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Sample records for change predict functional

  1. Diffusion changes predict cognitive and functional outcome

    DEFF Research Database (Denmark)

    Jokinen, Hanna; Schmidt, Reinhold; Ropele, Stefan; Fazekas, Franz; Gouw, Alida A; Barkhof, Frederik; Scheltens, Philip; Madureira, Sofia; Verdelho, Ana; Ferro, José M; Wallin, Anders; Poggesi, Anna; Inzitari, Domenico; Pantoni, Leonardo; Erkinjuntti, Timo; Group, LADIS Study; Waldemar, Gunhild

    2013-01-01

    A study was undertaken to determine whether diffusion-weighted imaging (DWI) abnormalities in normal-appearing brain tissue (NABT) and in white matter hyperintensities (WMH) predict longitudinal cognitive decline and disability in older individuals independently of the concomitant magnetic resona...

  2. A global remote sensing mission to detect and predict plant functional biodiversity change

    Science.gov (United States)

    Cavender-Bares, J.; Jetz, W.; Pavlick, R.; Schimel, D.; Gamon, J. A.; Hobbie, S. E.; Townsend, P. A.

    2015-12-01

    Global biodiversity is one of the most crucial and least-observed dimensions of the earth system and increasingly important for anticipating changes to both the climate system and ecosystem services. Parallel developments in biodiversity science and remote sensing show that new satellite observations could directly provide global monitoring of one key dimension of global biodiversity, plant functional trait diversity. Remote sensing has already proven a pivotal aid to address the biodiversity data gap. Data on plant productivity, phenology, land-cover and other environmental parameters from MODIS and Landsat satellites currently serve as highly effective covariates for spatiotemporal biodiversity models. The growing functional trait paradigm in ecology, supported by the development of a global plant trait database that includes information for more than one-third of the global flora, highlights the importance of detecting functional diversity globally. Functional traits such as nutrient concentrations, characteristic growth forms and wood density drive both, how organisms respond to environmental change and the effects of organisms on ecosystems. Additionally, the ever more complete tree of life for plants, which presents a link to the shared evolutionary history of plant traits within lineages, coupled with advances in macroevolutionary models and data gap filling techniques, allows predictions of traits that cannot be directly observed. Using experimental manipulations of plant functional and phylogenetic diversity, our team is testing the extent to which we can link above and belowground measurements of biodiversity to remotely sensed optical diversity using hyperspectral data. These efforts will provide the means to fruitfully harness functional diversity data from space from the envisioned Global Biodiversity Observatory (GBO) mission. In turn, remotely sensed hyperspectral data from GBO will allow fundamental breakthroughs and resolve one of the most

  3. Functional trade-offs in succulent stems predict responses to climate change in columnar cacti.

    Science.gov (United States)

    Williams, David G; Hultine, Kevin R; Dettman, David L

    2014-07-01

    Columnar cacti occur naturally in many habitats and environments in the Americas but are conspicuously dominant in very dry desert regions. These majestic plants are widely regarded for their cultural, economic, and ecological value and, in many ecosystems, support highly diverse communities of pollinators, seed dispersers, and frugivores. Massive amounts of water and other resources stored in the succulent photosynthetic stems of these species confer a remarkable ability to grow and reproduce during intensely hot and dry periods. Yet many columnar cacti are potentially under severe threat from environmental global changes, including climate change and loss of habitat. Stems in columnar cacti and other cylindrical-stemmed cacti are morphologically diverse; stem volume-to-surface area ratio (V:S) across these taxa varies by almost two orders of magnitude. Intrinsic functional trade-offs are examined here across a broad range of V:S in species of columnar cacti. It is proposed that variation in photosynthetic gas exchange, growth, and response to stress is highly constrained by stem V:S, establishing a mechanistic framework for understanding the sensitivity of columnar cacti to climate change and drought. Specifically, species that develop stems with low V:S, and thus have little storage capacity, are expected to express high mass specific photosynthesis and growth rates under favourable conditions compared with species with high V:S. But the trade-off of having little storage capacity is that low V:S species are likely to be less tolerant of intense or long-duration drought compared with high V:S species. The application of stable isotope measurements of cactus spines as recorders of growth, water relations, and metabolic responses to the environment across species of columnar cacti that vary in V:S is also reviewed. Taken together, our approach provides a coherent theory and required set of observations needed for predicting the responses of columnar cacti to

  4. Predictive Models for Pulmonary Function Changes After Radiotherapy for Breast Cancer and Lymphoma

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Nieto, Beatriz, E-mail: bsanchez@fis.puc.cl [Facultad de Fisica, Pontificia Universidad Catolica de Chile, Santiago (Chile); Goset, Karen C. [Unidad de Radioterapia, Clinica Alemana de Santiago, Santiago (Chile); Caviedes, Ivan [Servicio y Laboratorio Broncopulmonar, Clinica Alemana de Santiago, Santiago (Chile); Departamento de Medicina, Facultad de Medicina, Clinica Alemana-Universidad del Desarrollo, Santiago (Chile); Delgado, Iris O. [Instituto de Epidemiologia y Politicas de Salud Publica, Facultad de Medicina, Clinica Alemana-Universidad del Desarrollo, Santiago (Chile); Cordova, Andres [Unidad de Radioterapia, Clinica Alemana de Santiago, Santiago (Chile)

    2012-02-01

    Purpose: To propose multivariate predictive models for changes in pulmonary function tests ({Delta}PFTs) with respect to preradiotherapy (pre-RT) values in patients undergoing RT for breast cancer and lymphoma. Methods and Materials: A prospective study was designed to measure {Delta}PFTs of patients undergoing RT. Sixty-six patients were included. Spirometry, lung capacity (measured by helium dilution), and diffusing capacity of carbon monoxide tests were used to measure lung function. Two lung definitions were considered: paired lung vs. irradiated lung (IL). Correlation analysis of dosimetric parameters (mean lung dose and the percentage of lung volume receiving more than a threshold dose) and {Delta}PFTs was carried out to find the best dosimetric predictor. Chemotherapy, age, smoking, and the selected dose-volume parameter were considered as single and interaction terms in a multivariate analysis. Stability of results was checked by bootstrapping. Results: Both lung definitions proved to be similar. Modeling was carried out for IL. Acute and late damage showed the highest correlations with volumes irradiated above {approx}20 Gy (maximum R{sup 2} = 0.28) and {approx}40 Gy (maximum R{sup 2} = 0.21), respectively. RT alone induced a minor and transitory restrictive defect (p = 0.013). Doxorubicin-cyclophosphamide-paclitaxel (Taxol), when administered pre-RT, induced a late, large restrictive effect, independent of RT (p = 0.031). Bootstrap values confirmed the results. Conclusions: None of the dose-volume parameters was a perfect predictor of outcome. Thus, different predictor models for {Delta}PFTs were derived for the IL, which incorporated other nondosimetric parameters mainly through interaction terms. Late {Delta}PFTs seem to behave more serially than early ones. Large restrictive defects were demonstrated in patients pretreated with doxorubicin-cyclophosphamide-paclitaxel.

  5. Predictive Models for Pulmonary Function Changes After Radiotherapy for Breast Cancer and Lymphoma

    International Nuclear Information System (INIS)

    Purpose: To propose multivariate predictive models for changes in pulmonary function tests (ΔPFTs) with respect to preradiotherapy (pre-RT) values in patients undergoing RT for breast cancer and lymphoma. Methods and Materials: A prospective study was designed to measure ΔPFTs of patients undergoing RT. Sixty-six patients were included. Spirometry, lung capacity (measured by helium dilution), and diffusing capacity of carbon monoxide tests were used to measure lung function. Two lung definitions were considered: paired lung vs. irradiated lung (IL). Correlation analysis of dosimetric parameters (mean lung dose and the percentage of lung volume receiving more than a threshold dose) and ΔPFTs was carried out to find the best dosimetric predictor. Chemotherapy, age, smoking, and the selected dose-volume parameter were considered as single and interaction terms in a multivariate analysis. Stability of results was checked by bootstrapping. Results: Both lung definitions proved to be similar. Modeling was carried out for IL. Acute and late damage showed the highest correlations with volumes irradiated above ∼20 Gy (maximum R2 = 0.28) and ∼40 Gy (maximum R2 = 0.21), respectively. RT alone induced a minor and transitory restrictive defect (p = 0.013). Doxorubicin-cyclophosphamide-paclitaxel (Taxol), when administered pre-RT, induced a late, large restrictive effect, independent of RT (p = 0.031). Bootstrap values confirmed the results. Conclusions: None of the dose-volume parameters was a perfect predictor of outcome. Thus, different predictor models for ΔPFTs were derived for the IL, which incorporated other nondosimetric parameters mainly through interaction terms. Late ΔPFTs seem to behave more serially than early ones. Large restrictive defects were demonstrated in patients pretreated with doxorubicin-cyclophosphamide-paclitaxel.

  6. Predicted impacts of climatic change on ant functional diversity and distributions in eastern North American forests

    OpenAIRE

    Del Toro, Israel; Rogério R. Silva; Ellison, Aaron M.

    2015-01-01

    Aims: Climatic change is expected to rearrange species assemblages and ultimately affect organism-mediated ecosystem processes. We focus on identifying patterns and relationships between common ant species (representing 99% of total ant records) richness and functional diversity; model how these patterns may change at local and regional scales in future climatic conditions; and interpret how these changes might influence ant-mediated ecosystem processes. Location: Forested ecosystems of easte...

  7. Structural habitat predicts functional dispersal habitat of a large carnivore: how leopards change spots.

    Science.gov (United States)

    Fattebert, Julien; Robinson, Hugh S; Balme, Guy; Slotow, Rob; Hunter, Luke

    2015-10-01

    Natal dispersal promotes inter-population linkage, and is key to spatial distribution of populations. Degradation of suitable landscape structures beyond the specific threshold of an individual's ability to disperse can therefore lead to disruption of functional landscape connectivity and impact metapopulation function. Because it ignores behavioral responses of individuals, structural connectivity is easier to assess than functional connectivity and is often used as a surrogate for landscape connectivity modeling. However using structural resource selection models as surrogate for modeling functional connectivity through dispersal could be erroneous. We tested how well a second-order resource selection function (RSF) models (structural connectivity), based on GPS telemetry data from resident adult leopard (Panthera pardus L.), could predict subadult habitat use during dispersal (functional connectivity). We created eight non-exclusive subsets of the subadult data based on differing definitions of dispersal to assess the predictive ability of our adult-based RSF model extrapolated over a broader landscape. Dispersing leopards used habitats in accordance with adult selection patterns, regardless of the definition of dispersal considered. We demonstrate that, for a wide-ranging apex carnivore, functional connectivity through natal dispersal corresponds to structural connectivity as modeled by a second-order RSF. Mapping of the adult-based habitat classes provides direct visualization of the potential linkages between populations, without the need to model paths between a priori starting and destination points. The use of such landscape scale RSFs may provide insight into predicting suitable dispersal habitat peninsulas in human-dominated landscapes where mitigation of human-wildlife conflict should be focused. We recommend the use of second-order RSFs for landscape conservation planning and propose a similar approach to the conservation of other wide-ranging large

  8. Final technical report. Can microbial functional traits predict the response and resilience of decomposition to global change?

    Energy Technology Data Exchange (ETDEWEB)

    Allison, Steven D. [Univ. of California, Irvine, CA (United States)

    2015-09-24

    The role of specific micro-organisms in the carbon cycle, and their responses to environmental change, are unknown in most ecosystems. This knowledge gap limits scientists’ ability to predict how important ecosystem processes, like soil carbon storage and loss, will change with climate and other environmental factors. The investigators addressed this knowledge gap by transplanting microbial communities from different environments into new environments and measuring the response of community composition and carbon cycling over time. Using state-of-the-art sequencing techniques, computational tools, and nanotechnology, the investigators showed that microbial communities on decomposing plant material shift dramatically with natural and experimentally-imposed drought. Microbial communities also shifted in response to added nitrogen, but the effects were smaller. These changes had implications for carbon cycling, with lower rates of carbon loss under drought conditions, and changes in the efficiency of decomposition with nitrogen addition. Even when transplanted into the same conditions, microbial communities from different environments remained distinct in composition and functioning for up to one year. Changes in functioning were related to differences in enzyme gene content across different microbial groups. Computational approaches developed for this project allowed the conclusions to be tested more broadly in other ecosystems, and new computer models will facilitate the prediction of microbial traits and functioning across environments. The data and models resulting from this project benefit the public by improving the ability to predict how microbial communities and carbon cycling functions respond to climate change, nutrient enrichment, and other large-scale environmental changes.

  9. Complexity in relational processing predicts changes in functional brain network dynamics.

    Science.gov (United States)

    Cocchi, Luca; Halford, Graeme S; Zalesky, Andrew; Harding, Ian H; Ramm, Brentyn J; Cutmore, Tim; Shum, David H K; Mattingley, Jason B

    2014-09-01

    The ability to link variables is critical to many high-order cognitive functions, including reasoning. It has been proposed that limits in relating variables depend critically on relational complexity, defined formally as the number of variables to be related in solving a problem. In humans, the prefrontal cortex is known to be important for reasoning, but recent studies have suggested that such processes are likely to involve widespread functional brain networks. To test this hypothesis, we used functional magnetic resonance imaging and a classic measure of deductive reasoning to examine changes in brain networks as a function of relational complexity. As expected, behavioral performance declined as the number of variables to be related increased. Likewise, increments in relational complexity were associated with proportional enhancements in brain activity and task-based connectivity within and between 2 cognitive control networks: A cingulo-opercular network for maintaining task set, and a fronto-parietal network for implementing trial-by-trial control. Changes in effective connectivity as a function of increased relational complexity suggested a key role for the left dorsolateral prefrontal cortex in integrating and implementing task set in a trial-by-trial manner. Our findings show that limits in relational processing are manifested in the brain as complexity-dependent modulations of large-scale networks. PMID:23563963

  10. A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning

    Science.gov (United States)

    Wallenstein, Matthew D.; Hall, Edward K.

    2012-01-01

    As the earth system changes in response to human activities, a critical objective is to predict how biogeochemical process rates (e.g. nitrification, decomposition) and ecosystem function (e.g. net ecosystem productivity) will change under future conditions. A particular challenge is that the microbial communities that drive many of these processes are capable of adapting to environmental change in ways that alter ecosystem functioning. Despite evidence that microbes can adapt to temperature, precipitation regimes, and redox fluctuations, microbial communities are typically not optimally adapted to their local environment. For example, temperature optima for growth and enzyme activity are often greater than in situ temperatures in their environment. Here we discuss fundamental constraints on microbial adaptation and suggest specific environments where microbial adaptation to climate change (or lack thereof) is most likely to alter ecosystem functioning. Our framework is based on two principal assumptions. First, there are fundamental ecological trade-offs in microbial community traits that occur across environmental gradients (in time and space). These trade-offs result in shifting of microbial function (e.g. ability to take up resources at low temperature) in response to adaptation of another trait (e.g. limiting maintenance respiration at high temperature). Second, the mechanism and level of microbial community adaptation to changing environmental parameters is a function of the potential rate of change in community composition relative to the rate of environmental change. Together, this framework provides a basis for developing testable predictions about how the rate and degree of microbial adaptation to climate change will alter biogeochemical processes in aquatic and terrestrial ecosystems across the planet.

  11. Dose-volummetrics in the prediction of pulmonary function changes after radiotherapy in patients with lung cancer

    International Nuclear Information System (INIS)

    Objective: To study the correlation between dose-volummetrics and changes of pulmonary function tests (PFTs), and to study the ability of standard dose-volummetrics to predict these changes after radiotherapy. Methods: Pulmonary function was measured in 39 patients with inoperable lung cancer one week before and 2-4 months after radiotherapy. The pulmonary function parameters were the forced vital capacity (FVC), forced expiratory volume in 1 s ( FEV 1.0) and diffusion capacity of carbon monoxide (DLCO). Dose-volummetrics were V10, V15, V20, V25, V30, V35, V40, CTV100, CTV95, CTV90, CTV80, lung Dean, Veff and NTCP. Pearson and line regression analysis was performed to determine whether the correlation existed between the metrics and the changes of PFTs. Results: No correlation was found between the dose- volummetrics and the changes in PFTs. Excluding patients (n=15) with pretreatment atelectasis, significant correlation was found between the dose-volummetrics (V20, V25, V30, V35, V40, GTV, Veff and Dmean) and the PFTs changes(r=0.469-0.695, P≤0.05). Therefore, the re-expansion may have jesperdized the proper data to the present record. Multivariate analysis showed that V30 was the risk factor to affect the changes of FEV 1.0 and DLCO (P=0.046, 0.041). The pulmonary function of patients with V30≥18% was worse than patients with V30 30 is the risk factor to affect the pulmonary function changes in patients with lung cancer excluding those who have had pretreatment atelectasis. (authors)

  12. Does physical activity change predict functional recovery in low back pain? Protocol for a prospective cohort study

    Directory of Open Access Journals (Sweden)

    McDonough Suzanne M

    2009-11-01

    Full Text Available Abstract Background Activity advice and prescription are commonly used in the management of low back pain (LBP. Although there is evidence for advising patients with LBP to remain active, facilitating both recovery and return to work, to date no research has assessed whether objective measurements of free living physical activity (PA can predict outcome, recovery and course of LBP. Methods An observational longitudinal study will investigate PA levels in a cohort of community-dwelling working age adults with acute and sub-acute LBP. Each participant's PA level, functional status, mood, fear avoidance behaviours, and levels of pain, psychological distress and occupational activity will be measured on three occasions during for 1 week periods at baseline, 3 months, and 1 year. Physical activity levels will be measured by self report, RT3 triaxial accelerometer, and activity recall questionnaires. The primary outcome measure of functional recovery will be the Roland Morris Disability Questionnaire (RMDQ. Free living PA levels and changes in functional status will be quantified in order to look at predictive relationships between levels and changes in free living PA and functional recovery in a LBP population. Discussion This research will investigate levels and changes in activity levels of an acute LBP cohort and the predictive relationship to LBP recovery. The results will assess whether occupational, psychological and behavioural factors affect the relationship between free living PA and LBP recovery. Results from this research will help to determine the strength of evidence supporting international guidelines that recommend restoration of normal activity in managing LBP. Trial registration [Clinical Trial Registration Number, ACTRN12609000282280

  13. Initiating Moderate to Heavy Alcohol Use Predicts Changes in Neuropsychological Functioning for Adolescent Girls and Boys

    OpenAIRE

    Squeglia, L M; Spadoni, A D; Infante, M. A.; Myers, M. G.; Tapert, S. F.

    2009-01-01

    This study prospectively examines the influence of alcohol on neuropsychological functioning in a sample of boys and girls who were characterized prior to initiating drinking (N=76, ages 12–14). Adolescents who transitioned into heavy (n= 25; 11 female, 14 male) or moderate (n=11; 2 female, 9 male) drinking were compared to demographically-matched controls who remained non-users throughout the approximately 3-year follow-up period (n=40; 16 female, 24 male). For girls, more drinking days in t...

  14. Changing identity: predicting adjustment to organizational restructure as a function of subgroup and superordinate identification.

    Science.gov (United States)

    Jetten, Jolanda; O'Brien, Anne; Trindall, Nicole

    2002-06-01

    We investigated a work-team restructure within an organization obtaining measures before and after the change occurred. Pre-restructure analyses revealed that, in addition to informational variables, subgroup identification (work-team) and superordinate identification (organization) were important predictors of negative feelings towards the restructure. The more that employees identified with the subgroup, the more negative feelings they reported about the upcoming change. In contrast, the higher the identification with the superordinate group, the less negative employees felt. Longitudinal analysis revealed that compared with the pre-restructure, post-restructure levels of work-team identification, organizational identification, job satisfaction and perceived work-team performance were significantly lower. Pre-restructure work-team identification was a stronger predictor of post-restructure job satisfaction than pre-restructure organizational identification. In addition, it was found that pre-restructure work-team identification and organizational identification had opposing effects on post-restructure organizational identification. There was some evidence that high initial organizational identification protected long-term organizational commitment. PMID:12133229

  15. Predicting protein structure classes from function predictions

    DEFF Research Database (Denmark)

    Sommer, I.; Rahnenfuhrer, J.; de Lichtenberg, Ulrik;

    2004-01-01

    We introduce a new approach to using the information contained in sequence-to-function prediction data in order to recognize protein template classes, a critical step in predicting protein structure. The data on which our method is based comprise probabilities of functional categories; for given......-to-structure prediction methods....

  16. Are mean lung dose and changes in respiration during RT predictive for pulmonary function changes after RT?

    DEFF Research Database (Denmark)

    Jensen, K.; Bernchou, U.; Schytte, T.;

    2015-01-01

    Purpose/Objective: Radiotherapy (RT) of lung cancer patients could be improved if patient specific dose tolerances can be estimated during the first weeks of a fractionated treatment course. Such tolerances may be estimated from the delivered dose distribution and changes in ventilation and...... respiration patterns extracted from frequently recorded 4DCone Beam CT. Materials and Methods: This is a study of 140 non-small-cell lung cancer (NSCLC) patients, which were treated with 60-66 Gy in 30-33 fractions. Measures of ventilation were generated by the freeware tool elastix (http......) within the healthy lung region was used as a measure of the overall lung ventilation during the treatment course. Amsterdam Shrouds of the 4D-CBCT projections were generated by RTK-software, and the respiratory period (ReP) was estimated from the extracted respiratory signal. For each patient the slope...

  17. Predicting cognitive change within domains

    OpenAIRE

    Duff, Kevin; Beglinger, Leigh J.; Moser, David J.; Paulsen, Jane S.

    2010-01-01

    Standardized regression based (SRB) formulas, a method for predicting cognitive change across time, traditionally use baseline performance on a neuropsychological measure to predict future performance on that same measure. However, there are instances in which the same tests may not be given at follow-up assessments (e.g., lack of continuity of provider, avoiding practice effects). The current study sought to expand this methodology by developing SRBs to predict performance on different tests...

  18. Are Some Semantic Changes Predictable?

    DEFF Research Database (Denmark)

    Schousboe, Steen

    2010-01-01

      Historical linguistics is traditionally concerned with phonology and syntax. With the exception of grammaticalization - the development of auxiliary verbs, the syntactic rather than localistic use of prepositions, etc. - semantic change has usually not been described as a result of regular deve...... developments, but only as specific meaning changes in individual words. This paper will suggest some regularities in semantic change, regularities which, like sound laws, have predictive power and can be tested against recorded languages.......  Historical linguistics is traditionally concerned with phonology and syntax. With the exception of grammaticalization - the development of auxiliary verbs, the syntactic rather than localistic use of prepositions, etc. - semantic change has usually not been described as a result of regular...

  19. Stock Price Change Rate Prediction by Utilizing Social Network Activities

    OpenAIRE

    Shangkun Deng; Takashi Mitsubuchi; Akito Sakurai

    2014-01-01

    Predicting stock price change rates for providing valuable information to investors is a challenging task. Individual participants may express their opinions in social network service (SNS) before or after their transactions in the market; we hypothesize that stock price change rate is better predicted by a function of social network service activities and technical indicators than by a function of just stock market activities. The hypothesis is tested by accuracy of predictions as well as pe...

  20. Predictive Functional Control for Fractional Order System

    Directory of Open Access Journals (Sweden)

    Morteza Abdolhosseini

    2014-01-01

    Full Text Available The fractional calculus is the area of mathematics that handles derivatives and integrals of any arbitrary order (fractional or integer, real or complex order. Predictive Functional Control (PFC is one of the most popular methods of model predictive control. The implementation of the predictive functional controller (PFC on the fractional order systems has been presented in this paper. The effect of various approximations, sensitivity analysis, tuning of predictive functional controller parameters, the effect of delay and noise analysis of the fractional-order system has been considered. It has been shown that, in fractional order system, predictive functional control gives acceptable results

  1. An iterative approach of protein function prediction

    Directory of Open Access Journals (Sweden)

    Chi Xiaoxiao

    2011-11-01

    Full Text Available Abstract Background Current approaches of predicting protein functions from a protein-protein interaction (PPI dataset are based on an assumption that the available functions of the proteins (a.k.a. annotated proteins will determine the functions of the proteins whose functions are unknown yet at the moment (a.k.a. un-annotated proteins. Therefore, the protein function prediction is a mono-directed and one-off procedure, i.e. from annotated proteins to un-annotated proteins. However, the interactions between proteins are mutual rather than static and mono-directed, although functions of some proteins are unknown for some reasons at present. That means when we use the similarity-based approach to predict functions of un-annotated proteins, the un-annotated proteins, once their functions are predicted, will affect the similarities between proteins, which in turn will affect the prediction results. In other words, the function prediction is a dynamic and mutual procedure. This dynamic feature of protein interactions, however, was not considered in the existing prediction algorithms. Results In this paper, we propose a new prediction approach that predicts protein functions iteratively. This iterative approach incorporates the dynamic and mutual features of PPI interactions, as well as the local and global semantic influence of protein functions, into the prediction. To guarantee predicting functions iteratively, we propose a new protein similarity from protein functions. We adapt new evaluation metrics to evaluate the prediction quality of our algorithm and other similar algorithms. Experiments on real PPI datasets were conducted to evaluate the effectiveness of the proposed approach in predicting unknown protein functions. Conclusions The iterative approach is more likely to reflect the real biological nature between proteins when predicting functions. A proper definition of protein similarity from protein functions is the key to predicting

  2. Quality changes and predictive models of radial basis function neural networks for brined common carp (Cyprinus carpio) fillets during frozen storage.

    Science.gov (United States)

    Kong, Chunli; Wang, Huiyi; Li, Dapeng; Zhang, Yuemei; Pan, Jinfeng; Zhu, Beiwei; Luo, Yongkang

    2016-06-15

    To investigate and predict quality of 2% brined common carp (Cyprinus carpio) fillets during frozen storage, free fatty acids (FFA), salt extractable protein (SEP), total sulfhydryl (SH) content, and Ca(2+)-ATPase activity were determined at 261K, 253K, and 245K, respectively. There was a dramatic increase (Pfirst 3weeks. SEP decreased to 67.31% after 17weeks at 245K, whereas it took about 7weeks and 13weeks to decrease to the same extent at 261K and 253K, respectively. Ca(2+)-ATPase activity kept decreasing to 18.28% after 7weeks at 261K. Furthermore, radial basis function neural networks (RBFNNs) were developed to predict quality (FFA, SEP, SH, and Ca(2+)-ATPase activity) of brined carp fillets during frozen storage with relative errors all within ±5%. Thus, RBFNN is a promising method to predict quality of carp fillets during storage at 245-261K. PMID:26868584

  3. Contextual Factors Predict Patterns of Change in Functioning over 10 Years among Adolescents and Adults with Autism Spectrum Disorders

    Science.gov (United States)

    Woodman, Ashley C.; Smith, Leann E.; Greenberg, Jan S.; Mailick, Marsha R.

    2016-01-01

    In the present study, we jointly employ and integrate variable- and person-centered approaches to identify groups of individuals with autism spectrum disorders (ASD) who have similar profiles of change over a period of 10 years across three critical domains of functioning: maladaptive behaviors, autism symptoms, and daily living skills. Two…

  4. Predictive Functional Control for a Parallel Robot

    OpenAIRE

    Vivas, Oscar Andrès; Poignet, Philippe; Pierrot, François

    2003-01-01

    This paper presents an efficient application of a model based predictive control in parallel mechanisms. A predictive functional control control strategy based on a simplified dynamic model is implemented. Experimental results are shown for the H4 robot, a fully parallel structure providing 3 degrees of freedom (dof) in translation and 1 dof in rotation. Predictive functional control, computed torque control and PID control strategies are compared in complex machining tasks trajectories. The ...

  5. Climate Change as a Predictable Surprise

    International Nuclear Information System (INIS)

    In this article, I analyze climate change as a 'predictable surprise', an event that leads an organization or nation to react with surprise, despite the fact that the information necessary to anticipate the event and its consequences was available (Bazerman and Watkins, 2004). I then assess the cognitive, organizational, and political reasons why society fails to implement wise strategies to prevent predictable surprises generally and climate change specifically. Finally, I conclude with an outline of a set of response strategies to overcome barriers to change

  6. Parental Education Predicts Corticostriatal Functionality in Adulthood

    OpenAIRE

    Gianaros, Peter J.; Manuck, Stephen B.; Sheu, Lei K.; Kuan, Dora C. H.; Votruba-Drzal, Elizabeth; Craig, Anna E.; Hariri, Ahmad R.

    2010-01-01

    Socioeconomic disadvantage experienced in early development predicts ill health in adulthood. However, the neurobiological pathways linking early disadvantage to adult health remain unclear. Lower parental education—a presumptive indicator of early socioeconomic disadvantage—predicts health-impairing adult behaviors, including tobacco and alcohol dependencies. These behaviors depend, in part, on the functionality of corticostriatal brain systems that 1) show developmental plasticity and early...

  7. Year 2 Report: Protein Function Prediction Platform

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, C E

    2012-04-27

    Upon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. The PFP platform is a multi-scale computational modeling system for protein structure-function annotation and function prediction. As of this writing, PFP is the only existing fully automated, high-throughput, multi-scale modeling, whole-proteome annotation platform, and represents a significant advance in the field of genome annotation (Fig. 1). PFP modules perform protein functional annotations at the sequence, systems biology, protein structure, and atomistic levels of biological complexity (Fig. 2). Because these approaches provide orthogonal means of characterizing proteins and suggesting protein function, PFP processing maximizes the protein functional information that can currently be gained by computational means. Comprehensive annotation of pathogen genomes is essential for bio-defense applications in pathogen characterization, threat assessment, and medical countermeasure design and development in that it can short-cut the time and effort required to select and characterize protein biomarkers.

  8. Quantitative assessment of protein function prediction programs.

    Science.gov (United States)

    Rodrigues, B N; Steffens, M B R; Raittz, R T; Santos-Weiss, I C R; Marchaukoski, J N

    2015-01-01

    Fast prediction of protein function is essential for high-throughput sequencing analysis. Bioinformatic resources provide cheaper and faster techniques for function prediction and have helped to accelerate the process of protein sequence characterization. In this study, we assessed protein function prediction programs that accept amino acid sequences as input. We analyzed the classification, equality, and similarity between programs, and, additionally, compared program performance. The following programs were selected for our assessment: Blast2GO, InterProScan, PANTHER, Pfam, and ScanProsite. This selection was based on the high number of citations (over 500), fully automatic analysis, and the possibility of returning a single best classification per sequence. We tested these programs using 12 gold standard datasets from four different sources. The gold standard classification of the databases was based on expert analysis, the Protein Data Bank, or the Structure-Function Linkage Database. We found that the miss rate among the programs is globally over 50%. Furthermore, we observed little overlap in the correct predictions from each program. Therefore, a combination of multiple types of sources and methods, including experimental data, protein-protein interaction, and data mining, may be the best way to generate more reliable predictions and decrease the miss rate. PMID:26782400

  9. Stock price change rate prediction by utilizing social network activities.

    Science.gov (United States)

    Deng, Shangkun; Mitsubuchi, Takashi; Sakurai, Akito

    2014-01-01

    Predicting stock price change rates for providing valuable information to investors is a challenging task. Individual participants may express their opinions in social network service (SNS) before or after their transactions in the market; we hypothesize that stock price change rate is better predicted by a function of social network service activities and technical indicators than by a function of just stock market activities. The hypothesis is tested by accuracy of predictions as well as performance of simulated trading because success or failure of prediction is better measured by profits or losses the investors gain or suffer. In this paper, we propose a hybrid model that combines multiple kernel learning (MKL) and genetic algorithm (GA). MKL is adopted to optimize the stock price change rate prediction models that are expressed in a multiple kernel linear function of different types of features extracted from different sources. GA is used to optimize the trading rules used in the simulated trading by fusing the return predictions and values of three well-known overbought and oversold technical indicators. Accumulated return and Sharpe ratio were used to test the goodness of performance of the simulated trading. Experimental results show that our proposed model performed better than other models including ones using state of the art techniques. PMID:24790586

  10. Prediction Error During Functional and Non-Functional Action Sequences

    DEFF Research Database (Denmark)

    Nielbo, Kristoffer Laigaard; Sørensen, Jesper

    2013-01-01

    recurrent networks were made and the results are presented in this article. The simulations show that non-functional action sequences do indeed increase prediction error, but that context representations, such as abstract goal information, can modulate the error signal considerably. It is also shown......By means of the computational approach the present study investigates the difference between observation of functional behavior (i.e. actions involving necessary integration of subparts) and non-functional behavior (i.e. actions lacking necessary integration of subparts) in terms of prediction...... behavioral study has shown that human subjects segment non-functional behavior in a more fine-grained way than functional behavior. This increase in segmentation rate implies that non-functionality elicits a stronger error signal. To further explore the implications, two computer simulations using simple...

  11. Predicting coastal morphological changes with empirical orthogonal functionmethod

    Directory of Open Access Journals (Sweden)

    Fernando Alvarez

    2016-01-01

    Full Text Available In order to improve the accuracy of prediction when using the empirical orthogonal function (EOF method, this paper describes a novel approach for two-dimensional (2D EOF analysis based on extrapolating both the spatial and temporal EOF components for long-term prediction of coastal morphological changes. The approach was investigated with data obtained from a process-based numerical model, COAST2D, which was applied to an idealized study site with a group of shore-parallel breakwaters. The progressive behavior of the spatial and temporal EOF components, related to bathymetric changes over a training period, was demonstrated, and EOF components were extrapolated with combined linear and exponential functions for long-term prediction. The extrapolated EOF components were then used to reconstruct bathymetric changes. The comparison of the reconstructed bathymetric changes with the modeled results from the COAST2D model illustrates that the presented approach can be effective for long-term prediction of coastal morphological changes, and extrapolating both the spatial and temporal EOF components yields better results than extrapolating only the temporal EOF component.

  12. Predicting Functional Recovery after Acute Ankle Sprain

    OpenAIRE

    Sean R O'Connor; Bleakley, Chris M; Tully, Mark A; McDonough, Suzanne M

    2013-01-01

    INTRODUCTION:Ankle sprains are among the most common acute musculoskeletal conditions presenting to primary care. Their clinical course is variable but there are limited recommendations on prognostic factors. Our primary aim was to identify clinical predictors of short and medium term functional recovery after ankle sprain.METHODS:A secondary analysis of data from adult participants (N = 85) with an acute ankle sprain, enrolled in a randomized controlled trial was undertaken. The predictive v...

  13. Green's functions for topology change

    CERN Document Server

    Martín, J; Soares, I D; Martin, Jerome; Pinto-Neto, Nelson; Soares, Ivano Damiao

    2005-01-01

    We explicitly calculate Green's functions for quantum changes of topology in Friedman-Lemaitre-Robertson-Walker Universes, whose spacelike sections are compact but with distinct topologies depending on the curvature parameter $k$. We use the long-wavelength approximation at second order, and we demonstrate that quantum topological transitions from $k=-1$ to $k=1$ (and vice-versa) are allowed whereas no transition to a flat section is possible establishing thus a selection rule. Finally, a toy model is considered where all these properties are investigated concretely.

  14. Predicting estuarine benthic production using functional diversity

    Directory of Open Access Journals (Sweden)

    Marina Dolbeth

    2014-05-01

    Full Text Available We considered an estuarine system having naturally low levels of diversity, but attaining considerable high production levels, and being subjected to different sorts of anthropogenic impacts and climate events to investigate the relationship between diversity and secondary production. Functional diversity measures were used to predict benthic production, which is considered as a proxy of the ecosystem provisioning services. To this end, we used a 14-year dataset on benthic invertebrate community production from a seagrass and a sandflat habitat and we adopted a sequential modeling approach, where abiotic, trait community weighted means (CWM and functional diversity indices were tested by generalized linear models (GLM, and their significant variables were then combined to produce a final model. Almost 90% of variance of the benthic production could be predicted by combining the number of locomotion types, the absolute maximum atmospheric temperature (proxy of the heat waves occurrence, the type of habitat and the mean body mass, by order of importance. This result is in agreement with the mass ratio hypothesis, where ecosystem functions/services can be chiefly predicted by the dominant trait in the community, here measured as CWM. The increase of benthic production with the number of locomotion types may be seen as greater possibility of using the resources available in the system. Such greater efficiency would increase production. The other variables were also discussed in line of the previous hypothesis and taking into account the general positive relationship obtained between production and functional diversity indices. Overall, it was concluded that traits representative of wider possibilities of using available resources and higher functional diversity are related with higher benthic production.

  15. Predicting Contextual Sequences via Submodular Function Maximization

    CERN Document Server

    Dey, Debadeepta; Hebert, Martial; Bagnell, J Andrew

    2012-01-01

    Sequence optimization, where the items in a list are ordered to maximize some reward has many applications such as web advertisement placement, search, and control libraries in robotics. Previous work in sequence optimization produces a static ordering that does not take any features of the item or context of the problem into account. In this work, we propose a general approach to order the items within the sequence based on the context (e.g., perceptual information, environment description, and goals). We take a simple, efficient, reduction-based approach where the choice and order of the items is established by repeatedly learning simple classifiers or regressors for each "slot" in the sequence. Our approach leverages recent work on submodular function maximization to provide a formal regret reduction from submodular sequence optimization to simple cost-sensitive prediction. We apply our contextual sequence prediction algorithm to optimize control libraries and demonstrate results on two robotics problems: ...

  16. Linear Prediction Using Refined Autocorrelation Function

    Directory of Open Access Journals (Sweden)

    M. Shahidur Rahman

    2007-07-01

    Full Text Available This paper proposes a new technique for improving the performance of linear prediction analysis by utilizing a refined version of the autocorrelation function. Problems in analyzing voiced speech using linear prediction occur often due to the harmonic structure of the excitation source, which causes the autocorrelation function to be an aliased version of that of the vocal tract impulse response. To estimate the vocal tract characteristics accurately, however, the effect of aliasing must be eliminated. In this paper, we employ homomorphic deconvolution technique in the autocorrelation domain to eliminate the aliasing effect occurred due to periodicity. The resulted autocorrelation function of the vocal tract impulse response is found to produce significant improvement in estimating formant frequencies. The accuracy of formant estimation is verified on synthetic vowels for a wide range of pitch frequencies typical for male and female speakers. The validity of the proposed method is also illustrated by inspecting the spectral envelopes of natural speech spoken by high-pitched female speaker. The synthesis filter obtained by the current method is guaranteed to be stable, which makes the method superior to many of its alternatives.

