of EEG patterns such as sleep spindles and spike-wave discharges. This method provides an optimal selection of parameters based on objective functions and enables to extract the most informative features of the recognized structures. Different ways of increasing the quality of patterns recognition within the proposed serial adaptive technique are considered.

  19. Reaction and adaptation to the birth of a child: a couple-level analysis.

    PubMed

    Dyrdal, Gunvor Marie; Lucas, Richard E

    2013-04-01

    The present study explored how life satisfaction changes before and after childbirth among first-time parents from a nationally representative, longitudinal study of Germans. Life satisfaction increased before pregnancy to a peak just after birth and then returned to the baseline level within 2 years postpartum. The 2 members of the same couple reacted and adapted to childbirth in similar ways, suggesting that something about the event itself (rather than the individuals' personality) affects individual differences in these responses. However, some personality characteristics (including neuroticism and openness) did moderate reaction and adaptation effects.

  20. Habituation of visual adaptation

    PubMed Central

    Dong, Xue; Gao, Yi; Lv, Lili; Bao, Min

    2016-01-01

    Our sensory system adjusts its function driven by both shorter-term (e.g. adaptation) and longer-term (e.g. learning) experiences. Most past adaptation literature focuses on short-term adaptation. Only recently researchers have begun to investigate how adaptation changes over a span of days. This question is important, since in real life many environmental changes stretch over multiple days or longer. However, the answer to the question remains largely unclear. Here we addressed this issue by tracking perceptual bias (also known as aftereffect) induced by motion or contrast adaptation across multiple daily adaptation sessions. Aftereffects were measured every day after adaptation, which corresponded to the degree of adaptation on each day. For passively viewed adapters, repeated adaptation attenuated aftereffects. Once adapters were presented with an attentional task, aftereffects could either reduce for easy tasks, or initially show an increase followed by a later decrease for demanding tasks. Quantitative analysis of the decay rates in contrast adaptation showed that repeated exposure of the adapter appeared to be equivalent to adaptation to a weaker stimulus. These results suggest that both attention and a non-attentional habituation-like mechanism jointly determine how adaptation develops across multiple daily sessions. PMID:26739917

  1. Factorial and Hierarchical Cluster Analysis of the Adaptive Behavior Scales (Part I & II) in a Population of Older People (50 Years +) with Severe Intellectual Impairment (Mental Handicap).

    ERIC Educational Resources Information Center

    Moss, S. C.; Hogg, J.

    1990-01-01

    Principal components analysis was employed on the Adaptive Behavior Scales with scores of 122 older (mean age 63.5) individuals with severe intellectual impairment living in England. The study found the structure of adaptive skills and interpersonal maladaptive behaviors similar to that found for younger retarded adults. Two factors, personal…

  2. Spatiotemporal characteristics of form analysis in the human visual cortex revealed by rapid event-related fMRI adaptation.

    PubMed

    Kourtzi, Zoe; Huberle, Elisabeth

    2005-11-01

    The integration of local elements to coherent forms is at the core of understanding visual perception. Accumulating evidence suggests that both early retinotopic and higher occipitotemporal areas contribute to the integration of local elements to global forms. However, the spatiotemporal characteristics of form analysis in the human visual cortex remain largely unknown. The aim of this study was to investigate form analysis at different spatial (global vs. local structure) and temporal (different stimulus presentation rates) scales across stages of visual analysis (from V1 to the lateral occipital complex-LOC) in the human brain. We used closed contours rendered by Gabor elements and manipulated either the global contour structure or the orientation of the local Gabor elements. Our rapid event-related fMRI adaptation studies suggest that contour integration and form processing in early visual areas is transient and limited within the local neighborhood of their cells' receptive field. In contrast, higher visual areas appear to process the perceived global form in a more sustained manner. Finally, we demonstrate that these spatiotemporal properties of form processing in the visual cortex are modulated by attention. Attention to the global form maintains sustained processing in occipitotemporal areas, whereas attention to local elements enhances their integration in early visual areas. These findings provide novel neuroimaging evidence for form analysis at different spatiotemporal scales across human visual areas and validate the use of rapid event-related fMRI adaptation for investigating processing across stages of visual analysis in the human brain.

  3. Molecular diversity analysis and bacterial population dynamics of an adapted seawater microbiota during the degradation of Tunisian zarzatine oil.

    PubMed

    Zrafi-Nouira, Ines; Guermazi, Sonda; Chouari, Rakia; Safi, Nimer M D; Pelletier, Eric; Bakhrouf, Amina; Saidane-Mosbahi, Dalila; Sghir, Abdelghani

    2009-07-01

    The indigenous microbiota of polluted coastal seawater in Tunisia was enriched by increasing the concentration of zarzatine crude oil. The resulting adapted microbiota was incubated with zarzatine crude oil as the only carbon and energy source. Crude oil biodegradation capacity and bacterial population dynamics of the microbiota were evaluated every week for 28 days (day 7, day 14, day 21, and day 28). Results show that the percentage of petroleum degradation was 23.9, 32.1, 65.3, and 77.8%, respectively. At day 28, non-aromatic and aromatic hydrocarbon degradation rates reached 92.6 and 68.7%, respectively. Bacterial composition of the adapted microflora was analysed by 16S rRNA gene cloning and sequencing, using total genomic DNA extracted from the adapted microflora at days 0, 7, 14, 21, and 28. Five clone libraries were constructed and a total of 430 sequences were generated and grouped into OTUs using the ARB software package. Phylogenetic analysis of the adapted microbiota shows the presence of four phylogenetic groups: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Diversity indices show a clear decrease in bacterial diversity of the adapted microflora according to the incubation time. The Proteobacteria are the most predominant (>80%) at day 7, day 14 and day 21 but not at day 28 for which the microbiota was reduced to only one OTU affiliated with the genus Kocuria of the Actinobacteria. This study shows that the degradation of zarzatine crude oil components depends on the activity of a specialized and dynamic seawater consortium composed of different phylogenetic taxa depending on the substrate complexity.

  4. Integrated Physiological, Proteomic, and Metabolomic Analysis of Ultra Violet (UV) Stress Responses and Adaptation Mechanisms in Pinus radiata.

    PubMed

    Pascual, Jesús; Cañal, María Jesús; Escandón, Mónica; Meijón, Mónica; Weckwerth, Wolfram; Valledor, Luis

    2017-03-01

    Globally expected changes in environmental conditions, especially the increase of UV irradiation, necessitate extending our knowledge of the mechanisms mediating tree species adaptation to this stress. This is crucial for designing new strategies to maintain future forest productivity. Studies focused on environmentally realistic dosages of UV irradiation in forest species are scarce. Pinus spp. are commercially relevant trees and not much is known about their adaptation to UV. In this work, UV treatment and recovery of Pinus radiata plants with dosages mimicking future scenarios, based on current models of UV radiation, were performed in a time-dependent manner. The combined metabolome and proteome analysis were complemented with measurements of + physiological parameters and gene expression. Sparse PLS analysis revealed complex molecular interaction networks of molecular and physiological data. Early responses prevented phototoxicity by reducing photosystem activity and the electron transfer chain together with the accumulation of photoprotectors and photorespiration. Apart from the reduction in photosynthesis as consequence of the direct UV damage on the photosystems, the primary metabolism was rearranged to deal with the oxidative stress while minimizing ROS production. New protein kinases and proteases related to signaling, coordination, and regulation of UV stress responses were revealed. All these processes demonstrate a complex molecular interaction network extending the current knowledge on UV-stress adaptation in pine.

  5. Whole genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Backfat thickness affects preservation of the beef carcass after slaughter and confers organoleptic characteristics assessed by the consumer. One of the breeding goals for Canchim, a tropically adapted breed, is to comprehensively increase fat thickness. Our goal was to identify genomic regions ass...

  6. Transient analysis of an adaptive system for optimization of design parameters

    NASA Technical Reports Server (NTRS)

    Bayard, D. S.

    1992-01-01

    Averaging methods are applied to analyzing and optimizing the transient response associated with the direct adaptive control of an oscillatory second-order minimum-phase system. The analytical design methods developed for a second-order plant can be applied with some approximation to a MIMO flexible structure having a single dominant mode.

  7. Quantitative Analysis of the Adapted Physical Education Employment Market in Higher Education

    ERIC Educational Resources Information Center

    Zhang, Jiabei

    2010-01-01

    The purpose of this study was to analyze the employment market of adapted physical education (APE) careers in higher education since 1975 to see if the increase of this market has continued since 1998. Based on the data collected from the "Chronicle of Higher Education", a total of 887 APE job openings have been posted since 1975,…

  8. Adaptation of Ustilago maydis to extreme pH values: A transcriptomic analysis.

    PubMed

    Cervantes-Montelongo, Juan Antonio; Aréchiga-Carvajal, Elva Teresa; Ruiz-Herrera, José

    2016-11-01

    Fungi are capable to adapt to environments with different pH values. Here we used microarrays to analyze the transcriptomic response of the Basidiomycota Ustilago maydis when transferred from a neutral pH medium to acidic, or alkaline media. Yeast and hyphal monomorphic mutants were used as controls, permitting the identification of 301 genes differentially regulated during the transfer from neutral to an acidic medium, of which 162 were up-regulated and 139 down-regulated. When cells were transferred to an alkaline medium, we identified 797 differentially regulated genes, 335 up-regulated, and 462 down-regulated. The category showing the highest number of regulated genes during the change to either pH, besides "unclassified," was "metabolism," indicating that a very important factor for adaptation is a change in the metabolic machinery. These data reveal that adaptation of U. maydis to environments with different pH involves a severe modification of the transcription machinery to cope with the new conditions, and that the stress by an alkaline environment is more drastic than a change to an acidic medium. The data also revealed that only a minor proportion of the identified genes are under the apparent control of the Pal/Rim pathway, indicating that pH adaptation of this fungus involves other than this cannonical pathway.

  9. Adaptive thresholding for reliable topological inference in single subject fMRI analysis

    PubMed Central

    Gorgolewski, Krzysztof J.; Storkey, Amos J.; Bastin, Mark E.; Pernet, Cyril R.

    2012-01-01

    Single subject fMRI has proved to be a useful tool for mapping functional areas in clinical procedures such as tumor resection. Using fMRI data, clinicians assess the risk, plan and execute such procedures based on thresholded statistical maps. However, because current thresholding methods were developed mainly in the context of cognitive neuroscience group studies, most single subject fMRI maps are thresholded manually to satisfy specific criteria related to single subject analyzes. Here, we propose a new adaptive thresholding method which combines Gamma-Gaussian mixture modeling with topological thresholding to improve cluster delineation. In a series of simulations we show that by adapting to the signal and noise properties, the new method performs well in terms of total number of errors but also in terms of the trade-off between false negative and positive cluster error rates. Similarly, simulations show that adaptive thresholding performs better than fixed thresholding in terms of over and underestimation of the true activation border (i.e., higher spatial accuracy). Finally, through simulations and a motor test–retest study on 10 volunteer subjects, we show that adaptive thresholding improves reliability, mainly by accounting for the global signal variance. This in turn increases the likelihood that the true activation pattern can be determined offering an automatic yet flexible way to threshold single subject fMRI maps. PMID:22936908

  10. A 6-month analysis of training-intensity distribution and physiological adaptation in Ironman triathletes.

    PubMed

    Neal, Craig M; Hunter, Angus M; Galloway, Stuart D R

    2011-11-01

    In the present study, we analysed the training-intensity distribution and physiological adaptations over a 6-month period preceding an Ironman triathlon race. Ten athletes (mean ± s: age 43 ± 3 years, mass 78.3 ± 10.3 kg, stature 1.79 ± 0.05 m) participated in the study. The study consisted of three training periods (A, B, C), each of approximately 2 months' duration, and four testing weeks. Testing consisted of incremental tests to exhaustion for swimming, cycling and running, and assessments for anthropometry plus cardiovascular and pulmonary measures. The lactate threshold and the lactate turnpoint were used to demarcate three discipline-specific, exercise-intensity zones. The mean percentage of time spent in zones 1, 2, and 3 was 69 ± 9%, 25 ± 8%, and 6 ± 2% for periods A-C combined. Only modest physiological adaptation occurred throughout the 6-month period, with small to moderate effect sizes at best. Relationships between the training volume/training load and the training-intensity distribution with the changes in key measures of adaptation were weak and probably reflect differences in initial training status. Our results suggest that the effects of intensity distribution are small over short-term training periods and future experimental research is needed to clarify the potential impact of intensity distribution on physiological adaptation.

  11. Proteomic analysis of the adaptation to warming in the Antarctic bacteria Shewanella frigidimarina.

    PubMed

    García-Descalzo, Laura; García-López, Eva; Alcázar, Alberto; Baquero, Fernando; Cid, Cristina

    2014-12-01

    Antarctica is subjected to extremely variable conditions, but the importance of the temperature increase in cold adapted bacteria is still unknown. To study the molecular adaptation to warming of Antarctic bacteria, cultures of Shewanella frigidimarina were incubated at temperatures ranging from 0°C to 30°C, emulating the most extreme conditions that this strain could tolerate. A proteomic approach was developed to identify the soluble proteins obtained from cells growing at 4°C, 20°C and 28°C. The most drastic effect when bacteria were grown at 28°C was the accumulation of heat shock proteins as well as other proteins related to stress, redox homeostasis or protein synthesis and degradation, and the decrease of enzymes and components of the cell envelope. Furthermore, two main responses in the adaptation to warm temperature were detected: the presence of diverse isoforms in some differentially expressed proteins, and the composition of chaperone interaction networks at the limits of growth temperature. The abundance changes of proteins suggest that warming induces a stress situation in S. frigidimarina forcing cells to reorganize their molecular networks as an adaptive response to these environmental conditions.

  12. Understanding the host-adapted state of Citrobacter rodentium by transcriptomic analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Citrobacter rodentium (Cr) is a mouse pathogen that mimics many aspects of enteropathogenic Escherichia coli infections including producing attaching and effacing (A/E) lesions. Host-adapted (HA) Cr cells that are shed at the peak of infection have been reported to be hyperinfective. The exact mecha...

  13. Transcriptome analysis reveals diversified adaptation of Stipa purpurea along a drought gradient on the Tibetan Plateau.

    PubMed

    Yang, Yunqiang; Li, Xiong; Kong, Xiangxiang; Ma, Lan; Hu, Xiangyang; Yang, Yongping

    2015-05-01

    Natural selection drives species adaptations to biotic and abiotic stresses. Species distributed along a moisture gradient, such as Stipa purpurea, a dominant grass in alpine arid and semi-arid meadows on the Tibetan Plateau, provide an opportunity to evaluate the effects of long-term adaptation to differing degrees of drought stress on gene expression. However, the genetic basis of this divergence remains largely unknown. Next-generation sequencing technologies have provided important genome-wide insights on the evolution of organisms for which genomic information is lacking. To understand how S. purpurea responds to drought stress, we selected five populations distributed along the degressive rainfall line on the northwestern Tibetan Plateau that currently present evolutionary acclimation to localized drought pressure at the physiological and biochemical levels and compared their transcriptome responses. In addition, we performed de novo assembly of the S. purpurea transcriptome using short read sequencing technology and successfully assembled 84,298 unigenes from approximately 51 million sequencing reads. We quantified gene expression level to compare their transcriptome responses using mRNA-Seq and identified differentially expressed transcripts that are involved in primary and secondary plant metabolism, plant hormone synthesis, defense responses, and cell wall synthesis. Furthermore, physiological and biochemical evidence supports that abscisic acid (ABA) accumulation and cell wall strengthening derived from the differential transcripts contribute to the tolerance of S. purpurea to drought stress. The mechanisms by which S. purpurea adapts to drought stress provide new insight into how plants ecologically adapt and evolve.

  14. Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida

    SciTech Connect

    Wu X.; van der Lelie D.; Monchy, S.; Taghavi, S.; Zhu, W.; Ramos, J.

    2011-03-01

    Pseudomonas putida is a gram-negative rod-shaped gammaproteobacterium that is found throughout various environments. Members of the species P. putida show a diverse spectrum of metabolic activities, which is indicative of their adaptation to various niches, which includes the ability to live in soils and sediments contaminated with high concentrations of heavy metals and organic contaminants. Pseudomonas putida strains are also found as plant growth-promoting rhizospheric and endophytic bacteria. The genome sequences of several P. putida species have become available and provide a unique tool to study the specific niche adaptation of the various P. putida strains. In this review, we compare the genomes of four P. putida strains: the rhizospheric strain KT2440, the endophytic strain W619, the aromatic hydrocarbon-degrading strain F1 and the manganese-oxidizing strain GB-1. Comparative genomics provided a powerful tool to gain new insights into the adaptation of P. putida to specific lifestyles and environmental niches, and clearly demonstrated that horizontal gene transfer played a key role in this adaptation process, as many of the niche-specific functions were found to be encoded on clearly defined genomic islands.

  15. Acculturation Strategies, Social Support, and Cross-Cultural Adaptation: A Mediation Analysis

    ERIC Educational Resources Information Center

    Ng, Ting Kin; Tsang, Kwok Kuen; Lian, Yi

    2013-01-01

    Previous acculturation research has established the influences of acculturation strategies and social support on cross-cultural adaptation. The present study attempted to elaborate these direct associations by proposing that social support and the use of the integration and marginalization strategies might affect psychological adaptation…

  16. Acoustic and Perceptual Analysis of Speech Adaptation to an Artificial Palate

    ERIC Educational Resources Information Center

    McAuliffe, Megan J.; Robb, Michael P.; Murdoch, Bruce E.

    2007-01-01

    The study investigated adaptation to a standard electropalatographic (EPG) practise palate in a group of eight adults (mean age = 24 years). The participants read the phrase "a CVC" over four sampling conditions: prior to inserting the palate, immediately following insertion of the palate, 45 minutes after palate insertion, and 3 hours after…

  17. Biomolecular Mechanism, Cloning, Sequencing and Analysis of Adaptive Reflection cDNAs and Proteins from Squid

    DTIC Science & Technology

    2010-05-03

    drivers of these adaptive changes in reflectance that we will investigate include electromotive ion fluxes, pH change and exposures to metal ions and...found in L. pealeii. As is the case for the other reflectin proteins (16), Ref-Lp1 and 2 contain a series of conserved subdomains (SDs). Ref-Lp1

  18. Fault Tolerance Analysis of L1 Adaptive Control System for Unmanned Aerial Vehicles

    NASA Astrophysics Data System (ADS)

    Krishnamoorthy, Kiruthika

    Trajectory tracking is a critical element for the better functionality of autonomous vehicles. The main objective of this research study was to implement and analyze L1 adaptive control laws for autonomous flight under normal and upset flight conditions. The West Virginia University (WVU) Unmanned Aerial Vehicle flight simulation environment was used for this purpose. A comparison study between the L1 adaptive controller and a baseline conventional controller, which relies on position, proportional, and integral compensation, has been performed for a reduced size jet aircraft, the WVU YF-22. Special attention was given to the performance of the proposed control laws in the presence of abnormal conditions. The abnormal conditions considered are locked actuators (stabilator, aileron, and rudder) and excessive turbulence. Several levels of abnormal condition severity have been considered. The performance of the control laws was assessed over different-shape commanded trajectories. A set of comprehensive evaluation metrics was defined and used to analyze the performance of autonomous flight control laws in terms of control activity and trajectory tracking errors. The developed L1 adaptive control laws are supported by theoretical stability guarantees. The simulation results show that L1 adaptive output feedback controller achieves better trajectory tracking with lower level of control actuation as compared to the baseline linear controller under nominal and abnormal conditions.

  19. Person Fit Analysis in Computerized Adaptive Testing Using Tests for a Change Point

    ERIC Educational Resources Information Center

    Sinharay, Sandip

    2016-01-01

    Meijer and van Krimpen-Stoop noted that the number of person-fit statistics (PFSs) that have been designed for computerized adaptive tests (CATs) is relatively modest. This article partially addresses that concern by suggesting three new PFSs for CATs. The statistics are based on tests for a change point and can be used to detect an abrupt change…

  20. Adaptive engineering of a hyperthermophilic archaeon on CO and discovering the underlying mechanism by multi-omics analysis

    PubMed Central

    Lee, Seong Hyuk; Kim, Min-Sik; Lee, Jae-Hak; Kim, Tae Wan; Bae, Seung Seob; Lee, Sung-Mok; Jung, Hae Chang; Yang, Tae-Jun; Choi, Ae Ran; Cho, Yong-Jun; Lee, Jung-Hyun; Kwon, Kae Kyoung; Lee, Hyun Sook; Kang, Sung Gyun

    2016-01-01

    The hyperthermophilic archaeon Thermococcus onnurineus NA1 can grow and produce H2 on carbon monoxide (CO) and its H2 production rates have been improved through metabolic engineering. In this study, we applied adaptive evolution to enhance H2 productivity. After over 150 serial transfers onto CO medium, cell density, CO consumption rate and H2 production rate increased. The underlying mechanism for those physiological changes could be explained by using multi-omics approaches including genomic, transcriptomic and epigenomic analyses. A putative transcriptional regulator was newly identified to regulate the expression levels of genes related to CO oxidation. Transcriptome analysis revealed significant changes in the transcript levels of genes belonging to the categories of transcription, translation and energy metabolism. Our study presents the first genome-scale methylation pattern of hyperthermophilic archaea. Adaptive evolution led to highly enhanced H2 productivity at high CO flow rates using synthesis gas produced from coal gasification. PMID:26975345

  1. Adaptive engineering of a hyperthermophilic archaeon on CO and discovering the underlying mechanism by multi-omics analysis.