  17. Permafrost, climate, and change: predictive modelling approach.

    Science.gov (United States)

    Anisimov, O.

    2003-04-01

    Predicted by GCMs enhanced warming of the Arctic will lead to discernible impacts on permafrost and northern environment. Mathematical models of different complexity forced by scenarios of climate change may be used to predict such changes. Permafrost models that are currently in use may be divided into four groups: index-based models (e.g. frost index model, N-factor model); models of intermediate complexity based on equilibrium simplified solution of the Stephan problem ("Koudriavtcev's" model and its modifications), and full-scale comprehensive dynamical models. New approach of stochastic modelling came into existence recently and has good prospects for the future. Important task is to compare the ability of the models that are different in complexity, concept, and input data requirements to capture the major impacts of changing climate on permafrost. A progressive increase in the depth of seasonal thawing (often referred to as the active-layer thickness, ALT) could be a relatively short-term reaction to climatic warming. At regional and local scales, it may produce substantial effects on vegetation, soil hydrology and runoff, as the water storage capacity of near-surface permafrost will be changed. Growing public concerns are associated with the impacts that warming of permafrost may have on engineered infrastructure built upon it. At the global scale, increase of ALT could facilitate further climatic change if more greenhouse gases are released when the upper layer of the permafrost thaws. Since dynamic permafrost models require complete set of forcing data that is not readily available on the circumpolar scale, they could be used most effectively in regional studies, while models of intermediate complexity are currently best tools for the circumpolar assessments. Set of five transient scenarios of climate change for the period 1980 - 2100 has been constructed using outputs from GFDL, NCAR, CCC, HadCM, and ECHAM-4 models. These GCMs were selected in the course

  18. Holographic predictions for cosmological 3-point functions

    CERN Document Server

    Bzowski, Adam; Skenderis, Kostas

    2011-01-01

    We present the holographic predictions for cosmological 3-point correlators, involving both scalar and tensor modes, for a universe which started in a non-geometric holographic phase. Holographic formulae relate the cosmological 3-point functions to stress tensor correlation functions of a holographically dual three-dimensional non-gravitational QFT. We compute these correlators at 1-loop order for a theory containing massless scalars, fermions and gauge fields, and present an extensive analysis of the constraints due to Ward identities showing that they uniquely determine the correlators up to a few constants. We define shapes for all cosmological bispectra and compare the holographic shapes to the slow-roll ones, finding that some are distinguishable while others, perhaps surprisingly, are not.

  19. Executive functions predict conceptual learning of science.

    Science.gov (United States)

    Rhodes, Sinéad M; Booth, Josephine N; Palmer, Lorna Elise; Blythe, Richard A; Delibegovic, Mirela; Wheate, Nial J

    2016-06-01

    We examined the relationship between executive functions and both factual and conceptual learning of science, specifically chemistry, in early adolescence. Sixty-three pupils in their second year of secondary school (aged 12-13 years) participated. Pupils completed tasks of working memory (Spatial Working Memory), inhibition (Stop-Signal), attention set-shifting (ID/ED), and planning (Stockings of Cambridge), from the CANTAB. They also participated in a chemistry teaching session, practical, and assessment on the topic of acids and alkalis designed specifically for this study. Executive function data were related to (1) the chemistry assessment which included aspects of factual and conceptual learning and (2) a recent school science exam. Correlational analyses between executive functions and both the chemistry assessment and science grades revealed that science achievements were significantly correlated with working memory. Linear regression analysis revealed that visuospatial working memory ability was predictive of chemistry performance. Interestingly, this relationship was observed solely in relation to the conceptual learning condition of the assessment highlighting the role of executive functions in understanding and applying knowledge about what is learned within science teaching. PMID:26751597

  20. Predicting functional recovery after acute ankle sprain.

    Directory of Open Access Journals (Sweden)

    Sean R O'Connor

    Full Text Available INTRODUCTION: Ankle sprains are among the most common acute musculoskeletal conditions presenting to primary care. Their clinical course is variable but there are limited recommendations on prognostic factors. Our primary aim was to identify clinical predictors of short and medium term functional recovery after ankle sprain. METHODS: A secondary analysis of data from adult participants (N = 85 with an acute ankle sprain, enrolled in a randomized controlled trial was undertaken. The predictive value of variables (age, BMI, gender, injury mechanism, previous injury, weight-bearing status, medial joint line pain, pain during weight-bearing dorsiflexion and lateral hop test recorded at baseline and at 4 weeks post injury were investigated for their prognostic ability. Recovery was determined from measures of subjective ankle function at short (4 weeks and medium term (4 months follow ups. Multivariate stepwise linear regression analyses were undertaken to evaluate the association between the aforementioned variables and functional recovery. RESULTS: Greater age, greater injury grade and weight-bearing status at baseline were associated with lower function at 4 weeks post injury (p<0.01; adjusted R square=0.34. Greater age, weight-bearing status at baseline and non-inversion injury mechanisms were associated with lower function at 4 months (p<0.01; adjusted R square=0.20. Pain on medial palpation and pain on dorsiflexion at 4 weeks were the most valuable prognostic indicators of function at 4 months (p< 0.01; adjusted R square=0.49. CONCLUSION: The results of the present study provide further evidence that ankle sprains have a variable clinical course. Age, injury grade, mechanism and weight-bearing status at baseline provide some prognostic information for short and medium term recovery. Clinical assessment variables at 4 weeks were the strongest predictors of recovery, explaining 50% of the variance in ankle function at 4 months. Further

  1. Improving protein function prediction methods with integrated literature data

    Directory of Open Access Journals (Sweden)

    Gabow Aaron P

    2008-04-01

    Full Text Available Abstract Background Determining the function of uncharacterized proteins is a major challenge in the post-genomic era due to the problem's complexity and scale. Identifying a protein's function contributes to an understanding of its role in the involved pathways, its suitability as a drug target, and its potential for protein modifications. Several graph-theoretic approaches predict unidentified functions of proteins by using the functional annotations of better-characterized proteins in protein-protein interaction networks. We systematically consider the use of literature co-occurrence data, introduce a new method for quantifying the reliability of co-occurrence and test how performance differs across species. We also quantify changes in performance as the prediction algorithms annotate with increased specificity. Results We find that including information on the co-occurrence of proteins within an abstract greatly boosts performance in the Functional Flow graph-theoretic function prediction algorithm in yeast, fly and worm. This increase in performance is not simply due to the presence of additional edges since supplementing protein-protein interactions with co-occurrence data outperforms supplementing with a comparably-sized genetic interaction dataset. Through the combination of protein-protein interactions and co-occurrence data, the neighborhood around unknown proteins is quickly connected to well-characterized nodes which global prediction algorithms can exploit. Our method for quantifying co-occurrence reliability shows superior performance to the other methods, particularly at threshold values around 10% which yield the best trade off between coverage and accuracy. In contrast, the traditional way of asserting co-occurrence when at least one abstract mentions both proteins proves to be the worst method for generating co-occurrence data, introducing too many false positives. Annotating the functions with greater specificity is harder

  2. Developmental Changes in Executive Functioning

    Science.gov (United States)

    Lee, Kerry; Bull, Rebecca; Ho, Ringo M. H.

    2013-01-01

    Although early studies of executive functioning in children supported Miyake et al.'s (2000) three-factor model, more recent findings supported a variety of undifferentiated or two-factor structures. Using a cohort-sequential design, this study examined whether there were age-related differences in the structure of executive functioning among…

  3. Resting state functional connectivity predicts neurofeedback response

    Directory of Open Access Journals (Sweden)

    Dustin Scheinost

    2014-09-01

    Full Text Available Tailoring treatments to the specific needs and biology of individual patients – personalized medicine – requires delineation of reliable predictors of response. Unfortunately, these have been slow to emerge, especially in neuropsychiatric disorders. We have recently described a real-time functional magnetic resonance imaging (rt-fMRI neurofeedback protocol that can reduce contamination-related anxiety, a prominent symptom of many cases of obsessive-compulsive disorder (OCD. Individual response to this intervention is variable. Here we used patterns of brain functional connectivity, as measured by baseline resting-state fMRI (rs-fMRI, to predict improvements in contamination anxiety after neurofeedback training. Activity of a region of the orbitofrontal cortex (OFC and anterior prefrontal cortex, Brodmann area (BA 10, associated with contamination anxiety in each subject was measured in real time and presented as a neurofeedback signal, permitting subjects to learn to modulate this target brain region. We have previously reported both enhanced OFC/BA 10 control and improved anxiety in a group of subclinically anxious subjects after neurofeedback. Five individuals with contamination-related OCD who underwent the same protocol also showed improved clinical symptomatology. In both groups, these behavioral improvements were strongly correlated with baseline whole-brain connectivity in the OFC/BA 10, computed from rs-fMRI collected several days prior to neurofeedback training. These pilot data suggest that rs-fMRI can be used to identify individuals likely to benefit from rt-fMRI neurofeedback training to control contamination anxiety.

  4. Functional categories and categorial change

    DEFF Research Database (Denmark)

    Rijkhoff, Jan

    2016-01-01

    , communicative) acts.      A functional category consists of linguistic units (formally expressed as e.g. a clause, a phrase, a word or an affix) that are the products of an interpersonal act, which include SPEECH ACTS (Austin 1962), THETICAL ACTS (Kaltenböck et al. 2011), PROPOSITIONAL ACTS (predicating...... and semantic categories, functional categories (as defined here) have played a rather marginal role in linguistics. In the tentative typology of functional categories proposed below, linguistic forms and constructions are classified on the basis of various kinds of interpersonal (discourse...

  5. Predictive Function Control for Milling Process

    Directory of Open Access Journals (Sweden)

    Zhihuan Zhang

    2013-08-01

    Full Text Available The adaptive constant control for the cutting process is an effective way to improve the productivity of the Computer Numerical Control (CNC milling machine. This control is achieved through adjusting the feed rate online, and many scholars has been concentrated in the field. However, in of the existing adaptive constant control algorithms, the controller parameters are tuned only depends on the dynamic behavior of the controlled system, without giving effect to control the input and system output prospects. Therefore, milling force mutated because of the mutation of the depth or width of cut usually resulting in the overshooting of control system or overflow of control input. In this paper, we present a new solution to the problem, in which a mathematical model of milling process is established based on the characteristics of the CNC milling process. Then the predictive functional control law is introduced on the milling process and the controller parameters can be tuned online. The Simulation results show that the proposed method has the advantages of strong robustness to different interferences, good practicability for the milling process, and good real-time control responsibility.  

  6. Dynamical functional prediction and classification, with application to traffic flow prediction

    OpenAIRE

    Chiou, Jeng-Min

    2013-01-01

    Motivated by the need for accurate traffic flow prediction in transportation management, we propose a functional data method to analyze traffic flow patterns and predict future traffic flow. In this study we approach the problem by sampling traffic flow trajectories from a mixture of stochastic processes. The proposed functional mixture prediction approach combines functional prediction with probabilistic functional classification to take distinct traffic flow patterns into account. The proba...

  7. Hydrologic predictions in a changing environment: behavioral modeling

    Directory of Open Access Journals (Sweden)

    B. Schaefli

    2010-10-01

    Full Text Available Most hydrological models are valid at most only in a few places and cannot be reasonably transferred to other places or to far distant time periods. Transfer in space is difficult because the models are conditioned on past observations at particular places to define parameter values and unobservable processes that are needed to fully characterize the structure and functioning of the landscape. Transfer in time has to deal with the likely temporal changes to both parameters and processes under future changed conditions. This remains an important obstacle to addressing some of the most urgent prediction questions in hydrology, such as prediction in ungauged basins and prediction under global change. In this paper, we propose a new approach to catchment hydrological modeling, based on universal principles that do not change in time and that remain valid across many places. The key to this framework, which we call behavioral modeling, is to assume that these universal and time-invariant organizing principles can be used to identify the most appropriate model structure (including parameter values and responses for a given ecosystem at a given moment in time. The organizing principles may be derived from fundamental physical or biological laws, or from empirical laws that have been demonstrated to be time-invariant and to hold at many places and scales. Much fundamental research remains to be undertaken to help discover these organizing principles on the basis of exploration of observed patterns of landscape structure and hydrological behavior and their interpretation as legacy effects of past co-evolution of climate, soils, topography, vegetation and humans. Our hope is that the new behavioral modeling framework will be a step forward towards a new vision for hydrology where models are capable of more confidently predicting the behavior of catchments beyond what has been observed or experienced before.

  8. Predicting restoration of kidney function during CRRT-free intervals

    Directory of Open Access Journals (Sweden)

    Heise Daniel

    2012-01-01

    Full Text Available Abstract Background Renal failure is common in critically ill patients and frequently requires continuous renal replacement therapy (CRRT. CRRT is discontinued at regular intervals for routine changes of the disposable equipment or for replacing clogged filter membrane assemblies. The present study was conducted to determine if the necessity to continue CRRT could be predicted during the CRRT-free period. Materials and methods In the period from 2003 to 2006, 605 patients were treated with CRRT in our ICU. A total of 222 patients with 448 CRRT-free intervals had complete data sets and were used for analysis. Of the total CRRT-free periods, 225 served as an evaluation group. Twenty-nine parameters with an assumed influence on kidney function were analyzed with regard to their potential to predict the restoration of kidney function during the CRRT-free interval. Using univariate analysis and logistic regression, a prospective index was developed and validated in the remaining 223 CRRT-free periods to establish its prognostic strength. Results Only three parameters showed an independent influence on the restoration of kidney function during CRRT-free intervals: the number of previous CRRT cycles (medians in the two outcome groups: 1 vs. 2, the "Sequential Organ Failure Assessment"-score (means in the two outcome groups: 8.3 vs. 9.2 and urinary output after the cessation of CRRT (medians in two outcome groups: 66 ml/h vs. 10 ml/h. The prognostic index, which was calculated from these three variables, showed a satisfactory potential to predict the kidney function during the CRRT-free intervals; Receiver operating characteristic (ROC analysis revealed an area under the curve of 0.798. Conclusion Restoration of kidney function during CRRT-free periods can be predicted with an index calculated from three variables. Prospective trials in other hospitals must clarify whether our results are generally transferable to other patient populations.

  9. Farm functionality changes in relation to changes in Agricultural policies

    DEFF Research Database (Denmark)

    Andersen, Peter Stubkjær; Vejre, Henrik; Dalgaard, Tommy;

    2015-01-01

    Changes in European agriculture over the last 70 year have frequently been labelled with the keywords intensification, specialisation and concentration. A variety of empirical studies of the development in farm characteristics and landscape structures have been undertaken to describe the change in...... details. The structural changes in agriculture are well accounted for in national and European statistics, however changes in farm functions have also occurred. It has been suggested that European agriculture nowadays are undergoing changes from monofunctional focus on production to a wider...... functional focused analysis of the temporal changes in four selected farm functions – production, residence, habitat and recreation. The studies are based on data from an interview study conducted in the end 1990s and in 2008 in three study area in Denmark. To quantify the functional changes an indicator...

  10. Text mining improves prediction of protein functional sites.

    Directory of Open Access Journals (Sweden)

    Karin M Verspoor

    Full Text Available We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites. The structure analysis was carried out using Dynamics Perturbation Analysis (DPA, which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions.

  11. Fast dynamics perturbation analysis for prediction of protein functional sites

    Directory of Open Access Journals (Sweden)

    Cohn Judith D

    2008-01-01

    Full Text Available Abstract Background We present a fast version of the dynamics perturbation analysis (DPA algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites. Results The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm. Conclusion Compared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.

  12. Prediction uncertainty of environmental change effects on temperate European biodiversity.

    Science.gov (United States)

    Dormann, Carsten F; Schweiger, Oliver; Arens, P; Augenstein, I; Aviron, St; Bailey, Debra; Baudry, J; Billeter, R; Bugter, R; Bukácek, R; Burel, F; Cerny, M; Cock, Raphaël De; De Blust, Geert; DeFilippi, R; Diekötter, Tim; Dirksen, J; Durka, W; Edwards, P J; Frenzel, M; Hamersky, R; Hendrickx, Frederik; Herzog, F; Klotz, St; Koolstra, B; Lausch, A; Le Coeur, D; Liira, J; Maelfait, J P; Opdam, P; Roubalova, M; Schermann-Legionnet, Agnes; Schermann, N; Schmidt, T; Smulders, M J M; Speelmans, M; Simova, P; Verboom, J; van Wingerden, Walter; Zobel, M

    2008-03-01

    Observed patterns of species richness at landscape scale (gamma diversity) cannot always be attributed to a specific set of explanatory variables, but rather different alternative explanatory statistical models of similar quality may exist. Therefore predictions of the effects of environmental change (such as in climate or land cover) on biodiversity may differ considerably, depending on the chosen set of explanatory variables. Here we use multimodel prediction to evaluate effects of climate, land-use intensity and landscape structure on species richness in each of seven groups of organisms (plants, birds, spiders, wild bees, ground beetles, true bugs and hoverflies) in temperate Europe. We contrast this approach with traditional best-model predictions, which we show, using cross-validation, to have inferior prediction accuracy. Multimodel inference changed the importance of some environmental variables in comparison with the best model, and accordingly gave deviating predictions for environmental change effects. Overall, prediction uncertainty for the multimodel approach was only slightly higher than that of the best model, and absolute changes in predicted species richness were also comparable. Richness predictions varied generally more for the impact of climate change than for land-use change at the coarse scale of our study. Overall, our study indicates that the uncertainty introduced to environmental change predictions through uncertainty in model selection both qualitatively and quantitatively affects species richness projections. PMID:18070098

  13. "Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements.

    Science.gov (United States)

    Marcovitz, Amir; Jia, Robin; Bejerano, Gill

    2016-05-01

    Evolutionary changes in cis-regulatory elements are thought to play a key role in morphological and physiological diversity across animals. Many conserved noncoding elements (CNEs) function as cis-regulatory elements, controlling gene expression levels in different biological contexts. However, determining specific associations between CNEs and related phenotypes is a challenging task. Here, we present a computational "reverse genomics" approach that predicts the phenotypic functions of human CNEs. We identify thousands of human CNEs that were lost in at least two independent mammalian lineages (IL-CNEs), and match their evolutionary profiles against a diverse set of phenotypes recently annotated across multiple mammalian species. We identify 2,759 compelling associations between human CNEs and a diverse set of mammalian phenotypes. We discuss multiple CNEs, including a predicted ear element near BMP7, a pelvic CNE in FBN1, a brain morphology element in UBE4B, and an aquatic adaptation forelimb CNE near EGR2, and provide a full list of our predictions. As more genomes are sequenced and more traits are annotated across species, we expect our method to facilitate the interpretation of noncoding mutations in human disease and expedite the discovery of individual CNEs that play key roles in human evolution and development. PMID:26744417

  14. Platelet serotonin transporter function predicts default-mode network activity.

    Directory of Open Access Journals (Sweden)

    Christian Scharinger

    Full Text Available The serotonin transporter (5-HTT is abundantly expressed in humans by the serotonin transporter gene SLC6A4 and removes serotonin (5-HT from extracellular space. A blood-brain relationship between platelet and synaptosomal 5-HT reuptake has been suggested, but it is unknown today, if platelet 5-HT uptake can predict neural activation of human brain networks that are known to be under serotonergic influence.A functional magnetic resonance study was performed in 48 healthy subjects and maximal 5-HT uptake velocity (Vmax was assessed in blood platelets. We used a mixed-effects multilevel analysis technique (MEMA to test for linear relationships between whole-brain, blood-oxygen-level dependent (BOLD activity and platelet Vmax.The present study demonstrates that increases in platelet Vmax significantly predict default-mode network (DMN suppression in healthy subjects independent of genetic variation within SLC6A4. Furthermore, functional connectivity analyses indicate that platelet Vmax is related to global DMN activation and not intrinsic DMN connectivity.This study provides evidence that platelet Vmax predicts global DMN activation changes in healthy subjects. Given previous reports on platelet-synaptosomal Vmax coupling, results further suggest an important role of neuronal 5-HT reuptake in DMN regulation.

  15. Relationship between efficiency and predictability in stock price change

    Science.gov (United States)

    Eom, Cheoljun; Oh, Gabjin; Jung, Woo-Sung

    2008-09-01

    In this study, we evaluate the relationship between efficiency and predictability in the stock market. The efficiency, which is the issue addressed by the weak-form efficient market hypothesis, is calculated using the Hurst exponent and the approximate entropy (ApEn). The predictability corresponds to the hit-rate; this is the rate of consistency between the direction of the actual price change and that of the predicted price change, as calculated via the nearest neighbor prediction method. We determine that the Hurst exponent and the ApEn value are negatively correlated. However, predictability is positively correlated with the Hurst exponent.

  16. LSD-induced entropic brain activity predicts subsequent personality change.

    Science.gov (United States)

    Lebedev, A V; Kaelen, M; Lövdén, M; Nilsson, J; Feilding, A; Nutt, D J; Carhart-Harris, R L

    2016-09-01

    Personality is known to be relatively stable throughout adulthood. Nevertheless, it has been shown that major life events with high personal significance, including experiences engendered by psychedelic drugs, can have an enduring impact on some core facets of personality. In the present, balanced-order, placebo-controlled study, we investigated biological predictors of post-lysergic acid diethylamide (LSD) changes in personality. Nineteen healthy adults underwent resting state functional MRI scans under LSD (75µg, I.V.) and placebo (saline I.V.). The Revised NEO Personality Inventory (NEO-PI-R) was completed at screening and 2 weeks after LSD/placebo. Scanning sessions consisted of three 7.5-min eyes-closed resting-state scans, one of which involved music listening. A standardized preprocessing pipeline was used to extract measures of sample entropy, which characterizes the predictability of an fMRI time-series. Mixed-effects models were used to evaluate drug-induced shifts in brain entropy and their relationship with the observed increases in the personality trait openness at the 2-week follow-up. Overall, LSD had a pronounced global effect on brain entropy, increasing it in both sensory and hierarchically higher networks across multiple time scales. These shifts predicted enduring increases in trait openness. Moreover, the predictive power of the entropy increases was greatest for the music-listening scans and when "ego-dissolution" was reported during the acute experience. These results shed new light on how LSD-induced shifts in brain dynamics and concomitant subjective experience can be predictive of lasting changes in personality. Hum Brain Mapp 37:3203-3213, 2016. © 2016 Wiley Periodicals, Inc. PMID:27151536

  17. Predictive modeling of effects under global change.

    Science.gov (United States)

    Kickert, R N; Tonella, G; Simonov, A; Krupa, S V

    1999-01-01

    The status of computer simulation models from around the world for evaluating the possible ecological, environmental, and societal consequences of global change is presented in this paper. In addition, a brief synopsis of the state of the science of these impacts is included. Issues considered include future changes in climate and patterns of land use for societal needs. Models discussed relate to vegetation (e.g. crop), soil, bio-geochemistry, water, and wildlife responses to conventional, forecasted changes in temperature and precipitation. Also described are models of these responses, alone and interactively, to increased CO(2), other air pollutants and UV-B radiation, as the state of the science allows. Further, models of land-use change are included. Additionally, global multiple sector models of environment, natural resources, human population dynamics, economics, energy, and political relations are reviewed for integrated impact assessment. To the extent available, information on computer software and hardware requirements is presented for the various models. The paper concludes with comments about using these technologies as they relate to ecological risk assessment for policy decision analysis. Such an effort is hampered by considerable uncertainties with the output of existing models, because of the uncertainties associated with input data and the definitions of their dose-response relationships. The concluding suggestions point the direction for new developments in modeling and analyses that are needed for the 21st century. PMID:15093114

  18. On the prediction of stationary functional time series

    OpenAIRE

    Aue, A.; Norinho, DD; Hörmann, S

    2012-01-01

    © 2015, American Statistical Association. This article addresses the prediction of stationary functional time series. Existing contributions to this problem have largely focused on the special case of first-order functional autoregressive processes because of their technical tractability and the current lack of advanced functional time series methodology. It is shown here how standard multivariate prediction techniques can be used in this context. The connection between functional and multiva...

  19. Prediction of postoperative lung function after pulmonary resection

    International Nuclear Information System (INIS)

    Lung scintigraphy and ordinary lung function test as well as split lung function test by using bronchospirometry was performed in 78 patients with primary lung cancer and clinical significance of ventilation and perfusion scintigraphy was evaluated. Results obtained from this study are as follows. 1) The ratio of right VC to total VC obtained by preoperative bronchospirometry was well correlated to the ratio of right lung count to the total lung count obtained by ventiration and/or perfusion scintigraphy (r = 0.84, r = 0.69). 2) Evaluation of the data obtained from the patients undergoing pneumonectomy indicated that the right and left VC obtained preoperatively by bronchospirometry have their clinical significance only in the form of left to right ratio not in the form their absolure value. 3) As to the reliability of predicting the residual vital capacity after pneumonectomy on the basis of left-to-right of lung scintigraphy, ventilation scintigraphy is more reliable than perfusion scintigraphy. 4) Irrespective of using ventilation scintigraphy or perfusion scintigraphy, Ali's formular showed high reliability in predicting the residual vital capacity as well as FEV1.0 after lobectomy. 5) Reduction of the perfusion rate in the operated side of the lung is more marked than of the ventilation rate, resulting in a significant elevation of ventilation/perfusion ratio of the operated side of the lung. From the results descrived above, it can be said that lung ventilation and perfusion scintigraphy are very useful method to predict the residual lung function as well as the change of ventilation/perfusion ratio after pulmonary resection. (author)

  20. Changes in gastrointestinal tract function and structure in functional dyspepsia.

    Science.gov (United States)

    Vanheel, Hanne; Farré, Ricard

    2013-03-01

    Functional dyspepsia is an extremely common disorder of gastrointestinal function. The disorder is thought to be heterogeneous, with different pathophysiological mechanisms underlying varied symptom patterns. A diversity of changes in gastrointestinal tract function and structure has been described in functional dyspepsia. These involve alterations in the stomach, such as impaired accommodation, delayed gastric emptying and hypersensitivity, and alterations in the duodenum, such as increased sensitivity to duodenal acid and/or lipids and low-grade inflammation. In this Review, we summarize all these abnormalities in an attempt to provide an integrated overview of the pathophysiological mechanisms in functional dyspepsia. PMID:23318268

  1. Spatial adaption for predicting random functions

    OpenAIRE

    Müller-Gronbach, Thomas; Ritter, Klaus

    1998-01-01

    We study integration and reconstruction of Gaussian random functions with inhomogeneous local smoothness. A single realization may only be observed at a finite sampling design and the correct local smoothness is unknown. We construct adaptive two-stage designs that lead to asymptotically optimal methods. We show that every nonadaptive design is less efficient.

  2. Resting state functional connectivity predicts neurofeedback response

    OpenAIRE

    Scheinost, Dustin; Stoica, Teodora; Wasylink, Suzanne; Gruner, Patricia; Saksa, John; Pittenger, Christopher; Hampson, Michelle

    2014-01-01

    Tailoring treatments to the specific needs and biology of individual patients—personalized medicine—requires delineation of reliable predictors of response. Unfortunately, these have been slow to emerge, especially in neuropsychiatric disorders. We have recently described a real-time functional magnetic resonance imaging (rt-fMRI) neurofeedback protocol that can reduce contamination-related anxiety, a prominent symptom of many cases of obsessive-compulsive disorder (OCD). Individual response ...

  3. Probabilistic protein function prediction from heterogeneous genome-wide data.

    Directory of Open Access Journals (Sweden)

    Naoki Nariai

    Full Text Available Dramatic improvements in high throughput sequencing technologies have led to a staggering growth in the number of predicted genes. However, a large fraction of these newly discovered genes do not have a functional assignment. Fortunately, a variety of novel high-throughput genome-wide functional screening technologies provide important clues that shed light on gene function. The integration of heterogeneous data to predict protein function has been shown to improve the accuracy of automated gene annotation systems. In this paper, we propose and evaluate a probabilistic approach for protein function prediction that integrates protein-protein interaction (PPI data, gene expression data, protein motif information, mutant phenotype data, and protein localization data. First, functional linkage graphs are constructed from PPI data and gene expression data, in which an edge between nodes (proteins represents evidence for functional similarity. The assumption here is that graph neighbors are more likely to share protein function, compared to proteins that are not neighbors. The functional linkage graph model is then used in concert with protein domain, mutant phenotype and protein localization data to produce a functional prediction. Our method is applied to the functional prediction of Saccharomyces cerevisiae genes, using Gene Ontology (GO terms as the basis of our annotation. In a cross validation study we show that the integrated model increases recall by 18%, compared to using PPI data alone at the 50% precision. We also show that the integrated predictor is significantly better than each individual predictor. However, the observed improvement vs. PPI depends on both the new source of data and the functional category to be predicted. Surprisingly, in some contexts integration hurts overall prediction accuracy. Lastly, we provide a comprehensive assignment of putative GO terms to 463 proteins that currently have no assigned function.

  4. Using search engine technology for protein function prediction.

    Science.gov (United States)

    Chen, Ziyang; Cai, Zhao; Li, Min; Liu, Binbin

    2011-01-01

    Prediction of protein function is one of the most challenging problems in the post-genomic era. In this paper, we propose a novel algorithm Improved ProteinRank (IPR) for protein function prediction, which is based on the search engine technology and the preferential attachment criteria. In addition, an improved algorithm IPRW is developed from IPR to be used in the weighted protein?protein interaction (PPI) network. The proposed algorithms IPR and IPRW are applied to the PPI network of S.cerevisiae. The experimental results show that both IPR and IPRW outweigh the previous methods for the prediction of protein functions. PMID:21441099

  5. Regime shifts limit the predictability of land-system change

    DEFF Research Database (Denmark)

    Müller, Daniel; Sun, Zhanli; Vongvisouk, Thoumthone;

    2014-01-01

    and abrupt change that invalidate predictions calibrated on past trends. Rapid land-system change can occur when critical thresholds in broad-scale underlying drivers such as commodity prices and climate conditions are crossed or when sudden events such as political change or natural disasters punctuate long...... (China, Laos, Vietnam and Indonesia). The results show how sudden events and gradual changes in underlying drivers caused rapid, surprising and widespread land-system changes, including shifts to different regimes in China, Vietnam and Indonesia, whereas land systems in Laos remained stable in the study...... period but show recent signs of rapid change. The observed regime shifts were difficult to anticipate, which compromises the validity of predictions of future land-system changes and the assessment of their impact on greenhouse gas emissions, hydrological processes, agriculture, biodiversity...

  6. Mitochondrial function adaptations to changed metabolic conditions

    OpenAIRE

    Bakkman, Linda

    2010-01-01

    The skeletal muscle mitochondria play a decisive role for the metabolic capacity of the body. A capability to adapt to changed metabolic conditions and energy demands is crucial for weight control and physical exercise. The aim of this thesis was to describe how the mitochondria adapt its function to different environmental conditions and changed metabolic demands. In study I, the aim was to evaluate mitochondrial adaptations to hypoxic exercise. The effect of one-legged...

  7. The Mutational Spectrum of Holoprosencephaly-Associated Changes within the SHH Gene in Humans Predicts Loss-of-Function Through Either Key Structural Alterations of the Ligand or Its Altered Synthesis

    OpenAIRE

    Roessler, Erich; El-Jaick, Kenia B.; Dubourg, Christèle; Vélez, Jorge I.; Solomon, Benjamin D.; Pineda-Álvarez, Daniel E.; Lacbawan, Felicitas; Zhou, Nan; Ouspenskaia, Maia; Paulussen, Aimée; Smeets, Hubert J.; Hehr, Ute; Bendavid, Claude; Bale, Sherri; Odent, Sylvie

    2009-01-01

    Mutations within either the SHH gene or its related pathway components are the most common, and best understood, pathogenetic changes observed in holoprosencephaly patients; this fact is consistent with the essential functions of this gene during forebrain development and patterning. Here we summarize the nature and types of deleterious sequence alterations among over one hundred distinct mutations in the SHH gene (64 novel mutations) and compare these to over a dozen mutations in disease-rel...

  8. A new protein structure representation for efficient protein function prediction.

    Science.gov (United States)

    Maghawry, Huda A; Mostafa, Mostafa G M; Gharib, Tarek F

    2014-12-01

    One of the challenging problems in bioinformatics is the prediction of protein function. Protein function is the main key that can be used to classify different proteins. Protein function can be inferred experimentally with very small throughput or computationally with very high throughput. Computational methods are sequence based or structure based. Structure-based methods produce more accurate protein function prediction. In this article, we propose a new protein structure representation for efficient protein function prediction. The representation is based on three-dimensional patterns of protein residues. In the analysis, we used protein function based on enzyme activity through six mechanistically diverse enzyme superfamilies: amidohydrolase, crotonase, haloacid dehalogenase, isoprenoid synthase type I, and vicinal oxygen chelate. We applied three different classification methods, naïve Bayes, k-nearest neighbors, and random forest, to predict the enzyme superfamily of a given protein. The prediction accuracy using the proposed representation outperforms a recently introduced representation method that is based only on the distance patterns. The results show that the proposed representation achieved prediction accuracy up to 98%, with improvement of about 10% on average. PMID:25343279

  9. Predicting species’ range limits from functional traits for the tree flora of North America

    OpenAIRE

    Stahl, Ulrike; Reu, Björn; Wirth, Christian

    2014-01-01

    A species’ climate niche summarizes the observed climatic conditions at its range limits. This information can be used to predict range shifts of species under climate change, but it does not explain why they occur under a given climate or are absent from another. Functional traits associated with the climate niche, however, allow for such an explanation. We show that key plant functional traits predict the climate ranges of North American trees and discuss the underlying filter mechanisms th...

  10. Climate modelling, uncertainty and responses to predictions of change

    International Nuclear Information System (INIS)

    Article 4.1(F) of the Framework Convention on Climate Change commits all parties to take climate change considerations into account, to the extent feasible, in relevant social, economic and environmental policies and actions and to employ methods such as impact assessments to minimize adverse effects of climate change. This could be achieved by, inter alia, incorporating climate change risk assessment into development planning processes, i.e. relating climatic change to issues of habitability and sustainability. Adaptation is an ubiquitous and beneficial natural and human strategy. Future adaptation (adjustment) to climate is inevitable at the least to decrease the vulnerability to current climatic impacts. An urgent issue is the mismatch between the predictions of global climatic change and the need for information on local to regional change in order to develop adaptation strategies. Mitigation efforts are essential since the more successful mitigation activities are, the less need there will be for adaptation responses. And, mitigation responses can be global (e.g. a uniform percentage reduction in greenhouse gas emissions) while adaptation responses will be local to regional in character and therefore depend upon confident predictions of regional climatic change. The dilemma facing policymakers is that scientists have considerable confidence in likely global climatic changes but virtually zero confidence in regional changes. Mitigation and adaptation strategies relevant to climatic change can most usefully be developed in the context of sound understanding of climate, especially the near-surface continental climate, permitting discussion of societally relevant issues. But, climate models can't yet deliver this type of regionally and locationally specific prediction and some aspects of current research even seem to indicate increased uncertainty. These topics are explored in this paper using the specific example of the prediction of land-surface climate changes

  11. A Survey of Computational Intelligence Techniques in Protein Function Prediction

    Directory of Open Access Journals (Sweden)

    Arvind Kumar Tiwari

    2014-01-01

    Full Text Available During the past, there was a massive growth of knowledge of unknown proteins with the advancement of high throughput microarray technologies. Protein function prediction is the most challenging problem in bioinformatics. In the past, the homology based approaches were used to predict the protein function, but they failed when a new protein was different from the previous one. Therefore, to alleviate the problems associated with homology based traditional approaches, numerous computational intelligence techniques have been proposed in the recent past. This paper presents a state-of-the-art comprehensive review of various computational intelligence techniques for protein function predictions using sequence, structure, protein-protein interaction network, and gene expression data used in wide areas of applications such as prediction of DNA and RNA binding sites, subcellular localization, enzyme functions, signal peptides, catalytic residues, nuclear/G-protein coupled receptors, membrane proteins, and pathway analysis from gene expression datasets. This paper also summarizes the result obtained by many researchers to solve these problems by using computational intelligence techniques with appropriate datasets to improve the prediction performance. The summary shows that ensemble classifiers and integration of multiple heterogeneous data are useful for protein function prediction.

  12. A Unitary Executive Function Predicts Intelligence in Children

    Science.gov (United States)

    Brydges, Christopher R.; Reid, Corinne L.; Fox, Allison M.; Anderson, Mike

    2012-01-01

    Executive functions (EF) and intelligence are of critical importance to success in many everyday tasks. Working memory, or updating, which is one latent variable identified in confirmatory factor analytic models of executive functions, predicts intelligence (both fluid and crystallised) in adults, but inhibition and shifting do not (Friedman et…

  13. Prediction of human protein function according to Gene Ontology categories

    DEFF Research Database (Denmark)

    Jensen, Lars Juhl; Gupta, Ramneek; Stærfeldt, Hans Henrik; Brunak, Søren

    2003-01-01

    Motivation: The human genome project has led to the discovery of many human protein coding genes which were previously unknown. As a large fraction of these are functionally uncharacterized, it is of interest to develop methods for predicting their molecular function from sequence.Results: We have...... calculated from the amino acid composition. This allows for prediction of the function for orphan proteins where no homologs can be found. Using this method we propose two novel receptors in the human genome, and further demonstrate chromosomal clustering of related proteins....

  14. A large-scale evaluation of computational protein function prediction.

    Science.gov (United States)

    Radivojac, Predrag; Clark, Wyatt T; Oron, Tal Ronnen; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kaßner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Boehm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas A; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

    2013-03-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools. PMID:23353650

  15. Prospective prediction of functional difficulties among recently separated Veterans

    Directory of Open Access Journals (Sweden)

    Gerald E. Larson, PhD

    2014-06-01

    Full Text Available Reports of functional problems are common among Veterans who served post-9/11 (more than 25% report functional difficulties in at least one domain. However, little prospective work has examined the risk and protective factors for functional difficulties among Veterans. In a sample of recently separated Marines, we used stepwise logistic and multiple regressions to identify predictors of functional impairment, including work-related problems, financial problems, unlawful behavior, activity limitations due to mental health symptoms, and perceived difficulty reintegrating into civilian life. Posttraumatic stress disorder symptoms assessed both before and after military separation significantly predicted functional difficulties across all domains except unlawful behavior. Certain outcomes, such as unlawful behavior and activity limitations due to mental health symptoms, were predicted by other or additional predictors. Although several forms of functioning were examined, the list was not exhaustive. The results highlight a number of areas where targeted interventions may facilitate the reintegration of military servicemembers into civilian life.

  16. A traveling salesman approach for predicting protein functions

    Directory of Open Access Journals (Sweden)

    Johnson Olin

    2006-10-01

    Full Text Available Abstract Background Protein-protein interaction information can be used to predict unknown protein functions and to help study biological pathways. Results Here we present a new approach utilizing the classic Traveling Salesman Problem to study the protein-protein interactions and to predict protein functions in budding yeast Saccharomyces cerevisiae. We apply the global optimization tool from combinatorial optimization algorithms to cluster the yeast proteins based on the global protein interaction information. We then use this clustering information to help us predict protein functions. We use our algorithm together with the direct neighbor algorithm 1 on characterized proteins and compare the prediction accuracy of the two methods. We show our algorithm can produce better predictions than the direct neighbor algorithm, which only considers the immediate neighbors of the query protein. Conclusion Our method is a promising one to be used as a general tool to predict functions of uncharacterized proteins and a successful sample of using computer science knowledge and algorithms to study biological problems.

  17. The mutational spectrum of holoprosencephaly-associated changes within the SHH gene in humans predicts loss-of-function through either key structural alterations of the ligand or its altered synthesis.

    Science.gov (United States)

    Roessler, Erich; El-Jaick, Kenia B; Dubourg, Christèle; Vélez, Jorge I; Solomon, Benjamin D; Pineda-Alvarez, Daniel E; Lacbawan, Felicitas; Zhou, Nan; Ouspenskaia, Maia; Paulussen, Aimée; Smeets, Hubert J; Hehr, Ute; Bendavid, Claude; Bale, Sherri; Odent, Sylvie; David, Véronique; Muenke, Maximilian

    2009-10-01

    Mutations within either the SHH gene or its related pathway components are the most common, and best understood, pathogenetic changes observed in holoprosencephaly patients; this fact is consistent with the essential functions of this gene during forebrain development and patterning. Here we summarize the nature and types of deleterious sequence alterations among over one hundred distinct mutations in the SHH gene (64 novel mutations) and compare these to over a dozen mutations in disease-related Hedgehog family members IHH and DHH. This combined structural analysis suggests that dysfunction of Hedgehog signaling in human forebrain development can occur through truncations or major structural changes to the signaling domain, SHH-N, as well as due to defects in the processing of the mature ligand from its pre-pro-precursor or defective post-translation bi-lipid modifications with palmitate and cholesterol. PMID:19603532

  18. The predictability of molecular evolution during functional innovation

    OpenAIRE

    Blank, Diana; Wolf, Luise; Ackermann, Martin; Silander, Olin K.

    2014-01-01

    Understanding the genetic changes that underlie phenotypic functional innovations is a fundamental goal in evolutionary biology, giving insight into species’ past, present, and future evolutionary trajectories. One important unresolved question is whether such genetic changes typically affect protein expression or protein structure. Here we use large-scale laboratory evolution with bacteria to quantify the types of genetic changes that occur during functional innovation. We show that whether ...

  19. Predicting vulnerabilities of North American shorebirds to climate change.

    Directory of Open Access Journals (Sweden)

    Hector Galbraith

    Full Text Available Despite an increase in conservation efforts for shorebirds, there are widespread declines of many species of North American shorebirds. We wanted to know whether these declines would be exacerbated by climate change, and whether relatively secure species might become at-risk species. Virtually all of the shorebird species breeding in the USA and Canada are migratory, which means climate change could affect extinction risk via changes on the breeding, wintering, and/or migratory refueling grounds, and that ecological synchronicities could be disrupted at multiple sites. To predict the effects of climate change on shorebird extinction risks, we created a categorical risk model complementary to that used by Partners-in-Flight and the U.S. Shorebird Conservation Plan. The model is based on anticipated changes in breeding, migration, and wintering habitat, degree of dependence on ecological synchronicities, migration distance, and degree of specialization on breeding, migration, or wintering habitat. We evaluated 49 species, and for 3 species we evaluated 2 distinct populations each, and found that 47 (90% taxa are predicted to experience an increase in risk of extinction. No species was reclassified into a lower-risk category, although 6 species had at least one risk factor decrease in association with climate change. The number of species that changed risk categories in our assessment is sensitive to how much of an effect of climate change is required to cause the shift, but even at its least sensitive, 20 species were at the highest risk category for extinction. Based on our results it appears that shorebirds are likely to be highly vulnerable to climate change. Finally, we discuss both how our approach can be integrated with existing risk assessments and potential future directions for predicting change in extinction risk due to climate change.

  20. Combining specificity determining and conserved residues improves functional site prediction

    Directory of Open Access Journals (Sweden)

    Gelfand Mikhail S

    2009-06-01

    Full Text Available Abstract Background Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core. Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities. Results Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs, as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples. Conclusion The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.

  1. BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins

    Directory of Open Access Journals (Sweden)

    Kankainen Matti

    2012-02-01

    Full Text Available Abstract Background Automated function prediction has played a central role in determining the biological functions of bacterial proteins. Typically, protein function annotation relies on homology, and function is inferred from other proteins with similar sequences. This approach has become popular in bacterial genomics because it is one of the few methods that is practical for large datasets and because it does not require additional functional genomics experiments. However, the existing solutions produce erroneous predictions in many cases, especially when query sequences have low levels of identity with the annotated source protein. This problem has created a pressing need for improvements in homology-based annotation. Results We present an automated method for the functional annotation of bacterial protein sequences. Based on sequence similarity searches, BLANNOTATOR accurately annotates query sequences with one-line summary descriptions of protein function. It groups sequences identified by BLAST into subsets according to their annotation and bases its prediction on a set of sequences with consistent functional information. We show the results of BLANNOTATOR's performance in sets of bacterial proteins with known functions. We simulated the annotation process for 3090 SWISS-PROT proteins using a database in its state preceding the functional characterisation of the query protein. For this dataset, our method outperformed the five others that we tested, and the improved performance was maintained even in the absence of highly related sequence hits. We further demonstrate the value of our tool by analysing the putative proteome of Lactobacillus crispatus strain ST1. Conclusions BLANNOTATOR is an accurate method for bacterial protein function prediction. It is practical for genome-scale data and does not require pre-existing sequence clustering; thus, this method suits the needs of bacterial genome and metagenome researchers. The method and a

  2. Special Analysis For Predicting Changes In Mangrove Forest

    OpenAIRE

    Yumna; Irman Halid

    2015-01-01

    Abstract This study aims to determine the mangrove forest land cover change and farms based on the interpretation of satellite imagery and predict the extent and determine the area of mangrove rehabilitation based on the rate of change in land cover and land suitability analysis is based on the physical parameters of mangrove forests in the district Ponrang Luwu. Land suitability classification refers to the Land Suitability Classification Framework Method According to FAO 1976 are divided in...

  3. Changing the functionality of cocoa butter

    OpenAIRE

    De Clercq, Nathalie

    2011-01-01

    Cocoa butter is an essential ingredient in chocolate as it forms the continuous phase of chocolate. It’s therefore responsible for the gloss, texture and typical melting behaviour of ‘irresistible’ chocolate. The aim of this research was to change the functionality of cocoa butter by two different methods. In the first part, cocoa butter was modified by physical refining by using packed column steam refining with or without silica pretreatment. The physicochemical properties of the refined co...

  4. Partitioning of minimotifs based on function with improved prediction accuracy.

    Directory of Open Access Journals (Sweden)

    Sanguthevar Rajasekaran

    Full Text Available BACKGROUND: Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions. METHODOLOGY/PRINCIPAL FINDINGS: Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein have a related cellular or molecular function, the prediction is more likely to be accurate. This filter was implemented in Minimotif Miner using function annotations from the Gene Ontology. We have also combined two filters that are based on entirely different principles and this combined filter has a better predictability than the individual components. CONCLUSIONS/SIGNIFICANCE: Testing these functional filters on known and random minimotifs has revealed that they are capable of separating true motifs from false positives. In particular, for the cellular function filter, the percentage of known minimotifs that are not removed by the filter is approximately 4.6 times that of random minimotifs. For the molecular function filter this ratio is approximately 2.9. These results, together with the comparison with the published frequency score filter, strongly suggest that the new filters differentiate true motifs from random background with good confidence. A combination of the function filters and the frequency score filter performs better than these two individual filters.

  5. Phylogeny predicts future habitat shifts due to climate change.

    Directory of Open Access Journals (Sweden)

    Matjaž Kuntner

    Full Text Available BACKGROUND: Taxa may respond differently to climatic changes, depending on phylogenetic or ecological effects, but studies that discern among these alternatives are scarce. Here, we use two species pairs from globally distributed spider clades, each pair representing two lifestyles (generalist, specialist to test the relative importance of phylogeny versus ecology in predicted responses to climate change. METHODOLOGY: We used a recent phylogenetic hypothesis for nephilid spiders to select four species from two genera (Nephilingis and Nephilengys that match the above criteria, are fully allopatric but combined occupy all subtropical-tropical regions. Based on their records, we modeled each species niche spaces and predicted their ecological shifts 20, 40, 60, and 80 years into the future using customized GIS tools and projected climatic changes. CONCLUSIONS: Phylogeny better predicts the species current ecological preferences than do lifestyles. By 2080 all species face dramatic reductions in suitable habitat (54.8-77.1% and adapt by moving towards higher altitudes and latitudes, although at different tempos. Phylogeny and life style explain simulated habitat shifts in altitude, but phylogeny is the sole best predictor of latitudinal shifts. Models incorporating phylogenetic relatedness are an important additional tool to predict accurately biotic responses to global change.

  6. Changes in Neutrophil Functions in Astronauts

    Science.gov (United States)

    Kaur, Indreshpal; Simons, Elizabeth R.; Castro, Victoria; Pierson, Duane L.

    2002-01-01

    Neutrophil functions (phagocytosis, oxidative burst, degranulation) and expression of surface markers involved in these functions were studied in 25 astronauts before and after 4 space shuttle missions. Space flight duration ranged from 5 to 11 days. Blood specimens were obtained 10 days before launch (preflight or L-10), immediately after landing (landing or R+0), and again at 3 days after landing (postflight or R+3). Blood samples were also collected from 9 healthy low-stressed subjects at 3 time points simulating a 10-day shuttle mission. The number of neutrophils increased at landing by 85 percent when compared to the preflight numbers. Neutrophil functions were studied in whole blood using flow cytometric methods. Phagocytosis of E.coli-FITC and oxidative burst capacity of the neutrophils following the 9 to 11 day missions were lower at all three sampling points than the mean values for control subjects. Phagocytosis and oxidative burst capacity of the astronauts was decreased even 10-days before space flight. Mission duration appears to be a factor in phagocytic and oxidative functions. In contrast, following the short-duration (5-days) mission, these functions were unchanged from control values. No consistent changes in degranulation were observed following either short or medium length space missions. The expression of CD16, CD32, CD11a, CD11b, CD11c, L-selectin and CD36 was measured and found to be variable. Specifically, CD16 and CD32 did not correlate with the changes in oxidative burst and phagocytosis. We can conclude from this study that the stresses associated with space flight can alter the important functions of neutrophils.

  7. Accounting for Human Polymorphisms Predicted to Affect Protein Function

    OpenAIRE

    Ng, Pauline C.; Henikoff, Steven

    2002-01-01

    A major interest in human genetics is to determine whether a nonsynonymous single-base nucleotide polymorphism (nsSNP) in a gene affects its protein product and, consequently, impacts the carrier's health. We used the SIFT (Sorting Intolerant From Tolerant) program to predict that 25% of 3084 nsSNPs from dbSNP, a public SNP database, would affect protein function. Some of the nsSNPs predicted to affect function were variants known to be associated with disease. Others were artifacts of SNP di...

  8. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

    OpenAIRE

    Warde-Farley, David; Sylva L. Donaldson; Comes, Ovi; Zuberi, Khalid; Badrawi, Rashad; Chao, Pauline; Franz, Max; Grouios, Chris; Kazi, Farzana; Lopes, Christian Tannus; Maitland, Anson; Mostafavi, Sara; Montojo, Jason; Shao, Quentin; Wright, George

    2010-01-01

    GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis t...

  9. SitesIdentify: a protein functional site prediction tool

    Directory of Open Access Journals (Sweden)

    Doig Andrew J

    2009-11-01

    Full Text Available Abstract Background The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application. Results Here we present a functional site prediction tool (SitesIdentify, based on combining sequence conservation information with geometry-based cleft identification, that is freely available via a web-server. We have shown that SitesIdentify compares favourably to other functional site prediction tools in a comparison of seven methods on a non-redundant set of 237 enzymes with annotated active sites. Conclusion SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at http://www.manchester.ac.uk/bioinformatics/sitesidentify/

  10. Biochemical functional predictions for protein structures of unknown or uncertain function

    Directory of Open Access Journals (Sweden)

    Caitlyn L. Mills

    2015-01-01

    Full Text Available With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. This paper reviews the efforts to address the challenge of annotating the function at the molecular level of uncharacterized proteins. While sequence- and three-dimensional-structure-based methods for protein function prediction have been reviewed previously, the recent trends in local structure-based methods have received less attention. These local structure-based methods are the primary focus of this review. Computational methods have been developed to predict the residues important for catalysis and the local spatial arrangements of these residues can be used to identify protein function. In addition, the combination of different types of methods can help obtain more information and better predictions of function for proteins of unknown function. Global initiatives, including the Enzyme Function Initiative (EFI, COMputational BRidges to EXperiments (COMBREX, and the Critical Assessment of Function Annotation (CAFA, are evaluating and testing the different approaches to predicting the function of proteins of unknown function. These initiatives and global collaborations will increase the capability and reliability of methods to predict biochemical function computationally and will add substantial value to the current volume of structural genomics data by reducing the number of absent or inaccurate functional annotations.

  11. Drought Predictability and Prediction in a Changing Climate: Assessing Current Predictive Knowledge and Capabilities, User Requirements and Research Priorities

    Science.gov (United States)

    Schubert, Siegfried

    2011-01-01

    Drought is fundamentally the result of an extended period of reduced precipitation lasting anywhere from a few weeks to decades and even longer. As such, addressing drought predictability and prediction in a changing climate requires foremost that we make progress on the ability to predict precipitation anomalies on subseasonal and longer time scales. From the perspective of the users of drought forecasts and information, drought is however most directly viewed through its impacts (e.g., on soil moisture, streamflow, crop yields). As such, the question of the predictability of drought must extend to those quantities as well. In order to make progress on these issues, the WCRP drought information group (DIG), with the support of WCRP, the Catalan Institute of Climate Sciences, the La Caixa Foundation, the National Aeronautics and Space Administration, the National Oceanic and Atmospheric Administration, and the National Science Foundation, has organized a workshop to focus on: 1. User requirements for drought prediction information on sub-seasonal to centennial time scales 2. Current understanding of the mechanisms and predictability of drought on sub-seasonal to centennial time scales 3. Current drought prediction/projection capabilities on sub-seasonal to centennial time scales 4. Advancing regional drought prediction capabilities for variables and scales most relevant to user needs on sub-seasonal to centennial time scales. This introductory talk provides an overview of these goals, and outlines the occurrence and mechanisms of drought world-wide.

  12. Predicting real-world functional milestones in schizophrenia.

    Science.gov (United States)

    Olsson, Anna-Karin; Hjärthag, Fredrik; Helldin, Lars

    2016-08-30

    Schizophrenia is a severe disorder that often causes impairments in major areas of functioning, and most patients do not achieve expected real-world functional milestones. The aim of this study was to identify which variables of demography, illness activity, and functional capacity predict patients' ability to attain real-world functional milestones. Participants were 235 outpatients, 149 men and 86 women, diagnosed with schizophrenia spectrum disorder. Our results showed that younger patients managed to achieve a higher level of functioning in educational level, marital status, and social contacts. Patients' functional capacity was primarily associated with educational level and housing situation. We also found that women needed less support regarding housing and obtained a higher level of marital status as compared with men. Our findings demonstrate the importance of considering current symptoms, especially negative symptoms, and remission stability over time, together with age, duration of illness, gender, educational level, and current functional capacity, when predicting patients' future real-world functioning. We also conclude that there is an advantage in exploring symptoms divided into positive, negative, and general domains considering their probable impact on functional achievements. PMID:27235985

  13. Changes in Reflective Functioning during Psychoanalytic Psychotherapies.

    Science.gov (United States)

    Hörz-Sagstetter, Susanne; Mertens, Wolfgang; Isphording, Sybille; Buchheim, Anna; Taubner, Svenja

    2015-06-01

    This study examines how reflective functioning (RF) can be assessed in analytic sessions and throughout psychoanalytic psychotherapy. The goals are to replicate in part a study by Josephs and colleagues (2004) by applying the RF Scale to analytic sessions and to study fluctuations of RF within each session. Additionally, RF based on sessions was compared with the RF ratings based on the Adult Attachment Interview (AAI) during the course of two psychoanalytic psychotherapies with a duration of 240 hours. RF changes based on 10 sessions per patient, assessed at baseline and after 80, 160, and 240 hours of therapy, and RF changes based on AAI ratings measured at baseline and after 240 hours of therapy, and in one case at follow-up, were related to changes of symptoms and attachment classifications over time. Results showed that in both cases RF fluctuated within sessions. The average RF rating per session increased over the course of treatment, while the AAI-based RF rating needed longer to increase. Rather good correspondence was found between session-based RF ratings and independent AAI-based RF ratings. In both cases, changes in RF over time were compared to changes in attachment classification based on the AAI and to symptomatic change. Better correspondence between symptomatic and attachment changes was found with the AAI-based RF rating. It was tentatively interpreted that session-based RF ratings may represent a state of RF that is strongly influenced by the therapist-patient interaction, whereas AAI-based RF can be considered to have more trait characteristics. PMID:26185290

  14. Change in avian abundance predicted from regional forest inventory data

    Science.gov (United States)

    Twedt, Daniel J.; Tirpak, John M.; Jones-Farrand, D. Todd; Thompson, Frank R., III; Uihlein, William B.; Fitzgerald, Jane A.

    2010-01-01

    An inability to predict population response to future habitat projections is a shortcoming in bird conservation planning. We sought to predict avian response to projections of future forest conditions that were developed from nationwide forest surveys within the Forest Inventory and Analysis (FIA) program. To accomplish this, we evaluated the historical relationship between silvicolous bird populations and FIA-derived forest conditions within 25 ecoregions that comprise the southeastern United States. We aggregated forest area by forest ownership, forest type, and tree size-class categories in county-based ecoregions for 5 time periods spanning 1963-2008. We assessed the relationship of forest data with contemporaneous indices of abundance for 24 silvicolous bird species that were obtained from Breeding Bird Surveys. Relationships between bird abundance and forest inventory data for 18 species were deemed sufficient as predictive models. We used these empirically derived relationships between regional forest conditions and bird populations to predict relative changes in abundance of these species within ecoregions that are anticipated to coincide with projected changes in forest variables through 2040. Predicted abundances of these 18 species are expected to remain relatively stable in over a quarter (27%) of the ecoregions. However, change in forest area and redistribution of forest types will likely result in changed abundance of some species within many ecosystems. For example, abundances of 11 species, including pine warbler (Dendroica pinus), brown-headed nuthatch (Sitta pusilla), and chuckwills- widow (Caprimulgus carolinensis), are projected to increase within more ecoregions than ecoregions where they will decrease. For 6 other species, such as blue-winged warbler (Vermivora pinus), Carolina wren (Thryothorus ludovicianus), and indigo bunting (Passerina cyanea), we projected abundances will decrease within more ecoregions than ecoregions where they will

  15. Changes in functional imaging with aging

    International Nuclear Information System (INIS)

    Complex interactions between genetic information, endogenous chemical changes, and dietary intake of nutrients and toxins, along with additional factors such as radiation, find expression in the process known as aging. It is becoming clear that studies in nuclear medicine have a distinct role to play in evaluating age-associated changes. Certain functional indices, such as cardiac parameters, can be relatively simply derived and correlated with age and with variables such as height and weight. The images in nuclear medicine can also be subjected to quantitative assay, and age-associated variations are noted in health and disease. Of potential import is the area of immunoscintigraphy, not for tumors but for age-related antigenic markers. Information was presented in a previous paper on the unmasking of red cell antigens with cell aging. The opposite effect also occurs. That is, specific antigens can be lost as a function of age. The effect of age on hair-bulb tyrosinase activity has been studied. The hair bulbs of those with white hair did not express tyrosinase activity in vitro. To confirm that the enzyme protein was absent (in addition to absence of the catalytic effect), antibodies to tyrosinase established that tyrosinase antigen was not detectable in the hair bulbs. Extension of this approach may open up the ability to map functional versus nonfunctional enzyme sites versus age

  16. Predicting Changes in the Radio Emission Fluxes of Extragalactic Sources

    Science.gov (United States)

    Sukharev, A. L.; Ryabov, M. I.; Donskikh, G. I.

    2016-06-01

    Data from long-term monitoring with the 26-m University of Michigan radio telescope at a frequency of 14.5 GHz (1974-2011) is used to predict changes in the radio emission fluxes from the extragalactic sources 3C273, 3C120, 3C345, 3C446, 3C454.3, OJ287, OT081, and BLLac. The predictions are based on data on the major periods of variability and their durations obtained by wavelet analysis. The radio emission fluxes from the sources 3C345, 3C446, and 3C454.3, which have complicated variabilities, are predicted using an autoregression linear prediction method. This yields a forecast of the flux variations extending up to 5 years. Harmonic prediction is used for another group of sources, BLLac, OJ287, and OT081, with rapid variability. This approach yielded forecasts extending 4-9 years. For the sources 3C273 and 3C120, which have stable long periods, the harmonic method was also used and yielded a forecast extending up to 16 years. The reliability of the prediction was confirmed by independent observational data from the MOJAVE program for 2011-2015.

  17. Predicting IQ change from brain structure: A cross-validation study

    Science.gov (United States)

    Price, C.J.; Ramsden, S.; Hope, T.M.H.; Friston, K.J.; Seghier, M.L.

    2013-01-01

    Procedures that can predict cognitive abilities from brain imaging data are potentially relevant to educational assessments and studies of functional anatomy in the developing brain. Our aim in this work was to quantify the degree to which IQ change in the teenage years could be predicted from structural brain changes. Two well-known k-fold cross-validation analyses were applied to data acquired from 33 healthy teenagers – each tested at Time 1 and Time 2 with a 3.5 year interval. One approach, a Leave-One-Out procedure, predicted IQ change for each subject on the basis of structural change in a brain region that was identified from all other subjects (i.e., independent data). This approach predicted 53% of verbal IQ change and 14% of performance IQ change. The other approach used half the sample, to identify regions for predicting IQ change in the other half (i.e., a Split half approach); however – unlike the Leave-One-Out procedure – regions identified using half the sample were not significant. We discuss how these out-of-sample estimates compare to in-sample estimates; and draw some recommendations for k-fold cross-validation procedures when dealing with small datasets that are typical in the neuroimaging literature. PMID:23567505

  18. Mass Change Prediction Model of Concrete Subjected to Sulfate Attack

    Directory of Open Access Journals (Sweden)

    Kwang-Myong Lee

    2015-01-01

    Full Text Available The present study suggested a mass change prediction model for sulfate attack of concrete containing mineral admixtures through an immersion test in sulfate solutions. For this, 100% OPC as well as binary and ternary blended cement concrete specimens were manufactured by changing the types and amount of mineral admixture. The concrete specimens were immersed in fresh water, 10% sodium sulfate solution, and 10% magnesium sulfate solution, respectively, and mass change of the specimens was measured at 28, 56, 91, 182, and 365 days. The experimental results indicated that resistance of concrete containing mineral admixture against sodium sulfate attack was far greater than that of 100% OPC concrete. However, in terms of resistance against magnesium sulfate attack, concrete containing mineral admixture was lower than 100% OPC concrete due to the formation of magnesium silicate hydrate (M-S-H, the noncementitious material. Ultimately, based on the experimental results, a mass change prediction model was suggested and it was found that the prediction values using the model corresponded relatively well with the experimental results.

  19. Prediction of human protein function according to Gene Ontology categories

    DEFF Research Database (Denmark)

    Jensen, Lars Juhl; Gupta, Ramneek; Stærfeldt, Hans Henrik;

    2003-01-01

    developed a method for prediction of protein function for a subset of classes from the Gene Ontology classification scheme. This subset includes several pharmaceutically interesting categories-transcription factors, receptors, ion channels, stress and immune response proteins, hormones and growth factors...

  20. Sexual abuse predicts functional somatic symptoms : An adolescent population study

    NARCIS (Netherlands)

    Bonvanie, Irma J.; van Gils, Anne; Janssens, Karin A. M.; Rosmalen, Judith G. M.

    2015-01-01

    The main aim of this study was to investigate the effect of childhood sexual abuse on medically not well explained or functional somatic symptoms (FSSs) in adolescents. We hypothesized that sexual abuse predicts higher levels of FSSs and that anxiety and depression contribute to this relationship. I

  1. firestar--advances in the prediction of functionally important residues.

    Science.gov (United States)

    Lopez, Gonzalo; Maietta, Paolo; Rodriguez, Jose Manuel; Valencia, Alfonso; Tress, Michael L

    2011-07-01

    firestar is a server for predicting catalytic and ligand-binding residues in protein sequences. Here, we present the important developments since the first release of firestar. Previous versions of the server required human interpretation of the results; the server is now fully automatized. firestar has been implemented as a web service and can now be run in high-throughput mode. Prediction coverage has been greatly improved with the extension of the FireDB database and the addition of alignments generated by HHsearch. Ligands in FireDB are now classified for biological relevance. Many of the changes have been motivated by the critical assessment of techniques for protein structure prediction (CASP) ligand-binding prediction experiment, which provided us with a framework to test the performance of firestar. URL: http://firedb.bioinfo.cnio.es/Php/FireStar.php. PMID:21672959

  2. Regional differences in prediction models of lung function in Germany

    Directory of Open Access Journals (Sweden)

    Schäper Christoph

    2010-04-01

    Full Text Available Abstract Background Little is known about the influencing potential of specific characteristics on lung function in different populations. The aim of this analysis was to determine whether lung function determinants differ between subpopulations within Germany and whether prediction equations developed for one subpopulation are also adequate for another subpopulation. Methods Within three studies (KORA C, SHIP-I, ECRHS-I in different areas of Germany 4059 adults performed lung function tests. The available data consisted of forced expiratory volume in one second, forced vital capacity and peak expiratory flow rate. For each study multivariate regression models were developed to predict lung function and Bland-Altman plots were established to evaluate the agreement between predicted and measured values. Results The final regression equations for FEV1 and FVC showed adjusted r-square values between 0.65 and 0.75, and for PEF they were between 0.46 and 0.61. In all studies gender, age, height and pack-years were significant determinants, each with a similar effect size. Regarding other predictors there were some, although not statistically significant, differences between the studies. Bland-Altman plots indicated that the regression models for each individual study adequately predict medium (i.e. normal but not extremely high or low lung function values in the whole study population. Conclusions Simple models with gender, age and height explain a substantial part of lung function variance whereas further determinants add less than 5% to the total explained r-squared, at least for FEV1 and FVC. Thus, for different adult subpopulations of Germany one simple model for each lung function measures is still sufficient.

  3. Disorganized Symptoms and Executive Functioning Predict Impaired Social Functioning in Subjects at Risk for Psychosis

    OpenAIRE

    Eslami, Ali; Jahshan, Carol; Cadenhead, Kristin S.

    2011-01-01

    Predictors of social functioning deficits were assessed in 22 individuals “at risk” for psychosis. Disorganized symptoms and executive functioning predicted social functioning at follow-up. Early intervention efforts that focus on social and cognitive skills are indicated in this vulnerable population.

  4. Predicting Climate Change Impacts to the Canadian Boreal Forest

    Directory of Open Access Journals (Sweden)

    Trisalyn A. Nelson

    2014-03-01

    Full Text Available Climate change is expected to alter temperature, precipitation, and seasonality with potentially acute impacts on Canada’s boreal. In this research we predicted future spatial distributions of biodiversity in Canada’s boreal for 2020, 2050, and 2080 using indirect indicators derived from remote sensing and based on vegetation productivity. Vegetation productivity indices, representing annual amounts and variability of greenness, have been shown to relate to tree and wildlife richness in Canada’s boreal. Relationships between historical satellite-derived productivity and climate data were applied to modelled scenarios of future climate to predict and map potential future vegetation productivity for 592 regions across Canada. Results indicated that the pattern of vegetation productivity will become more homogenous, particularly west of Hudson Bay. We expect climate change to impact biodiversity along north/south gradients and by 2080 vegetation distributions will be dominated by processes of seasonality in the north and a combination of cumulative greenness and minimum cover in the south. The Hudson Plains, which host the world’s largest and most contiguous wetland, are predicted to experience less seasonality and more greenness. The spatial distribution of predicted trends in vegetation productivity was emphasized over absolute values, in order to support regional biodiversity assessments and conservation planning.

  5. A review of protein function prediction under machine learning perspective.

    Science.gov (United States)

    Bernardes, Juliana S; Pedreira, Carlos E

    2013-08-01

    Protein function prediction is one of the most challenging problems in the post-genomic era. The number of newly identified proteins has been exponentially increasing with the advances of the high-throughput techniques. However, the functional characterization of these new proteins was not incremented in the same proportion. To fill this gap, a large number of computational methods have been proposed in the literature. Early approaches have explored homology relationships to associate known functions to the newly discovered proteins. Nevertheless, these approaches tend to fail when a new protein is considerably different (divergent) from previously known ones. Accordingly, more accurate approaches, that use expressive data representation and explore sophisticate computational techniques are required. Regarding these points, this review provides a comprehensible description of machine learning approaches that are currently applied to protein function prediction problems. We start by defining several problems enrolled in understanding protein function aspects, and describing how machine learning can be applied to these problems. We aim to expose, in a systematical framework, the role of these techniques in protein function inference, sometimes difficult to follow up due to the rapid evolvement of the field. With this purpose in mind, we highlight the most representative contributions, the recent advancements, and provide an insightful categorization and classification of machine learning methods in functional proteomics. PMID:23848274

  6. Predicting plants -modeling traits as a function of environment

    Science.gov (United States)

    Franklin, Oskar

    2016-04-01

    A central problem in understanding and modeling vegetation dynamics is how to represent the variation in plant properties and function across different environments. Addressing this problem there is a strong trend towards trait-based approaches, where vegetation properties are functions of the distributions of functional traits rather than of species. Recently there has been enormous progress in in quantifying trait variability and its drivers and effects (Van Bodegom et al. 2012; Adier et al. 2014; Kunstler et al. 2015) based on wide ranging datasets on a small number of easily measured traits, such as specific leaf area (SLA), wood density and maximum plant height. However, plant function depends on many other traits and while the commonly measured trait data are valuable, they are not sufficient for driving predictive and mechanistic models of vegetation dynamics -especially under novel climate or management conditions. For this purpose we need a model to predict functional traits, also those not easily measured, and how they depend on the plants' environment. Here I present such a mechanistic model based on fitness concepts and focused on traits related to water and light limitation of trees, including: wood density, drought response, allocation to defense, and leaf traits. The model is able to predict observed patterns of variability in these traits in relation to growth and mortality, and their responses to a gradient of water limitation. The results demonstrate that it is possible to mechanistically predict plant traits as a function of the environment based on an eco-physiological model of plant fitness. References Adier, P.B., Salguero-Gómez, R., Compagnoni, A., Hsu, J.S., Ray-Mukherjee, J., Mbeau-Ache, C. et al. (2014). Functional traits explain variation in plant lifehistory strategies. Proc. Natl. Acad. Sci. U. S. A., 111, 740-745. Kunstler, G., Falster, D., Coomes, D.A., Hui, F., Kooyman, R.M., Laughlin, D.C. et al. (2015). Plant functional traits

  7. Predictive functional control of integrating process based on impulse response

    Institute of Scientific and Technical Information of China (English)

    Bin ZHANG; Ping LI; Weidong ZHANG

    2004-01-01

    The predictive model is built according to the characteristics of the impulse response of integrating process. In order to eliminate the permanent offset between the setpoint and the process output in the presence of the load disturbance, a novel error compensation method is proposed. Then predictive functional control of integrating process is designed. The method given generates a simple control structure, which can significantly reduce online computation. Furthermore, the tuning of the controller is fairly straightforward. Simulation results indicate that the designed control system is relatively robust to the parameters variation of the process.

  8. Predicting the effects of climate change on marine communities and the consequences for fisheries

    DEFF Research Database (Denmark)

    Jennings, Simon; Brander, Keith

    2010-01-01

    predicted for the community under the same climate scenario. The main weakness of the community approach is that the methods predict abundance and production by size-class rather than taxonomic group, and society would be particularly concerned if climate driven changes had a strong effect on the relative...... production of fishable and non-fishable species in the community. The main strength of the community approach is that it provides widely applicable ‘null’ models for assessing the biological effects of climate change and a baseline for model comparisons.......Climate effects on the structure and function of marine communities have received scant attention. The few existing approaches for predicting climate effects suggest that community responses might be predicted from the responses of component populations. These approaches require a very complex...

  9. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-05-25

    The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

  10. Age Related Change in Thyroid Function

    Directory of Open Access Journals (Sweden)

    Shakila Rahman, Nasim Jahan, Nayma Sultana

    2012-12-01

    Full Text Available AbstractBackground: Thyroid hormones play a vital role in metabolism, sensitivity of tissues to other hormones and also in oxygen consumption of almost all cells of the body. However, mild to moderate decrease in function of thyroid gland may occur with advancing age even in apparently healthy elderly subjects.Objectives: To observe age related change in thyroid function status in apparently healthy elderly subjects in Bangladesh.Methods: This cross sectional study was carried out in the Department of Physiology, Sir Salimullah Medical College, Dhaka between 1st January 2011 and 31st December 2011. Sixty apparently healthy elderly subjects of both sexes aged 50 to 75 years were taken as study group. They were collected from Probin Nibash Hitoishi Shangha, Agargaon, Dhaka. In addition, 30 apparently healthy young adult subjects aged 20-40 years were included as control. For assessment of thyroid function, serum free thyroxine (FT4, free triiodothyronine (FT3 and thyroid stimulating hormone (TSH levels were estimated by ELISA method. Statistical analysis was done by one way ANOVA, Bonferroni test and Pearson’s Correlation Coefficient test as applicable.Results: In this study, mean serum free thyroxine (FT4 and free triiodothyronine (FT3 levels were significantly (p<0.001 lower and serum thyroid stimulating hormone (TSH level was significantly (p<0.001 higher in apparently healthy elderly subjects in comparison to those of the healthy young subjects. Again, serum FT4 and FT3 levels were negatively correlated whereas serum TSH level was positively correlated with age of the subjects.Conclusion: The present study revealed a progressive decrease in thyroid function with advancement of age.

  11. Prediction of time trends in recovery of cognitive function after mild head injury

    DEFF Research Database (Denmark)

    Müller, Kay; Ingebrigtsen, Tor; Wilsgaard, Tom;

    2009-01-01

    . There was significant improvement of performance after 6 months. APOE-epsilon4 genotype was the only independent factor significantly predicting less improvement. CONCLUSION: The presence of the APOE-epsilon4 allele predicts less recovery of cognitive function after mild head injury....... change. RESULTS: A Glasgow Coma Scale score of less than 15, traumatic brain injury demonstrated with computed tomography, magnetic resonance imaging, and serum S-100B greater than 0.14 microg/L predicted impaired cognitive performance both at baseline and after 6 months; APOE genotype did not...

  12. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.

    Science.gov (United States)

    Warde-Farley, David; Donaldson, Sylva L; Comes, Ovi; Zuberi, Khalid; Badrawi, Rashad; Chao, Pauline; Franz, Max; Grouios, Chris; Kazi, Farzana; Lopes, Christian Tannus; Maitland, Anson; Mostafavi, Sara; Montojo, Jason; Shao, Quentin; Wright, George; Bader, Gary D; Morris, Quaid

    2010-07-01

    GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens and Saccharomyces cerevisiae) and hundreds of data sets have been collected from GEO, BioGRID, Pathway Commons and I2D, as well as organism-specific functional genomics data sets. Users can select arbitrary subsets of the data sets associated with an organism to perform their analyses and can upload their own data sets to analyze. The GeneMANIA algorithm performs as well or better than other gene function prediction methods on yeast and mouse benchmarks. The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make GeneMANIA a useful tool for any biologist. PMID:20576703

  13. Computational predictions of energy materials using density functional theory

    Science.gov (United States)

    Jain, Anubhav; Shin, Yongwoo; Persson, Kristin A.

    2016-01-01

    In the search for new functional materials, quantum mechanics is an exciting starting point. The fundamental laws that govern the behaviour of electrons have the possibility, at the other end of the scale, to predict the performance of a material for a targeted application. In some cases, this is achievable using density functional theory (DFT). In this Review, we highlight DFT studies predicting energy-related materials that were subsequently confirmed experimentally. The attributes and limitations of DFT for the computational design of materials for lithium-ion batteries, hydrogen production and storage materials, superconductors, photovoltaics and thermoelectric materials are discussed. In the future, we expect that the accuracy of DFT-based methods will continue to improve and that growth in computing power will enable millions of materials to be virtually screened for specific applications. Thus, these examples represent a first glimpse of what may become a routine and integral step in materials discovery.

  14. Predicting restoration of kidney function during CRRT-free intervals

    OpenAIRE

    Heise Daniel; Gries Daniel; Moerer Onnen; Bleckmann Annalen; Quintel Michael

    2012-01-01

    Abstract Background Renal failure is common in critically ill patients and frequently requires continuous renal replacement therapy (CRRT). CRRT is discontinued at regular intervals for routine changes of the disposable equipment or for replacing clogged filter membrane assemblies. The present study was conducted to determine if the necessity to continue CRRT could be predicted during the CRRT-free period. Materials and methods In the period from 2003 to 2006, 605 patients were treated with C...