    PubMed

    Lee, Seong Hyuk; Kim, Min-Sik; Lee, Jae-Hak; Kim, Tae Wan; Bae, Seung Seob; Lee, Sung-Mok; Jung, Hae Chang; Yang, Tae-Jun; Choi, Ae Ran; Cho, Yong-Jun; Lee, Jung-Hyun; Kwon, Kae Kyoung; Lee, Hyun Sook; Kang, Sung Gyun

    2016-03-15

    The hyperthermophilic archaeon Thermococcus onnurineus NA1 can grow and produce H2 on carbon monoxide (CO) and its H2 production rates have been improved through metabolic engineering. In this study, we applied adaptive evolution to enhance H2 productivity. After over 150 serial transfers onto CO medium, cell density, CO consumption rate and H2 production rate increased. The underlying mechanism for those physiological changes could be explained by using multi-omics approaches including genomic, transcriptomic and epigenomic analyses. A putative transcriptional regulator was newly identified to regulate the expression levels of genes related to CO oxidation. Transcriptome analysis revealed significant changes in the transcript levels of genes belonging to the categories of transcription, translation and energy metabolism. Our study presents the first genome-scale methylation pattern of hyperthermophilic archaea. Adaptive evolution led to highly enhanced H2 productivity at high CO flow rates using synthesis gas produced from coal gasification.

  2. Carrageenan analysis. Part 1: Characterisation of the carrageenan test material and stability in swine-adapted infant formula.

    PubMed

    Blakemore, William R; Davis, Steven R; Hroncich, Maggie M; Vurma, Mustafa

    2014-01-01

    A method was developed and validated in support of a 28-day feeding study of swine-adapted infant formula stabilised with carrageenan administered to neonatal piglets. Carrageenan concentrations in the test formulations were 0, 300, 1000 and 2250 mg kg(-1) formula. Extraction of carrageenan from swine-adapted infant formula was achieved by breaking carrageenan-protein cross-linkages using saturated sodium chloride, followed by separation of the non-gelling carrageenan fraction via centrifugation. The extraction of carrageenan from formula was successful with respect to consistent recovery of the non-gelling carrageenan fraction from both test and control formula samples. Molecular weight analysis (Mw) of the recovered carrageenan fractions from the test and control formula samples confirmed that the carrageenan used to manufacture the formula was not degraded during the infant formula production process and subsequent storage for 4 months covering the 28-day piglet dietary feeding study. Carrageenan has excellent stability in infant formulations.

  3. An Empirical Analysis of Farm Adaptation Response to Water Security Using a Natural Policy Experiment

    NASA Astrophysics Data System (ADS)

    Brady, M.

    2014-12-01

    The capacity of farm-level adaptation to mitigate the impacts of climate change in arid regions dominated by irrigated agriculture fed by snowpack is a critical challenge for developing accurate integrated engineering-economic modeling tools. Economic optimization models provide a valuable benchmark for the theoretical limit of adaptation given a set of clear objectives, conditions, and constraints. However, a major limitation to specifying tractable and accurate models is the large number of potential adaptation strategies that can be taken. There is a need for more empirical research that reveals preferred adaptation strategies in a way that identifies causal relationships. This research seeks to add to the empirical literature on adaptation by exploiting what in the econometric literature is called a "natural experiment" where a policy has isapplied to one group but not another in a way that is random relative to the variables of interest so as to reduce problems of bias in coefficient estimates caused by unobserved heterogeneity. The region of study is the Yakima Basin in Washington State which is a highly diverse region in terms of crop and irrigation technology. This creates significant complication for modeling adaptation since farmers have a wide array of choices including changing cropping patterns and irrigation technologies. Other strategies including water trading and deficit irrigation. Two irrigation districts in the Yakima Basin, Roza and Sunnyside, are adjacent to each other and are nearly identical in growing conditions. The difference is that Roza is severely curtailed during droughts while Sunnyside is not. With the availability of detailed field level data on cropping patterns, irrigation technologies, and land ownership this presents an opportunity to identify the effect of water security risk on farm-level decision making. Preliminary results show that after controlling for other features, a field in Roza is 5% more likely to have an efficient

  4. Finite Element Analysis of Adaptive-Stiffening and Shape-Control SMA Hybrid Composites

    NASA Technical Reports Server (NTRS)

    Gao, Xiu-Jie; Turner, Travis L.; Burton, Deborah; Brinson, L. Catherine

    2005-01-01

    The usage of shape memory materials has extended rapidly to many fields, including medical devices, actuators, composites, structures and MEMS devices. For these various applications, shape memory alloys (SMAs) are available in various forms: bulk, wire, ribbon, thin film, and porous. In this work, the focus is on SMA hybrid composites with adaptive-stiffening or morphing functions. These composites are created by using SMA ribbons or wires embedded in a polymeric based composite panel/beam. Adaptive stiffening or morphing is activated via selective resistance heating or uniform thermal loads. To simulate the thermomechanical behavior of these composites, a SMA model was implemented using ABAQUS user element interface and finite element simulations of the systems were studied. Several examples are presented which show that the implemented model can be a very useful design and simulation tool for SMA hybrid composites.

  5. Design and Analysis of Schemes for Adapting Migration Intervals in Parallel Evolutionary Algorithms.

    PubMed

    Mambrini, Andrea; Sudholt, Dirk

    2015-01-01

    The migration interval is one of the fundamental parameters governing the dynamic behaviour of island models. Yet, there is little understanding on how this parameter affects performance, and how to optimally set it given a problem in hand. We propose schemes for adapting the migration interval according to whether fitness improvements have been found. As long as no improvement is found, the migration interval is increased to minimise communication. Once the best fitness has improved, the migration interval is decreased to spread new best solutions more quickly. We provide a method for obtaining upper bounds on the expected running time and the communication effort, defined as the expected number of migrants sent. Example applications of this method to common example functions show that our adaptive schemes are able to compete with, or even outperform, the optimal fixed choice of the migration interval, with regard to running time and communication effort.

  6. Design and Performance Analysis of Adaptive Optical Telescopes Using Laser Guide Stars

    DTIC Science & Technology

    1989-01-01

    They subsequently verified their analytical expressions by predicting the brightness of an experimental guide star produced at Mauna Kea Observatory .4...of 1987 at the University of Hawaii’s Mauna Kea Observatory . The laser spots were generated by the University of Illinois monostatic lidar system and...at mauna kea observatory for adaptive imaging in astronomy," Nature, vol. 328, pp. 229-231, 1987. 5. C. S. Gardner, B. M. Welsh, and L. A. Thompson

  7. Maternal migration and child health: An analysis of disruption and adaptation processes in Benin

    PubMed Central

    Smith-Greenaway, Emily; Madhavan, Sangeetha

    2016-01-01

    Children of migrant mothers have lower vaccination rates compared to their peers with non-migrant mothers in low-income countries. Explanations for this finding are typically grounded in the disruption and adaptation perspectives of migration. Researchers argue that migration is a disruptive process that interferes with women’s economic well-being and social networks, and ultimately their health-seeking behaviors. With time, however, migrant women adapt to their new settings, and their health behaviors improve. Despite prominence in the literature, no research tests the salience of these perspectives to the relationship between maternal migration and child vaccination. We innovatively leverage Demographic and Health Survey data to test the extent to which disruption and adaptation processes underlie the relationship between maternal migration and child vaccination in the context of Benin—a West African country where migration is common and child vaccination rates have declined in recent years. By disaggregating children of migrants according to whether they were born before or after their mother’s migration, we confirm that migration does not lower children’s vaccination rates in Benin. In fact, children born after migration enjoy a higher likelihood of vaccination, whereas their peers born in the community from which their mother eventually migrates are less likely to be vaccinated. Although we find no support for the disruption perspective of migration, we do find evidence of adaptation: children born after migration have an increased likelihood of vaccination the longer their mother resides in the destination community prior to their birth. PMID:26463540

  8. SU-E-J-80: A Comparative Analysis of MIM and Pinnacle Software for Adaptive Planning

    SciTech Connect

    Stanford, J; Duggar, W; Morris, B; Yang, C

    2015-06-15

    Purpose: IMRT treatment is often administered with image guidance and small PTV margins. Change in body habitus such as weight loss and tumor response during the course of a treatment could be significant, thus warranting re-simulation and re-planning. Adaptive planning is challenging and places significant burden on the staff, as such some commercial vendors are now offering adaptive planning software to stream line the process of re-planning and dose accumulation between different CT data set. The purpose of this abstract is to compare the adaptive planning tools between Pinnacle version 9.8 and MIM 6.4 software. Methods: Head and Neck cases of previously treated patients that experienced anatomical changes during the course of their treatment were chosen for evaluation. The new CT data set from the re-simulation was imported to Pinnacle and MIM software. The dynamic planning tool in pinnacle was used to calculate the old plan with fixed MU setting on the new CT data. In MIM, the old CT was registered to the new data set, followed by a dose transformation to the new CT. The dose distribution to the PTV and critical structures from each software were analyzed and compared. Results: 9% difference was observed between the Global maximum doses reported by both software. Mean doses to organs at risk and PTV’s were within 6 % however pinnacle showed greater difference in PTV coverage change. Conclusion: MIM software adaptive planning corrects for geometrical changes without consideration for the effect of radiological path length on dose distribution; however Pinnacle corrects for both geometric and radiological effect on the dose distribution. Pinnacle gives a better estimate of the dosimetric impact due to anatomical changes.

  9. Transcriptomic Analysis Reveals Selective Metabolic Adaptation of Streptococcus suis to Porcine Blood and Cerebrospinal Fluid

    PubMed Central

    Koczula, Anna; Jarek, Michael; Visscher, Christian; Valentin-Weigand, Peter; Goethe, Ralph; Willenborg, Jörg

    2017-01-01

    Streptococcus suis is a zoonotic pathogen that can cause severe pathologies such as septicemia and meningitis in its natural porcine host as well as in humans. Establishment of disease requires not only virulence of the infecting strain but also an appropriate metabolic activity of the pathogen in its host environment. However, it is yet largely unknown how the streptococcal metabolism adapts to the different host niches encountered during infection. Our previous isotopologue profiling studies on S. suis grown in porcine blood and cerebrospinal fluid (CSF) revealed conserved activities of central carbon metabolism in both body fluids. On the other hand, they suggested differences in the de novo amino acid biosynthesis. This prompted us to further dissect S. suis adaptation to porcine blood and CSF by RNA deep sequencing (RNA-seq). In blood, the majority of differentially expressed genes were associated with transport of alternative carbohydrate sources and the carbohydrate metabolism (pentose phosphate pathway, glycogen metabolism). In CSF, predominantly genes involved in the biosynthesis of branched-chain and aromatic amino acids were differentially expressed. Especially, isoleucine biosynthesis seems to be of major importance for S. suis in CSF because several related biosynthetic genes were more highly expressed. In conclusion, our data revealed niche-specific metabolic gene activity which emphasizes a selective adaptation of S. suis to host environments. PMID:28212285

  10. Global Microarray Analysis of Alkaliphilic Halotolerant Bacterium Bacillus sp. N16-5 Salt Stress Adaptation.

    PubMed

    Yin, Liang; Xue, Yanfen; Ma, Yanhe

    2015-01-01

    The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 is often exposed to salt stress in its natural habitats. In this study, we used one-colour microarrays to investigate adaptive responses of Bacillus sp. N16-5 transcriptome to long-term growth at different salinity levels (0%, 2%, 8%, and 15% NaCl) and to a sudden salt increase from 0% to 8% NaCl. The common strategies used by bacteria to survive and grow at high salt conditions, such as K+ uptake, Na+ efflux, and the accumulation of organic compatible solutes (glycine betaine and ectoine), were observed in Bacillus sp. N16-5. The genes of SigB regulon involved in general stress responses and chaperone-encoding genes were also induced by high salt concentration. Moreover, the genes regulating swarming ability and the composition of the cytoplasmic membrane and cell wall were also differentially expressed. The genes involved in iron uptake were down-regulated, whereas the iron homeostasis regulator Fur was up-regulated, suggesting that Fur may play a role in the salt adaption of Bacillus sp. N16-5. In summary, we present a comprehensive gene expression profiling of alkaliphilic Bacillus sp. N16-5 cells exposed to high salt stress, which would help elucidate the mechanisms underlying alkaliphilic Bacillus spp. survival in and adaptation to salt stress.

  11. LEO Download Capacity Analysis for a Network of Adaptive Array Ground Stations

    NASA Technical Reports Server (NTRS)

    Ingram, Mary Ann; Barott, William C.; Popovic, Zoya; Rondineau, Sebastien; Langley, John; Romanofsky, Robert; Lee, Richard Q.; Miranda, Felix; Steffes, Paul; Mandl, Dan

    2005-01-01

    To lower costs and reduce latency, a network of adaptive array ground stations, distributed across the United States, is considered for the downlink of a polar-orbiting low earth orbiting (LEO) satellite. Assuming the X-band 105 Mbps transmitter of NASA s Earth Observing 1 (EO-1) satellite with a simple line-of-sight propagation model, the average daily download capacity in bits for a network of adaptive array ground stations is compared to that of a single 11 m dish in Poker Flats, Alaska. Each adaptive array ground station is assumed to have multiple steerable antennas, either mechanically steered dishes or phased arrays that are mechanically steered in azimuth and electronically steered in elevation. Phased array technologies that are being developed for this application are the space-fed lens (SFL) and the reflectarray. Optimization of the different boresight directions of the phased arrays within a ground station is shown to significantly increase capacity; for example, this optimization quadruples the capacity for a ground station with eight SFLs. Several networks comprising only two to three ground stations are shown to meet or exceed the capacity of the big dish, Cutting the data rate by half, which saves modem costs and increases the coverage area of each ground station, is shown to increase the average daily capacity of the network for some configurations.

  12. Adaptive Estimation of Active Contour Parameters Using Convolutional Neural Networks and Texture Analysis.

    PubMed

    Hoogi, Assaf; Subramaniam, Arjun; Veerapaneni, Rishi; Rubin, Daniel

    2016-11-11

    In this paper, we propose a generalization of the level set segmentation approach by supplying a novel method for adaptive estimation of active contour parameters. The presented segmentation method is fully automatic once the lesion has been detected. First, the location of the level set contour relative to the lesion is estimated using a convolutional neural network (CNN). The CNN has two convolutional layers for feature extraction, which lead into dense layers for classification. Second, the output CNN probabilities are then used to adaptively calculate the parameters of the active contour functional during the segmentation process. Finally, the adaptive window size surrounding each contour point is re-estimated by an iterative process that considers lesion size and spatial texture. We demonstrate the capabilities of our method on a dataset of 164 MRI and 112 CT images of liver lesions that includes low contrast and heterogeneous lesions as well as noisy images. To illustrate the strength of our method, we evaluated it against state of the art CNNbased and active contour techniques. For all cases, our method, as assessed by Dice similarity coefficients, performed significantly better than currently available methods. An average Dice improvement of 0.27 was found across the entire dataset over all comparisons. We also analyzed two challenging subsets of lesions and obtained a significant Dice improvement of ����.�������� with our method (p < 0.001, Wilcoxon).

  13. Adaptive Estimation of Active Contour Parameters Using Convolutional Neural Networks and Texture Analysis.

    PubMed

    Hoogi, Assaf; Subramaniam, Arjun; Veerapaneni, Rishi; Rubin, Daniel

    2016-11-11

    In this paper, we propose a generalization of the level set segmentation approach by supplying a novel method for adaptive estimation of active contour parameters. The presented segmentation method is fully automatic once the lesion has been detected. First, the location of the level set contour relative to the lesion is estimated using a convolutional neural network (CNN). The CNN has two convolutional layers for feature extraction, which lead into dense layers for classification. Second, the output CNN probabilities are then used to adaptively calculate the parameters of the active contour functional during the segmentation process. Finally, the adaptive window size surrounding each contour point is re-estimated by an iterative process that considers lesion size and spatial texture. We demonstrate the capabilities of our method on a dataset of 164 MRI and 112 CT images of liver lesions that includes low contrast and heterogeneous lesions as well as noisy images. To illustrate the strength of our method, we evaluated it against state of the art CNNbased and active contour techniques. For all cases, our method, as assessed by Dice similarity coefficients, performed significantly better than currently available methods. An average Dice improvement of 0.27 was found across the entire dataset over all comparisons. We also analyzed two challenging subsets of lesions and obtained a significant Dice improvement of 0.24 with our method (p < 0.001, Wilcoxon).

  14. Communication Range Dynamics and Performance Analysis for a Self-Adaptive Transmission Power Controller.

    PubMed

    Lucas Martínez, Néstor; Martínez Ortega, José-Fernán; Hernández Díaz, Vicente; Del Toro Matamoros, Raúl M

    2016-05-12

    The deployment of the nodes in a Wireless Sensor and Actuator Network (WSAN) is typically restricted by the sensing and acting coverage. This implies that the locations of the nodes may be, and usually are, not optimal from the point of view of the radio communication. Additionally, when the transmission power is tuned for those locations, there are other unpredictable factors that can cause connectivity failures, like interferences, signal fading due to passing objects and, of course, radio irregularities. A control-based self-adaptive system is a typical solution to improve the energy consumption while keeping good connectivity. In this paper, we explore how the communication range for each node evolves along the iterations of an energy saving self-adaptive transmission power controller when using different parameter sets in an outdoor scenario, providing a WSAN that automatically adapts to surrounding changes keeping good connectivity. The results obtained in this paper show how the parameters with the best performance keep a k-connected network, where k is in the range of the desired node degree plus or minus a specified tolerance value.

  15. Study of adaptation to altered gravity through systems analysis of motor control

    NASA Astrophysics Data System (ADS)

    Fox, R. A.; Daunton, N. G.; Corcoran, M. L.

    Maintenance of posture and production of functional, coordinated movement demand integration of sensory feedback with spinal and supra-spinal circuitry to produce adaptive motor control in altered gravity (G). To investigate neuroplastic processes leading to optimal performance in altered G we have studied motor control in adult rats using a battery of motor function tests following chronic exposure to various treatments (hyper-G, hindlimb suspension, chemical distruction of hair cells, space flight). These treatments differentially affect muscle fibers, vestibular receptors, and behavioral compensations and, in consequence, differentially disrupt air righting, swimming, posture and gait. The time-course of recovery from these disruptions varies depending on the function tested and the duration and type of treatment. These studies, with others (e.g., D'Amelio et al. in this volume), indicate that adaptation to altered gravity involves alterations in multiple sensory-motor systems that change at different rates. We propose that the use of parallel studies under different altered G conditions will most efficiently lead to an understanding of the modifications in central (neural) and peripheral (sensory and neuromuscular) systems that underlie sensory-motor adaptation in active, intact individuals.

  16. Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution

    PubMed Central

    Suzuki, Haruo; Lefébure, Tristan; Hubisz, Melissa Jane; Pavinski Bitar, Paulina; Lang, Ping; Siepel, Adam; Stanhope, Michael J.