  15. Platelet Serotonin Transporter Function Predicts Default-Mode Network Activity

    OpenAIRE

    Christian Scharinger; Ulrich Rabl; Christian H. Kasess; Meyer, Bernhard M.; Tina Hofmaier; Kersten Diers; Lucie Bartova; Gerald Pail; Wolfgang Huf; Zeljko Uzelac; Beate Hartinger; Klaudius Kalcher; Thomas Perkmann; Helmuth Haslacher; Andreas Meyer-Lindenberg

    2014-01-01

    Background The serotonin transporter (5-HTT) is abundantly expressed in humans by the serotonin transporter gene SLC6A4 and removes serotonin (5-HT) from extracellular space. A blood-brain relationship between platelet and synaptosomal 5-HT reuptake has been suggested, but it is unknown today, if platelet 5-HT uptake can predict neural activation of human brain networks that are known to be under serotonergic influence. Methods A functional magnetic resonance study was performed in 48 healthy...

  16. Global analysis of predicted proteomes: Functional adaptation of physical properties

    OpenAIRE

    Knight, Christopher G.; Kassen, Rees; Hebestreit, Holger; Rainey, Paul B.

    2004-01-01

    The physical characteristics of proteins are fundamentally important in organismal function. We used the complete predicted proteomes of >100 organisms spanning the three domains of life to investigate the comparative biology and evolution of proteomes. Theoretical 2D gels were constructed with axes of protein mass and charge (pI) and converted to density estimates comparable across all types and sizes of proteome. We asked whether we could detect general patterns of proteome conservation and...

  17. High precision prediction of functional sites in protein structures.

    Directory of Open Access Journals (Sweden)

    Ljubomir Buturovic

    Full Text Available We address the problem of assigning biological function to solved protein structures. Computational tools play a critical role in identifying potential active sites and informing screening decisions for further lab analysis. A critical parameter in the practical application of computational methods is the precision, or positive predictive value. Precision measures the level of confidence the user should have in a particular computed functional assignment. Low precision annotations lead to futile laboratory investigations and waste scarce research resources. In this paper we describe an advanced version of the protein function annotation system FEATURE, which achieved 99% precision and average recall of 95% across 20 representative functional sites. The system uses a Support Vector Machine classifier operating on the microenvironment of physicochemical features around an amino acid. We also compared performance of our method with state-of-the-art sequence-level annotator Pfam in terms of precision, recall and localization. To our knowledge, no other functional site annotator has been rigorously evaluated against these key criteria. The software and predictive models are incorporated into the WebFEATURE service at http://feature.stanford.edu/wf4.0-beta.

  18. White matter morphometric changes uniquely predict children's reading acquisition.

    Science.gov (United States)

    Myers, Chelsea A; Vandermosten, Maaike; Farris, Emily A; Hancock, Roeland; Gimenez, Paul; Black, Jessica M; Casto, Brandi; Drahos, Miroslav; Tumber, Mandeep; Hendren, Robert L; Hulme, Charles; Hoeft, Fumiko

    2014-10-01

    This study examined whether variations in brain development between kindergarten and Grade 3 predicted individual differences in reading ability at Grade 3. Structural MRI measurements indicated that increases in the volume of two left temporo-parietal white matter clusters are unique predictors of reading outcomes above and beyond family history, socioeconomic status, and cognitive and preliteracy measures at baseline. Using diffusion MRI, we identified the left arcuate fasciculus and superior corona radiata as key fibers within the two clusters. Bias-free regression analyses using regions of interest from prior literature revealed that volume changes in temporo-parietal white matter, together with preliteracy measures, predicted 56% of the variance in reading outcomes. Our findings demonstrate the important contribution of developmental differences in areas of left dorsal white matter, often implicated in phonological processing, as a sensitive early biomarker for later reading abilities, and by extension, reading difficulties. PMID:25212581

  19. Predicting when climate-driven phenotypic change affects population dynamics.

    Science.gov (United States)

    McLean, Nina; Lawson, Callum R; Leech, Dave I; van de Pol, Martijn

    2016-06-01

    Species' responses to climate change are variable and diverse, yet our understanding of how different responses (e.g. physiological, behavioural, demographic) relate and how they affect the parameters most relevant for conservation (e.g. population persistence) is lacking. Despite this, studies that observe changes in one type of response typically assume that effects on population dynamics will occur, perhaps fallaciously. We use a hierarchical framework to explain and test when impacts of climate on traits (e.g. phenology) affect demographic rates (e.g. reproduction) and in turn population dynamics. Using this conceptual framework, we distinguish four mechanisms that can prevent lower-level responses from impacting population dynamics. Testable hypotheses were identified from the literature that suggest life-history and ecological characteristics which could predict when these mechanisms are likely to be important. A quantitative example on birds illustrates how, even with limited data and without fully-parameterized population models, new insights can be gained; differences among species in the impacts of climate-driven phenological changes on population growth were not explained by the number of broods or density dependence. Our approach helps to predict the types of species in which climate sensitivities of phenotypic traits have strong demographic and population consequences, which is crucial for conservation prioritization of data-deficient species. PMID:27062059

  20. Prediction of subsurface water level change from satellite data

    Science.gov (United States)

    Saykawlard, Suphan; Honda, Kiyoshi; Das Gupta, Ashim; Eiumnoh, Apisit; Chen, Xiaoyong

    2005-03-01

    This study explores the potential for predicting the spatial variation in subsurface water level change with crop growth stage from satellite data in Thabua Irrigation Project, situated in the northern central region of Thailand. The relationship between subsurface water level change from pumping water to irrigate rice in the dry season and the age of the rice was analysed. The spatial model of subsurface water level change was developed from the classification using greenness or (normalized difference vegetation index NDVI) derived from Landsat 5 Thematic Mapper data. The NDVI of 52 rice fields was employed to assess its relationship to the age of the rice. It was found that NDVI and rice age have a good correlation (R2 = 0.73). The low NDVI values (-0.059 to 0.082) in these fields were related to the young rice stage (0-30 days). NDVI and subsurface water level change were also correlated in this study and found to have a high correlation (Water level change (m day-1) = 0.3442 × NDVI - 0.0372; R2 = 0.96). From this model, the water level change caused by rice at different growth stages was derived. This was used to show the spatial variation of water level change in the project during the 1998-99 dry-season cropping. This simple method of using NDVI relationships with water level change and crop growth stages proves to be useful in determining the areas prone to excessive lowering of the subsurface water level during the dry season. This could assist in the appropriate planning of the use of subsurface water resources in dry-season cropping.

  1. Conserved functional motifs and homology modelling to predict hidden moonlighting functional sites

    Directory of Open Access Journals (Sweden)

    Helen R Irving

    2015-06-01

    Full Text Available Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here we review how hidden moonlighting functional centers which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico which in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  2. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites

    KAUST Repository

    Wong, Aloysius Tze

    2015-06-09

    Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  3. Remote sensing of vegetation ecophysiological function for improved hydrologic prediction

    Science.gov (United States)

    Drewry, D.; Ruddell, B. L.

    2014-12-01

    Land surface hydrology in vegetated landscapes is strongly controlled by ecophysiological function. The coupling between photosynthesis, stomatal dynamics and leaf energy balance fundamentally links the hydrologic and carbon cycles, and provides a basis for examining the utility of observations of functional plant traits for hydrologic prediction. Here we explore the potential of solar induced fluorescence (SIF) and thermal infrared (TIR) remote sensing observations to improve the accuracy and reduce the uncertainty in hydrologic prediction. While SIF represents an emission of radiation associated with photosynthesis, TIR provides information on foliage temperature and is related to stomatal function and water stress. A set of remote observing system simulation experiments are conducted to quantify the value of remotely sensed observations of SIF and TIR when assimilated into a detailed vegetation biophysical model. The MLCan model discretizes a dense plant canopy to resolve vertical variation in photosynthesis, water vapor and energy exchange. Here we present extensions to MLCan that allow for direct computation of the canopy emission of both SIF and TIR. The detailed representation of the physical environment and biological functioning of structurally complex canopies makes MLCan an ideal simulation tool for exploring the impact of these two unique, and potentially synergistic observables. This work specifically addresses remote sensing capabilities on both recently launched (OCO-2) and near-term (ECOSTRESS) satellite platforms. We contrast the information gained through the assimilation of SIF and TIR observations to that of the assimilation of data related to physical states such as soil moisture and leaf area index.

  4. Change in BMI accurately predicted by social exposure to acquaintances.

    Directory of Open Access Journals (Sweden)

    Rahman O Oloritun

    Full Text Available Research has mostly focused on obesity and not on processes of BMI change more generally, although these may be key factors that lead to obesity. Studies have suggested that obesity is affected by social ties. However these studies used survey based data collection techniques that may be biased toward select only close friends and relatives. In this study, mobile phone sensing techniques were used to routinely capture social interaction data in an undergraduate dorm. By automating the capture of social interaction data, the limitations of self-reported social exposure data are avoided. This study attempts to understand and develop a model that best describes the change in BMI using social interaction data. We evaluated a cohort of 42 college students in a co-located university dorm, automatically captured via mobile phones and survey based health-related information. We determined the most predictive variables for change in BMI using the least absolute shrinkage and selection operator (LASSO method. The selected variables, with gender, healthy diet category, and ability to manage stress, were used to build multiple linear regression models that estimate the effect of exposure and individual factors on change in BMI. We identified the best model using Akaike Information Criterion (AIC and R(2. This study found a model that explains 68% (p<0.0001 of the variation in change in BMI. The model combined social interaction data, especially from acquaintances, and personal health-related information to explain change in BMI. This is the first study taking into account both interactions with different levels of social interaction and personal health-related information. Social interactions with acquaintances accounted for more than half the variation in change in BMI. This suggests the importance of not only individual health information but also the significance of social interactions with people we are exposed to, even people we may not consider as

  5. Cod Gadus morhua and climate change: processes, productivity and prediction

    DEFF Research Database (Denmark)

    Brander, Keith

    2010-01-01

    , predators, parasites and diseases are much more difficult to estimate and predict. Climate can affect all life-history stages through direct and indirect processes and although the consequences in terms of growth, survival and reproductive output can be monitored, it is often difficult to determine...... the causes. Investigation of cod Gadus morhua populations across the whole North Atlantic Ocean has shown large-scale patterns of change in productivity due to lower individual growth and condition, caused by large-scale climate forcing. If a population is being heavily exploited then a drop in productivity...... can push it into decline unless the level of fishing is reduced: the idea of a stable carrying capacity is a dangerous myth. Overexploitation can be avoided by keeping fishing mortality low and by monitoring and responding rapidly to changes in productivity. There are signs that this lesson has been...

  6. Models for predicting objective function weights in prostate cancer IMRT

    International Nuclear Information System (INIS)

    Purpose: To develop and evaluate the clinical applicability of advanced machine learning models that simultaneously predict multiple optimization objective function weights from patient geometry for intensity-modulated radiation therapy of prostate cancer. Methods: A previously developed inverse optimization method was applied retrospectively to determine optimal objective function weights for 315 treated patients. The authors used an overlap volume ratio (OV) of bladder and rectum for different PTV expansions and overlap volume histogram slopes (OVSR and OVSB for the rectum and bladder, respectively) as explanatory variables that quantify patient geometry. Using the optimal weights as ground truth, the authors trained and applied three prediction models: logistic regression (LR), multinomial logistic regression (MLR), and weighted K-nearest neighbor (KNN). The population average of the optimal objective function weights was also calculated. Results: The OV at 0.4 cm and OVSR at 0.1 cm features were found to be the most predictive of the weights. The authors observed comparable performance (i.e., no statistically significant difference) between LR, MLR, and KNN methodologies, with LR appearing to perform the best. All three machine learning models outperformed the population average by a statistically significant amount over a range of clinical metrics including bladder/rectum V53Gy, bladder/rectum V70Gy, and dose to the bladder, rectum, CTV, and PTV. When comparing the weights directly, the LR model predicted bladder and rectum weights that had, on average, a 73% and 74% relative improvement over the population average weights, respectively. The treatment plans resulting from the LR weights had, on average, a rectum V70Gy that was 35% closer to the clinical plan and a bladder V70Gy that was 29% closer, compared to the population average weights. Similar results were observed for all other clinical metrics. Conclusions: The authors demonstrated that the KNN and MLR

  7. Models for predicting objective function weights in prostate cancer IMRT

    Energy Technology Data Exchange (ETDEWEB)

    Boutilier, Justin J., E-mail: j.boutilier@mail.utoronto.ca; Lee, Taewoo [Department of Mechanical and Industrial Engineering, University of Toronto, 5 King’s College Road, Toronto, Ontario M5S 3G8 (Canada); Craig, Tim [Radiation Medicine Program, UHN Princess Margaret Cancer Centre, 610 University of Avenue, Toronto, Ontario M5T 2M9, Canada and Department of Radiation Oncology, University of Toronto, 148 - 150 College Street, Toronto, Ontario M5S 3S2 (Canada); Sharpe, Michael B. [Radiation Medicine Program, UHN Princess Margaret Cancer Centre, 610 University of Avenue, Toronto, Ontario M5T 2M9 (Canada); Department of Radiation Oncology, University of Toronto, 148 - 150 College Street, Toronto, Ontario M5S 3S2 (Canada); Techna Institute for the Advancement of Technology for Health, 124 - 100 College Street, Toronto, Ontario M5G 1P5 (Canada); Chan, Timothy C. Y. [Department of Mechanical and Industrial Engineering, University of Toronto, 5 King’s College Road, Toronto, Ontario M5S 3G8, Canada and Techna Institute for the Advancement of Technology for Health, 124 - 100 College Street, Toronto, Ontario M5G 1P5 (Canada)

    2015-04-15

    Purpose: To develop and evaluate the clinical applicability of advanced machine learning models that simultaneously predict multiple optimization objective function weights from patient geometry for intensity-modulated radiation therapy of prostate cancer. Methods: A previously developed inverse optimization method was applied retrospectively to determine optimal objective function weights for 315 treated patients. The authors used an overlap volume ratio (OV) of bladder and rectum for different PTV expansions and overlap volume histogram slopes (OVSR and OVSB for the rectum and bladder, respectively) as explanatory variables that quantify patient geometry. Using the optimal weights as ground truth, the authors trained and applied three prediction models: logistic regression (LR), multinomial logistic regression (MLR), and weighted K-nearest neighbor (KNN). The population average of the optimal objective function weights was also calculated. Results: The OV at 0.4 cm and OVSR at 0.1 cm features were found to be the most predictive of the weights. The authors observed comparable performance (i.e., no statistically significant difference) between LR, MLR, and KNN methodologies, with LR appearing to perform the best. All three machine learning models outperformed the population average by a statistically significant amount over a range of clinical metrics including bladder/rectum V53Gy, bladder/rectum V70Gy, and dose to the bladder, rectum, CTV, and PTV. When comparing the weights directly, the LR model predicted bladder and rectum weights that had, on average, a 73% and 74% relative improvement over the population average weights, respectively. The treatment plans resulting from the LR weights had, on average, a rectum V70Gy that was 35% closer to the clinical plan and a bladder V70Gy that was 29% closer, compared to the population average weights. Similar results were observed for all other clinical metrics. Conclusions: The authors demonstrated that the KNN and MLR

  8. Predictions of Excitation Functions of Super-Heavy Elements

    International Nuclear Information System (INIS)

    A long-standing theoretical change is predictions of optimum incident systems, optimum incident energies, as well as those of maximum residue cross sections for synthesis of super-heavy elements (SHE). Theoretical predictions, however, have ambiguities stemming from two causes: unknown masses or shell correction energies (SCE) of SHE nuclei themselves and unexplained mechanism of the fusion hindrance, experimentally known since many years ago. On the former, there are rather precise predictions by structure studies, but they are different with each other, so predicted SCE's are not reliable precisely, because 1 MeV difference in them results in change in residue cross section about one order of magnitude through so-called survival probability (It should be noted that fission barrier of SHE is given totally by SCE). On the latter, there was no reaction theory encompassing the hindrance mechanism. The present authors have proposed the two-step model for the fusion process, which explains the hindrance qualitatively [1], and which is applicable to the cold as well as to the hot fusion paths [2]. However, the model overestimates the absolute values of the cross sections, if the masses predicted by P. Moeller et al. [3] are used. Examples of the calculated excitations are shown in Fig. 1 [4] and 2, with only one free parameter f, a factor for SCE, in order to reproduce order of magnitude of the cross sections. As for the formation step of the spherical compound nucleus, the present authors recently have made a closer analysis of fusion dynamics from di-nucleus to mono-nucleus, which improves predictions of fusion probability quantitatively [5]. That is expected to make a free parameter f to be unnecessary to introduce. Furthermore, the neck dynamics is found to depend on mass-asymmetry and thus, fusion probability depends on incident channel with the neck dynamics unknown so far. In connection with the question on which path is more favorable when we proceed to heavier

  9. Functional traits predict relationship between plant abundance dynamic and long-term climate warming.

    Science.gov (United States)

    Soudzilovskaia, Nadejda A; Elumeeva, Tatiana G; Onipchenko, Vladimir G; Shidakov, Islam I; Salpagarova, Fatima S; Khubiev, Anzor B; Tekeev, Dzhamal K; Cornelissen, Johannes H C

    2013-11-01

    Predicting climate change impact on ecosystem structure and services is one of the most important challenges in ecology. Until now, plant species response to climate change has been described at the level of fixed plant functional types, an approach limited by its inflexibility as there is much interspecific functional variation within plant functional types. Considering a plant species as a set of functional traits greatly increases our possibilities for analysis of ecosystem functioning and carbon and nutrient fluxes associated therewith. Moreover, recently assembled large-scale databases hold comprehensive per-species data on plant functional traits, allowing a detailed functional description of many plant communities on Earth. Here, we show that plant functional traits can be used as predictors of vegetation response to climate warming, accounting in our test ecosystem (the species-rich alpine belt of Caucasus mountains, Russia) for 59% of variability in the per-species abundance relation to temperature. In this mountain belt, traits that promote conservative leaf water economy (higher leaf mass per area, thicker leaves) and large investments in belowground reserves to support next year's shoot buds (root carbon content) were the best predictors of the species increase in abundance along with temperature increase. This finding demonstrates that plant functional traits constitute a highly useful concept for forecasting changes in plant communities, and their associated ecosystem services, in response to climate change. PMID:24145400

  10. Should we believe model predictions of future climate change? (Invited)

    Science.gov (United States)

    Knutti, R.

    2009-12-01

    As computers get faster and our understanding of the climate system improves, climate models to predict the future are getting more complex by including more and more processes, and they are run at higher and higher resolution to resolve more of the small scale processes. As a result, some of the simulated features and structures, e.g. ocean eddies or tropical cyclones look surprisingly real. But are these deceptive? A pattern can look perfectly real but be in the wrong place. So can the current global models really provide the kind of information on local scales and on the quantities (e.g. extreme events) that the decision maker would need to know to invest for example in adaptation? A closer look indicates that evaluating skill of climate models and quantifying uncertainties in predictions is very difficult. This presentation shows that while models are improving in simulating the climate features we observe (e.g. the present day mean state, or the El Nino Southern Oscillation), the spread from multiple models in predicting future changes is often not decreasing. The main problem is that (unlike with weather forecasts for example) we cannot evaluate the model on a prediction (for example for the year 2100) and we have to use the present, or past changes as metrics of skills. But there are infinite ways of testing a model, and many metrics used to test models do not clearly relate to the prediction. Therefore there is little agreement in the community on metrics to separate ‘good’ and ‘bad’ models, and there is a concern that model development, evaluation and posterior weighting or ranking of models are all using the same datasets. While models are continuously improving in representing what we believe to be the key processes, many models also share ideas, parameterizations or even pieces of model code. The current models can therefore not be considered independent. Robustness of a model simulated result is often interpreted as increasing the confidence

  11. Predicting the Impacts of Climate Change on Central American Agriculture

    Science.gov (United States)

    Winter, J. M.; Ruane, A. C.; Rosenzweig, C.

    2011-12-01

    Agriculture is a vital component of Central America's economy. Poor crop yields and harvest reliability can produce food insecurity, malnutrition, and conflict. Regional climate models (RCMs) and agricultural models have the potential to greatly enhance the efficiency of Central American agriculture and water resources management under both current and future climates. A series of numerical experiments was conducted using Regional Climate Model Version 3 (RegCM3) and the Weather Research and Forecasting Model (WRF) to evaluate the ability of RCMs to reproduce the current climate of Central America and assess changes in temperature and precipitation under multiple future climate scenarios. Control simulations were thoroughly compared to a variety of observational datasets, including local weather station data, gridded meteorological data, and high-resolution satellite-based precipitation products. Future climate simulations were analyzed for both mean shifts in climate and changes in climate variability, including extreme events (droughts, heat waves, floods). To explore the impacts of changing climate on maize, bean, and rice yields in Central America, RCM output was used to force the Decision Support System for Agrotechnology Transfer Model (DSSAT). These results were synthesized to create climate change impacts predictions for Central American agriculture that explicitly account for evolving distributions of precipitation and temperature extremes.

  12. Does Change on the MOLEST and RAPE Scales Predict Sexual Recidivism?

    Science.gov (United States)

    Nunes, Kevin L; Pettersen, Cathrine; Hermann, Chantal A; Looman, Jan; Spape, Jessica

    2016-08-01

    The purpose of the current study was to examine whether the MOLEST and RAPE scales and change on these measures predicted sexual recidivism in a sample of 146 adult male sexual offenders who participated in a high-intensity treatment program while incarcerated. The majority of subjects had functional scores on the MOLEST and RAPE scales prior to treatment. Of those who had dysfunctional pre-treatment scores, the majority made significant gains. However, the MOLEST and RAPE scales did not significantly predict sexual recidivism. This was the case for pre-treatment scores, post-treatment scores, and change scores. Our findings are generally not consistent with the view that these measures assess dynamic risk factors for sexual recidivism. However, this is the first published study to examine the predictive validity of these scales and more rigorous research is needed before firm conclusions can be drawn. PMID:24996579

  13. Predicting implementation from organizational readiness for change: a study protocol

    Directory of Open Access Journals (Sweden)

    Kelly P Adam

    2011-07-01

    Full Text Available Abstract Background There is widespread interest in measuring organizational readiness to implement evidence-based practices in clinical care. However, there are a number of challenges to validating organizational measures, including inferential bias arising from the halo effect and method bias - two threats to validity that, while well-documented by organizational scholars, are often ignored in health services research. We describe a protocol to comprehensively assess the psychometric properties of a previously developed survey, the Organizational Readiness to Change Assessment. Objectives Our objective is to conduct a comprehensive assessment of the psychometric properties of the Organizational Readiness to Change Assessment incorporating methods specifically to address threats from halo effect and method bias. Methods and Design We will conduct three sets of analyses using longitudinal, secondary data from four partner projects, each testing interventions to improve the implementation of an evidence-based clinical practice. Partner projects field the Organizational Readiness to Change Assessment at baseline (n = 208 respondents; 53 facilities, and prospectively assesses the degree to which the evidence-based practice is implemented. We will conduct predictive and concurrent validities using hierarchical linear modeling and multivariate regression, respectively. For predictive validity, the outcome is the change from baseline to follow-up in the use of the evidence-based practice. We will use intra-class correlations derived from hierarchical linear models to assess inter-rater reliability. Two partner projects will also field measures of job satisfaction for convergent and discriminant validity analyses, and will field Organizational Readiness to Change Assessment measures at follow-up for concurrent validity (n = 158 respondents; 33 facilities. Convergent and discriminant validities will test associations between organizational readiness and

  14. Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

    Science.gov (United States)

    Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

    2016-06-01

    Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

  15. Prediction of detailed enzyme functions and identification of specificity determining residues by random forests.

    Directory of Open Access Journals (Sweden)

    Chioko Nagao

    Full Text Available Determining enzyme functions is essential for a thorough understanding of cellular processes. Although many prediction methods have been developed, it remains a significant challenge to predict enzyme functions at the fourth-digit level of the Enzyme Commission numbers. Functional specificity of enzymes often changes drastically by mutations of a small number of residues and therefore, information about these critical residues can potentially help discriminate detailed functions. However, because these residues must be identified by mutagenesis experiments, the available information is limited, and the lack of experimentally verified specificity determining residues (SDRs has hindered the development of detailed function prediction methods and computational identification of SDRs. Here we present a novel method for predicting enzyme functions by random forests, EFPrf, along with a set of putative SDRs, the random forests derived SDRs (rf-SDRs. EFPrf consists of a set of binary predictors for enzymes in each CATH superfamily and the rf-SDRs are the residue positions corresponding to the most highly contributing attributes obtained from each predictor. EFPrf showed a precision of 0.98 and a recall of 0.89 in a cross-validated benchmark assessment. The rf-SDRs included many residues, whose importance for specificity had been validated experimentally. The analysis of the rf-SDRs revealed both a general tendency that functionally diverged superfamilies tend to include more active site residues in their rf-SDRs than in less diverged superfamilies, and superfamily-specific conservation patterns of each functional residue. EFPrf and the rf-SDRs will be an effective tool for annotating enzyme functions and for understanding how enzyme functions have diverged within each superfamily.

  16. Predicting activity approach based on new atoms similarity kernel function.

    Science.gov (United States)

    Abu El-Atta, Ahmed H; Moussa, M I; Hassanien, Aboul Ella

    2015-07-01

    Drug design is a high cost and long term process. To reduce time and costs for drugs discoveries, new techniques are needed. Chemoinformatics field implements the informational techniques and computer science like machine learning and graph theory to discover the chemical compounds properties, such as toxicity or biological activity. This is done through analyzing their molecular structure (molecular graph). To overcome this problem there is an increasing need for algorithms to analyze and classify graph data to predict the activity of molecules. Kernels methods provide a powerful framework which combines machine learning with graph theory techniques. These kernels methods have led to impressive performance results in many several chemoinformatics problems like biological activity prediction. This paper presents a new approach based on kernel functions to solve activity prediction problem for chemical compounds. First we encode all atoms depending on their neighbors then we use these codes to find a relationship between those atoms each other. Then we use relation between different atoms to find similarity between chemical compounds. The proposed approach was compared with many other classification methods and the results show competitive accuracy with these methods. PMID:26117822

  17. Betting and Belief: Prediction Markets and Attribution of Climate Change

    CERN Document Server

    Nay, John J; Gilligan, Jonathan M

    2016-01-01

    Despite much scientific evidence, a large fraction of the American public doubts that greenhouse gases are causing global warming. We present a simulation model as a computational test-bed for climate prediction markets. Traders adapt their beliefs about future temperatures based on the profits of other traders in their social network. We simulate two alternative climate futures, in which global temperatures are primarily driven either by carbon dioxide or by solar irradiance. These represent, respectively, the scientific consensus and a hypothesis advanced by prominent skeptics. We conduct sensitivity analyses to determine how a variety of factors describing both the market and the physical climate may affect traders' beliefs about the cause of global climate change. Market participation causes most traders to converge quickly toward believing the "true" climate model, suggesting that a climate market could be useful for building public consensus.

  18. Habitual fat intake predicts memory function in younger women

    Directory of Open Access Journals (Sweden)

    Edward Leigh eGibson

    2013-12-01

    Full Text Available High intakes of fat have been linked to greater cognitive decline in old age, but such associations may already occur in younger adults. We tested memory and learning in 38 women (25-45 years old, recruited for a larger observational study in women with polycystic ovary syndrome. These women varied in health status, though not significantly between cases (n=23 and controls (n=15. Performance on tests sensitive to medial temporal lobe function (CANTABeclipse, Cambridge Cognition Ltd., i.e. verbal memory, visuo-spatial learning and delayed pattern matching, were compared with intakes of macronutrients from 7-day diet diaries and physiological indices of metabolic syndrome. Partial correlations were adjusted for age, activity and verbal IQ (National Adult Reading Test. Greater intakes of saturated and trans fats, and higher saturated to unsaturated fat ratio (Sat:UFA, were associated with more errors on the visuo-spatial task and with poorer word recall and recognition. Unexpectedly, higher UFA intake predicted poorer performance on the word recall and recognition measures. Fasting insulin was positively correlated with poorer word recognition only, whereas higher blood total cholesterol was associated only with visuo-spatial learning errors. None of these variables predicted performance on a delayed pattern matching test. The significant nutrient-cognition relationships were tested for mediation by total energy intake: saturated and trans fat intakes, and Sat:UFA, remained significant predictors specifically of visuo-spatial learning errors, whereas total fat and UFA intakes now predicted only poorer word recall. Examination of associations separately for mono- (MUFA and polyunsaturated fats suggested that only MUFA intake was predictive of poorer word recall. Saturated and trans fats, and fasting insulin, may already be associated with cognitive deficits in younger women. The findings need extending but may have important implications for public

  19. Reference change values and power functions

    DEFF Research Database (Denmark)

    Iglesias Canadell, Natàlia; Hyltoft Petersen, Per; Jensen, Esther;

    2004-01-01

    Repeated samplings and measurements in the monitoring of patients to look for changes are common clinical problems. The "reference change value", calculated as zp x [2 x (CVI2 + CVA2)](1/2), where zp is the z-statistic and CVI and CVA are within-subject and analytical coefficients of variation...

  20. Can Functional Cardiac Age be Predicted from ECG in a Normal Healthy Population

    Science.gov (United States)

    Schlegel, Todd; Starc, Vito; Leban, Manja; Sinigoj, Petra; Vrhovec, Milos

    2011-01-01

    In a normal healthy population, we desired to determine the most age-dependent conventional and advanced ECG parameters. We hypothesized that changes in several ECG parameters might correlate with age and together reliably characterize the functional age of the heart. Methods: An initial study population of 313 apparently healthy subjects was ultimately reduced to 148 subjects (74 men, 84 women, in the range from 10 to 75 years of age) after exclusion criteria. In all subjects, ECG recordings (resting 5-minute 12-lead high frequency ECG) were evaluated via custom software programs to calculate up to 85 different conventional and advanced ECG parameters including beat-to-beat QT and RR variability, waveform complexity, and signal-averaged, high-frequency and spatial/spatiotemporal ECG parameters. The prediction of functional age was evaluated by multiple linear regression analysis using the best 5 univariate predictors. Results: Ignoring what were ultimately small differences between males and females, the functional age was found to be predicted (R2= 0.69, P ECGs, functional cardiac age can be estimated by multiple linear regression analysis of mostly advanced ECG results. Because some parameters in the regression formula, such as QTcorr, high frequency QRS amplitude and P-wave width also change with disease in the same direction as with increased age, increased functional age of the heart may reflect subtle age-related pathologies in cardiac electrical function that are usually hidden on conventional ECG.

  1. Functional innovation from changes in protein domains and their combinations.

    Science.gov (United States)

    Lees, Jonathan G; Dawson, Natalie L; Sillitoe, Ian; Orengo, Christine A

    2016-06-01

    Domains are the functional building blocks of proteins. In this work we discuss how domains can contribute to the evolution of new functions. Domains themselves can evolve through various mechanisms, altering their intrinsic function. Domains can also facilitate functional innovations by combining with other domains to make novel proteins. We discuss the mechanisms by which domain and domain combinations support functional innovations. We highlight interesting examples where changes in domain combination promote changes at the domain level. PMID:27309309

  2. The use of specialisation indices to predict vulnerability of coral-feeding butterflyfishes to environmental change

    KAUST Repository

    Lawton, Rebecca J.

    2011-07-14

    In the absence of detailed assessments of extinction risk, ecological specialisation is often used as a proxy of vulnerability to environmental disturbances and extinction risk. Numerous indices can be used to estimate specialisation; however, the utility of these different indices to predict vulnerability to future environmental change is unknown. Here we compare the performance of specialisation indices using coral-feeding butterflyfishes as a model group. Our aims were to 1) quantify the dietary preferences of three butterflyfish species across habitats with differing levels of resource availability; 2) investigate how estimates of dietary specialisation vary with the use of different specialisation indices; 3) determine which specialisation indices best inform predictions of vulnerability to environmental change; and 4) assess the utility of resource selection functions to inform predictions of vulnerability to environmental change. The relative level of dietary specialisation estimated for all three species varied when different specialisation indices were used, indicating that the choice of index can have a considerable impact upon estimates of specialisation. Specialisation indices that do not consider resource abundance may fail to distinguish species that primarily use common resources from species that actively target resources disproportionately more than they are available. Resource selection functions provided the greatest insights into the potential response of species to changes in resource availability. Examination of resource selection functions, in addition to specialisation indices, indicated that Chaetodon trifascialis was the most specialised feeder, with highly conserved dietary preferences across all sites, suggesting that this species is highly vulnerable to the impacts of climate-induced coral loss on reefs. Our results indicate that vulnerability assessments based on some specialisation indices may be misleading and the best estimates of

  3. Estimating Stochastic Volatility Models using Prediction-based Estimating Functions

    DEFF Research Database (Denmark)

    Lunde, Asger; Brix, Anne Floor

    In this paper prediction-based estimating functions (PBEFs), introduced in Sørensen (2000), are reviewed and PBEFs for the Heston (1993) stochastic volatility model are derived. The finite sample performance of the PBEF based estimator is investigated in a Monte Carlo study, and compared to the...... performance of the GMM estimator based on conditional moments of integrated volatility from Bollerslev and Zhou (2002). The case where the observed log-price process is contaminated by i.i.d. market microstructure (MMS) noise is also investigated. First, the impact of MMS noise on the parameter estimates from...... the two estimation methods without noise correction are studied. Second, a noise robust GMM estimator is constructed by approximating integrated volatility by a realized kernel instead of realized variance. The PBEFs are also recalculated in the noise setting, and the two estimation methods ability to...

  4. Function and Phenotype prediction through Data and Knowledge Fusion

    KAUST Repository

    Vespoor, Karen

    2016-01-27

    The biomedical literature captures the most current biomedical knowledge and is a tremendously rich resource for research. With over 24 million publications currently indexed in the US National Library of Medicine’s PubMed index, however, it is becoming increasingly challenging for biomedical researchers to keep up with this literature. Automated strategies for extracting information from it are required. Large-scale processing of the literature enables direct biomedical knowledge discovery. In this presentation, I will introduce the use of text mining techniques to support analysis of biological data sets, and will specifically discuss applications in protein function and phenotype prediction, as well as analysis of genetic variants that are supported by analysis of the literature and integration with complementary structured resources.

  5. Pacific Walrus and climate change: observations and predictions.

    Science.gov (United States)

    Maccracken, James G

    2012-08-01

    The extent and duration of sea-ice habitats used by Pacific walrus (Odobenus rosmarus divergens) are diminishing resulting in altered walrus behavior, mortality, and distribution. I document changes that have occurred over the past several decades and make predictions to the end of the 21st century. Climate models project that sea ice will monotonically decline resulting in more ice-free summers of longer duration. Several stressors that may impact walruses are directly influenced by sea ice. How these stressors materialize were modeled as most likely-case, worst-case, and best-case scenarios for the mid- and late-21st century, resulting in four comprehensive working hypotheses that can help identify and prioritize management and research projects, identify comprehensive mitigation actions, and guide monitoring programs to track future developments and adjust programs as needed. In the short term, the most plausible hypotheses predict a continuing northward shift in walrus distribution, increasing use of coastal haulouts in summer and fall, and a population reduction set by the carrying capacity of the near shore environment and subsistence hunting. Alternatively, under worst-case conditions, the population will decline to a level where the probability of extinction is high. In the long term, walrus may seasonally abandon the Bering and Chukchi Seas for sea-ice refugia to the northwest and northeast, ocean warming and pH decline alter walrus food resources, and subsistence hunting exacerbates a large population decline. However, conditions that reverse current trends in sea ice loss cannot be ruled out. Which hypothesis comes to fruition depends on how the stressors develop and the success of mitigation measures. Best-case scenarios indicate that successful mitigation of unsustainable harvests and terrestrial haulout-related mortalities can be effective. Management and research should focus on monitoring, elucidating effects, and mitigation, while ultimately

  6. Predicted changes in energy demands for heating and cooling due to climate change

    Science.gov (United States)

    Dolinar, Mojca; Vidrih, Boris; Kajfež-Bogataj, Lučka; Medved, Sašo

    In the last 3 years in Slovenia we experienced extremely hot summers and demand for cooling the buildings have risen significantly. Since climate change scenarios predict higher temperatures for the whole country and for all seasons, we expect that energy demand for heating would decrease while demand for cooling would increase. An analysis for building with permitted energy demand and for low-energy demand building in two typical urban climates in Slovenia was performed. The transient systems simulation program (TRNSYS) was used for simulation of the indoor conditions and the energy use for heating and cooling. Climate change scenarios were presented in form of “future” Test Reference Years (TRY). The time series of hourly data for all meteorological variables for different scenarios were chosen from actual measurements, using the method of highest likelihood. The climate change scenarios predicted temperature rise (+1 °C and +3 °C) and solar radiation increase (+3% and +6%). With the selection of these scenarios we covered the spectra of possible predicted climate changes in Slovenia. The results show that energy use for heating would decrease from 16% to 25% (depends on the intensity of warming) in subalpine region, while in Mediterranean region the rate of change would not be significant. In summer time we would need up to six times more energy for cooling in subalpine region and approximately two times more in Mediterranean region. low-energy building proved to be very economical in wintertime while on average higher energy consumption for cooling is expected in those buildings in summertime. In case of significant warmer and more solar energy intensive climate, the good isolated buildings are more efficient than standard buildings. TRY proved not to be efficient for studying extreme conditions like installed power of the cooling system.

  7. Changes in sexual function after radiotherapy treatment of prostate cancer

    International Nuclear Information System (INIS)

    The objective was to assess sexual function before and after definitive irradiation for the treatment of cancer of the prostate. The study comprised 67 patients (mean age 68 years) treated in five radiotherapy departments and assessed with repeated questionnaires about their libido, arousal, frequency and quality of intercourse, and sexual satisfaction. Interviews were obtained before radiotherapy and at the end of the first year after treatment. Sixty-three patients were married and 50 had a sexually effective partner. Forty-six patients presented with another pathology or medical treatment capable of inducing sexual dysfunction. Before radiotherapy, 40 patients were sexually active, with good to acceptable intercourse. Between 10 and 24 months after the end of radiotherapy, no disease progression was observed and prostate-specific antigen levels remained high in only two patients. Sexual function was preserved in 67% of patients but only 50% observed no change. The functional prognosis seemed to be related to the initial frequency and quality of intercourse; more than three times per month, the prognosis remained good, under three per month, it was poor. The patient's age was a predictive factor for the frequency of intercourse. (author)

  8. Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach

    Science.gov (United States)

    Le Roux, Xavier; Bouskill, Nicholas J.; Niboyet, Audrey; Barthes, Laure; Dijkstra, Paul; Field, Chris B.; Hungate, Bruce A.; Lerondelle, Catherine; Pommier, Thomas; Tang, Jinyun; Terada, Akihiko; Tourna, Maria; Poly, Franck

    2016-01-01

    Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field experiment in a California grassland, we studied the main and interactive effects of three global change factors (increased atmospheric CO2 concentration, precipitation and nitrogen addition, and all their factorial combinations, based on global change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB). Using a trait-based model, we then tested whether categorizing NOB into a few functional groups unified by physiological traits enables understanding and predicting how soil NOB respond to global environmental change. Contrasted responses to global change treatments were observed between three main NOB functional types. In particular, putatively mixotrophic Nitrobacter, rare under most treatments, became dominant under the ‘High CO2+Nitrogen+Precipitation’ treatment. The mechanistic trait-based model, which simulated ecological niches of NOB types consistent with previous ecophysiological reports, helped predicting the observed effects of global change on NOB and elucidating the underlying biotic and abiotic controls. Our results are a starting point for representing the overwhelming diversity of soil bacteria by a few functional types that can be incorporated into models of terrestrial ecosystems and biogeochemical processes.

  9. The inventory-based approach for prediction of SOC change following land use change

    Directory of Open Access Journals (Sweden)

    van Wesemael B.

    2004-01-01

    Full Text Available This paper describes and illustrates an approach to predict soil organic carbon (SOC change in time after land use change as derived from SOC differences in space. The approach requires the availability of a SOC inventory for spatially explicit combinations of soil and land use type, further termed landscape units (LSU. SOC of LSU with equal soil type but different land use type are compared and the observed differences in SOC are interpreted as the expected SOC change after the corresponding land use change. From a confrontation with time series of agro-statistical data on crop and grassland areas and on animal manure production, we conclude that the approach is a low-cost alternative for more complex methods like multitemporal assessments and modelling, provided that (i an inventory reflecting current management and climate conditions and (ii additional information on the extent and type of recent land use changes are available. Examples of land use and land management changes are discussed, such as grassland – cropland conversions, the conversion of permanent to temporary grassland, or changes in manure application.

  10. Understanding the cost of change Function: A basis for using an effective small step change strategy

    OpenAIRE

    Pinto, Peter A.; Basheer M. Khumawala

    2005-01-01

    This paper develops the cost of change function under the Continuous Improvement (CI) paradigm advocated by quality gurus such as Deming, Taguchi, and Shingo. CI is considered to be focusing on "frame bending" or minor changes while Organizational Change (OC) is considered to be focusing on "frame breaking " or major changes. The cost of change function is modified to be a discrete function incorporating a "monitoring" cost component and a "doing" cost element, which leads to a better underst...

  11. Human functional neuroimaging of brain changes associated with practice

    OpenAIRE

    GARAVAN, HUGH PATRICK

    2005-01-01

    PUBLISHED The discovery that experience-driven changes in the human brain can occur from a neural to a cortical level throughout the lifespan has stimulated a proliferation of research into how neural function changes in response to experience, enabled by neuroimaging methods such as positron emission tomography and functional magnetic resonance imaging. Studies attempt to characterize these changes by examining how practice on a task affects the functional anatomy underlying performance. ...

  12. Feature Selection and the Class Imbalance Problem in Predicting Protein Function from Sequence

    NARCIS (Netherlands)

    Al-Shahib, A.; Breitling, R.; Gilbert, D.

    2005-01-01

    Abstract: When the standard approach to predict protein function by sequence homology fails, other alternative methods can be used that require only the amino acid sequence for predicting function. One such approach uses machine learning to predict protein function directly from amino acid sequence

  13. Sensitivity and specificity of the functional hallux limitus test to predict foot function.

    Science.gov (United States)

    Payne, Craig; Chuter, Vivienne; Miller, Kathryn

    2002-05-01

    Functional hallux limitus is an underrecognized entity that generally does not produce symptoms but can result in a variety of compensatory mechanisms that can produce symptoms. Clinically, hallux limitus can be determined by assessing the range of motion available at the first metatarsophalangeal joint while the first ray is prevented from plantarflexing. The aim of this study was to determine the sensitivity and specificity of this clinical test to predict abnormal excessive midtarsal joint function during gait. A total of 86 feet were examined for functional hallux limitus and abnormal pronation of the midtarsal joint during late midstance. The test had a sensitivity of 0.72 and a specificity of 0.66, suggesting that clinicians should consider functional hallux limitus when there is late midstance pronation of the midtarsal joint during gait. PMID:12015407

  14. Prediction of cloud condensation nuclei activity for organic compounds using functional group contribution methods

    Science.gov (United States)

    Petters, M. D.; Kreidenweis, S. M.; Ziemann, P. J.

    2016-01-01

    A wealth of recent laboratory and field experiments demonstrate that organic aerosol composition evolves with time in the atmosphere, leading to changes in the influence of the organic fraction to cloud condensation nuclei (CCN) spectra. There is a need for tools that can realistically represent the evolution of CCN activity to better predict indirect effects of organic aerosol on clouds and climate. This work describes a model to predict the CCN activity of organic compounds from functional group composition. Following previous methods in the literature, we test the ability of semi-empirical group contribution methods in Köhler theory to predict the effective hygroscopicity parameter, kappa. However, in our approach we also account for liquid-liquid phase boundaries to simulate phase-limited activation behavior. Model evaluation against a selected database of published laboratory measurements demonstrates that kappa can be predicted within a factor of 2. Simulation of homologous series is used to identify the relative effectiveness of different functional groups in increasing the CCN activity of weakly functionalized organic compounds. Hydroxyl, carboxyl, aldehyde, hydroperoxide, carbonyl, and ether moieties promote CCN activity while methylene and nitrate moieties inhibit CCN activity. The model can be incorporated into scale-bridging test beds such as the Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) to evaluate the evolution of kappa for a complex mix of organic compounds and to develop suitable parameterizations of CCN evolution for larger-scale models.

  15. Planning versus action: Different decision-making processes predict plans to change one's diet versus actual dietary behavior.

    Science.gov (United States)

    Kiviniemi, Marc T; Brown-Kramer, Carolyn R

    2015-05-01

    Most health decision-making models posit that deciding to engage in a health behavior involves forming a behavioral intention which then leads to actual behavior. However, behavioral intentions and actual behavior may not be functionally equivalent. Two studies examined whether decision-making factors predicting dietary behaviors were the same as or distinct from those predicting intentions. Actual dietary behavior was proximally predicted by affective associations with the behavior. By contrast, behavioral intentions were predicted by cognitive beliefs about behaviors, with no contribution of affective associations. This dissociation has implications for understanding individual regulation of health behaviors and for behavior change interventions. PMID:25903243

  16. Functional changes in littoral macroinvertebrate communities in response to watershed-level anthropogenic stress.

    Directory of Open Access Journals (Sweden)

    Katya E Kovalenko

    Full Text Available Watershed-scale anthropogenic stressors have profound effects on aquatic communities. Although several functional traits of stream macroinvertebrates change predictably in response to land development and urbanization, little is known about macroinvertebrate functional responses in lakes. We assessed functional community structure, functional diversity (Rao's quadratic entropy and voltinism in macroinvertebrate communities sampled across the full gradient of anthropogenic stress in Laurentian Great Lakes coastal wetlands. Functional diversity and voltinism significantly decreased with increasing development, whereas agriculture had smaller or non-significant effects. Functional community structure was affected by watershed-scale development, as demonstrated by an ordination analysis followed by regression. Because functional community structure affects energy flow and ecosystem function, and functional diversity is known to have important implications for ecosystem resilience to further environmental change, these results highlight the necessity of finding ways to remediate or at least ameliorate these effects.

  17. Genomic islands predict functional adaptation in marine actinobacteria

    Energy Technology Data Exchange (ETDEWEB)

    Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel; Gontang, Erin; McGlinchey, Ryan; Foster, Brian; Lapidus, Alla; Podell, Sheila; Allen, Eric; Moore, Bradley; Jensen, Paul

    2009-04-01

    Linking functional traits to bacterial phylogeny remains a fundamental but elusive goal of microbial ecology 1. Without this information, it becomes impossible to resolve meaningful units of diversity and the mechanisms by which bacteria interact with each other and adapt to environmental change. Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house functionally adaptive traits 2. In the case of environmental bacteria, these traits are largely inferred from bioinformatic or gene expression analyses 2, thus leaving few examples in which the functions of island genes have been experimentally characterized. Here we report the complete genome sequences of Salinispora tropica and S. arenicola, the first cultured, obligate marine Actinobacteria 3. These two species inhabit benthic marine environments and dedicate 8-10percent of their genomes to the biosynthesis of secondary metabolites. Despite a close phylogenetic relationship, 25 of 37 secondary metabolic pathways are species-specific and located within 21 genomic islands, thus providing new evidence linking secondary metabolism to ecological adaptation. Species-specific differences are also observed in CRISPR sequences, suggesting that variations in phage immunity provide fitness advantages that contribute to the cosmopolitan distribution of S. arenicola 4. The two Salinispora genomes have evolved by complex processes that include the duplication and acquisition of secondary metabolite genes, the products of which provide immediate opportunities for molecular diversification and ecological adaptation. Evidence that secondary metabolic pathways are exchanged by Horizontal Gene Transfer (HGT) yet are fixed among globally distributed populations 5 supports a functional role for their products and suggests that pathway acquisition represents a previously unrecognized force driving bacterial diversification

  18. Relating phylogenetic and functional diversity among denitrifiers and quantifying their capacity to predict community functioning

    Directory of Open Access Journals (Sweden)

    JoanaFalcão Salles

    2012-06-01

    Full Text Available Genetic diversity of phylogenetic or functional markers is widely used as a proxy of microbial diversity. However, it remains unclear at what extent functional diversity, gene sequence diversity and community functioning are linked. We analysed, for a range of denitrifying bacteria, the relationships between (i the similarity of functional traits evaluated from metabolic profiles (BIOLOG plates or from N2O accumulation patterns on different C sources, and (ii the similarity of phylogenetic (16S rRNA gene or functional (nir gene markers. We also calculated different proxies for the diversity of denitrifier community based on taxa richness, phylogenetic or functional similarities, and evaluated their performance in inferring the functioning of assembled denitrifying communities. For individual strains, the variation in the 16S rRNA gene sequence explained only 10% of the variation in metabolic patterns and were not related to N2O accumulation. The latter was correlated with the similarity of nitrite reductase residues. When nir genes were analysed separately, the similarity in amino acids coded by the nirS genes accounted for 48% of the variance of the observed pattern of N2O accumulation, whereas nirK amino acid residues were unrelated to N2O accumulation. For bacterial assemblages, phylogenetic diversity and mean community dissimilarity, calculated using 16S rRNA gene sequences, and functional diversity measures associated with BIOLOG, predicted poorly the variation in the functioning of assembled communities (below 15%. In contrast, the proxies of functional diversity based on N2O accumulation patterns performed better and explained from 23 to 42% of the variation in community functioning. Amongst those, community niche was the best metric, indicating the importance of complementarity for carbon resources among taxa in the context of denitrification.

  19. Changes in cardiopulmonary function induced by nanoparticles.

    Science.gov (United States)

    Mann, Erin E; Thompson, Leslie C; Shannahan, Jonathan H; Wingard, Christopher J

    2012-01-01

    Nanoparticles (NP) are highly applicable in a variety of technological and biomedical fields because of their unique physicochemical properties. The increased development and utilization of NP has amplified human exposure and raised concerns regarding their potential to generate toxicity. The biological impacts of NP exposures have been shown to be dependent on aerodynamic size, chemical composition, and the route of exposure (oral, dermal, intravenous, and inhalation), while recent research has demonstrated the cardiovascular (CV) system as an important site of toxicity. Proposed mechanisms responsible for these effects include inflammation, oxidative stress, autonomic dysregulation, and direct interactions of NP with CV cells. Specifically, NP have been shown to impact vascular endothelial cell (EC) integrity, which may disrupt the dynamic endothelial regulation of vascular tone, possibly altering systemic vascular resistance and impairing the appropriate distribution of blood flow throughout the circulation. Cardiac consequences of NP-induced toxicity include disruption of heart rate and electrical activity via catecholamine release, increased susceptibility to ischemia/reperfusion injury, and modified baroreceptor control of cardiac function. These and other CV outcomes likely contribute to adverse health effects promoting myocardial infarction, hypertension, cardiac arrhythmias, and thrombosis. This review will assess the current knowledge regarding the principle sites of CV toxicity following NP exposure. Furthermore, we will propose mechanisms contributing to altered CV function and hypothesize possible outcomes resulting in decrements in human health. PMID:22915448

  20. Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob Lewin; Roy, Scott William

    2009-01-01

    interspecific differences in these elements on the evolution of alternative splicing levels has not yet been investigated at genomic level. Here we study the effect of interspecific differences in predicted exonic splicing regulators (ESRs) on exon inclusion levels in human and chimpanzee. For this purpose, we...... compiled and studied comprehensive datasets of predicted ESRs, identified by several computational and experimental approaches, as well as microarray data for changes in alternative splicing levels between human and chimpanzee. Surprisingly, we found no association between changes in predicted ESRs and...... or no effect on splicing, and thus interspecific changes at short-time scales may primarily occur in these effectively neutral ESRs. These results underscore the difficulties of using current computational ESR prediction algorithms to identify truly functionally important motifs, and provide a...

  1. Predicting China’s Land-use Change and Soil Carbon Sequestration under Alternative Climate Change Scenarios

    OpenAIRE

    Li, Man; Wu, Junjie

    2010-01-01

    This paper examines and predicts the effects of climate change and climate extremes on China’s land use conversion and soil carbon sequestration under two alternative climate change scenarios. It intends to investigate the following three questions. 1) How did climate factors affect land-use conversion in China from 1988 to 2000 and what was the relative importance of these factors? 2) How would the predicted future climate change pattern affect land-use choice under alternative climate chang...

  2. Prediction of glass durability as a function of environmental conditions

    International Nuclear Information System (INIS)

    The author reports on thermodynamic model of glass durability applied to natural, ancient, and nuclear waste glasses. The durabilities of over 150 different natural and man-made glasses, including actual ancient Roman and Islamic glasses (Jalame ca. 350 A. D., Nishapur 10-11th century A. D., and Gorgon 9-11th century A.D.), have been compared. Glass durability had been shown to be a function of the thermodynamic hydration free energy. Δ Ghyd, which can be calculated from glass composition and solution pH. Using this approach, the durability of the most durable nuclear waste glasses examined was ≅106 years by comparison with the durability of the natural basalts of ≅106 years. The least durable waste glass formulations were comparable in durability to the most durable simulated medieval window glasses of ≅103 years. In this manner, the durability of nuclear waste glasses has been interpolated to be ≅106 years and no less than 103 years. Hydration thermodynamics are shown to be applicable to the dissolution of glass in various natural environments. Groundwater-glass interactions relative to geologic disposal of nuclear waste, hydration rind dating of obsidians, and/or other archeological studies can be modeled, e.g. the relative durabilities of six simulated medieval window glasses have been correctly predicted for both laboratory (one month) and burial (5 year) experiments

  3. A data mining based approach to predict spatiotemporal changes in satellite images

    Science.gov (United States)

    Boulila, W.; Farah, I. R.; Ettabaa, K. Saheb; Solaiman, B.; Ghézala, H. Ben

    2011-06-01

    The interpretation of remotely sensed images in a spatiotemporal context is becoming a valuable research topic. However, the constant growth of data volume in remote sensing imaging makes reaching conclusions based on collected data a challenging task. Recently, data mining appears to be a promising research field leading to several interesting discoveries in various areas such as marketing, surveillance, fraud detection and scientific discovery. By integrating data mining and image interpretation techniques, accurate and relevant information (i.e. functional relation between observed parcels and a set of informational contents) can be automatically elicited. This study presents a new approach to predict spatiotemporal changes in satellite image databases. The proposed method exploits fuzzy sets and data mining concepts to build predictions and decisions for several remote sensing fields. It takes into account imperfections related to the spatiotemporal mining process in order to provide more accurate and reliable information about land cover changes in satellite images. The proposed approach is validated using SPOT images representing the Saint-Denis region, capital of Reunion Island. Results show good performances of the proposed framework in predicting change for the urban zone.

  4. Hemostatic system changes predictive value in patients with ischemic brain disorders

    Directory of Open Access Journals (Sweden)

    Raičević Ranko

    2002-01-01

    Full Text Available The aim of this research was to determine the importance of tracking the dynamics of changes of the hemostatic system factors (aggregation of thrombocytes, D-dimer, PAI-1, antithrombin III, protein C and protein S, factor VII and factor VIII, fibrin degradation products, euglobulin test and the activated partial thromboplastin time – aPTPV in relation to the level of the severity of ischemic brain disorders (IBD and the level of neurological and functional deficiency in the beginning of IBD manifestation from 7 to 10 days, 19 to 21 day, and after 3 to 6 months. The research results confirmed significant predictive value of changes of hemostatic system with the predomination of procoagulant factors, together with the insufficiency of fibrinolysis. Concerning the IBD severity and it's outcome, the significant predictive value was shown in the higher levels of PAI-1 and the lower level of antithrombin III, and borderline significant value was shown in the accelerated aggregation of thrombocytes and the increased concentration of D-dimer. It could be concluded that the tracking of the dynamics of changes in parameters of hemostatic system proved to be an easily accessible method with the significant predictive value regarding the development of more severe. IBD cases and the outcome of the disease itself.

  5. Predicting changes in cardiac myocyte contractility during early drug discovery with in vitro assays

    International Nuclear Information System (INIS)

    Cardiovascular-related adverse drug effects are a major concern for the pharmaceutical industry. Activity of an investigational drug at the L-type calcium channel could manifest in a number of ways, including changes in cardiac contractility. The aim of this study was to define which of the two assay technologies – radioligand-binding or automated electrophysiology – was most predictive of contractility effects in an in vitro myocyte contractility assay. The activity of reference and proprietary compounds at the L-type calcium channel was measured by radioligand-binding assays, conventional patch-clamp, automated electrophysiology, and by measurement of contractility in canine isolated cardiac myocytes. Activity in the radioligand-binding assay at the L-type Ca channel phenylalkylamine binding site was most predictive of an inotropic effect in the canine cardiac myocyte assay. The sensitivity was 73%, specificity 83% and predictivity 78%. The radioligand-binding assay may be run at a single test concentration and potency estimated. The least predictive assay was automated electrophysiology which showed a significant bias when compared with other assay formats. Given the importance of the L-type calcium channel, not just in cardiac function, but also in other organ systems, a screening strategy emerges whereby single concentration ligand-binding can be performed early in the discovery process with sufficient predictivity, throughput and turnaround time to influence chemical design and address a significant safety-related liability, at relatively low cost. - Highlights: • The L-type calcium channel is a significant safety liability during drug discovery. • Radioligand-binding to the L-type calcium channel can be measured in vitro. • The assay can be run at a single test concentration as part of a screening cascade. • This measurement is highly predictive of changes in cardiac myocyte contractility

  6. Predicting changes in cardiac myocyte contractility during early drug discovery with in vitro assays

    Energy Technology Data Exchange (ETDEWEB)

    Morton, M.J., E-mail: michael.morton@astrazeneca.com [Discovery Sciences, AstraZeneca, Macclesfield, Cheshire SK10 4TG (United Kingdom); Armstrong, D.; Abi Gerges, N. [Drug Safety and Metabolism, AstraZeneca, Macclesfield, Cheshire SK10 4TG (United Kingdom); Bridgland-Taylor, M. [Discovery Sciences, AstraZeneca, Macclesfield, Cheshire SK10 4TG (United Kingdom); Pollard, C.E.; Bowes, J.; Valentin, J.-P. [Drug Safety and Metabolism, AstraZeneca, Macclesfield, Cheshire SK10 4TG (United Kingdom)

    2014-09-01

    Cardiovascular-related adverse drug effects are a major concern for the pharmaceutical industry. Activity of an investigational drug at the L-type calcium channel could manifest in a number of ways, including changes in cardiac contractility. The aim of this study was to define which of the two assay technologies – radioligand-binding or automated electrophysiology – was most predictive of contractility effects in an in vitro myocyte contractility assay. The activity of reference and proprietary compounds at the L-type calcium channel was measured by radioligand-binding assays, conventional patch-clamp, automated electrophysiology, and by measurement of contractility in canine isolated cardiac myocytes. Activity in the radioligand-binding assay at the L-type Ca channel phenylalkylamine binding site was most predictive of an inotropic effect in the canine cardiac myocyte assay. The sensitivity was 73%, specificity 83% and predictivity 78%. The radioligand-binding assay may be run at a single test concentration and potency estimated. The least predictive assay was automated electrophysiology which showed a significant bias when compared with other assay formats. Given the importance of the L-type calcium channel, not just in cardiac function, but also in other organ systems, a screening strategy emerges whereby single concentration ligand-binding can be performed early in the discovery process with sufficient predictivity, throughput and turnaround time to influence chemical design and address a significant safety-related liability, at relatively low cost. - Highlights: • The L-type calcium channel is a significant safety liability during drug discovery. • Radioligand-binding to the L-type calcium channel can be measured in vitro. • The assay can be run at a single test concentration as part of a screening cascade. • This measurement is highly predictive of changes in cardiac myocyte contractility.

  7. Demographic Metabolism: A Predictive Theory of Socio-economic Change

    OpenAIRE

    Lutz, Wolfgang

    2013-01-01

    This essay introduces a general theory of how societies change as a consequence of the changing composition of their members with respect to certain relevant and measurable characteristics. These characteristics can either change over the life course of individuals or from one generation to the next. While the former changes can be analytically identified and described by certain age- and duration-specific transition schedules, the latter changes resulting from cohort replacement can be mode...

  8. PREDICTION OF CHANGES IN VEGETATION DISTRIBUTION UNDER CLIMATE CHANGE SCENARIOS USING MODIS DATASET

    Directory of Open Access Journals (Sweden)

    H. Hirayama

    2016-06-01

    Full Text Available The distribution of vegetation is expected to change under the influence of climate change. This study utilizes vegetation maps derived from Terra/MODIS data to generate a model of current climate conditions suitable to beech-dominated deciduous forests, which are the typical vegetation of Japan’s cool temperate zone. This model will then be coordinated with future climate change scenarios to predict the future distribution of beech forests. The model was developed by using the presence or absence of beech forest as the dependent variable. Four climatic variables; mean minimum daily temperature of the coldest month (TMC,warmth index (WI, winter precipitation (PRW and summer precipitation (PRS: and five geophysical variables; topography (TOPO, surface geology (GEOL, soil (SOIL, slope aspect (ASP, and inclination (INCL; were adopted as independent variables. Previous vegetation distribution studies used point data derived from field surveys. The remote sensing data utilized in this study, however, should permit collecting of greater amounts of data, and also frequent updating of data and distribution maps. These results will hopefully show that use of remote sensing data can provide new insights into our understanding of how vegetation distribution will be influenced by climate change.

  9. Prediction of Changes in Vegetation Distribution Under Climate Change Scenarios Using Modis Dataset

    Science.gov (United States)

    Hirayama, Hidetake; Tomita, Mizuki; Hara, Keitarou

    2016-06-01

    The distribution of vegetation is expected to change under the influence of climate change. This study utilizes vegetation maps derived from Terra/MODIS data to generate a model of current climate conditions suitable to beech-dominated deciduous forests, which are the typical vegetation of Japan's cool temperate zone. This model will then be coordinated with future climate change scenarios to predict the future distribution of beech forests. The model was developed by using the presence or absence of beech forest as the dependent variable. Four climatic variables; mean minimum daily temperature of the coldest month (TMC) warmth index (WI) winter precipitation (PRW) and summer precipitation (PRS): and five geophysical variables; topography (TOPO), surface geology (GEOL), soil (SOIL), slope aspect (ASP), and inclination (INCL); were adopted as independent variables. Previous vegetation distribution studies used point data derived from field surveys. The remote sensing data utilized in this study, however, should permit collecting of greater amounts of data, and also frequent updating of data and distribution maps. These results will hopefully show that use of remote sensing data can provide new insights into our understanding of how vegetation distribution will be influenced by climate change.

  10. The conformational signature of β-arrestin2 predicts its trafficking and signalling functions.

    Science.gov (United States)

    Lee, Mi-Hye; Appleton, Kathryn M; Strungs, Erik G; Kwon, Joshua Y; Morinelli, Thomas A; Peterson, Yuri K; Laporte, Stephane A; Luttrell, Louis M

    2016-03-31

    Arrestins are cytosolic proteins that regulate G-protein-coupled receptor (GPCR) desensitization, internalization, trafficking and signalling. Arrestin recruitment uncouples GPCRs from heterotrimeric G proteins, and targets the proteins for internalization via clathrin-coated pits. Arrestins also function as ligand-regulated scaffolds that recruit multiple non-G-protein effectors into GPCR-based 'signalsomes'. Although the dominant function(s) of arrestins vary between receptors, the mechanism whereby different GPCRs specify these divergent functions is unclear. Using a panel of intramolecular fluorescein arsenical hairpin (FlAsH) bioluminescence resonance energy transfer (BRET) reporters to monitor conformational changes in β-arrestin2, here we show that GPCRs impose distinctive arrestin 'conformational signatures' that reflect the stability of the receptor-arrestin complex and role of β-arrestin2 in activating or dampening downstream signalling events. The predictive value of these signatures extends to structurally distinct ligands activating the same GPCR, such that the innate properties of the ligand are reflected as changes in β-arrestin2 conformation. Our findings demonstrate that information about ligand-receptor conformation is encoded within the population average β-arrestin2 conformation, and provide insight into how different GPCRs can use a common effector for different purposes. This approach may have application in the characterization and development of functionally selective GPCR ligands and in identifying factors that dictate arrestin conformation and function. PMID:27007854

  11. Prediction of crack density and electrical resistance changes in indium tin oxide/polymer thin films under tensile loading

    KAUST Repository

    Mora, Angel

    2014-06-11

    We present unified predictions for the crack onset strain, evolution of crack density, and changes in electrical resistance in indium tin oxide/polymer thin films under tensile loading. We propose a damage mechanics model to quantify and predict such changes as an alternative to fracture mechanics formulations. Our predictions are obtained by assuming that there are no flaws at the onset of loading as opposed to the assumptions of fracture mechanics approaches. We calibrate the crack onset strain and the damage model based on experimental data reported in the literature. We predict crack density and changes in electrical resistance as a function of the damage induced in the films. We implement our model in the commercial finite element software ABAQUS using a user subroutine UMAT. We obtain fair to good agreement with experiments. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  12. Impact of climatic change on alpine ecosystems: inference and prediction

    Directory of Open Access Journals (Sweden)

    Nigel G. Yoccoz

    2011-01-01

    Full Text Available Alpine ecosystems will be greatly impacted by climatic change, but other factors, such as land use and invasive species, are likely to play an important role too. Climate can influence ecosystems at several levels. We describe some of them, stressing methodological approaches and available data. Climate can modify species phenology, such as flowering date of plants and hatching date in insects. It can also change directly population demography (survival, reproduction, dispersal, and therefore species distribution. Finally it can effect interactions among species – snow cover for example can affect the success of some predators. One characteristic of alpine ecosystems is the presence of snow cover, but surprisingly the role played by snow is relatively poorly known, mainly for logistical reasons. Even if we have made important progress regarding the development of predictive models, particularly so for distribution of alpine plants, we still need to set up observational and experimental networks which properly take into account the variability of alpine ecosystems and of their interactions with climate.Les écosystèmes alpins vont être grandement influencés par les changements climatiques à venir, mais d’autres facteurs, tels que l’utilisation des terres ou les espèces invasives, pourront aussi jouer un rôle important. Le climat peut influencer les écosystèmes à différents niveaux, et nous en décrivons certains, en mettant l’accent sur les méthodes utilisées et les données disponibles. Le climat peut d’abord modifier la phénologie des espèces, comme la date de floraison des plantes ou la date d’éclosion des insectes. Il peut ensuite affecter directement la démographie des espèces (survie, reproduction, dispersion et donc à terme leur répartition. Il peut enfin agir sur les interactions entre espèces – le couvert neigeux par exemple modifie le succès de certains prédateurs. Une caractéristique des

  13. Cloud Prediction of Protein Structure and Function with PredictProtein for Debian

    OpenAIRE

    Cedric Staniewski; Burkhard Rost; Eva Reisinger; Christian Mertes; Julia Ertl; Simon Domke; Christof Angermüller; Ariane Böhm; Milot Mirdita; Martin Steinegger; László Kaján; Esmeralda Vicedo; Guy Yachdav

    2013-01-01

    We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also pre...

  14. Predicting ecological changes on benthic estuarine assemblages through decadal climate trends along Brazilian Marine Ecoregions

    Science.gov (United States)

    Bernardino, Angelo F.; Netto, Sérgio A.; Pagliosa, Paulo R.; Barros, Francisco; Christofoletti, Ronaldo A.; Rosa Filho, José S.; Colling, André; Lana, Paulo C.

    2015-12-01

    Estuaries are threatened coastal ecosystems that support relevant ecological functions worldwide. The predicted global climate changes demand actions to understand, anticipate and avoid further damage to estuarine habitats. In this study we reviewed data on polychaete assemblages, as a surrogate for overall benthic communities, from 51 estuaries along five Marine Ecoregions of Brazil (Amazonia, NE Brazil, E Brazil, SE Brazil and Rio Grande). We critically evaluated the adaptive capacity and ultimately the resilience to decadal changes in temperature and rainfall of the polychaete assemblages. As a support for theoretical predictions on changes linked to global warming we compared the variability of benthic assemblages across the ecoregions with a 40-year time series of temperature and rainfall data. We found a significant upward trend in temperature during the last four decades at all marine ecoregions of Brazil, while rainfall increase was restricted to the SE Brazil ecoregion. Benthic assemblages and climate trends varied significantly among and within ecoregions. The high variability in climate patterns in estuaries within the same ecoregion may lead to correspondingly high levels of noise on the expected responses of benthic fauna. Nonetheless, we expect changes in community structure and productivity of benthic species at marine ecoregions under increasing influence of higher temperatures, extreme events and pollution.

  15. Ways that Social Change Predicts Personal Quality of Life

    Science.gov (United States)

    Cheung, Chau-Kiu; Leung, Kwok

    2010-01-01

    A notable way that social change affects personal quality of life would rely on the person's experience with social change. This experience may influence societal quality of life and quality of work life, which may in turn affect personal quality of life. Additionally, the experience of social change is possibly less detrimental to personal…

  16. Reduced Cognitive Function Predicts Functional Decline in Patients with Heart Failure over 12 months

    Science.gov (United States)

    Alosco, Michael L.; Spitznagel, Mary Beth; Cohen, Ronald; Sweet, Lawrence H.; Colbert, Lisa H.; Josephson, Richard; Hughes, Joel; Rosneck, Jim; Gunstad, John

    2016-01-01

    Background Impaired activities of daily living (ADL) are common in heart failure (HF) patients and contribute to the elevated mortality and hospitalization rates in this population. Cognitive impairment is also prevalent in HF, though its ability to predict functional decline over time is unknown. Aims This study examined the longitudinal pattern of activities of daily living in HF persons and whether reduced baseline cognitive status predicts functional decline in this population. Methods 110 persons with HF completed the Lawton-Brody Activities of Daily Living Scale and were administered the Modified Mini-Mental Status Examination (3MS) at baseline and a 12-month follow-up. Three composite scores were derived from the Lawton-Brody, including total, instrumental, and basic ADLs. Results HF patients reported high rates of baseline impairments in instrumental ADLs, including shopping, food preparation, housekeeping duties, laundry, among others. Repeated measures analyses showed significant declines in total and instrumental ADLs from baseline to the 12-month follow-up in HF (p < .05). Hierarchical regression analyses showed that poorer baseline performance on the 3MS predicted worse total ADL performance at 12-months (β = .15, p = .049), including greater dependence in shopping, driving, feeding, and physical ambulation (p < .05 for all). Conclusion The current results show that HF patients report significant functional decline over a 12-month period and brief cognitive tests can identify those patients at highest risk for decline. If replicated, such findings encourage the use of cognitive screening measures to identify HF patients most likely to require assistance with ADL tasks. PMID:23754840

  17. VR-BFDT: A variance reduction based binary fuzzy decision tree induction method for protein function prediction.

    Science.gov (United States)

    Golzari, Fahimeh; Jalili, Saeed

    2015-07-21

    In protein function prediction (PFP) problem, the goal is to predict function of numerous well-sequenced known proteins whose function is not still known precisely. PFP is one of the special and complex problems in machine learning domain in which a protein (regarded as instance) may have more than one function simultaneously. Furthermore, the functions (regarded as classes) are dependent and also are organized in a hierarchical structure in the form of a tree or directed acyclic graph. One of the common learning methods proposed for solving this problem is decision trees in which, by partitioning data into sharp boundaries sets, small changes in the attribute values of a new instance may cause incorrect change in predicted label of the instance and finally misclassification. In this paper, a Variance Reduction based Binary Fuzzy Decision Tree (VR-BFDT) algorithm is proposed to predict functions of the proteins. This algorithm just fuzzifies the decision boundaries instead of converting the numeric attributes into fuzzy linguistic terms. It has the ability of assigning multiple functions to each protein simultaneously and preserves the hierarchy consistency between functional classes. It uses the label variance reduction as splitting criterion to select the best "attribute-value" at each node of the decision tree. The experimental results show that the overall performance of the proposed algorithm is promising. PMID:25865524

  18. Plant physiological models of heat, water and photoinhibition stress for climate change modelling and agricultural prediction

    Science.gov (United States)

    Nicolas, B.; Gilbert, M. E.; Paw U, K. T.

    2015-12-01

    Soil-Vegetation-Atmosphere Transfer (SVAT) models are based upon well understood steady state photosynthetic physiology - the Farquhar-von Caemmerer-Berry model (FvCB). However, representations of physiological stress and damage have not been successfully integrated into SVAT models. Generally, it has been assumed that plants will strive to conserve water at higher temperatures by reducing stomatal conductance or adjusting osmotic balance, until potentially damaging temperatures and the need for evaporative cooling become more important than water conservation. A key point is that damage is the result of combined stresses: drought leads to stomatal closure, less evaporative cooling, high leaf temperature, less photosynthetic dissipation of absorbed energy, all coupled with high light (photosynthetic photon flux density; PPFD). This leads to excess absorbed energy by Photosystem II (PSII) and results in photoinhibition and damage, neither are included in SVAT models. Current representations of photoinhibition are treated as a function of PPFD, not as a function of constrained photosynthesis under heat or water. Thus, it seems unlikely that current models can predict responses of vegetation to climate variability and change. We propose a dynamic model of damage to Rubisco and RuBP-regeneration that accounts, mechanistically, for the interactions between high temperature, light, and constrained photosynthesis under drought. Further, these predictions are illustrated by key experiments allowing model validation. We also integrated this new framework within the Advanced Canopy-Atmosphere-Soil Algorithm (ACASA). Preliminary results show that our approach can be used to predict reasonable photosynthetic dynamics. For instances, a leaf undergoing one day of drought stress will quickly decrease its maximum quantum yield of PSII (Fv/Fm), but it won't recover to unstressed levels for several days. Consequently, cumulative effect of photoinhibition on photosynthesis can cause

  19. Predicting risk selection following major changes in Medicare.

    Science.gov (United States)

    Pizer, Steven D; Frakt, Austin B; Feldman, Roger

    2008-04-01

    The Medicare Modernization Act of 2003 created several new types of private insurance plans within Medicare, starting in 2006. Some of these plan types previously did not exist in the commercial market and there was great uncertainty about their prospects. In this paper, we show that statistical models and historical data from the Medicare Current Beneficiary Survey can be used to predict the experience of new plan types with reasonable accuracy. This lays the foundation for the analysis of program modifications currently under consideration. We predict market share, risk selection, and stability for the most prominent new plan type, the stand-alone Medicare prescription drug plan (PDP). First, we estimate a model of consumer choice across Medicare insurance plans available in the data. Next, we modify the data to include PDPs and use the model to predict the probability of enrollment for each beneficiary in each plan type. Finally, we calculate mean-adjusted actual spending by plan type. We predict that adverse selection into PDPs will be substantial, but that enrollment and premiums will be stable. Our predictions correspond well to actual experience in 2006. PMID:17557273

  20. Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach

    DEFF Research Database (Denmark)

    Le Roux, Xavier; Bouskill, Nicholas J.; Niboyet, Audrey;

    2016-01-01

    change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB). Using a trait-based model, we then tested whether categorizing NOB into a few functional groups unified by physiological traits enables understanding and predicting...

  1. Lung function changes in wildland firefighters working at prescribed burns.

    Energy Technology Data Exchange (ETDEWEB)

    Adetona, Olorunfemi; Hall, Daniel, B.; Naeher, L,P.

    2011-10-01

    Although decline in lung function across workshift has been observed in wildland firefighters, measurements have been restricted to days when they worked at fires. Consequently, such results could have been confounded by normal circadian variation associated with lung function. We investigated the across-shift changes in lung function of wildland firefighters, and the effect of cumulative exposure on lung function during the burn season.

  2. Cue predictability changes scaling in eye-movement fluctuations.

    Science.gov (United States)

    Wallot, Sebastian; Coey, Charles A; Richardson, Michael J

    2015-10-01

    Recent research has provided evidence for scaling-relations in eye-movement fluctuations, but not much is known about what these scaling relations imply about cognition or eye-movement control. Generally, scaling relations in behavioral and neurophysiological data have been interpreted as an indicator for the coordination of neurophysiological and cognitive processes. In this study, we investigated the effect of predictability in timing and gaze-direction on eye-movement fluctuations. Participants performed a simple eye-movement task, in which a visual cue prompted their gaze to different locations on a spatial layout, and the predictability about temporal and directional aspects of the cue were manipulated. The results showed that scaling exponents in eye-movements decreased with predictability and were related to the participants' perceived effort during the task. In relation to past research, these findings suggest that scaling exponents reflect a relative demand for voluntary control during task performance. PMID:26337612

  3. Using niche-based modelling to assess the impact of climate change on tree functional diversity in Europe

    DEFF Research Database (Denmark)

    Thuiller, Wilfried; Lavorel, Sandra; Sykes, Martin T.;

    2006-01-01

    Rapid anthropogenic climate change is already affecting species distributions and ecosystem functioning worldwide. We applied niche-based models to analyse the impact of climate change on tree species and functional diversity in Europe. Present-day climate was used to predict the distributions...