    2011-01-01

    Comparative genomics of closely related bacterial species with different pathogenesis and host preference can provide a means of identifying the specifics of adaptive differences. Streptococcus dysgalactiae (SD) is comprised of two subspecies: S. dysgalactiae subsp. equisimilis is both a human commensal organism and a human pathogen, and S. dysgalactiae subsp. dysgalactiae is strictly an animal pathogen. Here, we present complete genome sequences for both taxa, with analyses involving other species of Streptococcus but focusing on adaptation in the SD species group. We found little evidence for enrichment in biochemical categories of genes carried by each SD strain, however, differences in the virulence gene repertoire were apparent. Some of the differences could be ascribed to prophage and integrative conjugative elements. We identified approximately 9% of the nonrecombinant core genome to be under positive selection, some of which involved known virulence factors in other bacteria. Analyses of proteomes by pooling data across genes, by biochemical category, clade, or branch, provided evidence for increased rates of evolution in several gene categories, as well as external branches of the tree. Promoters were primarily evolving under purifying selection but with certain categories of genes evolving faster. Many of these fast-evolving categories were the same as those associated with rapid evolution in proteins. Overall, these results suggest that adaptation to changing environments and new hosts in the SD species group has involved the acquisition of key virulence genes along with selection of orthologous protein-coding loci and operon promoters. PMID:21282711

  17. Communication Range Dynamics and Performance Analysis for a Self-Adaptive Transmission Power Controller †

    PubMed Central

    Lucas Martínez, Néstor; Martínez Ortega, José-Fernán; Hernández Díaz, Vicente; del Toro Matamoros, Raúl M.

    2016-01-01

    The deployment of the nodes in a Wireless Sensor and Actuator Network (WSAN) is typically restricted by the sensing and acting coverage. This implies that the locations of the nodes may be, and usually are, not optimal from the point of view of the radio communication. Additionally, when the transmission power is tuned for those locations, there are other unpredictable factors that can cause connectivity failures, like interferences, signal fading due to passing objects and, of course, radio irregularities. A control-based self-adaptive system is a typical solution to improve the energy consumption while keeping good connectivity. In this paper, we explore how the communication range for each node evolves along the iterations of an energy saving self-adaptive transmission power controller when using different parameter sets in an outdoor scenario, providing a WSAN that automatically adapts to surrounding changes keeping good connectivity. The results obtained in this paper show how the parameters with the best performance keep a k-connected network, where k is in the range of the desired node degree plus or minus a specified tolerance value. PMID:27187397

  18. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

    PubMed Central

    Tian, Xinpeng; Zhang, Zhewen; Yang, Tingting; Chen, Meili; Li, Jie; Chen, Fei; Yang, Jin; Li, Wenjie; Zhang, Bing; Zhang, Zhang; Wu, Jiayan; Zhang, Changsheng; Long, Lijuan; Xiao, Jingfa

    2016-01-01

    Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea’s genetic data sources. PMID:27446038

  19. Partial island submergence and speciation in an adaptive radiation: a multilocus analysis of the Cuban green anoles.

    PubMed Central

    Glor, Richard E.; Gifford, Matthew E.; Larson, Allan; Losos, Jonathan B.; Schettino, Lourdes Rodríguez; Chamizo Lara, Ada R.; Jackman, Todd R.

    2004-01-01

    Sympatric speciation is often proposed to account for species-rich adaptive radiations within lakes or islands, where barriers to gene flow or dispersal may be lacking. However, allopatric speciation may also occur in such situations, especially when ranges are fragmented by fluctuating water levels. We test the hypothesis that Miocene fragmentation of Cuba into three palaeo-archipelagos accompanied species-level divergence in the adaptive radiation of West Indian Anolis lizards. Analysis of morphology, mitochondrial DNA (mt DNA) and nuclear DNA in the Cuban green anoles (carolinensis subgroup) strongly supports three pre dictions made by this hypothesis. First, three geographical sets of populations, whose ranges correspond with palaeo-archipelago boundaries, are distinct and warrant recognition as independent evolutionary lineages or species. Coalescence of nuclear sequence fragments sampled from these species and the large divergences observed between their mtDNA haplotypes suggest separation prior to the subsequent unification of Cuba ca. 5 Myr ago. Second, molecular phylogenetic relationships among these species reflect historical geographical relationships rather than morphological similarity. Third, all three species remain distinct despite extensive geographical contact subsequent to island unification, occasional hybridization and introgression of mtDNA haplotypes. Allopatric speciation initiated during partial island submergence may play an important role in speciation during the adaptive radiation of Anolis lizards. PMID:15539351

  20. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level.

    PubMed

    Tian, Xinpeng; Zhang, Zhewen; Yang, Tingting; Chen, Meili; Li, Jie; Chen, Fei; Yang, Jin; Li, Wenjie; Zhang, Bing; Zhang, Zhang; Wu, Jiayan; Zhang, Changsheng; Long, Lijuan; Xiao, Jingfa

    2016-01-01

    Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea's genetic data sources.

  1. Comparing model-based adaptive LMS filters and a model-free hysteresis loop analysis method for structural health monitoring

    NASA Astrophysics Data System (ADS)

    Zhou, Cong; Chase, J. Geoffrey; Rodgers, Geoffrey W.; Xu, Chao

    2017-02-01

    The model-free hysteresis loop analysis (HLA) method for structural health monitoring (SHM) has significant advantages over the traditional model-based SHM methods that require a suitable baseline model to represent the actual system response. This paper provides a unique validation against both an experimental reinforced concrete (RC) building and a calibrated numerical model to delineate the capability of the model-free HLA method and the adaptive least mean squares (LMS) model-based method in detecting, localizing and quantifying damage that may not be visible, observable in overall structural response. Results clearly show the model-free HLA method is capable of adapting to changes in how structures transfer load or demand across structural elements over time and multiple events of different size. However, the adaptive LMS model-based method presented an image of greater spread of lesser damage over time and story when the baseline model is not well defined. Finally, the two algorithms are tested over a simpler hysteretic behaviour typical steel structure to quantify the impact of model mismatch between the baseline model used for identification and the actual response. The overall results highlight the need for model-based methods to have an appropriate model that can capture the observed response, in order to yield accurate results, even in small events where the structure remains linear.

  2. Adaptability and genotypic stability of Coffea arabica genotypes based on REML/BLUP analysis in Rio de Janeiro State, Brazil.

    PubMed

    Rodrigues, W P; Vieira, H D; Barbosa, D H S G; Souza Filho, G R; Candido, L S

    2013-07-15

    Biannuality in coffee culture causes temporal variability in plant productivity. Consequently, it is essential to evaluate genotypes during various crop years to ensure selection of productive and stable genotypes. We evaluated the effectiveness of simultaneous selection of coffee genotypes along harvests, based on productivity, stability, and adaptability, via mixed models, for indication of varieties suitable for Rio de Janeiro State. We evaluated 25 genotypes during 4 crop seasons (2009-2012), in a randomized block design with 5 replications. The ranking of genotypes was obtained on the basis of the adaptability and temporal stability methods (harmonic average of genetic values, relative performance of genetic values, and harmonic mean of the relative performance of the genetic values), obtained via restricted maximum likelihood/best linear unbiased procedure analysis. The selection accuracy (0.8717), associated with the high magnitude of mean heritability, indicate good reliability and prospects for success in the indication of agronomically superior genotypes. There was little variation in the ordering of genotypes among the environments, indicating low influence of harvests in the performance of the genotypes. Five of the 25 genotypes were superior and could be recommended for planting in the northwestern region of Rio de Janeiro State, due to high predicted productivity and stability. We recommend that these methodologies for evaluation of productivity, stability, and adaptability be included in the selection criteria for recommendation of genotypes for commercial plantings.

  3. Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas

    PubMed Central

    Gorkhali, Neena Amatya; Dong, Kunzhe; Yang, Min; Song, Shen; Kader, Adiljian; Shrestha, Bhola Shankar; He, Xiaohong; Zhao, Qianjun; Pu, Yabin; Li, Xiangchen; Kijas, James; Guan, Weijun; Han, Jianlin; Jiang, Lin; Ma, Yuehui

    2016-01-01

    Sheep has successfully adapted to the extreme high-altitude Himalayan region. To identify genes underlying such adaptation, we genotyped genome-wide single nucleotide polymorphisms (SNPs) of four major sheep breeds living at different altitudes in Nepal and downloaded SNP array data from additional Asian and Middle East breeds. Using a di value-based genomic comparison between four high-altitude and eight lowland Asian breeds, we discovered the most differentiated variants at the locus of FGF-7 (Keratinocyte growth factor-7), which was previously reported as a good protective candidate for pulmonary injuries. We further found a SNP upstream of FGF-7 that appears to contribute to the divergence signature. First, the SNP occurred at an extremely conserved site. Second, the SNP showed an increasing allele frequency with the elevated altitude in Nepalese sheep. Third, the electrophoretic mobility shift assays (EMSA) analysis using human lung cancer cells revealed the allele-specific DNA-protein interactions. We thus hypothesized that FGF-7 gene potentially enhances lung function by regulating its expression level in high-altitude sheep through altering its binding of specific transcription factors. Especially, FGF-7 gene was not implicated in previous studies of other high-altitude species, suggesting a potential novel adaptive mechanism to high altitude in sheep at the Himalayas. PMID:27444145

  4. Comprehensive Transcriptome Analysis of Six Catfish Species from an Altitude Gradient Reveals Adaptive Evolution in Tibetan Fishes

    PubMed Central

    Ma, Xiuhui; Dai, Wei; Kang, Jingliang; Yang, Liandong; He, Shunping

    2015-01-01

    Glyptosternoid fishes (Siluriformes), one of the three broad fish lineages (the two other are schizothoracines and Triplophysa), have a limited distribution in the rivers in the Tibetan Plateau and peripheral regions. To investigate the genetic mechanisms underlying adaptation to the Tibetan Plateau in several fish species from gradient altitudes, a total of 20,659,183–37,166,756 sequence reads from six species of catfish were generated by Illumina sequencing, resulting in six assemblies. Analysis of the 1,656 orthologs among the six assembled catfish unigene sets provided consistent evidence for genome-wide accelerated evolution in the three glyptosternoid lineages living at high altitudes. A large number of genes refer to functional categories related to hypoxia and energy metabolism exhibited rapid evolution in the glyptosternoid lineages relative to yellowhead catfish living in plains areas. Genes showing signatures of rapid evolution and positive selection in the glyptosternoid lineages were also enriched in functions associated with energy metabolism and hypoxia. Our analyses provide novel insights into highland adaptation in fishes and can serve as a foundation for future studies aiming to identify candidate genes underlying the genetic basis of adaptation in Tibetan fishes. PMID:26564948

  5. Structural Insight into and Mutational Analysis of Family 11 Xylanases: Implications for Mechanisms of Higher pH Catalytic Adaptation

    PubMed Central

    Bai, Wenqin; Zhou, Cheng; Zhao, Yueju; Wang, Qinhong; Ma, Yanhe

    2015-01-01

    To understand the molecular basis of higher pH catalytic adaptation of family 11 xylanases, we compared the structures of alkaline, neutral, and acidic active xylanases and analyzed mutants of xylanase Xyn11A-LC from alkalophilic Bacillus sp. SN5. It was revealed that alkaline active xylanases have increased charged residue content, an increased ratio of negatively to positively charged residues, and decreased Ser, Thr, and Tyr residue content relative to non-alkaline active counterparts. Between strands β6 and β7, alkaline xylanases substitute an α-helix for a coil or turn found in their non-alkaline counterparts. Compared with non-alkaline xylanases, alkaline active enzymes have an inserted stretch of seven amino acids rich in charged residues, which may be beneficial for xylanase function in alkaline conditions. Positively charged residues on the molecular surface and ionic bonds may play important roles in higher pH catalytic adaptation of family 11 xylanases. By structure comparison, sequence alignment and mutational analysis, six amino acids (Glu16, Trp18, Asn44, Leu46, Arg48, and Ser187, numbering based on Xyn11A-LC) adjacent to the acid/base catalyst were found to be responsible for xylanase function in higher pH conditions. Our results will contribute to understanding the molecular mechanisms of higher pH catalytic adaptation in family 11 xylanases and engineering xylanases to suit industrial applications. PMID:26161643

  6. Genomic, Transcriptomic, and Proteomic Analysis Provide Insights Into the Cold Adaptation Mechanism of the Obligate Psychrophilic Fungus Mrakia psychrophila

    PubMed Central

    Su, Yao; Jiang, Xianzhi; Wu, Wenping; Wang, Manman; Hamid, M. Imran; Xiang, Meichun; Liu, Xingzhong

    2016-01-01

    Mrakia psychrophila is an obligate psychrophilic fungus. The cold adaptation mechanism of psychrophilic fungi remains unknown. Comparative genomics analysis indicated that M. psychrophila had a specific codon usage preference, especially for codons of Gly and Arg and its major facilitator superfamily (MFS) transporter gene family was expanded. Transcriptomic analysis revealed that genes involved in ribosome and energy metabolism were upregulated at 4°, while genes involved in unfolded protein binding, protein processing in the endoplasmic reticulum, proteasome, spliceosome, and mRNA surveillance were upregulated at 20°. In addition, genes related to unfolded protein binding were alternatively spliced. Consistent with other psychrophiles, desaturase and glycerol 3-phosphate dehydrogenase, which are involved in biosynthesis of unsaturated fatty acid and glycerol respectively, were upregulated at 4°. Cold adaptation of M. psychrophila is mediated by synthesizing unsaturated fatty acids to maintain membrane fluidity and accumulating glycerol as a cryoprotectant. The proteomic analysis indicated that the correlations between the dynamic patterns between transcript level changes and protein level changes for some pathways were positive at 4°, but negative at 20°. The death of M. psychrophila above 20° might be caused by an unfolded protein response. PMID:27633791

  7. The Influence of Drivers and Barriers on Urban Adaptation and Mitigation Plans-An Empirical Analysis of European Cities.

    PubMed

    Reckien, Diana; Flacke, Johannes; Olazabal, Marta; Heidrich, Oliver

    2015-01-01

    Cities are recognised as key players in global adaptation and mitigation efforts because the majority of people live in cities. However, in Europe, which is highly urbanized and one of the most advanced regions in terms of environmental policies, there is considerable diversity in the regional distribution, ambition and scope of climate change responses. This paper explores potential factors contributing to such diversity in 200 large and medium-sized cities across 11 European countries. We statistically investigate institutional, socio-economic, environmental and vulnerability characteristics of cities as potential drivers of or barriers to the development of urban climate change plans. Our results show that factors such as membership of climate networks, population size, GDP per capita and adaptive capacity act as drivers of mitigation and adaptation plans. By contrast, factors such as the unemployment rate, warmer summers, proximity to the coast and projected exposure to future climate impacts act as barriers. We see that, overall, it is predominantly large and prosperous cities that engage in climate planning, while vulnerable cities and those at risk of severe climate impacts in the future are less active. Our analysis suggests that climate change planning in European cities is not proactive, i.e. not significantly influenced by anticipated future impacts. Instead, we found that the current adaptive capacity of a city significantly relates to climate planning. Along with the need to further explore these relations, we see a need for more economic and institutional support for smaller and less resourceful cities and those at high risk from climate change impacts in the future.

  8. The Influence of Drivers and Barriers on Urban Adaptation and Mitigation Plans—An Empirical Analysis of European Cities

    PubMed Central

    Reckien, Diana; Flacke, Johannes

    2015-01-01

    Cities are recognised as key players in global adaptation and mitigation efforts because the majority of people live in cities. However, in Europe, which is highly urbanized and one of the most advanced regions in terms of environmental policies, there is considerable diversity in the regional distribution, ambition and scope of climate change responses. This paper explores potential factors contributing to such diversity in 200 large and medium-sized cities across 11 European countries. We statistically investigate institutional, socio-economic, environmental and vulnerability characteristics of cities as potential drivers of or barriers to the development of urban climate change plans. Our results show that factors such as membership of climate networks, population size, GDP per capita and adaptive capacity act as drivers of mitigation and adaptation plans. By contrast, factors such as the unemployment rate, warmer summers, proximity to the coast and projected exposure to future climate impacts act as barriers. We see that, overall, it is predominantly large and prosperous cities that engage in climate planning, while vulnerable cities and those at risk of severe climate impacts in the future are less active. Our analysis suggests that climate change planning in European cities is not proactive, i.e. not significantly influenced by anticipated future impacts. Instead, we found that the current adaptive capacity of a city significantly relates to climate planning. Along with the need to further explore these relations, we see a need for more economic and institutional support for smaller and less resourceful cities and those at high risk from climate change impacts in the future. PMID:26317420

  9. Adaptation and transcriptome analysis of Aureobasidium pullulans in corncob hydrolysate for increased inhibitor tolerance to malic acid production.

    PubMed

    Zou, Xiang; Wang, Yongkang; Tu, Guangwei; Zan, Zhanquan; Wu, Xiaoyan

    2015-01-01

    Malic acid is a dicarboxylic acid widely used in the food industry, and is also a potential C4 platform chemical. Corncob is a low-cost renewable feedstock from agricultural industry. However, side-reaction products (furfural, 5-hydroxymethylfurfural (HMF), formic acid, and acetic acid) that severely hinder fermentation are formed during corncob pretreatment. The process for producing malic acid from a hydrolysate of corncob was investigated with a polymalic acid (PMA)-producing Aureobasidium pullulans strain. Under the optimal hydrolysate sugar concentration 110 g/L, A. pullulans was further adapted in an aerobic fibrous bed bioreactor (AFBB) by gradually increasing the sugar concentration of hydrolysate. After nine batches of fermentation, the production and productivity of malic acid reached 38.6 g/L and 0.4 g/L h, respectively, which was higher than that in the first batch (27.6 g/L and 0.29 g/L h, respectively). The adapted strain could grow under the stress of 0.5 g/L furfural, 3 g/L HMF, 2g/L acetic acid, and 0.5 g/L formic acid, whereas the wild type did not. Transcriptome analysis revealed that the differentially expressed genes were related to carbohydrate transport and metabolism, lipid transport and metabolism, signal transduction mechanism, redox metabolism, and energy production and conversion under 0.5 g/L furfural and 3 g/L HMF stress conditions. In total, 42 genes in the adapted strain were upregulated by 15-fold or more, and qRT-PCR also confirmed that the expression levels of key genes (i.e. SIR, GSS, CYS, and GSR) involved in sulfur assimilation pathway were upregulated by over 10-fold in adapted strain for cellular protection against oxidative stress.

  10. Adaptation and Transcriptome Analysis of Aureobasidium pullulans in Corncob Hydrolysate for Increased Inhibitor Tolerance to Malic Acid Production

    PubMed Central

    Zou, Xiang; Wang, Yongkang; Tu, Guangwei; Zan, Zhanquan; Wu, Xiaoyan

    2015-01-01

    Malic acid is a dicarboxylic acid widely used in the food industry, and is also a potential C4 platform chemical. Corncob is a low-cost renewable feedstock from agricultural industry. However, side-reaction products (furfural, 5-hydroxymethylfurfural (HMF), formic acid, and acetic acid) that severely hinder fermentation are formed during corncob pretreatment. The process for producing malic acid from a hydrolysate of corncob was investigated with a polymalic acid (PMA)-producing Aureobasidium pullulans strain. Under the optimal hydrolysate sugar concentration 110 g/L, A. pullulans was further adapted in an aerobic fibrous bed bioreactor (AFBB) by gradually increasing the sugar concentration of hydrolysate. After nine batches of fermentation, the production and productivity of malic acid reached 38.6 g/L and 0.4 g/L h, respectively, which was higher than that in the first batch (27.6 g/L and 0.29 g/L h, respectively). The adapted strain could grow under the stress of 0.5 g/L furfural, 3 g/L HMF, 2g/L acetic acid, and 0.5 g/L formic acid, whereas the wild type did not. Transcriptome analysis revealed that the differentially expressed genes were related to carbohydrate transport and metabolism, lipid transport and metabolism, signal transduction mechanism, redox metabolism, and energy production and conversion under 0.5 g/L furfural and 3 g/L HMF stress conditions. In total, 42 genes in the adapted strain were upregulated by 15-fold or more, and qRT-PCR also confirmed that the expression levels of key genes (i.e. SIR, GSS, CYS, and GSR) involved in sulfur assimilation pathway were upregulated by over 10-fold in adapted strain for cellular protection against oxidative stress. PMID:25793624

  11. Resilience through adaptation

    PubMed Central

    van Voorn, George A. K.; Ligtenberg, Arend; Molenaar, Jaap

    2017-01-01

    Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS). Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations with agent-based models (ABMs) provide a helpful tool. However, the value of ABMs for studying adaptation depends on the availability of methodologies for sensitivity analysis that can quantify resilience and adaptation in ABMs. In this paper we propose a sensitivity analysis methodology that is based on comparing time-dependent probability density functions of output of ABMs with and without agent adaptation. The differences between the probability density functions are quantified by the so-called earth-mover’s distance. We use this sensitivity analysis methodology to quantify the probability of occurrence of critical transitions and other long-term effects of agent adaptation. To test the potential of this new approach, it is used to analyse the resilience of an ABM of adaptive agents competing for a common-pool resource. Adaptation is shown to contribute positively to the resilience of this ABM. If adaptation proceeds sufficiently fast, it may delay or avert the collapse of this system. PMID:28196372

  12. Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba.