  4. Soil ecosystem functioning under climate change: plant species and community effects

    Energy Technology Data Exchange (ETDEWEB)

    Kardol, Paul [ORNL; Cregger, Melissa [ORNL; Campany, Courtney E [ORNL; Classen, Aimee T [ORNL

    2010-01-01

    impact of climate change on soil ecosystem functioning, and hence, these indirect effects should be taken into account when predicting how climate change will alter ecosystem functioning.

  5. Prediction Study on PCI Failure of Reactor Fuel Based on a Radial Basis Function Neural Network

    Directory of Open Access Journals (Sweden)

    Xinyu Wei

    2016-01-01

    Full Text Available Pellet-clad interaction (PCI is one of the major issues in fuel rod design and reactor core operation in water cooled reactors. The prediction of fuel rod failure by PCI is studied in this paper by the method of radial basis function neural network (RBFNN. The neural network is built through the analysis of the existing experimental data. It is concluded that it is a suitable way to reduce the calculation complexity. A self-organized RBFNN is used in our study, which can vary its structure dynamically in order to maintain the prediction accuracy. For the purpose of the appropriate network complexity and overall computational efficiency, the hidden neurons in the RBFNN can be changed online based on the neuron activity and mutual information. The presented method is tested by the experimental data from the reference, and the results demonstrate its effectiveness.

  6. The Prediction of Jet Noise Ground Effects Using an Acoustic Analogy and a Tailored Green's Function

    Science.gov (United States)

    Miller, Steven A. E.

    2013-01-01

    An assessment of an acoustic analogy for the mixing noise component of jet noise in the presence of an infinite surface is presented. The reflection of jet noise by the ground changes the distribution of acoustic energy and is characterized by constructive and destructive interference patterns. The equivalent sources are modeled based on the two-point cross- correlation of the turbulent velocity fluctuations and a steady Reynolds-Averaged Navier-Stokes (RANS) solution. Propagation effects, due to reflection by the surface and refaction by the jet shear layer, are taken into account by calculating the vector Green's function of the linearized Euler equations (LEE). The vector Green's function of the LEE is written in relation to Lilley's equation; that is, approximated with matched asymptotic solutions and the Green's function of the convective Helmholtz equation. The Green's function of the convective Helmholtz equation for an infinite flat plane with impedance is the Weyl-van der Pol equation. Predictions are compared with an unheated Mach 0.95 jet produced by a nozzle with an exit diameter of 0.3302 meters. Microphones are placed at various heights and distances from the nozzle exit in the peak jet noise direction above an acoustically hard and an asphalt surface. The predictions are shown to accurately capture jet noise ground effects that are characterized by constructive and destructive interference patterns in the mid- and far-field and capture overall trends in the near-field.

  7. Predicting plant invasion in an era of global change

    Science.gov (United States)

    Previous studies have indicated that ongoing global change will promote the spread of invasive plants. Recent research points to a more complex response. The components of global change that increase plant resources (e.g., rising CO2, N deposition) most consistently favor invasive species, but, chan...

  8. Predicting Change in Postpartum Depression: An Individual Growth Curve Approach.

    Science.gov (United States)

    Buchanan, Trey

    Recently, methodologists interested in examining problems associated with measuring change have suggested that developmental researchers should focus upon assessing change at both intra-individual and inter-individual levels. This study used an application of individual growth curve analysis to the problem of maternal postpartum depression.…

  9. Prediction of hospital mortality by changes in the estimated glomerular filtration rate (eGFR).

    LENUS (Irish Health Repository)

    Berzan, E

    2015-03-01

    Deterioration of physiological or laboratory variables may provide important prognostic information. We have studied whether a change in estimated glomerular filtration rate (eGFR) value calculated using the (Modification of Diet in Renal Disease (MDRD) formula) over the hospital admission, would have predictive value. An analysis was performed on all emergency medical hospital episodes (N = 61964) admitted between 1 January 2002 and 31 December 2011. A stepwise logistic regression model examined the relationship between mortality and change in renal function from admission to discharge. The fully adjusted Odds Ratios (OR) for 5 classes of GFR deterioration showed a stepwise increased risk of 30-day death with OR\\'s of 1.42 (95% CI: 1.20, 1.68), 1.59 (1.27, 1.99), 2.71 (2.24, 3.27), 5.56 (4.54, 6.81) and 11.9 (9.0, 15.6) respectively. The change in eGFR during a clinical episode, following an emergency medical admission, powerfully predicts the outcome.

  10. Two-point functions for flavour changing currents in QCD

    International Nuclear Information System (INIS)

    We complete the calculations of two-point functions in QCD by presenting the results for the flavour changing vector current, including perturbative and non-perturbative contributions (to first ordern in αsub(s)). (orig.)

  11. Early changes in pulmonary functions after mitral valve replacement

    OpenAIRE

    Saxena Pankaj; Luthra Suvitesh; Dhaliwal Rajinder; Rana Surinder; Behera Digambar

    2007-01-01

    Background: This study evaluates changes in pulmonary functions before and after mitral valve replacement (MVR). Materials and Methods: Twenty-five patients with rheumatic mitral lesions who had undergone MVR were divided into three groups, based on New York Heart Association (NYHA) class. They were evaluated for changes in pulmonary functions, preoperatively and postoperatively at 1 week, 1 month and 3 months to find any improvements after MVR. Results: Forced vital capacity (FVC), forc...

  12. Prediction of Factors Determining Changes in Stability in Protein Mutants

    OpenAIRE

    Parthiban, Vijayarangakannan

    2006-01-01

    Analysing the factors behind protein stability is a key research topic in molecular biology and has direct implications on protein structure prediction and protein-protein docking solutions. Protein stability upon point mutations were analysed using a distance dependant pair potential representing mainly through-space interactions and torsion angle potential representing neighbouring effects as a basic statistical mechanical setup for the analysis. The synergetic effect of accessible surface ...

  13. Quantitative MRI predicts long-term structural and functional outcome after experimental traumatic brain injury.

    Science.gov (United States)

    Immonen, Riikka J; Kharatishvili, Irina; Gröhn, Heidi; Pitkänen, Asla; Gröhn, Olli H J

    2009-03-01

    In traumatic brain injury (TBI) the initial impact causes both immediate damage and also launches a cascade of slowly progressive secondary damage. The chronic outcome disabilities vary greatly and can occur several years later. The aim of this study was to find predictive factors for the long-term outcome using multiparametric, non-invasive magnetic resonance imaging (MRI) methodology and a clinically relevant rat model of fluid percussion induced TBI. Our results demonstrated that the multiparametric quantitative MRI (T(2), T(1rho), trace of the diffusion tensor D(av), the extent of hyperintense lesion and intracerebral hemorrhage) acquired during acute and sub acute phases 3 h, 3 days, 9 days and 23 days post-injury has potential to predict the functional and histopathological outcome 6 to 12 months later. The acute D(av) changes in the ipsilateral hippocampus correlated with the chronic spatial learning and memory impairment evaluated using the Morris water maze (pwater maze performance (p<0.01). We conclude that, assessment of early quantitative MRI changes in the hippocampus and in the perifocal area may help to predict the long-term outcome after experimental TBI. PMID:19101638

  14. Cloud prediction of protein structure and function with PredictProtein for Debian.

    Science.gov (United States)

    Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Staniewski, Cedric; Rost, Burkhard

    2013-01-01

    We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome. PMID:23971032

  15. Cloud Prediction of Protein Structure and Function with PredictProtein for Debian

    Directory of Open Access Journals (Sweden)

    László Kaján

    2013-01-01

    Full Text Available We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd, nuclear localization signals (predictnls, and intrinsically disordered regions (norsnet. We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome.

  16. Impact of climatic change on alpine ecosystems: inference and prediction

    OpenAIRE

    YOCCOZ, Nigel G.; Anne Delestrade; Anne Loison

    2011-01-01

    Alpine ecosystems will be greatly impacted by climatic change, but other factors, such as land use and invasive species, are likely to play an important role too. Climate can influence ecosystems at several levels. We describe some of them, stressing methodological approaches and available data. Climate can modify species phenology, such as flowering date of plants and hatching date in insects. It can also change directly population demography (survival, reproduction, dispersal), and therefor...

  17. Functional brain imaging predicts public health campaign success.

    Science.gov (United States)

    Falk, Emily B; O'Donnell, Matthew Brook; Tompson, Steven; Gonzalez, Richard; Dal Cin, Sonya; Strecher, Victor; Cummings, Kenneth Michael; An, Lawrence

    2016-02-01

    Mass media can powerfully affect health decision-making. Pre-testing through focus groups or surveys is a standard, though inconsistent, predictor of effectiveness. Converging evidence demonstrates that activity within brain systems associated with self-related processing can predict individual behavior in response to health messages. Preliminary evidence also suggests that neural activity in small groups can forecast population-level campaign outcomes. Less is known about the psychological processes that link neural activity and population-level outcomes, or how these predictions are affected by message content. We exposed 50 smokers to antismoking messages and used their aggregated neural activity within a 'self-localizer' defined region of medial prefrontal cortex to predict the success of the same campaign messages at the population level (n = 400,000 emails). Results demonstrate that: (i) independently localized neural activity during health message exposure complements existing self-report data in predicting population-level campaign responses (model combined R(2) up to 0.65) and (ii) this relationship depends on message content-self-related neural processing predicts outcomes in response to strong negative arguments against smoking and not in response to compositionally similar neutral images. These data advance understanding of the psychological link between brain and large-scale behavior and may aid the construction of more effective media health campaigns. PMID:26400858

  18. Omega-6 and omega-3 fatty acids predict accelerated decline of peripheral nerve function in older persons

    OpenAIRE

    F. Lauretani; Bandinelli, S.; Benedetta, B.; Cherubini, A; Iorio, A. D.; Blè, A.; Giacomini, V.; Corsi, A. M.; Guralnik, J. M.; Ferrucci, L.

    2007-01-01

    Pre-clinical studies suggest that both omega-6 and omega-3 fatty acids have beneficial effects on peripheral nerve function. Rats feed a diet rich in polyunsaturated fatty acids (PUFAs) showed modification of phospholipid fatty acid composition in nerve membranes and improvement of sciatic nerve conduction velocity (NCV). We tested the hypothesis that baseline plasma omega-6 and omega-3 fatty acids levels predict accelerated decline of peripheral nerve function. Changes between baseline and t...

  19. Predicting plants – modeling traits as a function of environment

    OpenAIRE

    O. Franklin

    2016-01-01

    A central problem in understanding and modeling vegetation dynamics is how to represent the variation in plant properties and function across different environments. Addressing this problem there is a strong trend towards trait-based approaches, where vegetation properties are functions of the distributions of functional traits rather than of species. Recently there has been enormous progress in in quantifying trait variability and its drivers and effects (Van Bodegom et al. 2012; Adier et al...

  20. Predicting the Response of Electricity Load to Climate Change

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, Patrick [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Colman, Jesse [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Kalendra, Eric [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2015-07-28

    Our purpose is to develop a methodology to quantify the impact of climate change on electric loads in the United States. We perform simple linear regression, assisted by geospatial smoothing, on paired temperature and load time-series to estimate the heating- and coolinginduced sensitivity to temperature across 300 transmission zones and 16 seasonal and diurnal time periods. The estimated load sensitivities can be coupled with climate scenarios to quantify the potential impact of climate change on load, with a primary application being long-term electricity scenarios. The method allows regional and seasonal differences in climate and load response to be reflected in the electricity scenarios. While the immediate product of this analysis was designed to mesh with the spatial and temporal resolution of a specific electricity model to enable climate change scenarios and analysis with that model, we also propose that the process could be applied for other models and purposes.

  1. Western Mountain Initiative: predicting ecosystem responses to climate change

    Science.gov (United States)

    Baron, Jill S.; Peterson, David L.; Wilson, J.T.

    2008-01-01

    Mountain ecosystems of the western United States provide irreplaceable goods and services such as water, timber, biodiversity, and recreational opportunities, but their responses to climatic changes are complex and not well understood. The Western Mountain Initiative (WMI), a collaboration between USGS and U.S. Forest Service scientists, catalyzes assessment and synthesis of the effects of disturbance and climate change across western mountain areas, focusing on national parks and surrounding national forests. The WMI takes an ecosystem approach to science, integrating research across science disciplines at scales ranging from field studies to global trends.

  2. An Improved Optimal Slip Ratio Prediction considering Tyre Inflation Pressure Changes

    OpenAIRE

    Guoxing Li; Tie Wang; Ruiliang Zhang; Fengshou Gu; Jinxian Shen

    2015-01-01

    The prediction of optimal slip ratio is crucial to vehicle control systems. Many studies have verified there is a definitive impact of tyre pressure change on the optimal slip ratio. However, the existing method of optimal slip ratio prediction has not taken into account the influence of tyre pressure changes. By introducing a second-order factor, an improved optimal slip ratio prediction considering tyre inflation pressure is proposed in this paper. In order to verify and evaluate the perfor...

  3. Improving models to predict phenological responses to global change

    Energy Technology Data Exchange (ETDEWEB)

    Richardson, Andrew D. [Harvard College, Cambridge, MA (United States)

    2015-11-25

    The term phenology describes both the seasonal rhythms of plants and animals, and the study of these rhythms. Plant phenological processes, including, for example, when leaves emerge in the spring and change color in the autumn, are highly responsive to variation in weather (e.g. a warm vs. cold spring) as well as longer-term changes in climate (e.g. warming trends and changes in the timing and amount of rainfall). We conducted a study to investigate the phenological response of northern peatland communities to global change. Field work was conducted at the SPRUCE experiment in northern Minnesota, where we installed 10 digital cameras. Imagery from the cameras is being used to track shifts in plant phenology driven by elevated carbon dioxide and elevated temperature in the different SPRUCE experimental treatments. Camera imagery and derived products (“greenness”) is being posted in near-real time on a publicly available web page (http://phenocam.sr.unh.edu/webcam/gallery/). The images will provide a permanent visual record of the progression of the experiment over the next 10 years. Integrated with other measurements collected as part of the SPRUCE program, this study is providing insight into the degree to which phenology may mediate future shifts in carbon uptake and storage by peatland ecosystems. In the future, these data will be used to develop improved models of vegetation phenology, which will be tested against ground observations collected by a local collaborator.

  4. Structure-based activity prediction for an enzyme of unknown function

    OpenAIRE

    Hermann, Johannes C.; Marti-Arbona, Ricardo; Fedorov, Alexander A.; Fedorov, Elena; Almo, Steven C.; Shoichet, Brian K.; Raushel, Frank M.

    2007-01-01

    With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metaboli...

  5. Prediction of stability changes upon mutation in an icosahedral capsid.

    Science.gov (United States)

    Hickman, Samuel J; Ross, James F; Paci, Emanuele

    2015-09-01

    Identifying the contributions to thermodynamic stability of capsids is of fundamental and practical importance. Here we use simulation to assess how mutations affect the stability of lumazine synthase from the hyperthermophile Aquifex aeolicus, a T = 1 icosahedral capsid; in the simulations the icosahedral symmetry of the capsid is preserved by simulating a single pentamer and imposing crystal symmetry, in effect simulating an infinite cubic lattice of icosahedral capsids. The stability is assessed by estimating the free energy of association using an empirical method previously proposed to identify biological units in crystal structures. We investigate the effect on capsid formation of seven mutations, for which it has been experimentally assessed whether they disrupt capsid formation or not. With one exception, our approach predicts the effect of the mutations on the capsid stability. The method allows the identification of interaction networks, which drive capsid assembly, and highlights the plasticity of the interfaces between subunits in the capsid. PMID:26178267

  6. Cognitive declines precede and predict functional declines in aging and Alzheimer's disease.

    Directory of Open Access Journals (Sweden)

    Laura B Zahodne

    Full Text Available OBJECTIVE: To investigate the temporal ordering of cognitive and functional declines separately in older adults with or without Alzheimer's disease (AD. DESIGN AND SETTING: A community-based longitudinal study of aging and dementia in Northern Manhattan (Washington Heights/Hamilton Heights Inwood Columbia Aging Project and a multicenter, clinic-based longitudinal study of prevalent AD at Columbia University Medical Center, Johns Hopkins School of Medicine, Massachusetts General Hospital, and the Hôpital de la Salpêtrière in Paris, France (the Predictors Study. PARTICIPANTS: 3,443 initially non-demented older adults (612 with eventual incident dementia and 517 patients with AD. MAIN OUTCOME MEASURES: Cognitive measures included the modified Mini-Mental State Exam and composite scores of memory and language derived from a standardized neuropsychological battery. Function was measured with the Blessed Dementia Rating Scale, completed by the participant (in the sample of non-demented older adults or an informant (in the sample of prevalent AD patients. Data were analyzed with autoregressive cross-lagged panel analysis. RESULTS: Cognitive scores more consistently predicted subsequent functional abilities than vice versa in non-demented older adults, participants with eventual incident dementia, and patients with prevalent AD. CONCLUSIONS: Cognitive declines appear to precede and cause functional declines prior to and following dementia diagnosis. Standardized neuropsychological tests are valid predictors of later functional changes in both non-demented and demented older adults.

  7. Improving the reliability of fishery predictions under climate change

    DEFF Research Database (Denmark)

    Brander, Keith

    2015-01-01

    The increasing number of publications assessing impacts of climate change on marine ecosystems and fisheries attests to rising scientific and public interest. A selection of recent papers, dealing more with biological than social and economic aspects, is reviewed here, with particular attention to...... the reliability of projections of climate impacts on future fishery yields. The 2014 Intergovernmental Panel on Climate Change (IPCC) report expresses high confidence in projections that mid- and high-latitude fish catch potential will increase by 2050 and medium confidence that low-latitude catch...... understanding of climate impacts, such as how to improve coupled models from physics to fish and how to strengthen confidence in analysis of time series...

  8. Intrinsic functional connectivity predicts individual differences in distractibility.

    Science.gov (United States)

    Poole, Victoria N; Robinson, Meghan E; Singleton, Omar; DeGutis, Joseph; Milberg, William P; McGlinchey, Regina E; Salat, David H; Esterman, Michael

    2016-06-01

    Distractor suppression, the ability to filter and ignore task-irrelevant information, is critical for efficient task performance. While successful distractor suppression relies on a balance of activity in neural networks responsible for attention maintenance (dorsal attention network; DAN), reorientation (ventral attention network; VAN), and internal thought (default mode network, DMN), the degree to which intrinsic connectivity within and between these networks contributes to individual differences in distractor suppression ability is not well-characterized. For the purposes of understanding these interactions, the current study collected resting-state fMRI data from 32 Veterans and, several months later (7±5 months apart), performance on the additional singleton paradigm, a measure of distractor suppression. Using multivariate support vector regression models composed of resting state connectivity between regions of the DAN, VAN, and DMN, and a leave-one-subject-out cross-validation procedure, we were able to predict an individual's task performance, yielding a significant correlation between the actual and predicted distractor suppression (r=0.48, p=0.0053). Network-level analyses revealed that greater within-network DMN connectivity was predictive of better distractor suppression, while greater connectivity between the DMN and attention networks was predictive of poorer distractor suppression. The strongest connection hubs were determined to be the right frontal eye field and temporoparietal junction of the DAN and VAN, respectively, and medial (ventromedial prefrontal and posterior cingulate cortices) and bilateral prefrontal regions of the DMN. These results are amongst a small but growing number of studies demonstrating that resting state connectivity is related to stable individual differences in cognitive ability, and suggest that greater integrity and independence of the DMN is related to better attentional ability. PMID:27132070

  9. Stand Diameter Distribution Modelling and Prediction Based on Richards Function

    OpenAIRE

    Duan, Ai-guo; Zhang, Jian-Guo; Zhang, Xiong-qing; He, Cai-yun

    2013-01-01

    The objective of this study was to introduce application of the Richards equation on modelling and prediction of stand diameter distribution. The long-term repeated measurement data sets, consisted of 309 diameter frequency distributions from Chinese fir (Cunninghamia lanceolata) plantations in the southern China, were used. Also, 150 stands were used as fitting data, the other 159 stands were used for testing. Nonlinear regression method (NRM) or maximum likelihood estimates method (MLEM) we...

  10. Predicting Display Visibility Under Dynamically Changing Lighting Conditions

    OpenAIRE

    Aydin, Tunc O.; Myszkowski, Karol; Seidel, Hans-Peter

    2009-01-01

    Display devices, more than ever, are finding their ways into electronic consumer goods as a result of recent trends in providing more functionality and user interaction. Combined with the new developments in display technology towards higher reproducible luminance range, the mobility and variation in capability of display devices are constantly increasing. Consequently, in real life usage it is now very likely that the display emission to be distorted by spatially and t...

  11. Endothelial function predicts progression of carotid intima-media thickness

    DEFF Research Database (Denmark)

    Halcox, J.P.; Donald, A.E.; Ellins, E.;

    2009-01-01

    significant after adjustment for risk factors whether entered as separate variables or as Framingham Risk Score. Further adjustment for waist circumference, triglycerides, and employment grade had no significant effect. CONCLUSIONS: Systemic endothelial function was associated with progression of preclinical...

  12. SVM with Quadratic Polynomial Kernel Function Based Nonlinear Model One-step-ahead Predictive Control

    Institute of Scientific and Technical Information of China (English)

    钟伟民; 何国龙; 皮道映; 孙优贤

    2005-01-01

    A support vector machine (SVM) with quadratic polynomial kernel function based nonlinear model one-step-ahead predictive controller is presented. The SVM based predictive model is established with black-box identification method. By solving a cubic equation in the feature space, an explicit predictive control law is obtained through the predictive control mechanism. The effect of controller is demonstrated on a recognized benchmark problem and on the control of continuous-stirred tank reactor (CSTR). Simulation results show that SVM with quadratic polynomial kernel function based predictive controller can be well applied to nonlinear systems, with good performance in following reference trajectory as well as in disturbance-rejection.

  13. Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasets

    DEFF Research Database (Denmark)

    Swanton, C.; Larkin, J.M.; Gerlinger, M.;

    2010-01-01

    RNA screens to identify and validate functionally important genomic or transcriptomic predictive biomarkers of individual drug response in patients. PREDICT's approach to predictive biomarker discovery differs from conventional associative learning approaches, which can be susceptible to the detection of...... European network providing the technological and clinical platform for large-scale functional genomic biomarker discovery. Here we review our current understanding of molecular mechanisms driving resistance to anti-angiogenesis agents, the current limitations of laboratory and clinical trial strategies and...... how the PREDICT consortium will endeavour to identify a new generation of predictive biomarkers....

  14. Optimizing non-decomposable loss functions in structured prediction

    OpenAIRE

    Ranjbar, Mani

    2012-01-01

    Learning functional dependencies (mapping) between arbitrary input and output spaces is one of the main challenges in computational intelligence. There have been two main threads in the literature for solving this problem -- one focusing on designing more discriminative representation of the input and another one focusing on designing flexible mapping functions.Interestingly, for many applications, the outputs follow a structure, which can be exploited to narrow down the space of possible (mo...

  15. Wiggle-predicting functionally flexible regions from primary sequence.

    Directory of Open Access Journals (Sweden)

    Jenny Gu

    2006-07-01

    Full Text Available The Wiggle series are support vector machine-based predictors that identify regions of functional flexibility using only protein sequence information. Functionally flexible regions are defined as regions that can adopt different conformational states and are assumed to be necessary for bioactivity. Many advances have been made in understanding the relationship between protein sequence and structure. This work contributes to those efforts by making strides to understand the relationship between protein sequence and flexibility. A coarse-grained protein dynamic modeling approach was used to generate the dataset required for support vector machine training. We define our regions of interest based on the participation of residues in correlated large-scale fluctuations. Even with this structure-based approach to computationally define regions of functional flexibility, predictors successfully extract sequence-flexibility relationships that have been experimentally confirmed to be functionally important. Thus, a sequence-based tool to identify flexible regions important for protein function has been created. The ability to identify functional flexibility using a sequence based approach complements structure-based definitions and will be especially useful for the large majority of proteins with unknown structures. The methodology offers promise to identify structural genomics targets amenable to crystallization and the possibility to engineer more flexible or rigid regions within proteins to modify their bioactivity.

  16. Predictability Effects on Durations of Content and Function Words in Conversational English

    Energy Technology Data Exchange (ETDEWEB)

    Bell, Alan; Brenier, Jason; Gregory, Michelle L.; girand, cynthia; Jurafsky, Daniel

    2009-01-01

    Content and function word duration are affected differently by their frequency and predictability. Regression analyses of conversational speech show that content words are shorter when they are more frequent, but function words are not. Repeated content words are shorter, but function words are not. Furthermore, function words have shorter pronunciations, after controlling for frequency and predictability. both content and function words are strongly affected by predictability from the word following them, and only very frequent function words show sensitivity to predictability from the preceding word. The results support the view that content and function words are accessed by different production mechanisms. We argue that words’ form differences due to frequency or repetition stem from their faster or slower lexical access, mediated by a general mechanism that coordinates the pace of higher-level planning and the execution of the articulatory plan.

  17. Predictive functional control(PFC) and its application in Chlorinated polyethylene process

    Institute of Scientific and Technical Information of China (English)

    李鸿亮; 苏宏业; 刘军; 褚健

    2003-01-01

    The main principle and the characteristic of Predictive Functional Control (PFC) strategy are presented in this paper and the corresponding control system aid design software APC-PFC is also introduced. For a chlorinated polyethylene (CPE) process, a design scheme of cascade predictive functional control system is described and the control performance is improved obviously.

  18. Stages of Change or Changes of Stage? Predicting Transitions in Transtheoretical Model Stages in Relation to Healthy Food Choice

    Science.gov (United States)

    Armitage, Christopher J.; Sheeran, Paschal; Conner, Mark; Arden, Madelynne A.

    2004-01-01

    Relatively little research has examined factors that account for transitions between transtheoretical model (TTM) stages of change. The present study (N=787) used sociodemographic, TTM, and theory of planned behavior (TPB) variables, as well as theory-driven interventions to predict changes in stage. Longitudinal analyses revealed that…

  19. How the cerebral serotonin homeostasis predicts environmental changes

    DEFF Research Database (Denmark)

    Kalbitzer, Jan; Kalbitzer, Urs; Knudsen, Gitte Moos;

    2013-01-01

    Molecular imaging studies with positron emission tomography have revealed that the availability of serotonin transporter (5-HTT) in the human brain fluctuates over the course of the year. This effect is most pronounced in carriers of the short allele of the 5-HTT promoter region (5-HTTLPR), which...... with pronounced seasonal climatic changes, while this hypothesis does not rule out that genetic drift plays an additional or even exclusive role. We argue that s-allele manifests as an intermediate phenotype in terms of an increased responsiveness of the 5-HTT expression to number of daylight hours...

  20. Functional Brain Network Changes Associated with Maintenance of Cognitive Function in Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Santosh A Helekar

    2010-11-01

    Full Text Available In multiple sclerosis (MS functional changes in connectivity due to cortical reorganization could lead to cognitive impairment (CI, or reflect a re-adjustment to reduce the clinical effects of widespread tissue damage. Such alterations in connectivity could result in changes in neural activation as assayed by executive function tasks. We examined cognitive function in MS patients with mild to moderate cognitive impairment and age-matched controls. We evaluated brain activity using functional magnetic resonance imaging (fMRI during the successful performance of the Wisconsin-card sorting (WCS task by MS patients, showing compensatory maintenance of normal function, as measured by response latency and error rate. To assess changes in functional connectivity throughout the brain, we performed a global functional brain network analysis by computing voxel by voxel correlations on the fMRI time series data and carrying out a hierarchical cluster analysis. We found that during the WCS task there is a significant reduction in the number of smaller size brain functional networks, and a change in the brain areas representing the nodes of these networks in MS patients compared to age-matched controls. There is also a concomitant increase in the strength of functional connections between brain loci separated at intermediate scale distances in these patients. These functional alterations might reflect compensatory neuroplastic reorganization underlying maintenance of relatively normal cognitive function in the face of white matter lesions and cortical atrophy produced by MS.

  1. Changes in household composition as determinant of changes in functional ability among old men and women

    DEFF Research Database (Denmark)

    Avlund, Kirsten; Due, Pernille; Holstein, Bjørn Evald;

    2002-01-01

    The aims of this article were 1) to describe changes in functional ability from ages 75 to 80 among men and women in three Nordic localities, and 2) to analyze whether these changes are determined by changes in household composition from ages 70 to 75. The present analyses include the persons who...... functional ability are described as 1) sustained good, 2) decreased, 3) improved, and 4) sustained poor, and changes in household composition as 1) sustained living alone, 2) from living with others to living alone, and 3) sustained living with others. Number of chronic diseases and home help were included...

  2. Functional Neuroimaging Approaches to the Changing Borders of Consciousness

    OpenAIRE

    Noirhomme, Quentin; Soddu, Andrea; Vanhaudenhuyse, Audrey; Lehembre, Remy; Bruno, Marie-Aurélie; Gosseries, Olivia; Demertzi, Athina; Maudoux, Audrey; Schnakers, Caroline; Boveroux, Pierre; Boly, Mélanie; Laureys, Steven

    2010-01-01

    The bedside diagnosis of vegetative and minimally conscious patients is extremely challenging, and prediction of individual long-term outcome remains difficult. State-of the art neuroimaging methods could help disentangle complex cases and offer new prognostic criteria. These methods can be divided into to three categories: First, new anatomical MRI neuroimaging methods, like diffusion tensor imaging (DTI) or spectroscopy, and passive functional imaging methods (looking at the brain’...

  3. Geomagnetism, volcanoes, global climate change, and predictability. A progress report

    Directory of Open Access Journals (Sweden)

    G. P. Gregori

    1994-06-01

    Full Text Available A model is investigated, by which the encounters of the solar system with dense interstellar clouds ought to trigger either geomagnetic field reversals or excursions, that produce extra electric currents within the Earth dynamo, that cause extra Joule's heating, that supplies volcanoes and endogenous processes. Volcanoes increase the Earth degassing into the atmosphere, hence the concentration of the minor atmospheric constituents, including the greenhouse gases, hence they affect climate temperature, glacier melting, sea level and global change. This investigation implies both theoretical studies and observational data handling on different time scales, including present day phenomena, instrumental data series, historical records, proxy data, and geological and palaeontological evidences. The state of the art is briefly outlined, mentioning some already completed achievements, investigations in progress, and future perspectives.

  4. Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    GESTs (gene expression similarity and taxonomy similarity), a gene functional prediction approach previously proposed by us, is based on gene expression similarity and concept similarity of functional classes defined in Gene Ontology (GO). In this paper, we extend this method to protein-protein interac-tion data by introducing several methods to filter the neighbors in protein interaction networks for a protein of unknown function(s). Unlike other conventional methods, the proposed approach automati-cally selects the most appropriate functional classes as specific as possible during the learning proc-ess, and calls on genes annotated to nearby classes to support the predictions to some small-sized specific classes in GO. Based on the yeast protein-protein interaction information from MIPS and a dataset of gene expression profiles, we assess the performances of our approach for predicting protein functions to “biology process” by three measures particularly designed for functional classes organ-ized in GO. Results show that our method is powerful for widely predicting gene functions with very specific functional terms. Based on the GO database published in December 2004, we predict some proteins whose functions were unknown at that time, and some of the predictions have been confirmed by the new SGD annotation data published in April, 2006.

  5. Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile

    Institute of Scientific and Technical Information of China (English)

    GAO Lei; LI Xia; GUO Zheng; ZHU MingZhu; LI YanHui; RAO ShaoQi

    2007-01-01

    GESTs (gene expression similarity and taxonomy similarity), a gene functional prediction approach previously proposed by us, is based on gene expression similarity and concept similarity of functional classes defined in Gene Ontology (GO). In this paper, we extend this method to protein-protein interaction data by introducing several methods to filter the neighbors in protein interaction networks for a protein of unknown function(s). Unlike other conventional methods, the proposed approach automatically selects the most appropriate functional classes as specific as possible during the learning process, and calls on genes annotated to nearby classes to support the predictions to some small-sized specific classes in GO. Based on the yeast protein-protein interaction information from MIPS and a dataset of gene expression profiles, we assess the performances of our approach for predicting protein functions to "biology process" by three measures particularly designed for functional classes organized in GO. Results show that our method is powerful for widely predicting gene functions with very specific functional terms. Based on the GO database published in December 2004, we predict some proteins whose functions were unknown at that time, and some of the predictions have been confirmed by the new SGD annotation data published in April, 2006.

  6. Analysis and prediction of the alpha-function parameters used in cubic equations of state

    DEFF Research Database (Denmark)

    Privata, Romain; Viscontea, Maxime; Zazoua-Khames, Anis; Jauberta, Jean-Noël; Gani, Rafiqul

    2015-01-01

    evidenced and fixed. A new class of purely predictive alpha functions was derived by applying group-contribution (GC) methods to the prediction of alpha function parameters. The interest of such an approach is discussed and compared to another predictive approach (use of generalized alpha functions coupled......The performance of two generalized alpha functions (Soave and generalized Twu functions requiring the acentric factor as input parameter) and two parameterizable alpha functions (Mathias-Copeman and Twu) incorporated in cubic equations of state (Redlich-Kwong and Peng-Robinson) are evaluated and...... compared regarding their ability to reproduce vapor pressure, heat of vaporization, liquid heat capacity, liquid density and second virial coefficient data. To reach this objective, extensive databanks of alpha function parameters were created. In particular, pitfalls of Twu-type alpha functions were...

  7. Structural and Function Prediction of Musa acuminata subsp. Malaccensis Protein

    Directory of Open Access Journals (Sweden)

    Anum Munir

    2016-03-01

    Full Text Available Hypothetical proteins (HPs are the proteins whose presence has been anticipated, yet in vivo function has not been built up. Illustrating the structural and functional privileged insights of these HPs might likewise prompt a superior comprehension of the protein-protein associations or networks in diverse types of life. Bananas (Musa acuminata spp., including sweet and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister grouped to the all-around considered Poales, which incorporate oats. Bananas are crucial for nourishment security in numerous tropical and subtropical nations and the most prominent organic product in industrialized nations. In the present study, the hypothetical protein of M. acuminata (Banana was chosen for analysis and modeling by distinctive bioinformatics apparatuses and databases. As indicated by primary and secondary structure analysis, XP_009393594.1 is a stable hydrophobic protein containing a noteworthy extent of α-helices; Homology modeling was done utilizing SWISS-MODEL server where the templates identity with XP_009393594.1 protein was less which demonstrated novelty of our protein. Ab initio strategy was conducted to produce its 3D structure. A few evaluations of quality assessment and validation parameters determined the generated protein model as stable with genuinely great quality. Functional analysis was completed by ProtFun 2.2, and KEGG (KAAS, recommended that the hypothetical protein is a transcription factor with cytoplasmic domain as zinc finger. The protein was observed to be vital for translation process, involved in metabolism, signaling and cellular processes, genetic information processing and Zinc ion binding. It is suggested that further test approval would help to anticipate the structures and functions of other uncharacterized proteins of different plants and living being.

  8. Habitual fat intake predicts memory function in younger women

    OpenAIRE

    Edward Leigh Gibson; Suzanne Barr

    2013-01-01

    High intakes of fat have been linked to greater cognitive decline in old age, but such associations may already occur in younger adults. We tested memory and learning in 38 women (25 to 45 years old), recruited for a larger observational study in women with polycystic ovary syndrome. These women varied in health status, though not significantly between cases (n = 23) and controls (n = 15). Performance on tests sensitive to medial temporal lobe function (CANTABeclipse, Cambridge Cognition Ltd,...

  9. Amygdala Functional Connectivity Predicts Pharmacotherapy Outcome in Pediatric Bipolar Disorder

    OpenAIRE

    Wegbreit, Ezra; Ellis, James A.; Nandam, Aneesh; Fitzgerald, Jacklynn M.; Passarotti, Alessandra M.; Pavuluri, Mani N.; Stevens, Michael C.

    2011-01-01

    The aim of this study was to determine functional connectivity among patients with pediatric bipolar disorder (PBD) who are responders to pharmacotherapy and those who are nonresponders, and learn how they differ from healthy controls (HC) while performing a task that engages affective and cognitive neural systems. PBD participants (n=34; 13.4±2.3 years) were defined as responders if there was ≥50% improvement in Young Mania Rating Scale (YMRS) scores (n=22) versus nonresponders with

  10. The use of the Theory of Planned Behavior to Predict Engagement in Functional Behaviors in Schizophrenia

    OpenAIRE

    Mausbach, Brent T.; Moore, Raeanne C.; Davine, Taylor; Cardenas, Veronica; Bowie, Christopher R.; Ho, Jennifer; Jeste, Dilip V.; Patterson, Thomas L

    2012-01-01

    In Schizophrenia, low motivation may play a role in the initiation and frequency of functional behaviors. Several reviews support the efficacy of the Theory of Planned Behavior (TPB) to predict engagement in various behaviors, but little research has utilized the TPB to explain functional behavior in schizophrenia. This study tested the TPB for predicting prospective engagement in functional behaviors in a sample of 64 individuals with schizophrenia. Participants completed questionnaires asse...

  11. Microbial community functional change during vertebrate carrion decomposition.

    Directory of Open Access Journals (Sweden)

    Jennifer L Pechal

    Full Text Available Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects. Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition.

  12. A Romanian Prosody Prediction Module Based on a Functional Intonational Model

    Directory of Open Access Journals (Sweden)

    Doina Jitca

    2012-10-01

    Full Text Available This paper presents a prosodic prediction module used by the Romanian Text-to-Speech (TtS system in intonation synthesis. The prosody prediction refers to the surface generation of the F0 contour, based on the F0 patterns assigned to the functional categories of the prosodic units. Prior to the prediction module presentation, the paper includes a summary of these functional categories and the partial melodic contour descriptions based on functional labels. The block diagram of the prediction module outlines two main processing steps: the phrasing prediction for building the utterance tree and the selection of the melodic contours of its groups. Both processing steps are exemplified within a case study of Romanian text speech synthesis. The prosody prediction results are discussed and compared with natural F0 contours of different speakers.