    PubMed

    Carretero-Paulet, Lorenzo; Chang, Tien-Hao; Librado, Pablo; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Rozas, Julio; Albert, Victor A

    2015-01-09

    The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compared the U. gibba genome with that of four other eudicot species, defining a total of 17,324 gene families (orthogroups). These families were further classified as either 1) lineage-specific expanded/contracted or 2) stable in size. The U. gibba-expanded families are generically related to three main phenotypic features: 1) trap physiology, 2) key plant morphogenetic/developmental pathways, and 3) response to environmental stimuli, including adaptations to life in aquatic environments. Further scans for signatures of protein functional specialization permitted identification of seven candidate genes with amino acid changes putatively fixed by positive Darwinian selection in the U. gibba lineage. The Arabidopsis orthologs of these genes (AXR, UMAMIT41, IGS, TAR2, SOL1, DEG9, and DEG10) are involved in diverse plant biological functions potentially relevant for U. gibba phenotypic diversification, including 1) auxin metabolism and signal transduction, 2) flowering induction and floral meristem transition, 3) root development, and 4) peptidases. Taken together, our results suggest numerous candidate genes and gene families as interesting targets for further experimental confirmation of their functional and adaptive roles in the U. gibba's unique lifestyle and highly specialized body plan.

  13. Adaptive Markov chain Monte Carlo forward projection for statistical analysis in epidemic modelling of human papillomavirus.

    PubMed

    Korostil, Igor A; Peters, Gareth W; Cornebise, Julien; Regan, David G

    2013-05-20

    A Bayesian statistical model and estimation methodology based on forward projection adaptive Markov chain Monte Carlo is developed in order to perform the calibration of a high-dimensional nonlinear system of ordinary differential equations representing an epidemic model for human papillomavirus types 6 and 11 (HPV-6, HPV-11). The model is compartmental and involves stratification by age, gender and sexual-activity group. Developing this model and a means to calibrate it efficiently is relevant because HPV is a very multi-typed and common sexually transmitted infection with more than 100 types currently known. The two types studied in this paper, types 6 and 11, are causing about 90% of anogenital warts. We extend the development of a sexual mixing matrix on the basis of a formulation first suggested by Garnett and Anderson, frequently used to model sexually transmitted infections. In particular, we consider a stochastic mixing matrix framework that allows us to jointly estimate unknown attributes and parameters of the mixing matrix along with the parameters involved in the calibration of the HPV epidemic model. This matrix describes the sexual interactions between members of the population under study and relies on several quantities that are a priori unknown. The Bayesian model developed allows one to estimate jointly the HPV-6 and HPV-11 epidemic model parameters as well as unknown sexual mixing matrix parameters related to assortativity. Finally, we explore the ability of an extension to the class of adaptive Markov chain Monte Carlo algorithms to incorporate a forward projection strategy for the ordinary differential equation state trajectories. Efficient exploration of the Bayesian posterior distribution developed for the ordinary differential equation parameters provides a challenge for any Markov chain sampling methodology, hence the interest in adaptive Markov chain methods. We conclude with simulation studies on synthetic and recent actual data.

  14. Genome-wide analysis of cold adaptation in indigenous Siberian populations.

    PubMed

    Cardona, Alexia; Pagani, Luca; Antao, Tiago; Lawson, Daniel J; Eichstaedt, Christina A; Yngvadottir, Bryndis; Shwe, Ma Than Than; Wee, Joseph; Romero, Irene Gallego; Raj, Srilakshmi; Metspalu, Mait; Villems, Richard; Willerslev, Eske; Tyler-Smith, Chris; Malyarchuk, Boris A; Derenko, Miroslava V; Kivisild, Toomas

    2014-01-01

    Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66-69 Mb) contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.

  15. Genome-Wide Analysis of Cold Adaptation in Indigenous Siberian Populations

    PubMed Central

    Cardona, Alexia; Pagani, Luca; Antao, Tiago; Lawson, Daniel J.; Eichstaedt, Christina A.; Yngvadottir, Bryndis; Shwe, Ma Than Than; Wee, Joseph; Romero, Irene Gallego; Raj, Srilakshmi; Metspalu, Mait; Villems, Richard; Willerslev, Eske; Tyler-Smith, Chris; Malyarchuk, Boris A.; Derenko, Miroslava V.; Kivisild, Toomas

    2014-01-01

    Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66–69 Mb) contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture. PMID:24847810

  16. Adaptive surrogate modeling by ANOVA and sparse polynomial dimensional decomposition for global sensitivity analysis in fluid simulation

    SciTech Connect

    Tang, Kunkun; Congedo, Pietro M.; Abgrall, Rémi

    2016-06-01

    The Polynomial Dimensional Decomposition (PDD) is employed in this work for the global sensitivity analysis and uncertainty quantification (UQ) of stochastic systems subject to a moderate to large number of input random variables. Due to the intimate connection between the PDD and the Analysis of Variance (ANOVA) approaches, PDD is able to provide a simpler and more direct evaluation of the Sobol' sensitivity indices, when compared to the Polynomial Chaos expansion (PC). Unfortunately, the number of PDD terms grows exponentially with respect to the size of the input random vector, which makes the computational cost of standard methods unaffordable for real engineering applications. In order to address the problem of the curse of dimensionality, this work proposes essentially variance-based adaptive strategies aiming to build a cheap meta-model (i.e. surrogate model) by employing the sparse PDD approach with its coefficients computed by regression. Three levels of adaptivity are carried out in this paper: 1) the truncated dimensionality for ANOVA component functions, 2) the active dimension technique especially for second- and higher-order parameter interactions, and 3) the stepwise regression approach designed to retain only the most influential polynomials in the PDD expansion. During this adaptive procedure featuring stepwise regressions, the surrogate model representation keeps containing few terms, so that the cost to resolve repeatedly the linear systems of the least-squares regression problem is negligible. The size of the finally obtained sparse PDD representation is much smaller than the one of the full expansion, since only significant terms are eventually retained. Consequently, a much smaller number of calls to the deterministic model is required to compute the final PDD coefficients.

  17. Effect of Edge-Preserving Adaptive Image Filter on Low-Contrast Detectability in CT Systems: Application of ROC Analysis

    PubMed Central

    Okumura, Miwa; Ota, Takamasa; Kainuma, Kazuhisa; Sayre, James W.; McNitt-Gray, Michael; Katada, Kazuhiro

    2008-01-01

    Objective. For the multislice CT (MSCT) systems with a larger number of detector rows, it is essential to employ dose-reduction techniques. As reported in previous studies, edge-preserving adaptive image filters, which selectively eliminate only the noise elements that are increased when the radiation dose is reduced without affecting the sharpness of images, have been developed. In the present study, we employed receiver operating characteristic (ROC) analysis to assess the effects of the quantum denoising system (QDS), which is an edge-preserving adaptive filter that we have developed, on low-contrast resolution, and to evaluate to what degree the radiation dose can be reduced while maintaining acceptable low-contrast resolution. Materials and Methods. The low-contrast phantoms (Catphan 412) were scanned at various tube current settings, and ROC analysis was then performed for the groups of images obtained with/without the use of QDS at each tube current to determine whether or not a target could be identified. The tube current settings for which the area under the ROC curve (Az value) was approximately 0.7 were determined for both groups of images with/without the use of QDS. Then, the radiation dose reduction ratio when QDS was used was calculated by converting the determined tube current to the radiation dose. Results. The use of the QDS edge-preserving adaptive image filter allowed the radiation dose to be reduced by up to 38%. Conclusion. The QDS was found to be useful for reducing the radiation dose without affecting the low-contrast resolution in MSCT studies. PMID:19043565

  18. Expression and hypoxia adaptation analysis of the EPO gene in different tissues of plateau Tibetan pigs.

    PubMed

    Deji, B Z; Shang, P; Danzeng, W J; Zhang, H; Qiangba, Y Z

    2015-03-06

    This study aimed to observe the expression characteristics of the erythropoietin (EPO) gene in different tissues of Tibetan pigs and to explore the adaptation to hypoxic environments. The cDNA in heart, liver, lung, kidney, muscle, brain, and fat of Tibetan pigs was used as the template. Through the number of cycles of the polymerase chain reaction (PCR), annealing temperature, and system optimization, a stable and specific semi-quantitative PCR system was established. The EPO gene in different tissues of Tibetan pigs was detected using this system. The results showed that the EPO gene was expressed in heart, liver, lung, kidney, muscle, brain, and fat of the pigs. There were obvious differences in the expression in each tissue, and the expression sequence was as follows: kidney > muscle > lung > brain > liver > heart > fat. The results showed that the EPO gene was expressed in various tissues of Tibetan pigs. There were obvious differences in expression and each tissue may play a different regulatory role in the adaptation to hypoxia.

  19. Analysis of Adaptive Evolution in Lyssavirus Genomes Reveals Pervasive Diversifying Selection during Species Diversification

    PubMed Central

    Voloch, Carolina M.; Capellão, Renata T.; Mello, Beatriz; Schrago, Carlos G.

    2014-01-01

    Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups. PMID:25415197

  20. A texture-analysis-based design method for self-adaptive focus criterion function.

    PubMed

    Liang, Q; Qu, Y F

    2012-05-01

    Autofocusing (AF) criterion functions are critical to the performance of a passive autofocusing system in automatic video microscopy. Most of the autofocusing criterion functions proposed are dependent on the imaging system and image captured by the objective being focused or ranged. This dependence destabilizes the performance of the system when the criterion functions are applied to objectives with different characteristics. In this paper, a new design method for autofocusing criterion functions is introduced. This method enables the system to have the ability to tell the texture directional information of the objective. Based on this information, the optimal focus criterion function specific to one texture direction is designed, voiding blindly using autofocusing functions which cannot perform well when applied to the certain surface and can even lead to failure of the whole process. In this way, we improved the self-adaptability, robustness, reliability and focusing accuracy of the algorithm. First, the grey-level co-occurrence matrices of real-time images are calculated in four directions. Next, the contrast values of the four matrices are computed and then compared. The result reflects the directional information of the measured objective surfaces. Finally, with the directional information, an adaptive criterion function is constructed. To demonstrate the effectiveness of the new focus algorithm, we conducted experiments on different texture surfaces and compared the results with those obtained by existing algorithms. The proposed algorithm excellently performs with different measured objectives.

  1. [PROTEOMIC ANALYSIS OF ADAPTIVE MECHANISMS TO SALINITY STRESS IN MARINE GASTROPODS LITTORINA SAXATILIS].

    PubMed

    Muraeva, O A; Maltseva, A L; Mikhailova, N A; Granovitch, A I

    2015-01-01

    Salinity is one of the most important abiotic environmental factors affecting marine animals. If salinity deviate from optimum, adaptive mechanisms switch on to maintain organism's physiological activity. In this study, the reaction of the snails Littorina saxatilis from natural habitats and in response to experimental salinity decreasing was analyzed on proteomic level. The isolation of all snails inside their shells and gradually declining mortality was observed under acute experimental salinity decrease (down to 10 per hundred). Proteomic changes were evaluated in the surviving experimental mollusks compared to control individual using differential 2D gel-electrophoresis (DIGE) and subsequent LC-MS/MS-identification of proteins. Approximately 10% of analyzed proteins underwent up- or down regulation during the experiment. Proteins of folding, antioxidant response, intercellular matrix, cell adhesion, cell signaling and metabolic enzymes were identified among them. Proteome changes observed in experimental hypoosmotic stress partially reproduced in the proteomes of mollusks that live in conditions of natural freshening (estuaries). Possible mechanisms involved in the adaptation process of L. saxatilis individuals to hypo-osmotic stress are discussed.

  2. Global analysis of genes involved in freshwater adaptation in threespine sticklebacks (Gasterosteus aculeatus).

    PubMed

    DeFaveri, Jacquelin; Shikano, Takahito; Shimada, Yukinori; Goto, Akira; Merilä, Juha

    2011-06-01

    Examples of parallel evolution of phenotypic traits have been repeatedly demonstrated in threespine sticklebacks (Gasterosteus aculeatus) across their global distribution. Using these as a model, we performed a targeted genome scan--focusing on physiologically important genes potentially related to freshwater adaptation--to identify genetic signatures of parallel physiological evolution on a global scale. To this end, 50 microsatellite loci, including 26 loci within or close to (<6 kb) physiologically important genes, were screened in paired marine and freshwater populations from six locations across the Northern Hemisphere. Signatures of directional selection were detected in 24 loci, including 17 physiologically important genes, in at least one location. Although no loci showed consistent signatures of selection in all divergent population pairs, several outliers were common in multiple locations. In particular, seven physiologically important genes, as well as reference ectodysplasin gene (EDA), showed signatures of selection in three or more locations. Hence, although these results give some evidence for consistent parallel molecular evolution in response to freshwater colonization, they suggest that different evolutionary pathways may underlie physiological adaptation to freshwater habitats within the global distribution of the threespine stickleback.

  3. Understanding the host-adapted state of Citrobacter rodentium by transcriptomic analysis.

    PubMed

    Smith, Allen D; Yan, Xianghe; Chen, Celine; Dawson, Harry D; Bhagwat, Arvind A

    2016-05-01

    Citrobacter rodentium (Cr) is a mouse pathogen that mimics many aspects of enteropathogenic Escherichia coli infections including producing attaching and effacing (A/E) lesions. Host-adapted (HA) Cr cells that are shed at the peak of infection have been reported to be hyper-infective. The exact mechanism underlying this phenomenon has remained elusive since the pathogen loses its HA 'status' immediately upon subculturing in laboratory media. We sequenced the entire transcriptome of Cr directly from the feces of infected mice and analyzed the gene expression pattern. We observed that the entire transcriptional machinery as well as several transcriptional regulators to be differentially expressed when compared with the transcriptome of cells grown on laboratory media. Major adhesion and effector genes, tir and eae, were highly expressed in HA along with many genes located on all five loci of enterocyte effacement regions (LEE 1-5). Notable absent among the HA expressed genes were 19 fimbrial operons and non-fimbrial adhesions and several non-LEE encoded effectors. These results demonstrate that host-adapted Cr has a unique transcriptome that is associated with increased host transmission.

  4. Automatic nevi segmentation using adaptive mean shift filters and feature analysis

    NASA Astrophysics Data System (ADS)

    King, Michael A.; Lee, Tim K.; Atkins, M. Stella; McLean, David I.

    2004-05-01

    A novel automatic method of segmenting nevi is explained and analyzed in this paper. The first step in nevi segmentation is to iteratively apply an adaptive mean shift filter to form clusters in the image and to remove noise. The goal of this step is to remove differences in skin intensity and hairs from the image, while still preserving the shape of nevi present on the skin. Each iteration of the mean shift filter changes pixel values to be a weighted average of pixels in its neighborhood. Some new extensions to the mean shift filter are proposed to allow for better segmentation of nevi from the skin. The kernel, that describes how the pixels in its neighborhood will be averaged, is adaptive; the shape of the kernel is a function of the local histogram. After initial clustering, a simple merging of clusters is done. Finally, clusters that are local minima are found and analyzed to determine which clusters are nevi. When this algorithm was compared to an assessment by an expert dermatologist, it showed a sensitivity rate and diagnostic accuracy of over 95% on the test set, for nevi larger than 1.5mm.

  5. Analysis of steps adapted protocol in cardiac rehabilitation in the hospital phase

    PubMed Central

    Winkelmann, Eliane Roseli; Dallazen, Fernanda; Bronzatti, Angela Beerbaum Steinke; Lorenzoni, Juliara Cristina Werner; Windmöller, Pollyana

    2015-01-01

    Objective To analyze a cardiac rehabilitation adapted protocol in physical therapy during the postoperative hospital phase of cardiac surgery in a service of high complexity, in aspects regarded to complications and mortality prevalence and hospitalization days. Methods This is an observational cross-sectional, retrospective and analytical study performed by investigating 99 patients who underwent cardiac surgery for coronary artery bypass graft, heart valve replacement or a combination of both. Step program adapted for rehabilitation after cardiac surgery was analyzed under the command of the physiotherapy professional team. Results In average, a patient stays for two days in the Intensive Care Unit and three to four days in the hospital room, totalizing six days of hospitalization. Fatalities occurred in a higher percentage during hospitalization (5.1%) and up to two years period (8.6%) when compared to 30 days after hospital discharge (1.1%). Among the postoperative complications, the hemodynamic (63.4%) and respiratory (42.6%) were the most prevalent. 36-42% of complications occurred between the immediate postoperative period and the second postoperative day. The hospital discharge started from the fifth postoperative day. We can observe that in each following day, the patients are evolving in achieving the Steps, where Step 3 was the most used during the rehabilitation phase I. Conclusion This evolution program by steps can to guide the physical rehabilitation at the hospital in patients after cardiac surgery. PMID:25859866

  6. Importance of catalase in the adaptive response to hydrogen peroxide: analysis of acatalasaemic Saccharomyces cerevisiae.

    PubMed Central

    Izawa, S; Inoue, Y; Kimura, A

    1996-01-01

    Controversy about the importance of catalase in the detoxification of H2O2 in human erythrocytes continues. It has been suggested that catalase has no role in the clearance of H2O2 in erythrocytes. In the present study we investigated the role of catalase in the defence mechanism against oxidative stress using Saccharomyces cerevisiae. S. cerevisiae has two catalases, catalase A and catalase T. We constructed a double mutant (acatalasaemic mutant) unable to produce either catalase A or catalase T, and compared it with wild-type and single-mutant cells. The acatalasaemic mutant cells showed a similar growth rate to wild-type cells under non-oxidative stress conditions, and showed a similar susceptibility to H2O2 stress in the exponential growth phase. The acatalasaemic mutant cells at stationary phase were, however, much more sensitive to H2O2 stress than wild-type and single-mutant cells. Moreover, the ability of acatalasaemic and single-mutant cells to show adaptation to 2 mM H2O2 was distinctly inferior to that of wild-type cells. These results suggest that catalase is not essential for yeast cells under normal conditions, but plays an important role in the acquisition of tolerance to oxidative stress in the adaptive response of these cells. PMID:8947468

  7. Error estimation and adaptive mesh refinement for parallel analysis of shell structures

    NASA Technical Reports Server (NTRS)

    Keating, Scott C.; Felippa, Carlos A.; Park, K. C.

    1994-01-01

    The formulation and application of element-level, element-independent error indicators is investigated. This research culminates in the development of an error indicator formulation which is derived based on the projection of element deformation onto the intrinsic element displacement modes. The qualifier 'element-level' means that no information from adjacent elements is used for error estimation. This property is ideally suited for obtaining error values and driving adaptive mesh refinements on parallel computers where access to neighboring elements residing on different processors may incur significant overhead. In addition such estimators are insensitive to the presence of physical interfaces and junctures. An error indicator qualifies as 'element-independent' when only visible quantities such as element stiffness and nodal displacements are used to quantify error. Error evaluation at the element level and element independence for the error indicator are highly desired properties for computing error in production-level finite element codes. Four element-level error indicators have been constructed. Two of the indicators are based on variational formulation of the element stiffness and are element-dependent. Their derivations are retained for developmental purposes. The second two indicators mimic and exceed the first two in performance but require no special formulation of the element stiffness mesh refinement which we demonstrate for two dimensional plane stress problems. The parallelizing of substructures and adaptive mesh refinement is discussed and the final error indicator using two-dimensional plane-stress and three-dimensional shell problems is demonstrated.

  8. Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit

    PubMed Central

    Baerenfaller, Katja; Massonnet, Catherine; Walsh, Sean; Baginsky, Sacha; Bühlmann, Peter; Hennig, Lars; Hirsch-Hoffmann, Matthias; Howell, Katharine A; Kahlau, Sabine; Radziejwoski, Amandine; Russenberger, Doris; Rutishauser, Dorothea; Small, Ian; Stekhoven, Daniel; Sulpice, Ronan; Svozil, Julia; Wuyts, Nathalie; Stitt, Mark; Hilson, Pierre; Granier, Christine; Gruissem, Wilhelm

    2012-01-01

    Leaves have a central role in plant energy capture and carbon conversion and therefore must continuously adapt their development to prevailing environmental conditions. To reveal the dynamic systems behaviour of leaf development, we profiled Arabidopsis leaf number six in depth at four different growth stages, at both the end-of-day and end-of-night, in plants growing in two controlled experimental conditions: short-day conditions with optimal soil water content and constant reduced soil water conditions. We found that the lower soil water potential led to reduced, but prolonged, growth and an adaptation at the molecular level without a drought stress response. Clustering of the protein and transcript data using a decision tree revealed different patterns in abundance changes across the growth stages and between end-of-day and end-of-night that are linked to specific biological functions. Correlations between protein and transcript levels depend on the time-of-day and also on protein localisation and function. Surprisingly, only very few of >1700 quantified proteins showed diurnal abundance fluctuations, despite strong fluctuations at the transcript level. PMID:22929616

  9. An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes

    PubMed Central

    Shafqat-Abbasi, Hamdah; Kowalewski, Jacob M; Kiss, Alexa; Gong, Xiaowei; Hernandez-Varas, Pablo; Berge, Ulrich; Jafari-Mamaghani, Mehrdad; Lock, John G; Strömblad, Staffan

    2016-01-01

    Mesenchymal (lamellipodial) migration is heterogeneous, although whether this reflects progressive variability or discrete, 'switchable' migration modalities, remains unclear. We present an analytical toolbox, based on quantitative single-cell imaging data, to interrogate this heterogeneity. Integrating supervised behavioral classification with multivariate analyses of cell motion, membrane dynamics, cell-matrix adhesion status and F-actin organization, this toolbox here enables the detection and characterization of two quantitatively distinct mesenchymal migration modes, termed 'Continuous' and 'Discontinuous'. Quantitative mode comparisons reveal differences in cell motion, spatiotemporal coordination of membrane protrusion/retraction, and how cells within each mode reorganize with changed cell speed. These modes thus represent distinctive migratory strategies. Additional analyses illuminate the macromolecular- and cellular-scale effects of molecular targeting (fibronectin, talin, ROCK), including 'adaptive switching' between Continuous (favored at high adhesion/full contraction) and Discontinuous (low adhesion/inhibited contraction) modes. Overall, this analytical toolbox now facilitates the exploration of both spontaneous and adaptive heterogeneity in mesenchymal migration. DOI: http://dx.doi.org/10.7554/eLife.11384.001 PMID:26821527

  10. Finite Element Analysis of Folded Airbag in Frontal Impact of Adapted Vehicles for Disabled Drivers

    NASA Astrophysics Data System (ADS)

    Masiá, J.; Eixerés, B.; Dols, J. F.; Esquerdo, T. V.

    2009-11-01

    The car control adaptations are used in vehicles in order to facilitate the driving to persons with physical handicaps. This does not have to suppose a decrease of the passive safety that is required to the vehicles. In order to analyze this relation there will be characterized the different control adaptations that are in use together with the different devices of passive safety that can be mounted in the vehicles in diverse cases of impact in order to generate models of simulation. The methodology used to generate this simulation consists of the first phase in which there develops the three-dimensional model of the driving place. For it, there has been used a commercial software of three-dimensional design. Once realized this one divides, the model is imported to the finite elements software in which meshing is generated. Finally, dynamic simulation software is used to assign the most important characteristics like material properties, contact interfaces, gas expansion models, airbag fold types, etc.

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

    PubMed Central

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

    2016-01-01

    Arsenic (As) resistance determinant ars operon is present in many bacteria and has been demonstrated to enhance As(V) resistance of bacteria. However, whole molecular mechanism adaptations of bacteria in response to As(V) stress remain largely unknown. In this study, transcriptional profiles of Enterobacteriaceae strain LSJC7 responding to As(V) stress were analyzed using RNA-seq and qRT-PCR. As expected, genes involved in As(V) uptake were down-regulated, those involved in As(V) reduction and As(III) efflux were up-regulated, which avoided cellular As accumulation. Reactive oxygen species and nitric oxide (NO) were induced, which caused cellular damages including DNA, protein, and Fe–S cluster damage in LSJC7. The expression of specific genes encoding transcriptional regulators, such as nsrR and soxRS were also induced. NsrR and SoxRS modulated many critical metabolic activities in As(V) stressed LSJC7 cells, including reactive species scavenging and repairing damaged DNA, proteins, and Fe–S clusters. Therefore, besides As uptake, reduction, and efflux; oxidative stress defense and damage repair were the main cellular adaptive responses of LSJC7 to As(V) stress. PMID:27199962

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

    PubMed

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

    2016-01-01

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

  13. Multi-Fault Detection of Rolling Element Bearings under Harsh Working Condition Using IMF-Based Adaptive Envelope Order Analysis

    PubMed Central

    Zhao, Ming; Lin, Jing; Xu, Xiaoqiang; Li, Xuejun

    2014-01-01

    When operating under harsh condition (e.g., time-varying speed and load, large shocks), the vibration signals of rolling element bearings are always manifested as low signal noise ratio, non-stationary statistical parameters, which cause difficulties for current diagnostic methods. As such, an IMF-based adaptive envelope order analysis (IMF-AEOA) is proposed for bearing fault detection under such conditions. This approach is established through combining the ensemble empirical mode decomposition (EEMD), envelope order tracking and fault sensitive analysis. In this scheme, EEMD provides an effective way to adaptively decompose the raw vibration signal into IMFs with different frequency bands. The envelope order tracking is further employed to transform the envelope of each IMF to angular domain to eliminate the spectral smearing induced by speed variation, which makes the bearing characteristic frequencies more clear and discernible in the envelope order spectrum. Finally, a fault sensitive matrix is established to select the optimal IMF containing the richest diagnostic information for final decision making. The effectiveness of IMF-AEOA is validated by simulated signal and experimental data from locomotive bearings. The result shows that IMF-AEOA could accurately identify both single and multiple faults of bearing even under time-varying rotating speed and large extraneous shocks. PMID:25353982

  14. A system identification analysis of neural adaptation dynamics and nonlinear responses in the local reflex control of locust hind limbs.

    PubMed

    Dewhirst, Oliver P; Angarita-Jaimes, Natalia; Simpson, David M; Allen, Robert; Newland, Philip L

    2013-02-01

    Nonlinear type system identification models coupled with white noise stimulation provide an experimentally convenient and quick way to investigate the often complex and nonlinear interactions between the mechanical and neural elements of reflex limb control systems. Previous steady state analysis has allowed the neurons in such systems to be categorised by their sensitivity to position, velocity or acceleration (dynamics) and has improved our understanding of network function. These neurons, however, are known to adapt their output amplitude or spike firing rate during repetitive stimulation and this transient response may be more important than the steady state response for reflex control. In the current study previously used system identification methods are developed and applied to investigate both steady state and transient dynamic and nonlinear changes in the neural circuit responsible for controlling reflex movements of the locust hind limbs. Through the use of a parsimonious model structure and Monte Carlo simulations we conclude that key system dynamics remain relatively unchanged during repetitive stimulation while output amplitude adaptation is occurring. Whilst some evidence of a significant change was found in parts of the systems nonlinear response, the effect was small and probably of little physiological relevance. Analysis using biologically more realistic stimulation reinforces this conclusion.

  15. Successful adaption of a forensic toxicological screening workflow employing nontargeted liquid chromatography-tandem mass spectrometry to water analysis.

    PubMed

    Steger, Julia; Arnhard, Kathrin; Haslacher, Sandra; Geiger, Klemens; Singer, Klaus; Schlapp, Michael; Pitterl, Florian; Oberacher, Herbert

    2016-04-01

    Forensic toxicology and environmental water analysis share the common interest and responsibility in ensuring comprehensive and reliable confirmation of drugs and pharmaceutical compounds in samples analyzed. Dealing with similar analytes, detection and identification techniques should be exchangeable between scientific disciplines. Herein, we demonstrate the successful adaption of a forensic toxicological screening workflow employing nontargeted LC/MS/MS under data-dependent acquisition control and subsequent database search to water analysis. The main modification involved processing of an increased sample volume with SPE (500 mL vs. 1-10 mL) to reach LODs in the low ng/L range. Tandem mass spectra acquired with a qTOF instrument were submitted to database search. The targeted data mining strategy was found to be sensitive and specific; automated search produced hardly any false results. To demonstrate the applicability of the adapted workflow to complex samples, 14 wastewater effluent samples collected on seven consecutive days at the local wastewater-treatment plant were analyzed. Of the 88,970 fragment ion mass spectra produced, 8.8% of spectra were successfully assigned to one of the 1040 reference compounds included in the database, and this enabled the identification of 51 compounds representing important illegal drugs, members of various pharmaceutical compound classes, and metabolites thereof.

  16. Multi-fault detection of rolling element bearings under harsh working condition using IMF-based adaptive envelope order analysis.

    PubMed

    Zhao, Ming; Lin, Jing; Xu, Xiaoqiang; Li, Xuejun

    2014-10-28

    When operating under harsh condition (e.g., time-varying speed and load, large shocks), the vibration signals of rolling element bearings are always manifested as low signal noise ratio, non-stationary statistical parameters, which cause difficulties for current diagnostic methods. As such, an IMF-based adaptive envelope order analysis (IMF-AEOA) is proposed for bearing fault detection under such conditions. This approach is established through combining the ensemble empirical mode decomposition (EEMD), envelope order tracking and fault sensitive analysis. In this scheme, EEMD provides an effective way to adaptively decompose the raw vibration signal into IMFs with different frequency bands. The envelope order tracking is further employed to transform the envelope of each IMF to angular domain to eliminate the spectral smearing induced by speed variation, which makes the bearing characteristic frequencies more clear and discernible in the envelope order spectrum. Finally, a fault sensitive matrix is established to select the optimal IMF containing the richest diagnostic information for final decision making. The effectiveness of IMF-AEOA is validated by simulated signal and experimental data from locomotive bearings. The result shows that IMF-AEOA could accurately identify both single and multiple faults of bearing even under time-varying rotating speed and large extraneous shocks.

  17. Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice

    PubMed Central

    Zhang, Zheng-Feng; Li, Yuan-Yuan; Xiao, Ben-Ze

    2016-01-01

    Drought stress is one of the major adverse environmental factors reducing plant growth. With the aim to elucidate the underlying molecular basis of rice response to drought stress, comparative transcriptome analysis was conducted between drought susceptible rice cultivar Zhenshan97 and tolerant cultivar IRAT109 at the seedling stage. 436 genes showed differential expression and mainly enriched in the Gene Ontology (GO) terms of stress defence. A large number of variations exist between these two genotypes including 2564 high-quality insertion and deletions (INDELs) and 70,264 single nucleotide polymorphism (SNPs). 1041 orthologous gene pairs show the ratio of nonsynonymous nucleotide substitution rate to synonymous nucleotide substitutions rate (Ka/Ks) larger than 1.5, indicating the rapid adaptation to different environments during domestication. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of positive selection genes suggested that photosynthesis represents the most significant category. The collocation of positively selected genes with the QTLs of photosynthesis and the different photosynthesis performance of these two cultivars further illuminate the crucial function of photosynthesis in rice adaptation to drought stress. Our results also provide fruitful functional markers and candidate genes for future genetic research and improvement of drought tolerance in rice. PMID:26777777

  18. Adaptable structural synthesis using advanced analysis and optimization coupled by a computer operating system

    NASA Technical Reports Server (NTRS)

    Sobieszczanski-Sobieski, J.; Bhat, R. B.

    1979-01-01

    A finite element program is linked with a general purpose optimization program in a 'programing system' which includes user supplied codes that contain problem dependent formulations of the design variables, objective function and constraints. The result is a system adaptable to a wide spectrum of structural optimization problems. In a sample of numerical examples, the design variables are the cross-sectional dimensions and the parameters of overall shape geometry, constraints are applied to stresses, displacements, buckling and vibration characteristics, and structural mass is the objective function. Thin-walled, built-up structures and frameworks are included in the sample. Details of the system organization and characteristics of the component programs are given.

  19. Analysis of Modified SMI Method for Adaptive Array Weight Control. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Dilsavor, Ronald Louis

    1989-01-01

    An adaptive array is used to receive a desired signal in the presence of weak interference signals which need to be suppressed. A modified sample matrix inversion (SMI) algorithm controls the array weights. The modification leads to increased interference suppression by subtracting a fraction of the noise power from the diagonal elements of the covariance matrix. The modified algorithm maximizes an intuitive power ratio criterion. The expected values and variances of the array weights, output powers, and power ratios as functions of the fraction and the number of snapshots are found and compared to computer simulation and real experimental array performance. Reduced-rank covariance approximations and errors in the estimated covariance are also described.

  20. Efficiency analysis of homodyne detection for a coherent lidar with adaptive optics

    NASA Astrophysics Data System (ADS)

    Liu, Wei; Wang, Liang; Yao, Kainan; Cao, Jingtai; Huang, Danian; Gu, Haijun

    2016-12-01

    For a coherent lidar, the efficiency of homodyne detection is a significant factor. Adaptive optics (AO) is an effective way to correct the turbulence-induced wavefront distortions. Based on our previous works, an expression for the homodyne detection efficiency is given. The results of the numerical simulation show that the atmospheric coherent length has an influence on the homodyne detection efficiency for a fixed atmospheric Greenwood frequency and a closed-loop control bandwidth. In addition, an experimental AO system is employed to verify the effect of the AO on the coherent lidar. The results show that the homodyne detection efficiency is obviously improved after aberrations are corrected. The conclusion of this paper provides a reference for designing an AO system for a coherent lidar.

  1. Adaptive relaxation for the steady-state analysis of Markov chains

    NASA Technical Reports Server (NTRS)

    Horton, Graham

    1994-01-01

    We consider a variant of the well-known Gauss-Seidel method for the solution of Markov chains in steady state. Whereas the standard algorithm visits each state exactly once per iteration in a predetermined order, the alternative approach uses a dynamic strategy. A set of states to be visited is maintained which can grow and shrink as the computation progresses. In this manner, we hope to concentrate the computational work in those areas of the chain in which maximum improvement in the solution can be achieved. We consider the adaptive approach both as a solver in its own right and as a relaxation method within the multi-level algorithm. Experimental results show significant computational savings in both cases.

  2. Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts

    PubMed Central

    Ma, Liang; Chen, Zehua; Huang, Da Wei; Kutty, Geetha; Ishihara, Mayumi; Wang, Honghui; Abouelleil, Amr; Bishop, Lisa; Davey, Emma; Deng, Rebecca; Deng, Xilong; Fan, Lin; Fantoni, Giovanna; Fitzgerald, Michael; Gogineni, Emile; Goldberg, Jonathan M.; Handley, Grace; Hu, Xiaojun; Huber, Charles; Jiao, Xiaoli; Jones, Kristine; Levin, Joshua Z.; Liu, Yueqin; Macdonald, Pendexter; Melnikov, Alexandre; Raley, Castle; Sassi, Monica; Sherman, Brad T.; Song, Xiaohong; Sykes, Sean; Tran, Bao; Walsh, Laura; Xia, Yun; Yang, Jun; Young, Sarah; Zeng, Qiandong; Zheng, Xin; Stephens, Robert; Nusbaum, Chad; Birren, Bruce W.; Azadi, Parastoo; Lempicki, Richard A.; Cuomo, Christina A.; Kovacs, Joseph A.

    2016-01-01

    Pneumocystis jirovecii is a major cause of life-threatening pneumonia in immunosuppressed patients including transplant recipients and those with HIV/AIDS, yet surprisingly little is known about the biology of this fungal pathogen. Here we report near complete genome assemblies for three Pneumocystis species that infect humans, rats and mice. Pneumocystis genomes are highly compact relative to other fungi, with substantial reductions of ribosomal RNA genes, transporters, transcription factors and many metabolic pathways, but contain expansions of surface proteins, especially a unique and complex surface glycoprotein superfamily, as well as proteases and RNA processing proteins. Unexpectedly, the key fungal cell wall components chitin and outer chain N-mannans are absent, based on genome content and experimental validation. Our findings suggest that Pneumocystis has developed unique mechanisms of adaptation to life exclusively in mammalian hosts, including dependence on the lungs for gas and nutrients and highly efficient strategies to escape both host innate and acquired immune defenses. PMID:26899007

  3. A Multiagent Approach to Adaptive Continuous Analysis of Streaming Data in Complex Uncertain Environments

    NASA Astrophysics Data System (ADS)

    Kiselev, Igor; Alhajj, Reda

    The data mining task of online unsupervised learning of streaming data continually arriving at the system in complex dynamic environments under conditions of uncertainty is an NP-hard optimization problem for general metric spaces and is computationally intractable for real-world problems of practical interest. The primary contribution of this work is a multi-agent method for continuous agglomerative hierarchical clustering of streaming data, and a knowledge-based selforganizing competitive multi-agent system for implementing it. The reported experimental results demonstrate the applicability and efficiency of the implemented adaptive multi-agent learning system for continuous online clustering of both synthetic datasets and datasets from the following real-world domains: the RoboCup Soccer competition, and gene expression datasets from a bioinformatics test bed.

  4. Component Analysis of Simple Span vs. Complex Span Adaptive Working Memory Exercises: A Randomized, Controlled Trial

    PubMed Central

    Gibson, Bradley S.; Kronenberger, William G.; Gondoli, Dawn M.; Johnson, Ann C.; Morrissey, Rebecca A.; Steeger, Christine M.

    2012-01-01

    There has been growing interest in using adaptive training interventions such as Cogmed-RM to increase the capacity of working memory (WM), but this intervention may not be optimally designed. For instance, Cogmed-RM can target the primary memory (PM) component of WM capacity, but not the secondary memory (SM) component. The present study hypothesized that Cogmed-RM does not target SM capacity because the simple span exercises it uses may not cause a sufficient amount of information to be lost from PM during training. To investigate, we randomly assigned participants to either a standard (simple span; N = 31) or a modified (complex span; N = 30) training condition. The main findings showed that SM capacity did not improve, even in the modified training condition. Hence, the potency of span-based WM interventions cannot be increased simply by converting simple span exercises into complex span exercises. PMID:23066524

  5. [Multivariate Adaptive Regression Splines (MARS), an alternative for the analysis of time series].

    PubMed

    Vanegas, Jairo; Vásquez, Fabián

    2016-12-19

    Multivariate Adaptive Regression Splines (MARS) is a non-parametric modelling method that extends the linear model, incorporating nonlinearities and interactions between variables. It is a flexible tool that automates the construction of predictive models: selecting relevant variables, transforming the predictor variables, processing missing values and preventing overshooting using a self-test. It is also able to predict, taking into account structural factors that might influence the outcome variable, thereby generating hypothetical models. The end result could identify relevant cut-off points in data series. It is rarely used in health, so it is proposed as a tool for the evaluation of relevant public health indicators. For demonstrative purposes, data series regarding the mortality of children under 5 years of age in Costa Rica were used, comprising the period 1978-2008.

  6. An Adaptive Learning Rate for RBFNN Using Time-Domain Feedback Analysis

    PubMed Central

    Ali, Syed Saad Azhar; Moinuddin, Muhammad; Raza, Kamran

    2014-01-01

    Radial basis function neural networks are used in a variety of applications such as pattern recognition, nonlinear identification, control and time series prediction. In this paper, the learning algorithm of radial basis function neural networks is analyzed in a feedback structure. The robustness of the learning algorithm is discussed in the presence of uncertainties that might be due to noisy perturbations at the input or to modeling mismatch. An intelligent adaptation rule is developed for the learning rate of RBFNN which gives faster convergence via an estimate of error energy while giving guarantee to the l 2 stability governed by the upper bounding via small gain theorem. Simulation results are presented to support our theoretical development. PMID:24987745

  7. A Preliminary Analysis of Adaptive Responding under Open and Closed Economies

    PubMed Central

    2005-01-01

    In the current investigation, we evaluated the effects of open and closed economies on the adaptive behavior of 2 individuals with developmental disabilities. Across both types of economy, progressive-ratio (PR) schedules were used in which the number of responses required to obtain reinforcement increased as the session progressed. In closed-economy sessions, participants were able to obtain reinforcement only through interaction with the PR schedule requirements (i.e., more work resulted in more reinforcer access). In open-economy sessions, participants obtained reinforcers by responding on the PR schedule and were given supplemental (free) access to the reinforcers after completion of the session. In general, more responding was associated with the closed economy. PMID:16270843

  8. Self-adaptive predictor-corrector algorithm for static nonlinear structural analysis

    NASA Technical Reports Server (NTRS)

    Padovan, J.

    1981-01-01

    A multiphase selfadaptive predictor corrector type algorithm was developed. This algorithm enables the solution of highly nonlinear structural responses including kinematic, kinetic and material effects as well as pro/post buckling behavior. The strategy involves three main phases: (1) the use of a warpable hyperelliptic constraint surface which serves to upperbound dependent iterate excursions during successive incremental Newton Ramphson (INR) type iterations; (20 uses an energy constraint to scale the generation of successive iterates so as to maintain the appropriate form of local convergence behavior; (3) the use of quality of convergence checks which enable various self adaptive modifications of the algorithmic structure when necessary. The restructuring is achieved by tightening various conditioning parameters as well as switch to different algorithmic levels to improve the convergence process. The capabilities of the procedure to handle various types of static nonlinear structural behavior are illustrated.