  13. Changes in brain functional network connectivity after stroke

    Institute of Scientific and Technical Information of China (English)

    Wei Li; Yapeng Li; Wenzhen Zhu; Xi Chen

    2014-01-01

    Studies have shown that functional network connection models can be used to study brain net-work changes in patients with schizophrenia. In this study, we inferred that these models could also be used to explore functional network connectivity changes in stroke patients. We used independent component analysis to find the motor areas of stroke patients, which is a novel way to determine these areas. In this study, we collected functional magnetic resonance imaging datasets from healthy controls and right-handed stroke patients following their ifrst ever stroke. Using independent component analysis, six spatially independent components highly correlat-ed to the experimental paradigm were extracted. Then, the functional network connectivity of both patients and controls was established to observe the differences between them. The results showed that there were 11 connections in the model in the stroke patients, while there were only four connections in the healthy controls. Further analysis found that some damaged connections may be compensated for by new indirect connections or circuits produced after stroke. These connections may have a direct correlation with the degree of stroke rehabilitation. Our ifndings suggest that functional network connectivity in stroke patients is more complex than that in hea-lthy controls, and that there is a compensation loop in the functional network following stroke. This implies that functional network reorganization plays a very important role in the process of rehabilitation after stroke.

  14. Medium- and Long-term Prediction of LOD Change by the Leap-step Autoregressive Model

    Science.gov (United States)

    Wang, Qijie

    2015-08-01

    The accuracy of medium- and long-term prediction of length of day (LOD) change base on combined least-square and autoregressive (LS+AR) deteriorates gradually. Leap-step autoregressive (LSAR) model can significantly reduce the edge effect of the observation sequence. Especially, LSAR model greatly improves the resolution of signals’ low-frequency components. Therefore, it can improve the efficiency of prediction. In this work, LSAR is used to forecast the LOD change. The LOD series from EOP 08 C04 provided by IERS is modeled by both the LSAR and AR models. The results of the two models are analyzed and compared. When the prediction length is between 10-30 days, the accuracy improvement is less than 10%. When the prediction length amounts to above 30 day, the accuracy improved obviously, with the maximum being around 19%. The results show that the LSAR model has higher prediction accuracy and stability in medium- and long-term prediction.

  15. Developmental changing in the form and function of rowing hydromedusae

    Science.gov (United States)

    Colin, S. P.; Weston, J.; Costello, J. H.; Dabiri, J. O.

    2007-12-01

    Among medusan lineages bell morphology and propulsion appear to be interdependent traits. In general, taxa that possess large oblate bells swim via rowing propulsion and taxa with small prolate bells swim via jet propulsion. However, hydromedusae from the order, Leptomedusae, experience large changes in bell size and shape throughout their development, metamorphosing from small prolate juveniles into large oblate adults. To examine how propulsion changes throughout the development of leptomedusae, we investigated the fluid interactions and swimming characteristics of two leptomedusan species, Aequorea victorea and Eutonina indicans, throughout their development. As expected, these species start off as small prolate juveniles ( 1.5 cm diameter). In addition to changes in morphology, we observed changes in Reynolds number, wake structure, propulsion and swimming kinematics. These changes were consistent with the previously described relationship between bell morphology and function.

  16. Changes in defensive functioning in completed psychoanalyses: the penn psychoanalytic treatment collection.

    Science.gov (United States)

    Roy, Carmella A; Perry, Christopher J; Luborsky, Lester; Banon, Elisabeth

    2009-04-01

    Theory predicts that patients completing psychoanalysis should improve in their dynamic functioning. The aim of this naturalistic study is to examine whether a sample of 17 subjects from the Penn Psychoanalytic Treatment Collection with completed, tape-recorded psychoanalyses demonstrated improvement in one dynamic aspect: their defense mechanisms. The pre-post effect size for the change in overall defensive functioning (ODF) of the sample was large (.76) and statistically significant (p = .01). The percentage of subjects who improved in their ODF (71%) was similar to that found by others who studied the same sample using general functioning measures. These findings provide the first empirical evidence to support a trait-like change in dynamic personality functioning in patients who have undergone psychoanalysis. Randomized controlled studies with homogeneous samples are needed to further confirm these findings. PMID:19516058

  17. Changes in occupational functioning in patients after psychotherapy

    DEFF Research Database (Denmark)

    Fenger, Morten Munthe; Poulsen, Stig Bernt; Mortensen, Erik Lykke;

    2012-01-01

    Introduction Mental disorders are a primary cause of occupational impairments. This study investigated long-term changes in occupational functioning for patients referred to psychotherapeutic treatment at a Danish mental healthcare centre in 2004 and 2005. Method We recruited 761 consecutive pati...

  18. P-1138 - Changes in occupational functioning in patients after psychotherapy

    DEFF Research Database (Denmark)

    Fenger, Morten Munthe; Poulsen, Stig Bernt; Mortensen, Erik Lykke;

    2012-01-01

    Introduction Mental disorders are a primary cause of occupational impairments. This study investigated long-term changes in occupational functioning for patients referred to psychotherapeutic treatment at a Danish mental healthcare centre in 2004 and 2005. Method We recruited 761 consecutive pati...

  19. [Change in pancreatic exocrine function in acute appendicitis].

    Science.gov (United States)

    Ivanov, Iu A

    1979-10-01

    In order to study changes in the functional state of the pancreas 1572 investigations of the blood and urine amylase, atoxylresistant lipase of the blood serum before operation were performed in different postoperative periods in 131 patients with acute appendicitis. The enzyme activity was established to increase, especially in destructive forms of appendicitis and in elderly patients. PMID:505800

  20. Changes in pulmonary function after definitive radiotherapy for NSCLC

    DEFF Research Database (Denmark)

    Schytte, Tine; Bentzen, Søren M; Brink, Carsten; Hansen, Olfred

    2015-01-01

    INTRODUCTION: The objective of this study was to identify factors associated with early and long-term pulmonary function (PF) changes after definitive radiotherapy for NSCLC patients. PF was measured by spirometry i.e. forced expiratory volume in 1s (FEV1), and forced vital capacity (FVC...

  1. Prediction-Market-Based Quantification of Climate Change Consensus and Uncertainty

    Science.gov (United States)

    Boslough, M.

    2012-12-01

    Intrade is an online trading exchange that includes climate prediction markets. One such family of contracts can be described as "Global temperature anomaly for 2012 to be greater than x °C or more," where the figure x ranges in increments of .05 from .30 to 1.10 (relative to the 1951-1980 base period), based on data published by NASA GISS. Each market will settle at 10.00 if the published global temperature anomaly for 2012 is equal to or greater than x, and will otherwise settle at 0.00. Similar contracts will be available for 2013. Global warming hypotheses can be cast as probabilistic predictions for future temperatures. The first modern such climate prediction is that of Broecker (1975), whose temperatures are easily separable from his CO2 growth scenario—which he overestimated—by interpolating his table of temperature as a function of CO2 concentration and projecting the current trend into the near future. For the current concentration of 395 ppm, Broecker's equilibrium temperature anomaly prediction relative to pre-industrial is 1.05 °C, or about 0.75 °C relative to the GISS base period. His neglect of lag in response to the changes in radiative forcing was partially compensated by his low sensitivity of 2.4 °C, leading to a slight overestimate. Simple linear extrapolation of the current trend since 1975 yields an estimate of .65 ± .09 °C (net warming of .95 °C) for anthropogenic global warming with a normal distribution of random natural variability. To evaluate an extreme case, we can estimate the prediction Broecker would have made if he had used the Lindzen & Choi (2009) climate sensitivity of 0.5 °C. The net post-industrial warming by 2012 would have been 0.21 °C, for an expected change of -0.09 from the GISS base period. This is the temperature to which the Earth would be expected to revert if the observed warming since the 19th century was merely due to random natural variability that coincidentally mimicked Broecker's anthropogenic

  2. Jinzhai County Household Technical Change and Efficiency Change Analysis: Stochastic Frontier Production Function Approach

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Stochastic frontier production function approach is adopted, 93 farmer samples have been collected, pure efficiency, technical efficiency, technical change and scale efficiency and the institutional contribution have been calculated. The results indicated that increasing productivity is the sole measurement to reduce poverty, institution and technical change are the two key factors. Therefore, stable institution, improving technical changes are required. At present, it is urgent to make technical progre...

  3. FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies

    OpenAIRE

    Redfern, O. C.; Dessailly, B. H.; Dallman, T. J.; Sillitoe, I.; Orengo, C A

    2009-01-01

    Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure e...

  4. Stability of executive function and predictions to adaptive behavior from middle childhood to pre-adolescence

    Directory of Open Access Journals (Sweden)

    Madeline eHarms

    2014-04-01

    Full Text Available The shift from childhood to adolescence is characterized by rapid remodeling of the brain and increased risk-taking behaviors. Current theories hypothesize that developmental enhancements in sensitivity to affective environmental cues in adolescence may undermine executive function (EF and increase the likelihood of problematic behaviors. In the current study, we examined the extent to which EF in childhood predicts EF in early adolescence. We also tested whether individual differences in neural responses to affective cues (rewards/punishments in childhood serve as a biological marker for EF, sensation-seeking, academic performance, and social skills in early adolescence. At age 8, 84 children completed a gambling task while event-related potentials (ERPs were recorded. We examined the extent to which selections resulting in rewards or losses in this task elicited (i the P300, a post-stimulus waveform reflecting the allocation of attentional resources toward a stimulus, and (ii the SPN, a pre-stimulus anticipatory waveform reflecting a neural representation of a hunch about an outcome that originates in insula and ventromedial PFC. Children also completed a Dimensional Change Card-Sort (DCCS and Flanker task to measure EF. At age 12, 78 children repeated the DCCS and Flanker and completed a battery of questionnaires. Flanker and DCCS accuracy at age 8 predicted Flanker and DCCS performance at age 12, respectively. Individual differences in the magnitude of P300 (to losses vs. rewards and SPN (preceding outcomes with a high probability of punishment at age 8 predicted self-reported sensation seeking (lower and teacher-rated academic performance (higher at age 12. We suggest there is stability in EF from age 8 to 12, and that childhood neural sensitivity to reward and punishment predicts individual differences in sensation seeking and adaptive behaviors in children entering adolescence.

  5. Determining the Importance of Calibration for Predicting Relative Changes in Streamflow from Land Use/Cover Changes

    Science.gov (United States)

    Niraula, R.; Meixner, T.; Norman, L. M.

    2012-12-01

    Human-induced land use/cover (LULC) change and climate change can have significant impacts on water quantity and quality. Prediction of impacts due to anticipated LULC and climate change on water in arid and semi-arid regions are crucial to understand due to scarce water resources. Watershed models are often used to analyze the effects of land use/cover and climate change on water resources, commonly in terms of relative changes; and provide important information for decision making. These models are often calibrated and validated with available data which can be time consuming and sometimes even very difficult. The objective of this study is to quantify the variation of estimated relative changes in streamflow associated with LULC with uncalibrated, single outlet calibrated and spatially-calibrated watershed model. Soil and Water Assessment Tool (SWAT) was applied in an uncalibrated, single outlet calibrated, and spatially-calibrated (at 7 USGS stream-gaging stations) mode to compare and quantify the relative change in terms of magnitude and direction of flow in a 9000 km2 semi-arid Santa Cruz watershed on the border of southern Arizona, United States, and northern Sonora, Mexico. While the average annual precipitation over the whole watershed is approximately 430 mm, the average annual discharge ranges between 0.17 and 2.64 m3/s. The effect due to three LULC scenarios, where urbanization is expected to increase from ~12% in 1999 to range of 35-40% in 2050 was analyzed. For the 7 USGS stations, all 3 calibration scenarios demonstrated an increase in predicted flow but magnitude of predicted change varied. The uncalibrated model predicted the increase from 4% to 15%, the single-outlet calibrated model predicted between 5% and 105%, and the spatially-calibrated model predicted the increase to be between 4% and 170%. While the results were similar between uncalibrated and single outlet calibration at some stations, the results were more similar to single outlet and

  6. Scoring protein relationships in functional interaction networks predicted from sequence data.

    Directory of Open Access Journals (Sweden)

    Gaston K Mazandu

    Full Text Available UNLABELLED: The abundance of diverse biological data from various sources constitutes a rich source of knowledge, which has the power to advance our understanding of organisms. This requires computational methods in order to integrate and exploit these data effectively and elucidate local and genome wide functional connections between protein pairs, thus enabling functional inferences for uncharacterized proteins. These biological data are primarily in the form of sequences, which determine functions, although functional properties of a protein can often be predicted from just the domains it contains. Thus, protein sequences and domains can be used to predict protein pair-wise functional relationships, and thus contribute to the function prediction process of uncharacterized proteins in order to ensure that knowledge is gained from sequencing efforts. In this work, we introduce information-theoretic based approaches to score protein-protein functional interaction pairs predicted from protein sequence similarity and conserved protein signature matches. The proposed schemes are effective for data-driven scoring of connections between protein pairs. We applied these schemes to the Mycobacterium tuberculosis proteome to produce a homology-based functional network of the organism with a high confidence and coverage. We use the network for predicting functions of uncharacterised proteins. AVAILABILITY: Protein pair-wise functional relationship scores for Mycobacterium tuberculosis strain CDC1551 sequence data and python scripts to compute these scores are available at http://web.cbio.uct.ac.za/~gmazandu/scoringschemes.

  7. Morphological changes of gastric mucosa depending on functional dyspepsia syndrome

    Directory of Open Access Journals (Sweden)

    Svintsitskyy A.

    2014-06-01

    Full Text Available Background. Chronic gastritis process of cell renewal in the mucosa is disturbed, leading to rapid movement of the generative cell zone without full differentiation into mature specialized area accommodation epithelial cells. The result of this process is the inability to fully function gastric glands. Crucial in the diagnosis of gastritis given the nature of the morphological changes of the gastric mucosa and preferential localization of these changes. Objective. To assess histological changes of gastric mucosa in patients with clinically different types of functional dyspepsia. Methods. Adult patients (18-65 years with confirmed diagnosis of functional dyspepsia were eligible to participate. Biopsy specimens were taken from stomach due to the Houston-updated gastric biopsy sampling protocol for the next histological examination. One expert gastrointestinal pathologist assessed all tissue samples. Atrophy was assessed due to Operative Link for Gastritis Assessment (OLGA staging system. Results. 75 patients were recruited, 42 of which had epigastric pain (I group and 33 – postprandial distress syndrome (II group due to Rome III criteria (2006. Antral and corpus atrophy were detected at the same frequency in both groups (p>0.05, however the stage of atrophy didn’t exceed I in all cases. Complete antral metaplasia was revealed in 11 (26.2% patients of the I group and 11 (33.3% patients of the II one. Incomplete antral metaplasia was seen in 2 (4.7% patients of the I group and 2 (6.1% patients of the II one. No cases of corpus metaplasia or dysplasia were found. Conclusion. Our study didn’t reveal statistically significant correlation between stage of gastritis, atrophic or metaplastic changes and clinical symptoms of functional dyspepsia. Citation: Svintsitskyy A, Korendovych I, Kuryk O, Solovyova G. [Morphological changes of gastric mucosa depending on functional dyspepsia syndrome]. Morphologia. 2014;8(2:50-5. Ukrainian.

  8. Amphiphile regulation of ion channel function by changes in the bilayer spring constant

    DEFF Research Database (Denmark)

    Lundbæk, Jens August; Koeppe, R.E.; Andersen, Oluf Sten

    2010-01-01

    predicted from measurements of isolated changes in such properties. Thus, the bilayer contribution to the promiscuous regulation of membrane proteins by drugs and other amphiphiles remains unknown. To overcome this problem, we use gramicidin A (gA) channels as molecular force probes to measure the net...... altering the energetic cost (Delta G(bilayer)) of bilayer deformations associated with protein conformational changes that involve the protein-bilayer interface. But amphiphiles have complex effects on the physical properties of lipid bilayers, meaning that the net change in Delta G(bilayer) cannot be......-dependent sodium channels in living cells. The use of gA channels as molecular force probes provides a tool for quantitative, predictive studies of bilayer-mediated regulation of membrane protein function by amphiphiles....

  9. PREDICTING CHANGE IN MANAGEMENT ACCOUNTING SYSTEMS: THE EFFECTS OF COMPETITIVE STRATEGY

    OpenAIRE

    Nelson Waweru

    2008-01-01

    This study reports on a survey that investigated changes in management accounting and control systems in 31 Canadian manufacturing companies. Six variables that may influence changes in management accounting and control systems are identified from contingency theory literature. The findings indicate considerable changes in the organizations’ management accounting systems during the three year period. Changes in management accounting were best predicted by organizational capacity to learn. S...

  10. Lung perfusion SPECT in predicting postoperative pulmonary function in lung cancer

    International Nuclear Information System (INIS)

    The aim of this prospective study is to evaluate the availability of preoperative perfusion SPECT in predicting postoperative pulmonary function following resection. Twenty-three patients with lung cancer who were candidates for lobectomy were investigated preoperatively with spirometry, x-ray computed tomography and 99mTc-macroaggregated albumin SPECT. Their postoperative pulmonary functions were predicted with these examinations. The forced vital capacity and the forced expiratory volume in one second were selected as parameters for overall pulmonary function. The postoperative pulmonary function was predicted by the following formula: Predicted postoperative value=observed preoperative value x precent perfusion of the lung not to be resected. The patients were reinvestigated with spirometry at 3 months and 6 months after lobectomy, and the values obtained were statistically compared with the predicted values. Close relationships were found between predicted and observed forced vital capacity (r=0.87, p<0.001), and predicted and observed forced expiratory volume in one second (r=0.90, p<0.001). The accurate prediction of pulmonary function after lobectomy could be achieved by means of lung perfusion SPECT. (author)

  11. Changes in the ecosystem structure of the Black Sea under predicted climatological and anthropogenic variations

    Science.gov (United States)

    Akoglu, Ekin; Salihoglu, Baris; Fach Salihoglu, Bettina; Libralato, Simone; Cannaby, Heather; Oguz, Temel; Solidoro, Cosimo

    2014-05-01

    A dynamic Ecopath with Ecosim higher-trophic-level (HTL) model representation of the Black Sea ecosystem was coupled to the physical (BIMS-CIR) and biogeochemical (BIMS-ECO) models of the Black Sea in order to investigate historical anthropogenic and climatological interactions and feedbacks in the ecosystem. Further, the coupled models were used to assess the likely consequences of these interactions on the ecosystem's structure and functioning under predicted future climate (IPCC A1B) and fishing variability. Therefore, two model scenarios were used; i) a hindcast scenario (1980-1999) to evaluate and understand the impacts of the short-term climate and physical variability and the introduction of invasive species on the Black Sea ecosystem, and ii) a forecast scenario (2080-2099) to investigate the potential implications of climate change and anthropogenic exploitation on living resources of the Black Sea ecosystem by the end of the 21st century. According to the outcomes of the hindcast simulation, fisheries were found to be the main driver in determining the structure and functioning of the Black Sea ecosystem under changing environmental conditions. The coupled physical-biogeochemical forecast simulations predicted a slight but statistically significant basin-wide increase in the Black Sea's primary productivity by the end of the century due to increased stratification induced by basin-wide temperature increase and reduced Cold Intermediate Layer (CIL) formation which increased the residence time of riverine nutrients within the euphotic zone. Despite this increased primary productivity, the HTL model forecast simulation predicted a significant decrease in the commercial fish stocks primarily due to fisheries exploitation if current catch rates are maintained into the future. Results further suggested that some economically important small pelagic fish species are likely to disappear from the ecosystem making the recovery of the already-collapsed piscivorous

  12. Dimensional changes as a function of charge injection for trans-polyacetylene: A density functional theory study

    Science.gov (United States)

    Sun, Guangyu; Kurti, Jeno; Kertesz, Miklos; Baughman, Ray H.

    2002-10-01

    Charge-induced dimensional changes allow conducting polymers and single walled carbon nanotubes to function as electromechanical actuators. The unit cell of the prototypical conducting polymer, trans-polyacetylene, was calculated as a function of charge injection using density functional theory in combination with ultrasoft pseudopotentials using the solid-state Vienna ab initio simulation package. Test calculations on the charged pyridinium molecular ion give results in good agreement with the experimental geometry. Strain versus charge relationships are predicted from dimensional changes calculated using a uniform background charge ("jellium") for representing the counterions, which we show provides results consistent with experiment for doped polyacetylenes. These jellium calculations are consistent with further presented calculations that include specific counterions, showing that hybridization between the guest dopant ions and the host polyacetylene chains is unimportant. The lack of guest-host orbital hybridization allows a qualitative rigid band interpretation of the amount of charge transfer for both acceptor and donor doping. For polyacetylene, asymmetry of strain along the chain with respect to the sign of the charge is predicted: negative charge elongates and positive charge shortens the polymer. For charge less than 0.05e per carbon, an approximately linear dependence is obtained for the dependence of chain-direction strain on the amount of injected charge.

  13. FLORA: a novel method to predict protein function from structure in diverse superfamilies.

    Directory of Open Access Journals (Sweden)

    Oliver C Redfern

    2009-08-01

    Full Text Available Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure embellishments to a common structural core. The majority of prediction algorithms employ local templates built on known or predicted functional residues. Here, we present a novel method (FLORA that automatically generates structural motifs associated with different functional sub-families (FSGs within functionally diverse domain superfamilies. Templates are created purely on the basis of their specificity for a given FSG, and the method makes no prior prediction of functional sites, nor assumes specific physico-chemical properties of residues. FLORA is able to accurately discriminate between homologous domains with different functions and substantially outperforms (a 2-3 fold increase in coverage at low error rates popular structure comparison methods and a leading function prediction method. We benchmark FLORA on a large data set of enzyme superfamilies from all three major protein classes (alpha, beta, alphabeta and demonstrate the functional relevance of the motifs it identifies. We also provide novel predictions of enzymatic activity for a large number of structures solved by the Protein Structure Initiative. Overall, we show that FLORA is able to effectively detect functionally similar protein domain structures by purely using patterns of structural conservation of all residues.

  14. Predicted impacts of climate change on malaria transmission in West Africa

    Science.gov (United States)

    Yamana, T. K.; Eltahir, E. A. B.

    2014-12-01

    Increases in temperature and changes in precipitation due to climate change are expected to alter the spatial distribution of malaria transmission. This is especially true in West Africa, where malaria prevalence follows the current north-south gradients in temperature and precipitation. We assess the skill of GCMs at simulating past and present climate in West Africa in order to select the most credible climate predictions for the periods 2030-2060 and 2070-2100. We then use the Hydrology, Entomology and Malaria Transmission Simulator (HYDREMATS), a mechanistic model of malaria transmission, to translate the predicted changes in climate into predicted changes availability of mosquito breeding sites, mosquito populations, and malaria prevalence. We investigate the role of acquired immunity in determining a population's response to changes in exposure to the malaria parasite.

  15. Modeling Spatial Recharge in the Arid Southern Okanagan Basin and Impacts of Future Predicted Climate Change

    Science.gov (United States)

    Allen, D. M.; Toews, M. W.

    2007-12-01

    Groundwater systems in arid regions will be particularly sensitive to climate change owing to the strong dependence of evapotranspiration rates on temperature, and potential shifts in the precipitation amounts and timing. In this study, future predicted climate change from three GCMs (CGCM1 GHG+A, CGCM3.1 A2, and HadCM3 A2) are used to evaluate the sensitivity of recharge in the Oliver region of the Okanagan Valley, south- central British Columbia, where annual precipitation is approximately 300~mm. Temperature data were downscaled using Statistical Downscaling Model (SDSM), while precipitation and solar radiation changes were estimated directly from the GCM data. Results for the region suggest that temperature will increase up to 4°C by the end of the century. Precipitation is expected to decrease in the spring, and increase in the fall. Solar radiation may decrease in the late summer. Shifts in climate, from present to future-predicted, were applied to the LARS-WG stochastic weather generator to generate daily stochastic weather series. Recharge was modeled spatially using output from the HELP hydrologic model applied to one-dimensional soil columns. An extensive valley-bottom soil database was used to determine both the spatial variation and vertical assemblage of soil horizons in the Oliver region. Soil hydraulic parameters were estimated from soil descriptions using pedotransfer functions through the ROSETTA program. Leaf area index (LAI) was estimated from ground-truthed Landsat 5 TM imagery, and surface slope was estimated from a digital elevation model. Irrigation application rates were modified for each climate scenario based on estimates of seasonal crop water demand. Daily irrigation was added to precipitation in irrigation districts using proportions of crop types along with daily climate and evapotranspiration data from LARS-WG. The two dominant crop classes are orchard (including peaches, cherries and apples) and vineyards (grapes). Recharge in

  16. Prediction of postoperative pulmonary function using 99mTc-MAA perfusion lung SPECT

    International Nuclear Information System (INIS)

    In order to predict postoperative pulmonary function, 99mTc-MAA perfusion lung SPECT and spirometry were performed preoperatively in 52 patients with resectable primary lung cancer; 44 underwent lobectomy, eight pneumonectomy. Local pulmonary function (called local effective volume) was evaluated according to the degree of radionuclide distribution of each voxel in the SPECT images. The total effective volume was defined as the sum of the local effective volume, and the residual effective volume was the total effective volume excluding loss after operation. Predicted pulmonary function (VC and FEV 1.0) was calculated by the following formula: Predicted value=preoperative value x percent of the residual effective volume. Postoperative pulmonary function was predicted in the same patients by means of 99mTc-MAA perfusion lung planar scintigraphy and X-ray CT. The patients were reinvestigated with spirometry at one and four months after surgery, and the values were compared with the predicted values. The correlations between the predicted values using SPECT and measured postoperative pulmonary function were highly significant (VC: r=0.867, FEV1.0: r=0.864 one month after operation; VC: r=0.860, FEV1.0: r=0.907 4 months after operation). The predicted values calculated using SPECT were accurate compared with the predicted values calculated using planar scintigraphy or X-ray CT. The patients with predicted FEV1.0 of less than 0.8 liter required home oxygen therapy. This method is valuable for the prediction of postoperative pulmonary function before the surgical procedure. (author)

  17. Performance Improvements of a Permanent Magnet Synchronous Machine via Functional Model Predictive Control

    OpenAIRE

    A. A. Hassan; Ahmed M. Kassem

    2012-01-01

    This paper investigates the application of the model predictive control (MPC) approach to control the speed of a permanent magnet synchronous motor (PMSM) drive system. The MPC is used to calculate the optimal control actions including system constraints. To alleviate computational effort and to reduce numerical problems, particularly in large prediction horizon, an exponentially weighted functional model predictive control (FMPC) is employed. In order to validate the effectiveness of the pro...

  18. Comparison of Per Cent Predicted and Percentile Values for Pulmonary Function Test Interpretation

    OpenAIRE

    Smita Pakhale; Zoheir Bshouty; Marras, Theodore K

    2009-01-01

    BACKGROUND: Pulmonary function tests (PFTs) are commonly interpreted as a fraction of predicted normal values, with an abnormal test often defined as less than 80% or greater than 120% of the predicted value. However, recommendations of the American Thoracic Society/European Respiratory Society suggest using a percentile-based approach to define an abnormal test (less than the fifth or greater than the 95th percentiles).OBJECTIVE: To compare PFT values obtained by the per cent predicted metho...

  19. Climate change and plant distribution: local models predict high-elevation persistence

    DEFF Research Database (Denmark)

    Randin, Christophe F.; Engler, Robin; Normand, Signe;

    2009-01-01

    of habitat loss have been predicted, with associated risk of species extinction. Few coordinated across-scale comparisons have been made using data of different resolutions and geographic extents. Here, we assess whether climate change-induced habitat losses predicted at the European scale (10 × 10' grid...... in the area. Proportion of habitat loss depends on climate change scenario and study area. We find good agreement between the mismatch in predictions between scales and the fine-grain elevation range within 10 × 10' cells. The greatest prediction discrepancy for alpine species occurs in the area...... with the largest nival zone. Our results suggest elevation range as the main driver for the observed prediction discrepancies. Local-scale projections may better reflect the possibility for species to track their climatic requirement toward higher elevations....

  20. Medium- and Long-term Prediction of LOD Change with the Leap-step Autoregressive Model

    Science.gov (United States)

    Liu, Q. B.; Wang, Q. J.; Lei, M. F.

    2015-09-01

    It is known that the accuracies of medium- and long-term prediction of changes of length of day (LOD) based on the combined least-square and autoregressive (LS+AR) decrease gradually. The leap-step autoregressive (LSAR) model is more accurate and stable in medium- and long-term prediction, therefore it is used to forecast the LOD changes in this work. Then the LOD series from EOP 08 C04 provided by IERS (International Earth Rotation and Reference Systems Service) is used to compare the effectiveness of the LSAR and traditional AR methods. The predicted series resulted from the two models show that the prediction accuracy with the LSAR model is better than that from AR model in medium- and long-term prediction.

  1. Machine learning classification of resting state functional connectivity predicts smoking status

    Directory of Open Access Journals (Sweden)

    Vani ePariyadath

    2014-06-01

    Full Text Available Machine learning-based approaches are now able to examine functional magnetic resonance imaging data in a multivariate manner and extract features predictive of group membership. We applied support vector machine-based classification to resting state functional connectivity data from nicotine-dependent smokers and healthy controls to identify brain-based features predictive of nicotine dependence. By employing a network-centered approach, we observed that within-network functional connectivity measures offered maximal information for predicting smoking status, as opposed to between-network connectivity, or the representativeness of each individual node with respect to its parent network. Further, our analysis suggests that connectivity measures within the executive control and frontoparietal networks are particularly informative in predicting smoking status. Our findings suggest that machine learning-based approaches to classifying resting state functional connectivity data offer a valuable alternative technique to understanding large-scale differences in addiction-related neurobiology.

  2. Effect of land use change on soil properties and functions

    Science.gov (United States)

    Tonutare, Tonu; Kõlli, Raimo; Köster, Tiina; Rannik, Kaire; Szajdak, Lech; Shanskiy, Merrit

    2014-05-01

    For good base of sustainable land management and ecologically sound protection of soils are researches on soil properties and functioning. Ecosystem approach to soil properties and functioning is equally important in both natural and cultivated land use conditions. Comparative analysis of natural and agro-ecosystems formed on similar soil types enables to elucidate principal changes caused by land use change (LUC) and to elaborate the best land use practices for local pedo-ecological conditions. Taken for actual analysis mineral soils' catena - rendzina → brown soils → pseudopodzolic soils → gley-podzols - represent ca 1/3 of total area of Estonian normal mineral soils. All soils of this catena differ substantially each from other by calcareousness, acidity, nutrition conditions, fabric and humus cover type. This catena (representative to Estonian pedo-ecological conditions) starts with drought-prone calcareous soils. Brown (distributed in northern and central Estonia) and pseudopodzolic soils (in southern Estonia) are the most broadly acknowledged for agricultural use medium-textured high-quality automorphic soils. Dispersedly distributed gley-podzols are permanently wet and strongly acid, low-productivity sandy soils. In presentation four complex functions of soils are treated: (1) being a suitable soil environment for plant cover productivity (expressed by annual increment, Mg ha-1 yr-1); (2) forming adequate conditions for decomposition, transformation and conversion of fresh falling litter (characterized by humus cover type); (3) deposition of humus, individual organic compounds, plant nutrition elements, air and water, and (4) forming (bio)chemically variegated active space for soil type specific edaphon. Capacity of soil cover as depositor (3) depends on it thickness, texture, calcareousness and moisture conditions. Biological activity of soil (4) is determined by fresh organic matter influx, quality and quantity of biochemical substances and humus

  3. Fusion prediction based on the attribute clustering net-work and the radial basis function

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A fusion prediction method is introduced on the basis of attribute clustering network and radial basis functions. An algorithm of quasi-self organization for developing the model for the fusion prediction is introduced. Some simulation results for chaotic time series are presented to show the performance of the method.

  4. Nurses' Assessment of Rehabilitation Potential and Prediction of Functional Status at Discharge from Inpatient Rehabilitation

    Science.gov (United States)

    Myers, Jamie S.; Grigsby, Jim; Teel, Cynthia S.; Kramer, Andrew M.

    2009-01-01

    The goals of this study were to evaluate the accuracy of nurses' predictions of rehabilitation potential in older adults admitted to inpatient rehabilitation facilities and to ascertain whether the addition of a measure of executive cognitive function would enhance predictive accuracy. Secondary analysis was performed on prospective data collected…

  5. Comparison of statistical and clinical predictions of functional outcome after ischemic stroke.

    Directory of Open Access Journals (Sweden)

    Douglas D Thompson

    Full Text Available To determine whether the predictions of functional outcome after ischemic stroke made at the bedside using a doctor's clinical experience were more or less accurate than the predictions made by clinical prediction models (CPMs.A prospective cohort study of nine hundred and thirty one ischemic stroke patients recruited consecutively at the outpatient, inpatient and emergency departments of the Western General Hospital, Edinburgh between 2002 and 2005. Doctors made informal predictions of six month functional outcome on the Oxford Handicap Scale (OHS. Patients were followed up at six months with a validated postal questionnaire. For each patient we calculated the absolute predicted risk of death or dependence (OHS≥3 using five previously described CPMs. The specificity of a doctor's informal predictions of OHS≥3 at six months was good 0.96 (95% CI: 0.94 to 0.97 and similar to CPMs (range 0.94 to 0.96; however the sensitivity of both informal clinical predictions 0.44 (95% CI: 0.39 to 0.49 and clinical prediction models (range 0.38 to 0.45 was poor. The prediction of the level of disability after stroke was similar for informal clinical predictions (ordinal c-statistic 0.74 with 95% CI 0.72 to 0.76 and CPMs (range 0.69 to 0.75. No patient or clinician characteristic affected the accuracy of informal predictions, though predictions were more accurate in outpatients.CPMs are at least as good as informal clinical predictions in discriminating between good and bad functional outcome after ischemic stroke. The place of these models in clinical practice has yet to be determined.

  6. Effects of prenatal alcohol exposure on the development of white matter volume and change in executive function

    OpenAIRE

    P. Gautam; S.C. Nuñez; Narr, K.L.; E.C. Kan; Sowell, E.R.

    2014-01-01

    Prenatal alcohol exposure can cause a wide range of deficits in executive function that persist throughout life, but little is known about how changes in brain structure relate to cognition in affected individuals. In the current study, we predicted that the rate of white matter volumetric development would be atypical in children with fetal alcohol spectrum disorders (FASD) when compared to typically developing children, and that the rate of change in cognitive function would relate to diffe...

  7. Spatially distributed flame transfer functions for predicting combustion dynamics in lean premixed gas turbine combustors

    Energy Technology Data Exchange (ETDEWEB)

    Kim, K.T.; Lee, J.G.; Quay, B.D.; Santavicca, D.A. [Center for Advanced Power Generation, Department of Mechanical and Nuclear Engineering, Pennsylvania State University, University Park, PA (United States)

    2010-09-15

    The present paper describes a methodology to improve the accuracy of prediction of the eigenfrequencies and growth rates of self-induced instabilities and demonstrates its application to a laboratory-scale, swirl-stabilized, lean-premixed, gas turbine combustor. The influence of the spatial heat release distribution is accounted for using local flame transfer function (FTF) measurements. The two-microphone technique and CH{sup *} chemiluminescence intensity measurements are used to determine the input (inlet velocity perturbation) and the output functions (heat release oscillation), respectively, for the local flame transfer functions. The experimentally determined local flame transfer functions are superposed using the flame transfer function superposition principle, and the result is incorporated into an analytic thermoacoustic model, in order to predict the linear stability characteristics of a given system. Results show that when the flame length is not acoustically compact the model prediction calculated using the local flame transfer functions is better than the prediction made using the global flame transfer function. In the case of a flame in the compact flame regime, accurate predictions of eigenfrequencies and growth rates can be obtained using the global flame transfer function. It was also found that the general response characteristics of the local FTF (gain and phase) are qualitatively the same as those of the global FTF. (author)

  8. Probabilistic methods for predicting protein functions in protein-protein interaction networks

    OpenAIRE

    Best, Christoph; Zimmer, Ralf; Apostolakis, Joannis

    2005-01-01

    We discuss probabilistic methods for predicting protein functions from protein-protein interaction networks. Previous work based on Markov Randon Fields is extended and compared to a general machine-learning theoretic approach. Using actual protein interaction networks for yeast from the MIPS database and GO-SLIM function assignments, we compare the predictions of the different probabilistic methods and of a standard support vector machine. It turns out that, with the currently available netw...

  9. Is Personality Fixed? Personality Changes as Much as "Variable" Economic Factors and More Strongly Predicts Changes to Life Satisfaction

    Science.gov (United States)

    Boyce, Christopher J.; Wood, Alex M.; Powdthavee, Nattavudh

    2013-01-01

    Personality is the strongest and most consistent cross-sectional predictor of high subjective well-being. Less predictive economic factors, such as higher income or improved job status, are often the focus of applied subjective well-being research due to a perception that they can change whereas personality cannot. As such there has been limited…

  10. Osteoprotegerin Levels Change During STEMI and Reflect Cardiac Function

    DEFF Research Database (Denmark)

    Lindberg, Søren; Jensen, Jan S; Hoffmann, Søren; Iversen, Allan Z; Pedersen, Sune H; Mogelvang, Rasmus; Galatius, Søren; Flyvbjerg, Allan; Bjerre, Mette

    2014-01-01

    BACKGROUND: High levels of circulating osteoprotegerin (OPG) predicts long-term outcome in patients with ST-elevation myocardial infarction (STEMI), possibly because of increased vascular inflammation resulting in myocardial damage. In the present study we aimed at elucidating the dynamic progress...... of OPG levels during STEMI treated with percutaneous coronary intervention (PCI) and additionally, the effect of OPG levels on cardiac function. METHODS: We prospectively included 42 patients with STEMI treated with primary PCI. Four consecutive blood samples were obtained before and after PCI...... treatment. Plasma OPG levels were determined using an in-house immunoassay. Cardiac function was increased according to echocardiography, estimating left ventricular ejection fraction (LVEF) 1-3 days after STEMI. RESULTS: During STEMI, OPG levels peaked after PCI and then decreased; mean concentrations (95...

  11. A new statistical tool to predict phenology under climate change scenarios

    NARCIS (Netherlands)

    Gienapp, P.; Hemerik, L.; Visser, M.E.