  9. Adaptive arrays - A new approach to the steady-state analysis

    NASA Technical Reports Server (NTRS)

    Zohar, S.

    1982-01-01

    A closed-form expression for the steady-state output signal-to-noise ratio (SNR) of an n-element adaptive array excited by one desired narrow-band signal and K - 1 narrow-band jammers is obtained. This is facilitated by representing each excitation by a complex n-dimensional vector - the excitation vector. It is shown that the important system parameters are functions of scalar products of pairs of these excitation vectors. In particular, the normalized output SNR of the array is shown to be the ratio of determinants whose elements involve these scaler products. Such determinants are also shown to be involved in the expressions for the optimal array weights.

  10. Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis

    PubMed Central

    2011-01-01

    Background Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea and it can reside in human, fish, frogs and water. In this study, we performed an in-depth annotation of the genes in its genome related to adaptation to the various environmental niches. Results L. hongkongensis possessed genes for DNA repair and recombination, basal transcription, alternative σ-factors and 109 putative transcription factors, allowing DNA repair and global changes in gene expression in response to different environmental stresses. For acid stress, it possessed a urease gene cassette and two arc gene clusters. For alkaline stress, it possessed six CDSs for transporters of the monovalent cation/proton antiporter-2 and NhaC Na+:H+ antiporter families. For heavy metals acquisition and tolerance, it possessed CDSs for iron and nickel transport and efflux pumps for other metals. For temperature stress, it possessed genes related to chaperones and chaperonins, heat shock proteins and cold shock proteins. For osmotic stress, 25 CDSs were observed, mostly related to regulators for potassium ion, proline and glutamate transport. For oxidative and UV light stress, genes for oxidant-resistant dehydratase, superoxide scavenging, hydrogen peroxide scavenging, exclusion and export of redox-cycling antibiotics, redox balancing, DNA repair, reduction of disulfide bonds, limitation of iron availability and reduction of iron-sulfur clusters are present. For starvation, it possessed phosphorus and, despite being asaccharolytic, carbon starvation-related CDSs. Conclusions The L. hongkongensis genome possessed a high variety of genes for adaptation to acid, alkaline, temperature, osmotic, oxidative, UV light and starvation stresses and acquisition of and tolerance to heavy metals. PMID:21711489

  11. A fuzzy set preference model for market share analysis

    NASA Technical Reports Server (NTRS)

    Turksen, I. B.; Willson, Ian A.

    1992-01-01

    Consumer preference models are widely used in new product design, marketing management, pricing, and market segmentation. The success of new products depends on accurate market share prediction and design decisions based on consumer preferences. The vague linguistic nature of consumer preferences and product attributes, combined with the substantial differences between individuals, creates a formidable challenge to marketing models. The most widely used methodology is conjoint analysis. Conjoint models, as currently implemented, represent linguistic preferences as ratio or interval-scaled numbers, use only numeric product attributes, and require aggregation of individuals for estimation purposes. It is not surprising that these models are costly to implement, are inflexible, and have a predictive validity that is not substantially better than chance. This affects the accuracy of market share estimates. A fuzzy set preference model can easily represent linguistic variables either in consumer preferences or product attributes with minimal measurement requirements (ordinal scales), while still estimating overall preferences suitable for market share prediction. This approach results in flexible individual-level conjoint models which can provide more accurate market share estimates from a smaller number of more meaningful consumer ratings. Fuzzy sets can be incorporated within existing preference model structures, such as a linear combination, using the techniques developed for conjoint analysis and market share estimation. The purpose of this article is to develop and fully test a fuzzy set preference model which can represent linguistic variables in individual-level models implemented in parallel with existing conjoint models. The potential improvements in market share prediction and predictive validity can substantially improve management decisions about what to make (product design), for whom to make it (market segmentation), and how much to make (market share

  12. A randomized trial examining the effects of Conjoint Behavioral Consultation in rural schools: Student outcomes and the mediating role of the teacher-parent relationship.

    PubMed

    Sheridan, Susan M; Witte, Amanda L; Holmes, Shannon R; Coutts, Michael J; Dent, Amy L; Kunz, Gina M; Wu, ChaoRong

    2017-04-01

    The results of a large-scale randomized controlled trial of Conjoint Behavioral Consultation (CBC) on student outcomes and teacher-parent relationships in rural schools are presented. CBC is an indirect service delivery model that addresses concerns shared by teachers and parents about students. In the present study, the intervention was aimed at promoting positive school-related social-behavioral skills and strengthening teacher-parent relationships in rural schools. Participants were 267 students in grades K-3, their parents, and 152 teachers in 45 Midwest rural schools. Results revealed that, on average, improvement among students whose parents and teachers experienced CBC significantly outpaced that of control students in their teacher-reported school problems and observational measures of their inappropriate (off-task and motor activity) and appropriate (on-task and social interactions) classroom behavior. In addition, teacher responses indicated significantly different rates of improvement in their relationship with parents in favor of the CBC group. Finally, the teacher-parent relationship was found to partially mediate effects of CBC on several student outcomes. Unique contributions of this study, implications of findings for rural students, study limitations and suggestions for future research are discussed.

  13. Revisiting the Psychology of Intelligence Analysis: From Rational Actors to Adaptive Thinkers

    ERIC Educational Resources Information Center

    Puvathingal, Bess J.; Hantula, Donald A.

    2012-01-01

    Intelligence analysis is a decision-making process rife with ambiguous, conflicting, irrelevant, important, and excessive information. The U.S. Intelligence Community is primed for psychology to lend its voice to the "analytic transformation" movement aimed at improving the quality of intelligence analysis. Traditional judgment and decision making…

  14. A differential role for neuropeptides in acute and chronic adaptive responses to alcohol: behavioural and genetic analysis in Caenorhabditis elegans.

    PubMed

    Mitchell, Philippa; Mould, Richard; Dillon, James; Glautier, Steven; Andrianakis, Ioannis; James, Christopher; Pugh, Amanda; Holden-Dye, Lindy; O'Connor, Vincent

    2010-05-03

    Prolonged alcohol consumption in humans followed by abstinence precipitates a withdrawal syndrome consisting of anxiety, agitation and in severe cases, seizures. Withdrawal is relieved by a low dose of alcohol, a negative reinforcement that contributes to alcohol dependency. This phenomenon of 'withdrawal relief' provides evidence of an ethanol-induced adaptation which resets the balance of signalling in neural circuits. We have used this as a criterion to distinguish between direct and indirect ethanol-induced adaptive behavioural responses in C. elegans with the goal of investigating the genetic basis of ethanol-induced neural plasticity. The paradigm employs a 'food race assay' which tests sensorimotor performance of animals acutely and chronically treated with ethanol. We describe a multifaceted C. elegans 'withdrawal syndrome'. One feature, decrease reversal frequency is not relieved by a low dose of ethanol and most likely results from an indirect adaptation to ethanol caused by inhibition of feeding and a food-deprived behavioural state. However another aspect, an aberrant behaviour consisting of spontaneous deep body bends, did show withdrawal relief and therefore we suggest this is the expression of ethanol-induced plasticity. The potassium channel, slo-1, which is a candidate ethanol effector in C. elegans, is not required for the responses described here. However a mutant deficient in neuropeptides, egl-3, is resistant to withdrawal (although it still exhibits acute responses to ethanol). This dependence on neuropeptides does not involve the NPY-like receptor npr-1, previously implicated in C. elegans ethanol withdrawal. Therefore other neuropeptide pathways mediate this effect. These data resonate with mammalian studies which report involvement of a number of neuropeptides in chronic responses to alcohol including corticotrophin-releasing-factor (CRF), opioids, tachykinins as well as NPY. This suggests an evolutionarily conserved role for neuropeptides

  15. Comparative genomic analysis of Saccharomyces cerevisiae yeasts isolated from fermentations of traditional beverages unveils different adaptive strategies.

    PubMed

    Ibáñez, Clara; Pérez-Torrado, Roberto; Chiva, Rosana; Guillamón, José Manuel; Barrio, Eladio; Querol, Amparo

    2014-02-03

    Saccharomyces cerevisiae strains are the main responsible of most traditional alcohol fermentation processes performed around the world. The characteristics of the diverse traditional fermentations are very different according to their sugar composition, temperature, pH or nitrogen sources. During the adaptation of yeasts to these new environments provided by human activity, their different compositions likely imposed selective pressures that shaped the S. cerevisiae genome. In the present work we performed a comparative genomic hybridization analysis to explore the genome constitution of six S. cerevisiae strains isolated from different traditional fermentations (masato, mescal, cachaça, sake, wine, and sherry wine) and one natural strain. Our results indicate that gene copy numbers (GCN) are very variable among strains, and most of them were observed in subtelomeric and intrachromosomal gene families involved in metabolic functions related to cellular homeostasis, cell-to-cell interactions, and transport of solutes such as ions, sugars and metals. In many cases, these genes are not essential but they can play an important role in the adaptation to new environmental conditions. However, the most interesting result is the association observed between GCN changes in genes involved in the nitrogen metabolism and the availability of nitrogen sources in the different traditional fermentation processes. This is clearly illustrated by the differences in copy numbers not only in gene PUT1, the main player in the assimilation of proline as a nitrogen source, but also in CAR2, involved in arginine catabolism. Strains isolated from fermentations where proline is more abundant contain a higher number of PUT1 copies and are more efficient in assimilating this amino acid as a nitrogen source. A strain isolated from sugarcane juice fermentations, in which arginine is a rare amino acid, contains less copies of CAR2 and showed low efficiency in arginine assimilation. These

  16. Genomic Expression Analysis Reveals Strategies of Burkholderia cenocepacia to Adapt to Cystic Fibrosis Patients' Airways and Antimicrobial Therapy

    PubMed Central

    Mira, Nuno P.; Madeira, Andreia; Moreira, Ana Sílvia; Coutinho, Carla P.; Sá-Correia, Isabel

    2011-01-01

    Pulmonary colonization of cystic fibrosis (CF) patients with Burkholderia cenocepacia or other bacteria of the Burkholderia cepacia complex (Bcc) is associated with worse prognosis and increased risk of death. During colonization, the bacteria may evolve under the stressing selection pressures exerted in the CF lung, in particular, those resulting from challenges of the host immune defenses, antimicrobial therapy, nutrient availability and oxygen limitation. Understanding the adaptive mechanisms that promote successful colonization and long-term survival of B. cenocepacia in the CF lung is essential for an improved therapeutic outcome of chronic infections. To get mechanistic insights into these adaptive strategies a transcriptomic analysis, based on DNA microarrays, was explored in this study. The genomic expression levels in two clonal variants isolated during long-term colonization of a CF patient who died from the cepacia syndrome were compared. One of the isolates examined, IST439, is the first B. cenocepacia isolate retrieved from the patient and the other isolate, IST4113, was obtained three years later and is more resistant to different classes of antimicrobials. Approximately 1000 genes were found to be differently expressed in the two clonal variants reflecting a marked reprogramming of genomic expression. The up-regulated genes in IST4113 include those involved in translation, iron uptake (in particular, in ornibactin biosynthesis), efflux of drugs and in adhesion to epithelial lung tissue and to mucin. Alterations related with adaptation to the nutritional environment of the CF lung and to an oxygen-limited environment are also suggested to be a key feature of transcriptional reprogramming occurring during long-term colonization, antibiotic therapy and the progression of the disease. PMID:22216120

  17. Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol

    PubMed Central

    2012-01-01

    Bacterial strains that were genetically blocked in important metabolic pathways and grown under selective conditions underwent a process of adaptive evolution: certain pathways may have been deregulated and therefore allowed for the circumvention of the given block. A block of endogenous pyruvate synthesis from glycerol was realized by a knockout of pyruvate kinase and phosphoenolpyruvate carboxylase in E. coli. The resulting mutant strain was able to grow on a medium containing glycerol and lactate, which served as an exogenous pyruvate source. Heterologous expression of a pyruvate carboxylase gene from Corynebacterium glutamicum was used for anaplerosis of the TCA cycle. Selective conditions were controlled in a continuous culture with limited lactate feed and an excess of glycerol feed. After 200–300 generations pyruvate-prototrophic mutants were isolated. The genomic analysis of an evolved strain revealed that the genotypic basis for the regained pyruvate-prototrophy was not obvious. A constraint-based model of the metabolism was employed to compute all possible detours around the given metabolic block by solving a hierarchy of linear programming problems. The regulatory network was expected to be responsible for the adaptation process. Hence, a Boolean model of the transcription factor network was connected to the metabolic model. Our model analysis only showed a marginal impact of transcriptional control on the biomass yield on substrate which is a key variable in the selection process. In our experiment, microarray analysis confirmed that transcriptional control probably played a minor role in the deregulation of the alternative pathways for the circumvention of the block. PMID:23033959

  18. Transcriptional Analysis of The Adaptive Digestive System of The Migratory Locust in Response to Plant Defensive Protease Inhibitors.

    PubMed

    Spit, Jornt; Holtof, Michiel; Badisco, Liesbet; Vergauwen, Lucia; Vogel, Elise; Knapen, Dries; Vanden Broeck, Jozef

    2016-09-01

    Herbivorous insects evolved adaptive mechanisms to compensate for the presence of plant defensive protease inhibitors (PI) in their food. The underlying regulatory mechanisms of these compensatory responses remain largely elusive. In the current study, we investigated the initiation of this adaptive response in the migratory locust, Locusta migratoria, via microarray analysis of gut tissues. Four hours after dietary uptake of PIs, 114 and 150 transcripts were respectively found up- or downregulated. The results suggest a quick trade-off between compensating for potential loss of digestive activity on the one hand, and stress tolerance, defense, and structural integrity of the gut on the other hand. We additionally addressed the role of a group of related upregulated hexamerin-like proteins in the PI-induced response. Simultaneous knockdown of corresponding transcripts by means of RNA interference resulted in a reduced capacity of the locust nymphs to cope with the effects of PI. Moreover, since insect hexamerins have been shown to bind Juvenile Hormone (JH), we also investigated the effect of JH on the proteolytic digestion in L. migratoria. Our results indicate that JH has a stimulatory effect on the expression of three homologous chymotrypsin genes, while knocking down the JH receptor (methoprene tolerant) led to opposite effects.

  19. Environmental Adaptation: Genomic Analysis of the Piezotolerant and Psychrotolerant Deep-Sea Iron Reducing Bacterium Shewanella piezotolerans WP3

    PubMed Central

    Jian, Huahua; Zhang, Bing; Li, Shengkang; Wang, Feng; Zeng, Xiaowei; Gao, Lei; Bartlett, Douglas Hoyt; Yu, Jun; Hu, Songnian; Xiao, Xiang

    2008-01-01

    Shewanella species are widespread in various environments. Here, the genome sequence of Shewanella piezotolerans WP3, a piezotolerant and psychrotolerant iron reducing bacterium from deep-sea sediment was determined with related functional analysis to study its environmental adaptation mechanisms. The genome of WP3 consists of 5,396,476 base pairs (bp) with 4,944 open reading frames (ORFs). It possesses numerous genes or gene clusters which help it to cope with extreme living conditions such as genes for two sets of flagellum systems, structural RNA modification, eicosapentaenoic acid (EPA) biosynthesis and osmolyte transport and synthesis. And WP3 contains 55 open reading frames encoding putative c-type cytochromes which are substantial to its wide environmental adaptation ability. The mtr-omc gene cluster involved in the insoluble metal reduction in the Shewanella genus was identified and compared. The two sets of flagellum systems were found to be differentially regulated under low temperature and high pressure; the lateral flagellum system was found essential for its motility and living at low temperature. PMID:18398463

  20. Transcriptional Analysis of The Adaptive Digestive System of The Migratory Locust in Response to Plant Defensive Protease Inhibitors

    NASA Astrophysics Data System (ADS)

    Spit, Jornt; Holtof, Michiel; Badisco, Liesbet; Vergauwen, Lucia; Vogel, Elise; Knapen, Dries; vanden Broeck, Jozef

    2016-09-01

    Herbivorous insects evolved adaptive mechanisms to compensate for the presence of plant defensive protease inhibitors (PI) in their food. The underlying regulatory mechanisms of these compensatory responses remain largely elusive. In the current study, we investigated the initiation of this adaptive response in the migratory locust, Locusta migratoria, via microarray analysis of gut tissues. Four hours after dietary uptake of PIs, 114 and 150 transcripts were respectively found up- or downregulated. The results suggest a quick trade-off between compensating for potential loss of digestive activity on the one hand, and stress tolerance, defense, and structural integrity of the gut on the other hand. We additionally addressed the role of a group of related upregulated hexamerin-like proteins in the PI-induced response. Simultaneous knockdown of corresponding transcripts by means of RNA interference resulted in a reduced capacity of the locust nymphs to cope with the effects of PI. Moreover, since insect hexamerins have been shown to bind Juvenile Hormone (JH), we also investigated the effect of JH on the proteolytic digestion in L. migratoria. Our results indicate that JH has a stimulatory effect on the expression of three homologous chymotrypsin genes, while knocking down the JH receptor (methoprene tolerant) led to opposite effects.

  1. Transcriptional Analysis of The Adaptive Digestive System of The Migratory Locust in Response to Plant Defensive Protease Inhibitors

    PubMed Central

    Spit, Jornt; Holtof, Michiel; Badisco, Liesbet; Vergauwen, Lucia; Vogel, Elise; Knapen, Dries; Vanden Broeck, Jozef

    2016-01-01

    Herbivorous insects evolved adaptive mechanisms to compensate for the presence of plant defensive protease inhibitors (PI) in their food. The underlying regulatory mechanisms of these compensatory responses remain largely elusive. In the current study, we investigated the initiation of this adaptive response in the migratory locust, Locusta migratoria, via microarray analysis of gut tissues. Four hours after dietary uptake of PIs, 114 and 150 transcripts were respectively found up- or downregulated. The results suggest a quick trade-off between compensating for potential loss of digestive activity on the one hand, and stress tolerance, defense, and structural integrity of the gut on the other hand. We additionally addressed the role of a group of related upregulated hexamerin-like proteins in the PI-induced response. Simultaneous knockdown of corresponding transcripts by means of RNA interference resulted in a reduced capacity of the locust nymphs to cope with the effects of PI. Moreover, since insect hexamerins have been shown to bind Juvenile Hormone (JH), we also investigated the effect of JH on the proteolytic digestion in L. migratoria. Our results indicate that JH has a stimulatory effect on the expression of three homologous chymotrypsin genes, while knocking down the JH receptor (methoprene tolerant) led to opposite effects. PMID:27581362

  2. Proteome analysis of sugar beet (Beta vulgaris L.) elucidates constitutive adaptation during the first phase of salt stress.

    PubMed

    Wakeel, Abdul; Asif, Abdul R; Pitann, Britta; Schubert, Sven

    2011-04-15

    Salinity is one of the major stress factors responsible for growth reduction of most of the higher plants. In this study, the effect of salt stress on protein pattern in shoots and roots of sugar beet (Beta vulgaris L.) was examined. Sugar beet plants were grown in hydroponics under control and 125 mM salt treatments. A significant growth reduction of shoots and roots was observed. The changes in protein expression, caused by salinity, were monitored using two-dimensional gel-electrophoresis. Most of the detected proteins in sugar beet showed stability under salt stress. The statistical analysis of detected proteins showed that the expression of only six proteins from shoots and three proteins from roots were significantly altered. At this stage, the significantly changed protein expressions we detected could not be attributed to sugar beet adaptation under salt stress. However, unchanged membrane bound proteins under salt stress did reveal the constitutive adaptation of sugar beet to salt stress at the plasma membrane level.

  3. Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3.

    PubMed

    Wang, Fengping; Wang, Jianbin; Jian, Huahua; Zhang, Bing; Li, Shengkang; Wang, Feng; Zeng, Xiaowei; Gao, Lei; Bartlett, Douglas Hoyt; Yu, Jun; Hu, Songnian; Xiao, Xiang

    2008-04-09

    Shewanella species are widespread in various environments. Here, the genome sequence of Shewanella piezotolerans WP3, a piezotolerant and psychrotolerant iron reducing bacterium from deep-sea sediment was determined with related functional analysis to study its environmental adaptation mechanisms. The genome of WP3 consists of 5,396,476 base pairs (bp) with 4,944 open reading frames (ORFs). It possesses numerous genes or gene clusters which help it to cope with extreme living conditions such as genes for two sets of flagellum systems, structural RNA modification, eicosapentaenoic acid (EPA) biosynthesis and osmolyte transport and synthesis. And WP3 contains 55 open reading frames encoding putative c-type cytochromes which are substantial to its wide environmental adaptation ability. The mtr-omc gene cluster involved in the insoluble metal reduction in the Shewanella genus was identified and compared. The two sets of flagellum systems were found to be differentially regulated under low temperature and high pressure; the lateral flagellum system was found essential for its motility and living at low temperature.

  4. Flood risk and adaptation strategies under climate change and urban expansion: A probabilistic analysis using global data.

    PubMed

    Muis, Sanne; Güneralp, Burak; Jongman, Brenden; Aerts, Jeroen C J H; Ward, Philip J

    2015-12-15

    An accurate understanding of flood risk and its drivers is crucial for effective risk management. Detailed risk projections, including uncertainties, are however rarely available, particularly in developing countries. This paper presents a method that integrates recent advances in global-scale modeling of flood hazard and land change, which enables the probabilistic analysis of future trends in national-scale flood risk. We demonstrate its application to Indonesia. We develop 1000 spatially-explicit projections of urban expansion from 2000 to 2030 that account for uncertainty associated with population and economic growth projections, as well as uncertainty in where urban land change may occur. The projections show that the urban extent increases by 215%-357% (5th and 95th percentiles). Urban expansion is particularly rapid on Java, which accounts for 79% of the national increase. From 2000 to 2030, increases in exposure will elevate flood risk by, on average, 76% and 120% for river and coastal floods. While sea level rise will further increase the exposure-induced trend by 19%-37%, the response of river floods to climate change is highly uncertain. However, as urban expansion is the main driver of future risk, the implementation of adaptation measures is increasingly urgent, regardless of the wide uncertainty in climate projections. Using probabilistic urban projections, we show that spatial planning can be a very effective adaptation strategy. Our study emphasizes that global data can be used successfully for probabilistic risk assessment in data-scarce countries.

  5. Probabilistic Sensitivity Analysis for Launch Vehicles with Varying Payloads and Adapters for Structural Dynamics and Loads

    NASA Technical Reports Server (NTRS)

    McGhee, David S.; Peck, Jeff A.; McDonald, Emmett J.

    2012-01-01

    This paper examines Probabilistic Sensitivity Analysis (PSA) methods and tools in an effort to understand their utility in vehicle loads and dynamic analysis. Specifically, this study addresses how these methods may be used to establish limits on payload mass and cg location and requirements on adaptor stiffnesses while maintaining vehicle loads and frequencies within established bounds. To this end, PSA methods and tools are applied to a realistic, but manageable, integrated launch vehicle analysis where payload and payload adaptor parameters are modeled as random variables. This analysis is used to study both Regional Response PSA (RRPSA) and Global Response PSA (GRPSA) methods, with a primary focus on sampling based techniques. For contrast, some MPP based approaches are also examined.

  6. Low Speed Analysis of Mission Adaptive Flaps on a High Speed Civil Transport Configuration

    NASA Technical Reports Server (NTRS)

    Lessard, Victor R.

    1999-01-01

    Thin-layer Navier-Stokes analyses were done on a high speed civil transport configuration with mission adaptive leading-edge flaps. The flow conditions simulated were Mach = 0.22 and Reynolds number of 4.27 million for angles-of-attack ranging from 0 to 18 degrees. Two turbulence closure models were used. Analyses were done exclusively with the Baldwin-Lomax turbulence model at low angle-of-attack conditions. At high angles-of-attack where considerable flow separation and vortices occurred the Spalart-Allmaras turbulence model was also considered. The effects of flow transition were studied. Predicted aerodynamic forces, moment, and pressure are compared to experimental data obtained in the 14- by 22-Foot Subsonic Tunnel at NASA Langley. The forces and moments correlated well with experimental data in terms of trends. Drag and pitching moment were consistently underpredicted. Predicted surface pressures compared well with experiment at low angles-of-attack. Above 10 angle-of-attack the pressure comparisons were not as favorable. The two turbulent models affected the pressures on the flap considerably and neither produced correct results at the high angles-of-attack.

  7. Transient analysis of distribution class Adaptive Var Compensators: Simulation and field test results

    SciTech Connect

    Kagalwala, R.A.; Venkata, S.S.; El-Sharkawi, M.A.; Butler, N.G.; Van Leuven, A.; Rodriguez, A.P.; Kerszenbaum, I.; Smith, D.

    1995-04-01

    Simulation studies are performed to analyze the transient behavior of the Adaptive Var Compensator (AVC), a power electronic device installed at the distribution level, during its design, installation and field testing stages. The simulation model includes detailed models for power apparatus, power semiconductor devices and low signal level electronics. Hence, by using this model, a wide range of simulation studies which contribute towards the development of the AVC and its effectiveness in the field can all be performed on the same platform. A new power electronics simulator called SABER has proven to be very effective for this study because of its model-independent structure and extensive library that covers various disciplines of engineering. The simulation studies are aimed at gaining a better understanding of the interaction between the AVC and the distribution system. They cover a range of phenomena such as switching transients due to mechanical capacitor bank closing, fast transients due to reverse recovery of the power diodes of the AVC, power system harmonics and voltage flicker problem. This paper also briefly describes the criteria for selection of the simulation tool and the models developed.

  8. Metabolomic analysis indicates a pivotal role of the hepatotoxin microcystin in high light adaptation of Microcystis.

    PubMed

    Meissner, Sven; Steinhauser, Dirk; Dittmann, Elke

    2015-05-01

    Microcystis is a freshwater cyanobacterium frequently forming nuisance blooms in the summer months. The genus belongs to the predominant producers of the potent hepatotoxin microcystin. The success of Microcystis and its remarkable resistance to high light conditions are not well understood. Here, we have compared the metabolic response of Microcystis aeruginosa PCC7806, its microcystin-deficient ΔmcyB mutant (Mut) and the cyanobacterial model organism Synechocystis PCC6803 to high light exposure of 250 μmol photons m(-2)  s(-1) using GC/MS-based metabolomics. Microcystis wild type and Mut show pronounced differences in their metabolic reprogramming upon high light. Seventeen per cent of the detected metabolites showed significant differences between the two genotypes after high light exposure. Whereas the microcystin-producing wild type shows a faster accumulation of glycolate upon high light illumination, loss of microcystin leads to an accumulation of general stress markers such as trehalose and sucrose. The study further uncovers differences in the high light adaptation of the bloom-forming cyanobacterium Microcystis and the model cyanobacterium Synechocystis. Most notably, Microcystis invests more into carbon reserves such as glycogen after high light exposure. Our data shed new light on the lifestyle of bloom-forming cyanobacteria, the role of the widespread toxin microcystin and the metabolic diversity of cyanobacteria.

  9. The cost of model reference adaptive control - Analysis, experiments, and optimization

    NASA Technical Reports Server (NTRS)

    Messer, R. S.; Haftka, R. T.; Cudney, H. H.

    1993-01-01

    In this paper the performance of Model Reference Adaptive Control (MRAC) is studied in numerical simulations and verified experimentally with the objective of understanding how differences between the plant and the reference model affect the control effort. MRAC is applied analytically and experimentally to a single degree of freedom system and analytically to a MIMO system with controlled differences between the model and the plant. It is shown that the control effort is sensitive to differences between the plant and the reference model. The effects of increased damping in the reference model are considered, and it is shown that requiring the controller to provide increased damping actually decreases the required control effort when differences between the plant and reference model exist. This result is useful because one of the first attempts to counteract the increased control effort due to differences between the plant and reference model might be to require less damping, however, this would actually increase the control effort. Optimization of weighting matrices is shown to help reduce the increase in required control effort. However, it was found that eventually the optimization resulted in a design that required an extremely high sampling rate for successful realization.

  10. Leaf Dimorphism Of Microgramma Squamulosa (Polypodiaceae): a qualitative and quantitative analysis focusing on adaptations to epiphytism.

    PubMed

    Rocha, Ledyane Dalgallo; Droste, Annette; Gehlen, Günther; Schmitt, Jairo Lizandro

    2013-03-01

    The epiphytic fern Microgramma squamulosa occurs in the Neotropics and shows dimorphic sterile and fertile leaves. The present study aimed to describe and compare qualitatively and quantitatively macroscopic and microscopic structural characteristics of the dimorphic leaves of M. squamulosa, to point more precisely those characteristics which may contribute to epiphytic adaptations. In June 2009, six isolated host trees covered by M squamulosa were selected close to the edge of a semi-deciduous seasonal forest fragment in the municipality of Novo Hamburgo, State of Rio Grande do Sul, Brazil. Macroscopic and microscopic analyzes were performed from 192 samples for each leaf type, and permanent and semi-permanent slides were prepared. Sections were observed under light microscopy using image capture software to produce illustrations and scales, as well as to perform quantitative analyses. Fertile and sterile leaves had no qualitative structural differences, being hypostomatous and presenting uniseriate epidermis, homogeneous chlorenchyma, amphicribal vascular bundle, and hypodermis. The presence of hypodermal tissue and the occurrence of stomata at the abaxial face are typical characteristics ofxeromorphic leaves. Sterile leaves showed significantly larger areas (14.80cm2), higher sclerophylly index (0.13g/cm2) and higher stomatal density (27.75stomata/mm2) than fertile leaves. The higher sclerophylly index and the higher stomatal density observed in sterile leaves are features that make these leaves more xeromorphic, enhancing their efficiency to deal with limited water availability in the epiphytic environment, compared to fertile leaves.

  11. Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation

    PubMed Central

    Tschitschko, Bernhard; Williams, Timothy J; Allen, Michelle A; Páez-Espino, David; Kyrpides, Nikos; Zhong, Ling; Raftery, Mark J; Cavicchioli, Ricardo

    2015-01-01

    Despite knowledge that viruses are abundant in natural ecosystems, there is limited understanding of which viruses infect which hosts, and how both hosts and viruses respond to those interactions—interactions that ultimately shape community structure and dynamics. In Deep Lake, Antarctica, intergenera gene exchange occurs rampantly within the low complexity, haloarchaea-dominated community, strongly balanced by distinctions in niche adaptation which maintain sympatric speciation. By performing metaproteomics for the first time on haloarchaea, genomic variation of S-layer, archaella and other cell surface proteins was linked to mechanisms of infection evasion. CRISPR defense systems were found to be active, with haloarchaea responding to at least eight distinct types of viruses, including those infecting between genera. The role of BREX systems in defending against viruses was also examined. Although evasion and defense were evident, both hosts and viruses also may benefit from viruses carrying and expressing host genes, thereby potentially enhancing genetic variation and phenotypic differences within populations. The data point to a complex inter-play leading to a dynamic optimization of host–virus interactions. This comprehensive overview was achieved only through the integration of results from metaproteomics, genomics and metagenomics. PMID:26125682

  12. A quantitative proteomic analysis of biofilm adaptation by the periodontal pathogen Tannerella forsythia.

    PubMed

    Pham, Trong Khoa; Roy, Sumita; Noirel, Josselin; Douglas, Ian; Wright, Phillip C; Stafford, Graham P

    2010-09-01

    Tannerella forsythia is a Gram-negative anaerobe that is one of the most prominent inhabitants of the sub-gingival plaque biofilm, which is crucial for causing periodontitis. We have used iTRAQ proteomics to identify and quantify alterations in global protein expression of T. forsythia during growth in a biofilm. This is the first proteomic study concentrating on biofilm growth in this key periodontal pathogen, and this study has identified several changes in protein expression. Moreover, we introduce a rigorous statistical method utilising peptide-level intensities of iTRAQ reporters to determine which proteins are significantly regulated. In total, 348 proteins were identified and quantified with the expression of 44 proteins being significantly altered between biofilm and planktonic cells. We identified proteins from all cell compartments, and highlighted a marked upregulation in the relative abundances of predicted outer membrane proteins in biofilm cells. These included putative transport systems and the T. forsythia S-layer proteins. These data and our finding that the butyrate production pathway is markedly downregulated in biofilms indicate possible alterations in host interaction capability. We also identified upregulation of putative oxidative stress response proteins, and showed that biofilm cells are 10 to 20 fold more resistant to oxidative stress. This may represent an important adaptation of this organism to prolonged persistence and immune evasion in the oral cavity.

  13. Evaluating Cognitive Action Control Using Eye-Movement Analysis: An Oculomotor Adaptation of the Simon Task

    PubMed Central

    Duprez, Joan; Houvenaghel, Jean-François; Naudet, Florian; Dondaine, Thibaut; Auffret, Manon; Robert, Gabriel; Drapier, Dominique; Argaud, Soizic; Vérin, Marc; Sauleau, Paul

    2016-01-01

    Cognitive action control has been extensively studied using conflict tasks such as the Simon task. In most recent studies, this process has been investigated in the light of the dual route hypothesis and more specifically of the activation-suppression model using distributional analyses. Some authors have suggested that cognitive action control assessment is not specific to response modes. In this study we adapted the Simon task, using oculomotor responses instead of manual responses, in order to evaluate whether the resolution of conflict induced by a two-dimensional stimulus yielded similar results to what is usually reported in tasks with manual responses. Results obtained from 43 young healthy participants revealed the typical congruence effect, with longer reaction times (RT) and lesser accuracy in the incongruent condition. Conditional accuracy functions (CAF) also revealed a higher proportion of fast errors in the incongruent condition and delta plots confirmed that conflict resolution was easier, as the time taken to respond increased. These results are very similar to what has been reported in the literature. Furthermore, our observations are in line with the assumptions of the activation-suppression model, in which automatic activation in conflict situations is captured in the fastest responses and selective inhibition of cognitive action control needs time to build up. Altogether, our results suggest that conflict resolution has core mechanisms whatever the response mode, manual or oculomotor. Using oculomotor responses in such tasks could be of interest when investigating cognitive action control in patients with severe motor disorders. PMID:26973499

  14. Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation.

    PubMed

    Tschitschko, Bernhard; Williams, Timothy J; Allen, Michelle A; Páez-Espino, David; Kyrpides, Nikos; Zhong, Ling; Raftery, Mark J; Cavicchioli, Ricardo

    2015-09-01

    Despite knowledge that viruses are abundant in natural ecosystems, there is limited understanding of which viruses infect which hosts, and how both hosts and viruses respond to those interactions-interactions that ultimately shape community structure and dynamics. In Deep Lake, Antarctica, intergenera gene exchange occurs rampantly within the low complexity, haloarchaea-dominated community, strongly balanced by distinctions in niche adaptation which maintain sympatric speciation. By performing metaproteomics for the first time on haloarchaea, genomic variation of S-layer, archaella and other cell surface proteins was linked to mechanisms of infection evasion. CRISPR defense systems were found to be active, with haloarchaea responding to at least eight distinct types of viruses, including those infecting between genera. The role of BREX systems in defending against viruses was also examined. Although evasion and defense were evident, both hosts and viruses also may benefit from viruses carrying and expressing host genes, thereby potentially enhancing genetic variation and phenotypic differences within populations. The data point to a complex inter-play leading to a dynamic optimization of host-virus interactions. This comprehensive overview was achieved only through the integration of results from metaproteomics, genomics and metagenomics.

  15. Time-Varying, Multi-Scale Adaptive System Reliability Analysis of Lifeline Infrastructure Networks

    SciTech Connect

    Gearhart, Jared Lee; Kurtz, Nolan Scot

    2014-09-01

    The majority of current societal and economic needs world-wide are met by the existing networked, civil infrastructure. Because the cost of managing such infrastructure is high and increases with time, risk-informed decision making is essential for those with management responsibilities for these systems. To address such concerns, a methodology that accounts for new information, deterioration, component models, component importance, group importance, network reliability, hierarchical structure organization, and efficiency concerns has been developed. This methodology analyzes the use of new information through the lens of adaptive Importance Sampling for structural reliability problems. Deterioration, multi-scale bridge models, and time-variant component importance are investigated for a specific network. Furthermore, both bridge and pipeline networks are studied for group and component importance, as well as for hierarchical structures in the context of specific networks. Efficiency is the primary driver throughout this study. With this risk-informed approach, those responsible for management can address deteriorating infrastructure networks in an organized manner.

  16. Output-Based Adaptive Meshing Applied to Space Launch System Booster Separation Analysis

    NASA Technical Reports Server (NTRS)

    Dalle, Derek J.; Rogers, Stuart E.

    2015-01-01

    This paper presents details of Computational Fluid Dynamic (CFD) simulations of the Space Launch System during solid-rocket booster separation using the Cart3D inviscid code with comparisons to Overflow viscous CFD results and a wind tunnel test performed at NASA Langley Research Center's Unitary PlanWind Tunnel. The Space Launch System (SLS) launch vehicle includes two solid-rocket boosters that burn out before the primary core stage and thus must be discarded during the ascent trajectory. The main challenges for creating an aerodynamic database for this separation event are the large number of basis variables (including orientation of the core, relative position and orientation of the boosters, and rocket thrust levels) and the complex flow caused by the booster separation motors. The solid-rocket boosters are modified from their form when used with the Space Shuttle Launch Vehicle, which has a rich flight history. However, the differences between the SLS core and the Space Shuttle External Tank result in the boosters separating with much narrower clearances, and so reducing aerodynamic uncertainty is necessary to clear the integrated system for flight. This paper discusses an approach that has been developed to analyze about 6000 wind tunnel simulations and 5000 flight vehicle simulations using Cart3D in adaptive-meshing mode. In addition, a discussion is presented of Overflow viscous CFD runs used for uncertainty quantification. Finally, the article presents lessons learned and improvements that will be implemented in future separation databases.

  17. Automated Detection of Microaneurysms Using Scale-Adapted Blob Analysis and Semi-Supervised Learning

    SciTech Connect

    Adal, Kedir M.; Sidebe, Desire; Ali, Sharib; Chaum, Edward; Karnowski, Thomas Paul; Meriaudeau, Fabrice

    2014-01-07

    Despite several attempts, automated detection of microaneurysm (MA) from digital fundus images still remains to be an open issue. This is due to the subtle nature of MAs against the surrounding tissues. In this paper, the microaneurysm detection problem is modeled as finding interest regions or blobs from an image and an automatic local-scale selection technique is presented. Several scale-adapted region descriptors are then introduced to characterize these blob regions. A semi-supervised based learning approach, which requires few manually annotated learning examples, is also proposed to train a classifier to detect true MAs. The developed system is built using only few manually labeled and a large number of unlabeled retinal color fundus images. The performance of the overall system is evaluated on Retinopathy Online Challenge (ROC) competition database. A competition performance measure (CPM) of 0.364 shows the competitiveness of the proposed system against state-of-the art techniques as well as the applicability of the proposed features to analyze fundus images.

  18. Analysis and research on thermal infrared properties and adaptability of the camouflage net

    NASA Astrophysics Data System (ADS)

    Cui, Guangzhen; Hu, Jianghua; Jian, Chaochao; Yang, Juntang

    2016-10-01

    As camouflage equipment, camouflage net which covers or obstruct the enemy reconnaissance and attack, have the compatibility such as optics, infrared, radar wave band performance. To improve the adaptive between the camouflage net with background in infrared wavelengths, the heat shield and heat integration requirements on the surface of the camouflage net was analyzed. The condition that satisfied the heat shield was when the average thermal infrared transmittance was less than 25.38% on camouflage screen surface. Studies have shown that camouflage nets and the background field fused together when infrared radiation temperature difference control is within the scope of ± 4K . Experiment on temperature contrast was tested in situ background, thermal camouflage spots and camouflage net with sponge material, the infrared heat maps was recorded in the period of experiment through the thermal imager. Results showed that the thermal inertia of camouflage net was markedly lower than the background and the exposed signs were obvious. It was difficult to reach camouflage thermal infrared fusion requirements by relying on camouflage spot emissivity, but sponge which mix with polymer resin can reduce target significance in the context of mottled and realize the fusion effect.

  19. Autoradiographic analysis of hepatocytes in mirex-induced adaptive liver growth

    SciTech Connect

    Wilson, D.; Yarbrough, J.D. )

    1988-07-01

    The relationships between ({sup 3}H)thymidine incorporation into hepatocyte nuclei, cell enlargement, and mitotic index were studied in intact (INT) and adrenalectomized (ADX) mirex-dosed rats. In INT mirex-dosed rats the sequence of events included the following: a biphasic response in nuclear labeling of mononuclear hepatocyes with peaks at 48 and 66 h postmirex dose, a peak in mitotic activity 66 h postmirex dose, and a significant increase in binuclear hepatocyte size 48 h postmirex dose. In ADX mirex-dosed rats the sequence of events included the following: a biphasic response in nuclear labeling mononuclear hepatocytes with peaks at 24 and 48 h postmirex dose, a peak in mitotic activity 60 h postmirex dose, and a marginal increase in binuclear hepatocyte size 48 h postmirex dose. Corticosterone supplements to ADX mirex-dosed rats significantly reduced nuclear labeling of the mononuclear hepatocytes and increased the size of binuclear hepatocytes to that observed in INT mirex-dosed rats. This study demonstrates that adaptive liver growth consists of a hyperplastic response that involves mononuclear hepatocytes and a hypertrophic response that involves binuclear hepatocytes. Both responses appear to be modulated by corticosterone.

  20. Proteome-wide analysis of functional divergence in bacteria: exploring a host of ecological adaptations.

    PubMed

    Caffrey, Brian E; Williams, Tom A; Jiang, Xiaowei; Toft, Christina; Hokamp, Karsten; Fares, Mario A

    2012-01-01

    Functional divergence is the process by which new genes and functions originate through the modification of existing ones. Both genetic and environmental factors influence the evolution of new functions, including gene duplication or changes in the ecological requirements of an organism. Novel functions emerge at the expense of ancestral ones and are generally accompanied by changes in the selective forces at constrained protein regions. We present software capable of analyzing whole proteomes, identifying putative amino acid replacements leading to functional change in each protein and performing statistical tests on all tabulated data. We apply this method to 750 complete bacterial proteomes to identify high-level patterns of functional divergence and link these patterns to ecological adaptations. Proteome-wide analyses of functional divergence in bacteria with different ecologies reveal a separation between proteins involved in information processing (Ribosome biogenesis etc.) and those which are dependent on the environment (energy metabolism, defense etc.). We show that the evolution of pathogenic and symbiotic bacteria is constrained by their association with the host, and also identify unusual events of functional divergence even in well-studied bacteria such as Escherichia coli. We present a description of the roles of phylogeny and ecology in functional divergence at the level of entire proteomes in bacteria.

  1. Design and analysis of self-adapted task scheduling strategies in wireless sensor networks.

    PubMed

    Guo, Wenzhong; Xiong, Naixue; Chao, Han-Chieh; Hussain, Sajid; Chen, Guolong

    2011-01-01

    In a wireless sensor network (WSN), the usage of resources is usually highly related to the execution of tasks which consume a certain amount of computing and communication bandwidth. Parallel processing among sensors is a promising solution to provide the demanded computation capacity in WSNs. Task allocation and scheduling is a typical problem in the area of high performance computing. Although task allocation and scheduling in wired processor networks has been well studied in the past, their counterparts for WSNs remain largely unexplored. Existing traditional high performance computing solutions cannot be directly implemented in WSNs due to the limitations of WSNs such as limited resource availability and the shared communication medium. In this paper, a self-adapted task scheduling strategy for WSNs is presented. First, a multi-agent-based architecture for WSNs is proposed and a mathematical model of dynamic alliance is constructed for the task allocation problem. Then an effective discrete particle swarm optimization (PSO) algorithm for the dynamic alliance (DPSO-DA) with a well-designed particle position code and fitness function is proposed. A mutation operator which can effectively improve the algorithm's ability of global search and population diversity is also introduced in this algorithm. Finally, the simulation results show that the proposed solution can achieve significant better performance than other algorithms.

  2. Time scale matters: genetic analysis does not support adaptation-by-time as the mechanism for adaptive seasonal declines in kokanee reproductive life span

    PubMed Central

    Morbey, Yolanda E; Jensen, Evelyn L; Russello, Michael A

    2014-01-01

    Seasonal declines of fitness-related traits are often attributed to environmental effects or individual-level decisions about reproductive timing and effort, but genetic variation may also play a role. In populations of Pacific salmon (Oncorhynchus spp.), seasonal declines in reproductive life span have been attributed to adaptation-by-time, in which divergent selection for different traits occurs among reproductively isolated temporal components of a population. We evaluated this hypothesis in kokanee (freshwater obligate Oncorhynchus nerka) by testing for temporal genetic structure in neutral and circadian-linked loci. We detected no genetic differences in presumably neutral loci among kokanee with different arrival and maturation dates within a spawning season. Similarly, we detected no temporal genetic structure in OtsClock1b, Omy1009uw, or OmyFbxw11, candidate loci associated with circadian function. The genetic evidence from this study and others indicates a lack of support for adaptation-by-time as an important evolutionary mechanism underlying seasonal declines in reproductive life span and a need for greater consideration of other mechanisms such as time-dependent, adaptive adjustment of reproductive effort. PMID:25478160

  3. Defining climate modeling user needs: which data are actually required to support impact analysis and adaptation policy development?

    NASA Astrophysics Data System (ADS)

    Swart, R. J.; Pagé, C.

    2010-12-01

    -scientific stakeholders in government, civil society and the private sector, in a context which is different in many European countries. In the IS-ENES effort, a dialogue is set up between the communities in Europe, building on various existing research networks in the area of climate change impacts, vulnerability and adaptation. Generally, the data needs have not been well articulated. If asked, people working on impacts and adaptation routinely seem to ask for data with the highest possible resolution. However, in reality for many impact and adaptation applications this is not needed, and the large resulting data sets may exceed the analytical capacity of the impact researchers. For impact analysis often various types of climate indices, derived from primary climate model output variables, are required, including indices for extremes and in probabilistic format. Rather than making output from climate modeling generically available, e.g. through a climate service e-portal, context-specific tailoring of information for specific applications is important for effective use. This may require some level of interaction between the users and the data providers, dependent on the specific questions to be addressed.

  4. Molecular evolution and host adaptation of Bordetella spp.: phylogenetic analysis using multilocus enzyme electrophoresis and typing with three insertion sequences.

    PubMed Central

    van der Zee, A; Mooi, F; Van Embden, J; Musser, J

    1997-01-01

    A total of 188 Bordetella strains were characterized by the electrophoretic mobilities of 15 metabolic enzymes and the distribution and variation in positions and copy numbers of three insertion sequences (IS). The presence or absence of IS elements within certain lineages was congruent with estimates of overall genetic relationships as revealed by multilocus enzyme electrophoresis. Bordetella pertussis and ovine B. parapertussis each formed separate clusters, while human B. parapertussis was most closely related to IS1001-containing B. bronchiseptica isolates. The results of the analysis provide support for the hypothesis that the population structure of Bordetella is predominantly clonal, with relatively little effective horizontal gene flow. Only a few examples of putative recombinational exchange of an IS element were detected. Based on the results of this study, we tried to reconstruct the evolutionary history of different host-adapted lineages. PMID:9352907

  5. Visual Adaptation

    PubMed Central

    Webster, Michael A.

    2015-01-01

    Sensory systems continuously mold themselves to the widely varying contexts in which they must operate. Studies of these adaptations have played a long and central role in vision science. In part this is because the specific adaptations remain a powerful tool for dissecting vision, by exposing the mechanisms that are adapting. That is, “if it adapts, it's there.” Many insights about vision have come from using adaptation in this way, as a method. A second important trend has been the realization that the processes of adaptation are themselves essential to how vision works, and thus are likely to operate at all levels. That is, “if it's there, it adapts.” This has focused interest on the mechanisms of adaptation as the target rather than the probe. Together both approaches have led to an emerging insight of adaptation as a fundamental and ubiquitous coding strategy impacting all aspects of how we see. PMID:26858985

  6. Problem-solving style and adaptation in breast cancer survivors: a prospective analysis

    PubMed Central

    Armer, Jane M.; Mallinckrodt, Brent

    2010-01-01

    Introduction Emotional care of the breast cancer patient is not well understood; this lack of understanding results in both a high cost to the patient, as well as the health care system. This study examined the role of problem-solving style as a predictor of emotional distress, adjustment to breast cancer, and physical function immediately post-surgery and 12 months later. Methods The sample consisted of 121 women diagnosed with breast cancer and undergoing surgery as a primary treatment. The survivors completed a measure of problem-solving style and three outcome measures immediately post-surgery, as well as at 1 year later. There was a 95.6% retention rate at 1 year. Results Multiple hierarchical regressions revealed, after controlling for patient demographics and stage of cancer, that problem-solving style (particularly personal control) was associated with emotional distress, adjustment to chronic illness, and physical function immediately following surgical intervention. In addition, a more positive problem-solving style was associated with less emotional distress, but not a better adaptation to a chronic illness or physical functioning 12 months later; the Personal Control again was the best single predictor of the emotional distress, adding 10% of the variance in predicting this outcome. Conclusions The utility of post-surgery assessment may help identify those in need for problem-solving training to improve these outcomes at 1 year. Future studies need to determine the impact of interventions tailored to levels of problem-solving styles in cancer survivors over time. Implications for Cancer Survivors Understanding the role of problem solving style in breast cancer survivors deserves attention as it is associated with emotional distress immediately and one year after medical intervention. Problem-solving style should be evaluated early, and interventions established for those most at risk for emotional distress. PMID:19396549

  7. Adaptive echolocation behavior in bats for the analysis of auditory scenes

    PubMed Central

    Chiu, Chen; Xian, Wei; Moss, Cynthia F.

    2009-01-01

    Summary Echolocating bats emit sonar pulses and listen to returning echoes to probe their surroundings. Bats adapt their echolocation call design to cope with dynamic changes in the acoustic environment, including habitat change or the presence of nearby conspecifics/heterospecifics. Seven pairs of big brown bats, Eptesicus fuscus, were tested in this study to examine how they adjusted their echolocation calls when flying and competing with a conspecific for food. Results showed that differences in five call parameters, start/end frequencies, duration, bandwidth and sweep rate, significantly increased in the two-bat condition compared with the baseline data. In addition, the magnitude of spectral separation of calls was negatively correlated with the baseline call design differences in individual bats. Bats with small baseline call frequency differences showed larger increases in call frequency separation when paired than those with large baseline call frequency differences, suggesting that bats actively change their sonar call structure if pre-existing differences in call design are small. Call design adjustments were also influenced by physical spacing between two bats. Calls of paired bats exhibited the largest design separations when inter-bat distance was shorter than 0.5 m, and the separation decreased as the spacing increased. All individuals modified at least one baseline call parameter in response to the presence of another conspecific. We propose that dissimilarity between the time–frequency features of sonar calls produced by different bats aids each individual in segregating echoes of its own sonar vocalizations from the acoustic signals of neighboring bats. PMID:19376960

  8. Analysis of modes and behavior of a multiconjugate adaptive optics system.

    PubMed

    Le Louarn, Miska; Tallon, Michel

    2002-05-01

    We study the so-called three-dimensional mapping of turbulence, a method solving the cone effect (or focus anisoplanatism) by using multiple laser guide stars (LGSs). This method also permits a widening of the corrected field of view much beyond the isoplanatic field. Multiple deformable mirrors, conjugated to planes at chosen altitudes among the turbulent layers, are used to correct in real time the wave fronts measured from the LGSs. We construct an interaction matrix describing the multiconjugate adaptive optics system and analyze the eigenmodes of the system. We show that the global tilt mode is singular because it cannot be localized in altitude, so that it must be corrected only once at any altitude. Furthermore, when the tilt from the LGS cannot be measured, the singularity of the global tilt yields the delocalization of particular forms of defocus and astigmatism. This imposes the use of a single natural guide star located anywhere in the corrected field to measure these modes. We show as an example that the cone effect can be corrected with a Strehl of 0.8 with four LGSs (tilt ignored) on an 8-m telescope in the visible when a single laser star provides a Strehl of 0.1. The maximum field of view of 100 arc sec in diameter can be reconstructed with an on-axis Strehl ratio of 30%. We also show that the measurement of the height of the layers can be done with current techniques and that additional layers, not accounted for, do not significantly degrade the performance in the configuration that we model.

  9. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation

    SciTech Connect

    Stein, Lisa Y; Arp, D J; Berube, PM; Chain, Patrick S. G.; Hauser, Loren John; Jetten, MSM; Klotz, Martin G; Larimer, Frank W; Norton, Jeanette M.; Op den Camp, HJM; Shin, M; Wei, Xueming

    2007-12-01

    Analysis of the structure and inventory of the genome of Nitrosomonas eutropha C91 revealed distinctive features that may explain the adaptation of N. eutropha-like bacteria to N-saturated ecosystems. Multiple gene-shuffling events are apparent, including mobilized and replicated transposition, as well as plasmid or phage integration events into the 2.66 Mbp chromosome and two plasmids (65 and 56 kbp) of N. eutropha C91. A 117 kbp genomic island encodes multiple genes for heavy metal resistance, including clusters for copper and mercury transport, which are absent from the genomes of other ammonia-oxidizing bacteria (AOB). Whereas the sequences of the two ammonia monooxygenase and three hydroxylamine oxidoreductase gene clusters in N. eutropha C91 are highly similar to those of Nitrosomonas europaea ATCC 19718, a break of synteny in the regions flanking these clusters in each genome is evident. Nitrosomonas eutropha C91 encodes four gene clusters for distinct classes of haem-copper oxidases, two of which are not found in other aerobic AOB. This diversity of terminal oxidases may explain the adaptation of N. eutropha to environments with variable O2 concentrations and/or high concentrations of nitrogen oxides. As with N. europaea, the N. eutropha genome lacks genes for urease metabolism, likely disadvantaging nitrosomonads in low-nitrogen or acidic ecosystems. Taken together, this analysis revealed significant genomic variation between N. eutropha C91 and other AOB, even the closely related N. europaea, and several distinctive properties of the N. eutropha genome that are supportive of niche specialization.

  10. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation.

    PubMed

    Stein, Lisa Y; Arp, Daniel J; Berube, Paul M; Chain, Patrick S G; Hauser, Loren; Jetten, Mike S M; Klotz, Martin G; Larimer, Frank W; Norton, Jeanette M; Op den Camp, Huub J M; Shin, Maria; Wei, Xueming

    2007-12-01

    Analysis of the structure and inventory of the genome of Nitrosomonas eutropha C91 revealed distinctive features that may explain the adaptation of N. eutropha-like bacteria to N-saturated ecosystems. Multiple gene-shuffling events are apparent, including mobilized and replicated transposition, as well as plasmid or phage integration events into the 2.66 Mbp chromosome and two plasmids (65 and 56 kbp) of N. eutropha C91. A 117 kbp genomic island encodes multiple genes for heavy metal resistance, including clusters for copper and mercury transport, which are absent from the genomes of other ammonia-oxidizing bacteria (AOB). Whereas the sequences of the two ammonia monooxygenase and three hydroxylamine oxidoreductase gene clusters in N. eutropha C91 are highly similar to those of Nitrosomonas europaea ATCC 19718, a break of synteny in the regions flanking these clusters in each genome is evident. Nitrosomonas eutropha C91 encodes four gene clusters for distinct classes of haem-copper oxidases, two of which are not found in other aerobic AOB. This diversity of terminal oxidases may explain the adaptation of N. eutropha to environments with variable O(2) concentrations and/or high concentrations of nitrogen oxides. As with N. europaea, the N. eutropha genome lacks genes for urease metabolism, likely disadvantaging nitrosomonads in low-nitrogen or acidic ecosystems. Taken together, this analysis revealed significant genomic variation between N. eutropha C91 and other AOB, even the closely related N. europaea, and several distinctive properties of the N. eutropha genome that are supportive of niche specialization.

  11. Quantitative Proteomic Analysis Reveals Molecular Adaptations in the Hippocampal Synaptic Active Zone of Chronic Mild Stress-Unsusceptible Rats

    PubMed Central

    Zhou, Jian; Liu, Zhao; Yu, Jia; Han, Xin; Fan, Songhua; Shao, Weihua; Chen, Jianjun; Qiao, Rui

    2016-01-01

    Background: While stressful events are recognized as an important cause of major depressive disorder, some individuals exposed to life stressors maintain normal psychological functioning. The molecular mechanism(s) underlying this phenomenon remain unclear. Abnormal transmission and plasticity of hippocampal synapses have been implied to play a key role in the pathoetiology of major depressive disorder. Methods: A chronic mild stress protocol was applied to separate susceptible and unsusceptible rat subpopulations. Proteomic analysis using an isobaric tag for relative and absolute quantitation coupled with tandem mass spectrometry was performed to identify differential proteins in enriched hippocampal synaptic junction preparations. Results: A total of 4318 proteins were quantified, and 89 membrane proteins were present in differential amounts. Of these, SynaptomeDB identified 81 (91%) having a synapse-specific localization. The unbiased profiles identified several candidate proteins within the synaptic junction that may be associated with stress vulnerability or insusceptibility. Subsequent functional categorization revealed that protein systems particularly involved in membrane trafficking at the synaptic active zone exhibited a positive strain as potential molecular adaptations in the unsusceptible rats. Moreover, through STRING and immunoblotting analysis, membrane-associated GTP-bound Rab3a and Munc18-1 appear to coregulate syntaxin-1/SNAP25/VAMP2 assembly at the hippocampal presynaptic active zone of unsusceptible rats, facilitating SNARE-mediated membrane fusion and neurotransmitter release, and may be part of a stress-protection mechanism in actively maintaining an emotional homeostasis. Conclusions: The present results support the concept that there is a range of potential protein adaptations in the hippocampal synaptic active zone of unsusceptible rats, revealing new investigative targets that may contribute to a better understanding of stress

  12. Maritime adaptations and dietary variation in prehistoric Western Alaska: stable isotope analysis of permafrost-preserved human hair.

    PubMed

    Britton, Kate; Knecht, Rick; Nehlich, Olaf; Hillerdal, Charlotta; Davis, Richard S; Richards, Michael P

    2013-07-01

    The reconstruction of diet and subsistence strategies is integral in understanding early human colonizations and cultural adaptations, especially in the Arctic-one of the last areas of North America to be permanently inhabited. However, evidence for early subsistence practices in Western Alaska varies, particularly with regards to the emergence, importance, and intensity of sea mammal hunting. Here, we present stable carbon and nitrogen isotope data from permafrost-preserved human hair from two new prehistoric sites in Western Alaska, providing a direct measure of diet. The isotope evidence indicates a heavy reliance on sea mammal protein among the earlier Norton-period group (1,750 ± 40 cal BP), confirming that the complex hunting technologies required to intensively exploit these animals were most likely already in place in this region by at least the beginning of 1st millennium AD. In contrast, analysis of the more recent Thule-period hair samples (650 ± 40 cal BP; 570 ± 30 cal BP) reveals a more mixed diet, including terrestrial animal protein. Sequential isotope analysis of two longer human hair locks indicates seasonal differences in diet in a single Norton-period individual but demonstrates little dietary variation in a Thule-period individual. These analyses provide direct evidence for dietary differences among Alaska's early Eskimo groups and confirm the antiquity of specialized sea mammal hunting and procurement technologies. The results of this study have implications for our understanding of human adaptation to maritime and high-latitude environments, and the geographical and temporal complexity in early Arctic subsistence.

  13. BESC public portal: an integrative analysis of a resequenced ethanol adapted Clostridium thermocellum mutant

    SciTech Connect

    Syed, Mustafa H; Karpinets, Tatiana V; Leuze, Michael Rex; Park, Byung; Hyatt, Philip Douglas; Brown, Steven D; Uberbacher, Edward C

    2012-01-01

    The BioEnergy Science Center (BESC) is undertaking large experimental campaigns to understand the biosynthesis and biodegradation of biomass and to develop biofuel solutions. BESC is generating large volumes of diverse data, including genome sequences, omics data and assay results. The purpose of the BESC Knowledgebase is to serve as a centralized repository for experimentally generated data and to provide an integrated, interactive and user-friendly analysis framework. The Portal makes available tools for visualization, integration and analysis of data either produced by BESC or obtained from external resources.

  14. Multigroup Confirmatory Factor Analysis for the Teacher Form, Ages 5 to 21, of the Adaptive Behavior Assessment System-II

    ERIC Educational Resources Information Center

    Aricak, O. Tolga; Oakland, Thomas

    2010-01-01

    The American Association on Intellectual and Developmental Disabilities has promulgated various models of adaptive behavior, including its 1992 model that highlighted 10 adaptive skills and its 2002 model that highlighted three conceptual domains. The Adaptive Behavior Assessment System-II (ABAS-II) was designed to be consistent with these models.…

  15. Can local adaptation research in plants inform selection of native plant materials? An analysis of experimental methodologies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Local adaptation research in plants: limitations to synthetic understanding Local adaptation is used as a criterion to select plant materials that will display high fitness in new environments. A large body of research has explored local adaptation in plants, however, to what extent findings can inf...

  16. Self-adaptive method for high frequency multi-channel analysis of surface wave method

    Technology Transfer Automated Retrieval System (TEKTRAN)