    2005-01-01

    Climate change will likely affect the phenology of trophic levels differently and thereby disrupt the phenological synchrony between predators and prey. To predict this disruption of the synchrony under different climate change scenarios, good descriptive models for the phenology of the different sp

  12. The predictive skill of species distribution models for plankton in a changing climate

    DEFF Research Database (Denmark)

    Brun, Philipp Georg; Kiørboe, Thomas; Licandro, Priscilla;

    2016-01-01

    Statistical species distribution models (SDMs) are increasingly used to project spatial relocations of marine taxa under future climate change scenarios. However, tests of their predictive skill in the real-world are rare. Here, we use data from the Continuous Plankton Recorder program, one of the...... null models, is essential to assess the robustness of projections of marine planktonic species under climate change...

  13. Changes in Biston robustum and Camellia japonica distributions, according to climate change predictions in South Korea

    OpenAIRE

    Tae Guen Kim; Yong-Gu Han; Jong Chul Jeong; Youngjin Kim; Ohseok Kwon; Youngho Cho

    2015-01-01

    We investigated the current and potential spatial distributions and habitable areas of Biston robustum and Camellia japonica in South Korea in order to provide useful data for the conservation of C. japonica and minimize the damage caused by B. robustum. It was predicted that, by 2070, although B. robustum would be widely distributed throughout the Korean Peninsula, except for the western and eastern coa...

  14. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps

    OpenAIRE

    Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian P.; Kasif, Simon; Roberts, Richard J.; Steffen, Martin

    2015-01-01

    The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene functi...

  15. A new approach to assess and predict the functional roles of proteins across all known structures.

    Science.gov (United States)

    Julfayev, Elchin S; McLaughlin, Ryan J; Tao, Yi-Ping; McLaughlin, William A

    2011-03-01

    The three dimensional atomic structures of proteins provide information regarding their function; and codified relationships between structure and function enable the assessment of function from structure. In the current study, a new data mining tool was implemented that checks current gene ontology (GO) annotations and predicts new ones across all the protein structures available in the Protein Data Bank (PDB). The tool overcomes some of the challenges of utilizing large amounts of protein annotation and measurement information to form correspondences between protein structure and function. Protein attributes were extracted from the Structural Biology Knowledgebase and open source biological databases. Based on the presence or absence of a given set of attributes, a given protein's functional annotations were inferred. The results show that attributes derived from the three dimensional structures of proteins enhanced predictions over that using attributes only derived from primary amino acid sequence. Some predictions reflected known but not completely documented GO annotations. For example, predictions for the GO term for copper ion binding reflected used information a copper ion was known to interact with the protein based on information in a ligand interaction database. Other predictions were novel and require further experimental validation. These include predictions for proteins labeled as unknown function in the PDB. Two examples are a role in the regulation of transcription for the protein AF1396 from Archaeoglobus fulgidus and a role in RNA metabolism for the protein psuG from Thermotoga maritima. PMID:21445639

  16. PRISM offers a comprehensive genomic approach to transcription factor function prediction

    KAUST Repository

    Wenger, A. M.

    2013-02-04

    The human genome encodes 1500-2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant target genes, that most binding is distal, and that binding is context specific. Because of the effort and cost involved, ChIP-seq is seldom used in search of novel TF function. Such exploration is instead done using expression perturbation and genetic screens. Here we propose a comprehensive computational framework for transcription factor function prediction. We curate 332 high-quality nonredundant TF binding motifs that represent all major DNA binding domains, and improve cross-species conserved binding site prediction to obtain 3.3 million conserved, mostly distal, binding site predictions. We combine these with 2.4 million facts about all human and mouse gene functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh null are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach obtains 2543 TF function predictions in a large variety of contexts, at a false discovery rate of 16%. The predictions are highly enriched for validated TF roles, and 45 of 67 (67%) tested binding site regions in five different contexts act as enhancers in functionally matched cells.

  17. Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates.

    Directory of Open Access Journals (Sweden)

    Manuel Irimia

    Full Text Available Alternative splicing is tightly regulated in a spatio-temporal and quantitative manner. This regulation is achieved by a complex interplay between spliceosomal (trans factors that bind to different sequence (cis elements. cis-elements reside in both introns and exons and may either enhance or silence splicing. Differential combinations of cis-elements allows for a huge diversity of overall splicing signals, together comprising a complex 'splicing code'. Many cis-elements have been identified, and their effects on exon inclusion levels demonstrated in reporter systems. However, the impact of interspecific differences in these elements on the evolution of alternative splicing levels has not yet been investigated at genomic level. Here we study the effect of interspecific differences in predicted exonic splicing regulators (ESRs on exon inclusion levels in human and chimpanzee. For this purpose, we compiled and studied comprehensive datasets of predicted ESRs, identified by several computational and experimental approaches, as well as microarray data for changes in alternative splicing levels between human and chimpanzee. Surprisingly, we found no association between changes in predicted ESRs and changes in alternative splicing levels. This observation holds across different ESR exon positions, exon lengths, and 5' splice site strengths. We suggest that this lack of association is mainly due to the great importance of context for ESR functionality: many ESR-like motifs in primates may have little or no effect on splicing, and thus interspecific changes at short-time scales may primarily occur in these effectively neutral ESRs. These results underscore the difficulties of using current computational ESR prediction algorithms to identify truly functionally important motifs, and provide a cautionary tale for studies of the effect of SNPs on splicing in human disease.

  18. Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates.

    Science.gov (United States)

    Irimia, Manuel; Rukov, Jakob Lewin; Roy, Scott William

    2009-01-01

    Alternative splicing is tightly regulated in a spatio-temporal and quantitative manner. This regulation is achieved by a complex interplay between spliceosomal (trans) factors that bind to different sequence (cis) elements. cis-elements reside in both introns and exons and may either enhance or silence splicing. Differential combinations of cis-elements allows for a huge diversity of overall splicing signals, together comprising a complex 'splicing code'. Many cis-elements have been identified, and their effects on exon inclusion levels demonstrated in reporter systems. However, the impact of interspecific differences in these elements on the evolution of alternative splicing levels has not yet been investigated at genomic level. Here we study the effect of interspecific differences in predicted exonic splicing regulators (ESRs) on exon inclusion levels in human and chimpanzee. For this purpose, we compiled and studied comprehensive datasets of predicted ESRs, identified by several computational and experimental approaches, as well as microarray data for changes in alternative splicing levels between human and chimpanzee. Surprisingly, we found no association between changes in predicted ESRs and changes in alternative splicing levels. This observation holds across different ESR exon positions, exon lengths, and 5' splice site strengths. We suggest that this lack of association is mainly due to the great importance of context for ESR functionality: many ESR-like motifs in primates may have little or no effect on splicing, and thus interspecific changes at short-time scales may primarily occur in these effectively neutral ESRs. These results underscore the difficulties of using current computational ESR prediction algorithms to identify truly functionally important motifs, and provide a cautionary tale for studies of the effect of SNPs on splicing in human disease. PMID:19495418

  19. Changes in family functions in patients with secondary premature ejaculation

    OpenAIRE

    Mustafa Arı; Yasin Bez; Yusuf Kaya; Yüksel Kıvrak

    2011-01-01

    We aimed to inverstigate changes in family functions in patients with premature ejaculation.Materials and methods: In the present study, study group were randomly selected from Mustafa Kemal University Medical School Research and Training Hospital Urology Department outpatients clinic. Control group were selected among healthy volunteers. Totally 30 patients were included in the PE group and 30 healthy volunteers were included in the control group. Subjects were examined by the same psychiatr...

  20. Visual functional changes during acute elevation of intraocular pressure

    Institute of Scientific and Technical Information of China (English)

    Tian-De SHOU

    2006-01-01

    Glaucoma is closely related to elevation of intraocular pressure (IOP). Many studies have done on the effect of chronic elevation of IOP on the retina and optic nerve, but less attention was paid to the effect of acute elevated IOP. Here we briefly review experimental studies on functional changes of the visual system from the retina to the visual cortex under acute elevated IOP condition, which is similar to that of acute primary angle-closure glaucoma.

  1. Functional and histopathologic changes in the liver during sepsis.

    Science.gov (United States)

    Caruana, J A; Montes, M; Camara, D S; Ummer, A; Potmesil, S H; Gage, A A

    1982-05-01

    Although liver failure from sepsis is a frequent occurrence in serious ill, hospitalized patients, little information is available on the histologic changes of the liver. We examined the histopathology of the liver of 19 patients who died of clinical sepsis and attempted to relate certain features of the illness or treatment to the observed histopathologic changes. The most striking finding was midzonal and peripheral necrosis of a moderate to marked degree in 11 of 19 patients. Other important changes were acute inflammation and cholestasis. The severity of hepatocellular necrosis did not appear to be influenced by the premortem circulating pathogen, by the nutritional support administered or by the arterial blood pressure. It is suggested that hepatocellular necrosis is characteristic of sepsis and may be caused by loss of specific factors which normally maintain liver function and structure. PMID:6803371

  2. Change in Depression Symptomatology and Cognitive Function in Twins

    DEFF Research Database (Denmark)

    Petersen, Inge; McGue, Matt; Tan, Qihua;

    2016-01-01

    of correlated traits. Here, we have applied twin modeling approaches to shed light on the genetic correlation between both level and change of depression symptomatology and cognitive functioning, and to further explore the bidirectionality of any such correlation using assessments of both phenotypes at two......A complex interrelation exists between change in depression symptomatology and cognitive decline. Studies indicate either that depression is a direct risk factor for cognitive change over time, or vice versa. Longitudinal twin studies provide the possibility to unravel cause and effect......-sectional heritability estimates of approximately 60% for general cognitive abilities and 30% for affective depressive symptoms. There was a considerable decline in the mean cognitive performance over 10 years, whereas the mean affective depression symptoms score was stable and with no genetic contribution to any...

  3. Predicting changes of body weight, body fat, energy expenditure and metabolic fuel selection in C57BL/6 mice.

    Directory of Open Access Journals (Sweden)

    Juen Guo

    Full Text Available The mouse is an important model organism for investigating the molecular mechanisms of body weight regulation, but a quantitative understanding of mouse energy metabolism remains lacking. Therefore, we created a mathematical model of mouse energy metabolism to predict dynamic changes of body weight, body fat, energy expenditure, and metabolic fuel selection. Based on the principle of energy balance, we constructed ordinary differential equations representing the dynamics of body fat mass (FM and fat-free mass (FFM as a function of dietary intake and energy expenditure (EE. The EE model included the cost of tissue deposition, physical activity, diet-induced thermogenesis, and the influence of FM and FFM on metabolic rate. The model was calibrated using previously published data and validated by comparing its predictions to measurements in five groups of male C57/BL6 mice (N = 30 provided ad libitum access to either chow or high fat diets for varying time periods. The mathematical model accurately predicted the observed body weight and FM changes. Physical activity was predicted to decrease immediately upon switching from the chow to the high fat diet and the model coefficients relating EE to FM and FFM agreed with previous independent estimates. Metabolic fuel selection was predicted to depend on a complex interplay between diet composition, the degree of energy imbalance, and body composition. This is the first validated mathematical model of mouse energy metabolism and it provides a quantitative framework for investigating energy balance relationships in mouse models of obesity and diabetes.

  4. A combined approach for genome wide protein function annotation/prediction

    DEFF Research Database (Denmark)

    Benso, Alfredo; Di Carlo, Stefano; Ur Rehman, Hafeez;

    2013-01-01

    predictive power of our model we also compute and integrate term specific relationships among functional terms based on Gene Ontology (GO). RESULTS: We tested our method on Saccharomyces Cerevisiae and Homo sapiens species proteins. The aggregation of different structural and functional evidence with GO...... relationships outperforms, in terms of precision and accuracy of prediction than the other methods reported in literature. The predicted precision and accuracy is 100% for more than half of the input set for both species; overall, we obtained 85.38% precision and 81.95% accuracy for Homo sapiens and 79...

  5. Antireflux surgery does not change ongoing renal functional deterioration.

    Science.gov (United States)

    Arslansoyu Çamlar, Seçil; Çağlar, Sevinç; Soylu, Alper; Türkmen, Mehmet Atilla; Kavukçu, Salih

    2016-04-01

    Aim Treatment modalities of vesicoureteral reflux (VUR) consist of antimicrobial prophylaxis and antireflux surgery. In this study, we aimed to determine if antireflux surgery changes the course of renal functional deterioration in children with VUR and urinary tract infections (UTI). Methods Medical files of patients with VUR diagnosed during evaluation for UTI were evaluated retrospectively for gender, age, follow-up period, and renal ultrasonography (US) and serial 99mTc-dimercaptosuccinic acid (99mTc-DMSA) scintigraphy findings. Estimated glomerular filtration rate and urinary protein levels were determined at the initial and last visits, and before the operation in children who had antireflux surgery. The patients were divided into two groups as solely medically treated (Group 1) and both medically and surgically treated (Group 2). Group 2 was further divided as those with stable renal function (Group 2a) and with progressive renal injury (Group 2b). Results There were 140 patients (77 female; mean age 51.6 ± 51.9 months). Group 1 and Group 2 included 82 and 58 patients, respectively. In Group 2, the number of patients with the abnormal US, DMSA scintigraphy, and renal function was higher than in Group 1. Recurrent UTI rate was similar, but progressive scarring was more prominent in the antireflux surgery group. In Group 2, 31 patients had a stable renal function (Group 2a) while 27 had progressive deterioration of renal functions (Group 2b). These subgroups were not different with respect to the rate of high-grade VUR, the presence of a renal scar in DMSA, and UTI recurrence. However, the bilateral renal scar was more common in Group 2b. Conclusion Antireflux surgery does not change the course of ongoing renal injury and renal functional deterioration. PMID:26786885

  6. An evaluation of utility of residual liver function prediction using dynamic SPECT

    International Nuclear Information System (INIS)

    A method for evaluating and predicting residual liver function was devised for dynamic single photon emission computed tomography (SPECT). The ratio of residual volume to total effective liver volume, K value and predictive index using dynamic SPECT were compared with respective values using dynamic planar scintigraphy. The coefficients of correlation were 0.86 (the ratio), 0.91 (K value) and 0.88 (predictive index). The predictive index, measured by dynamic SPECT, was as useful as by dynamic planar scintigraphy. In addition, the resecting line using SPECT was more accurate than using planar scintigraphy. Dynamic SPECT was more useful than dynamic planar scintigraphy. (author)

  7. Determination of intensity functions for predicting subsidence from coal mining, potash mining, and groundwater withdrawal using the influence function technique

    Energy Technology Data Exchange (ETDEWEB)

    Triplett, T.; Yurchak, D. [Twin Cities Research Center, Bureau of Mines, US Dept. of the Interior, Minneapolis, MN (United States)

    1996-12-31

    This paper presents research, conducted by the Bureau of Mines, on modifying the influence function method to predict subsidence. According to theory, this technique must incorporate an intensity function to represent the relative significance of the causes of subsidence. This paper shows that the inclusion of a reasonable intensity function increases the accuracy of the technique, then presents the required functions for case studies of longwall coal mining subsidence in Illinois, USA, potash mining subsidence in new Mexico, USA, and subsidence produced by ground water withdrawal in California, USA. Finally, the paper discusses a method to predict the resultant strain from a simply measured site constant and ground curvatures calculated by the technique. (orig.)

  8. Optical Spectroscopy Approach for the Predictive Assessment of Kidney Functional Recovery Following Ischemic Injury

    Energy Technology Data Exchange (ETDEWEB)

    Raman, R N; Pivetti, C D; Rubenchik, A M; Matthews, D L; Troppmann, C; Demos, S G

    2010-02-11

    Tissue that has undergone significant yet unknown amount of ischemic injury is frequently encountered in organ transplantation and trauma clinics. With no reliable real-time method of assessing the degree of injury incurred in tissue, surgeons generally rely on visual observation which is subjective. In this work, we investigate the use of optical spectroscopy methods as a potentially more reliable approach. Previous work by various groups was strongly suggestive that tissue autofluorescence from NADH obtained under UV excitation is sensitive to metabolic response changes. To test and expand upon this concept, we monitored autofluorescence and light scattering intensities of injured vs. uninjured rat kidneys via multimodal imaging under 355 nm, 325 nm, and 266 nm excitation as well as scattering under 500 nm illumination. 355 nm excitation was used to probe mainly NADH, a metabolite, while 266 nm excitation was used to probe mainly tryptophan to correct for non-metabolic signal artifacts. The ratio of autofluorescence intensities derived under these two excitation wavelengths was calculated and its temporal profile was fit to a relaxation model. Time constants were extracted, and longer time constants were associated with kidney dysfunction. Analysis of both the autofluorescence and light scattering images suggests that changes in microstructure tissue morphology, blood absorption spectral characteristics, and pH contribute to the behavior of the observed signal which may be used to obtain tissue functional information and offer predictive capability.

  9. Enhancing protein function prediction with taxonomic constraints--The Argot2.5 web server.

    Science.gov (United States)

    Lavezzo, Enrico; Falda, Marco; Fontana, Paolo; Bianco, Luca; Toppo, Stefano

    2016-01-15

    Argot2.5 (Annotation Retrieval of Gene Ontology Terms) is a web server designed to predict protein function. It is an updated version of the previous Argot2 enriched with new features in order to enhance its usability and its overall performance. The algorithmic strategy exploits the grouping of Gene Ontology terms by means of semantic similarity to infer protein function. The tool has been challenged over two independent benchmarks and compared to Argot2, PANNZER, and a baseline method relying on BLAST, proving to obtain a better performance thanks to the contribution of some key interventions in critical steps of the working pipeline. The most effective changes regard: (a) the selection of the input data from sequence similarity searches performed against a clustered version of UniProt databank and a remodeling of the weights given to Pfam hits, (b) the application of taxonomic constraints to filter out annotations that cannot be applied to proteins belonging to the species under investigation. The taxonomic rules are derived from our in-house developed tool, FunTaxIS, that extends those provided by the Gene Ontology consortium. The web server is free for academic users and is available online at http://www.medcomp.medicina.unipd.it/Argot2-5/. PMID:26318087

  10. Moderate land use changes plant functional composition without loss of functional diversity in India's Western Ghats.

    Science.gov (United States)

    Mandle, Lisa; Ticktin, Tamara

    2015-09-01

    The fields of ecology and conservation science increasingly recognize the importance of managing for functional composition and functional diversity to maintain critical ecosystem processes and services. However, little is known about the degree to which widespread but moderate forms of land use that maintain overall vegetation structure are compatible with the conservation of functional diversity. We assessed differences in plani functional composition and functional diversity across savanna woodlands in the Western Ghats, India, managed with varying degrees of biomass extraction, livestock grazing, and ground fire. Across the gradient of moderate land uses, we found shifts in functional composition but no overall decline in functional diversity with land, use intensification. Biomass extraction was associated with changes in dispersal mode, reduced seed mass, and lower overstory functional diversity. Livestock grazing was associated with shorter overstory species, reduced seed mass, and increased understory functional diversity. Nonnative invasive species contributed to shifts in understory functional composition with livestock grazing and increased functional diversity with more intensive land use. Our study highlights both the utility and some limitations of assessing conservation value with functional diversity. These results suggest that moderate-intensity local land use can be compatible with maintenance of functional diversity in savanna woodlands of the Western Ghats, and further efforts to maximize this compatibility would benefit conservation in South India's extensive human-managed landscapes. However, using functional diversity as the sole metric by which to gauge conservation value can mask threats from invasive species and loss of diversity within categories of biotic dispersal. Therefore, functional diversity metrics are likely to provide a valuable complement to, but not replacement for, other management targets such as species composition. PMID

  11. Age-related changes in predictive capacity versus internal model adaptability: electrophysiological evidence that individual differences outweigh effects of age

    Directory of Open Access Journals (Sweden)

    Ina eBornkessel-Schlesewsky

    2015-11-01

    Full Text Available Hierarchical predictive coding has been identified as a possible unifying principle of brain function, and recent work in cognitive neuroscience has examined how it may be affected by age–related changes. Using language comprehension as a test case, the present study aimed to dissociate age-related changes in prediction generation versus internal model adaptation following a prediction error. Event-related brain potentials (ERPs were measured in a group of older adults (60–81 years; n=40 as they read sentences of the form The opposite of black is white/yellow/nice. Replicating previous work in young adults, results showed a target-related P300 for the expected antonym (white; an effect assumed to reflect a prediction match, and a graded N400 effect for the two incongruous conditions (i.e. a larger N400 amplitude for the incongruous continuation not related to the expected antonym, nice, versus the incongruous associated condition, yellow. These effects were followed by a late positivity, again with a larger amplitude in the incongruous non-associated versus incongruous associated condition. Analyses using linear mixed-effects models showed that the target-related P300 effect and the N400 effect for the incongruous non-associated condition were both modulated by age, thus suggesting that age-related changes affect both prediction generation and model adaptation. However, effects of age were outweighed by the interindividual variability of ERP responses, as reflected in the high proportion of variance captured by the inclusion of by-condition random slopes for participants and items. We thus argue that – at both a neurophysiological and a functional level – the notion of general differences between language processing in young and older adults may only be of limited use, and that future research should seek to better understand the causes of interindividual variability in the ERP responses of older adults and its relation to cognitive

  12. Gene ontology-based protein function prediction by using sequence composition information.

    Science.gov (United States)

    Dong, Qiwen; Zhou, Shuigeng; Deng, Lei; Guan, Jihong

    2010-06-01

    The prediction of protein function is a difficult and important problem in computational biology. In this study, an efficient method is presented to predict protein function with sequence composition information. Four kinds of basic building blocks of protein sequences are investigated, including N-grams, binary profiles, PFAM domains and InterPro domains. The protein sequences are mapped into high-dimensional vectors by using the occurrence frequencies of each kind of building blocks. The resulting vectors are then taken as input to support vector machine to predict their function based on gene ontology. Experiments are conducted over the subset of GOA database. The experimental results show that the protein function can be predicted from primary sequence information. The method based on InterPro domains outperforms the other building blocks, and gets an overall accuracy of 0.87 and ROC score is 0.93. We also demonstrate that the use of feature extraction algorithms such as latent semantic analysis and nonnegative matrix factorization, can efficiently remove noise and improve the prediction efficiency without significantly degrading the performance. The results obtained here are helpful for the prediction of protein function by using only sequence information. PMID:19995340

  13. Impairment of executive function and attention predicts onset of affective disorder in healthy high-risk twins

    DEFF Research Database (Denmark)

    Vinberg, Maj; Miskowiak, Kamilla W; Kessing, Lars Vedel

    2013-01-01

    To investigate whether measures of cognitive function can predict onset of affective disorder in individuals at heritable risk.......To investigate whether measures of cognitive function can predict onset of affective disorder in individuals at heritable risk....

  14. Functional Task Test: 1. Sensorimotor changes Associated with Postflight Alterations in Astronaut Functional Task Performance

    Science.gov (United States)

    Bloomberg, J. J.; Arzeno, N. H.; Buxton, R. E.; Feiveson, A. H.; Kofman, I. S.; Lee, S. M. C.; Miller, C. A.; Mulavara, A. P.; Platts, S. H.; Peters, B. T.; Phillips, T.; Ploutz-Snyder, L. L.; Reschke, M. F.; Ryder, J. W.; Spiering, B. A.; Stenger, M. B.; Taylor, L. C.; Wickwire, P. J.; Wood, S. J.

    2011-01-01

    Space flight is known to cause alterations in multiple physiological systems including changes in sensorimotor, cardiovascular, and neuromuscular systems. These changes may affect a crewmember s ability to perform critical mission tasks immediately after landing on a planetary surface. The overall goal of this project is to determine the effects of space flight on functional tests that are representative of high priority exploration mission tasks and to identify the key underlying physiological factors that contribute to decrements in performance. This presentation will focus on the sensorimotor contributions to postflight functional performance.

  15. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

    Science.gov (United States)

    Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian P; Kasif, Simon; Roberts, Richard J; Steffen, Martin

    2016-01-01

    The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼ 3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue. PMID:26635392

  16. Woody plants and the prediction of climate-change impacts on bird diversity

    DEFF Research Database (Denmark)

    Kissling, W. Daniel; Field, R.; Korntheuer, H.;

    2010-01-01

    Current methods of assessing climate-induced shifts of species distributions rarely account for species interactions and usually ignore potential differences in response times of interacting taxa to climate change. Here, we used species-richness data from 1005 breeding bird and 1417 woody plant...... species in Kenya and employed model-averaged coefficients from regression models and median climatic forecasts assembled across 15 climate-change scenarios to predict bird species richness under climate change. Forecasts assuming an instantaneous response of woody plants and birds to climate change...... suggested increases in future bird species richness across most of Kenya whereas forecasts assuming strongly lagged woody plant responses to climate change indicated a reversed trend, i.e. reduced bird species richness. Uncertainties in predictions of future bird species richness were geographically...

  17. Corrosion fatigue behavior and life prediction method under changing temperature condition

    International Nuclear Information System (INIS)

    Axially strain controlled low cycle fatigue tests of a carbon steel in oxygenated high temperature water were carried out under changing temperature conditions. Two patterns of triangular wave were selected for temperature cycling. One was in-phase pattern synchronizing with strain cycling and the other was an out-of-phase pattern in which temperature was changed in anti-phase to the strain cycling. The fatigue life under changing temperature condition was in the range of the fatigue life under various constant temperature within the range of the changing temperature. The fatigue life of in-phase pattern was equivalent to that of out-of-phase pattern. The corrosion fatigue life prediction method was proposed for changing temperature condition, and was based on the assumption that the fatigue damage increased in linear proportion to increment of strain during cycling. The fatigue life predicted by this method was in good agreement with the test results

  18. Sweat gland function as a measure of radiation change

    International Nuclear Information System (INIS)

    Radiotherapy may result in dryness of the skin even when no other change can be detected. We describe a system for recording the electrical conductance of skin as a measure of sweat gland function. In 22 normal volunteers close agreement was obtained between measurements obtained from comparable sites on both sides of the chest. Measurements were subsequently made in 38 patients treated by radiotherapy to one side of the chest for tumours of the breast or lung using one of five different fractionation schedules. Simultaneous readings were obtained from both sides of the chest with the non irradiated side acting as a control. A dose response relationship was demonstrated: five patients who received the equivalent total dose of 15 Gy in 2-Gy fractions showed no change in conductance. Sixteen out of 23 who received an equivalent total dose of 42-46 Gy in 2-Gy fractions had a greater than 22% reduction in mean skin conductance compared with that of the control areas despite the skin appearing normal in the large majority. Marked changes in skin conductance were seen after higher total doses. In a prospective study 18 women receiving breast irradiation underwent weekly readings during treatment. A mean reduction of 40% in skin conductance was noted by the end of the second week of treatment prior to any clinical evidence of radiation change. Skin conductance returned to normal in 44% of patients by 6 months. In the remainder, those patients who showed the greatest reduction in skin conductance during treatment demonstrated the least recovery. Changes in sweat gland function can be detected and quantified in skin which may otherwise appear normal. Differences may so be demonstrated between areas treated using different fractionation schedules and the method may be applied to the detection during radiotherapy of unusually sensitive patient. (author)

  19. Exploiting Structural Classifications for Function Prediction: Towards a Domain Grammar for Protein Function

    OpenAIRE

    Dessailly, Benoît H.; Redfern, Oliver C.; Cuff, Alison; Orengo, Christine A.

    2009-01-01

    The ability to assign function to proteins has become a major bottleneck for comprehensively understanding cellular mechanisms at the molecular level. Here we discuss the extent to which structural domain classifications can help in deciphering the complex relationship between the functions of proteins and their sequences and structures. Structural classifications are particularly helpful in understanding the mosaic manner in which new proteins and functions emerge through evolution. This is ...

  20. Macroecological scale effects of biodiversity on ecosystem functions under environmental change.

    Science.gov (United States)

    Burley, Hugh M; Mokany, Karel; Ferrier, Simon; Laffan, Shawn W; Williams, Kristen J; Harwood, Tom D

    2016-04-01

    Conserving different spatial and temporal dimensions of biological diversity is considered necessary for maintaining ecosystem functions under predicted global change scenarios. Recent work has shifted the focus from spatially local (α-diversity) to macroecological scales (β- and γ-diversity), emphasizing links between macroecological biodiversity and ecosystem functions (MB-EF relationships). However, before the outcomes of MB-EF analyses can be useful to real-world decisions, empirical modeling needs to be developed for natural ecosystems, incorporating a broader range of data inputs, environmental change scenarios, underlying mechanisms, and predictions. We outline the key conceptual and technical challenges currently faced in developing such models and in testing and calibrating the relationships assumed in these models using data from real ecosystems. These challenges are explored in relation to two potential MB-EF mechanisms: "macroecological complementarity" and "spatiotemporal compensation." Several regions have been sufficiently well studied over space and time to robustly test these mechanisms by combining cutting-edge spatiotemporal methods with remotely sensed data, including plant community data sets in Australia, Europe, and North America. Assessing empirical MB-EF relationships at broad spatiotemporal scales will be crucial in ensuring these macroecological processes can be adequately considered in the management of biodiversity and ecosystem functions under global change. PMID:27066246

  1. Phagonaute: A web-based interface for phage synteny browsing and protein function prediction.

    Science.gov (United States)

    Delattre, Hadrien; Souiai, Oussema; Fagoonee, Khema; Guerois, Raphaël; Petit, Marie-Agnès

    2016-09-01

    Distant homology search tools are of great help to predict viral protein functions. However, due to the lack of profile databases dedicated to viruses, they can lack sensitivity. We constructed HMM profiles for more than 80,000 proteins from both phages and archaeal viruses, and performed all pairwise comparisons with HHsearch program. The whole resulting database can be explored through a user-friendly "Phagonaute" interface to help predict functions. Results are displayed together with their genetic context, to strengthen inferences based on remote homology. Beyond function prediction, this tool permits detections of co-occurrences, often indicative of proteins completing a task together, and observation of conserved patterns across large evolutionary distances. As a test, Herpes simplex virus I was added to Phagonaute, and 25% of its proteome matched to bacterial or archaeal viral protein counterparts. Phagonaute should therefore help virologists in their quest for protein functions and evolutionary relationships. PMID:27254594

  2. Executive functioning predicts reading, mathematics, and theory of mind during the elementary years.

    Science.gov (United States)

    Cantin, Rachelle H; Gnaedinger, Emily K; Gallaway, Kristin C; Hesson-McInnis, Matthew S; Hund, Alycia M

    2016-06-01

    The goal of this study was to specify how executive functioning components predict reading, mathematics, and theory of mind performance during the elementary years. A sample of 93 7- to 10-year-old children completed measures of working memory, inhibition, flexibility, reading, mathematics, and theory of mind. Path analysis revealed that all three executive functioning components (working memory, inhibition, and flexibility) mediated age differences in reading comprehension, whereas age predicted mathematics and theory of mind directly. In addition, reading mediated the influence of executive functioning components on mathematics and theory of mind, except that flexibility also predicted mathematics directly. These findings provide important details about the development of executive functioning, reading, mathematics, and theory of mind during the elementary years. PMID:26914106

  3. The evaluation of changes in functional health status in patients with abdominal complaints.

    Science.gov (United States)

    Jacobs, H M; Touw-Otten, F W; de Melker, R A

    1996-02-01

    Measuring functional status changes in various patient subgroups is important in stratifying risk, assessing disease severity, and predicting and defining clinically relevant outcomes. Data from a multi-centered study of 980 primary care patients presenting with nonspecific abdominal complaints were studied to demonstrate the importance of such an assessment procedure. Patients were prospectively followed for 6 months. Five diagnostic categories based on illness duration and seriousness were derived from the clinical course of these patients. The functional status of each patient was determined at baseline, 1 month, and 6 months using the Sickness Impact Profile (SIP). Intraclass correlation coefficients accounted for two aspects of the reliability of the SIP regarding the measurement of change over time: differences between patients which are stable over time (reproducibility) and different effects of treatment between subsets (responsiveness). A priori formulated expectations about the degree of health status change in patient subgroups were evaluated with the help of effect-size calculations. Patient impairment only partially depended on the final diagnosis and was also influenced by the presence of co-morbidity, psycho-social determinants, and other complaints. The health status change in the patient subgroups agreed with a priori formulated expectations. Standardized effect-size calculations revealed that the degree of change over time in SIP scores was in accordance with these expectations. We conclude: (a) the SIP appeared to be a reliable clinimetric instrument in detecting change over time resulting from different clinical courses, (b) clinical studies that use clinimetric instruments to assess the effects of clinical interventions must adequately control for the influence of baseline "functional status" as well as traditional demographic features such as gender and age, and (c) evaluating a priori formulated clinical expectations concerning functional

  4. On predicting future economic losses from tropical cyclones: Comparing damage functions for the Eastern USA

    Science.gov (United States)

    Geiger, Tobias; Levermann, Anders; Frieler, Katja

    2015-04-01

    Recent years have seen an intense scientific debate of what to expect from future tropical cyclone activity under climate change [1,2]. Besides the projection of cyclones' genesis points and trajectories it is the cyclone's impact on future societies that needs to be quantified. In our present work, where we focus on the Eastern USA, we start out with a comprehensive comparison of a variety of presently available and novel functional relationships that are used to link cyclones' physical properties with their damage caused on the ground. These so-called damage functions make use of high quality data sets consisting of gridded population data, exposed capital at risk, and information on the cyclone's extension and its translational and locally resolved maximum wind speed. Based on a cross-validation ansatz we train a multitude of damage functions on a large variety of data sets in order to evaluate their performance on an equally sized test sample. Although different damage analyses have been conducted in the literature [3,4,5,6], the efforts have so far primarily been focused on determining fit parameters for individual data sets. As our analysis consists of a wide range of damage functions implemented on identical data sets, we can rigorously evaluate which (type of) damage function (for which set of parameters) does best in reproducing damages and should therefore be used for future loss analysis with highest certainty. We find that the benefits of using locally resolved data input tend to be outweighed by the large uncertainties that accompany the data. More coarse and generalized data input therefore captures the diversity of cyclonic features better. Furthermore, our analysis shows that a non-linear relation between wind speed and damage outperforms the linear as well as the exponential relationship discussed in the literature. In a second step, the damage function with the highest predictive quality is implemented to predict potential future cyclone losses

  5. Prediction of solvent-induced morphological changes of polyelectrolyte diblock copolymer micelles.

    Science.gov (United States)

    Li, Nan K; Fuss, William H; Tang, Lei; Gu, Renpeng; Chilkoti, Ashutosh; Zauscher, Stefan; Yingling, Yaroslava G

    2015-11-14

    Self-assembly processes of polyelectrolyte block copolymers are ubiquitous in industrial and biological processes; understanding their physical properties can also provide insights into the design of polyelectrolyte materials with novel and tailored properties. Here, we report systematic analysis on how the ionic strength of the solvent and the length of the polyelectrolyte block affect the self-assembly and morphology of the polyelectrolyte block copolymer materials by constructing a salt-dependent morphological phase diagram using an implicit solvent ionic strength (ISIS) method for dissipative particle dynamics (DPD) simulations. This diagram permits the determination of the conditions for the morphological transition into a specific shape, namely vesicles or lamellar aggregates, wormlike/cylindrical micelles, and spherical micelles. The scaling behavior for the size of spherical micelles is predicted, in terms of radius of gyration (R(g,m)) and thickness of corona (Hcorona), as a function of solvent ionic strength (c(s)) and polyelectrolyte length (NA), which are R(g,m) ∼ c(s)(-0.06)N(A)(0.54) and Hcorona ∼ c(s)(-0.11)N(A)(0.75). The simulation results were corroborated through AFM and static light scattering measurements on the example of the self-assembly of monodisperse, single-stranded DNA block-copolynucleotides (polyT50-b-F-dUTP). Overall, we were able to predict the salt-responsive morphology of polyelectrolyte materials in aqueous solution and show that a spherical-cylindrical-lamellar change in morphology can be obtained through an increase in solvent ionic strength or a decrease of polyelectrolyte length. PMID:26315065

  6. A Novel Modelling Approach for Predicting Forest Growth and Yield under Climate Change.

    Directory of Open Access Journals (Sweden)

    M Irfan Ashraf

    Full Text Available Global climate is changing due to increasing anthropogenic emissions of greenhouse gases. Forest managers need growth and yield models that can be used to predict future forest dynamics during the transition period of present-day forests under a changing climatic regime. In this study, we developed a forest growth and yield model that can be used to predict individual-tree growth under current and projected future climatic conditions. The model was constructed by integrating historical tree growth records with predictions from an ecological process-based model using neural networks. The new model predicts basal area (BA and volume growth for individual trees in pure or mixed species forests. For model development, tree-growth data under current climatic conditions were obtained using over 3000 permanent sample plots from the Province of Nova Scotia, Canada. Data to reflect tree growth under a changing climatic regime were projected with JABOWA-3 (an ecological process-based model. Model validation with designated data produced model efficiencies of 0.82 and 0.89 in predicting individual-tree BA and volume growth. Model efficiency is a relative index of model performance, where 1 indicates an ideal fit, while values lower than zero means the predictions are no better than the average of the observations. Overall mean prediction error (BIAS of basal area and volume growth predictions was nominal (i.e., for BA: -0.0177 cm(2 5-year(-1 and volume: 0.0008 m(3 5-year(-1. Model variability described by root mean squared error (RMSE in basal area prediction was 40.53 cm(2 5-year(-1 and 0.0393 m(3 5-year(-1 in volume prediction. The new modelling approach has potential to reduce uncertainties in growth and yield predictions under different climate change scenarios. This novel approach provides an avenue for forest managers to generate required information for the management of forests in transitional periods of climate change. Artificial intelligence

  7. Spatial Predictive Process Models Yield Improved Forecasts of Vegetation Response to Climate Change

    Science.gov (United States)

    Swanson, A.; Dobrowski, S. Z.; Mynsberge, A.

    2010-12-01

    Species distribution models (SDMs) relate the presence and absence of plant species to environmental covariates, and are commonly used to forecast climate change impacts on biota. Such models have predicted increased extinction risk and dramatic shifts in habitat for many species, but their validity relies on the assumption that SDM projections are transferable through space and time, an assumption that is largely untested due to the rarity of independent data for assessing transferability. In practice, there are many obstacles to the SDM approach that can limit their transferability. For example, most SDMs are non-spatial, treating observations as independent even when close in space. This can lead to biased parameter estimates, overconfidence in predictions, and invalid tests of predictor significance. SDMs also fail to account for biotic effects known to be important in shaping species distributions. Spatial ‘predictive process’ models show promise in increasing both the biological and statistical realism of species distribution models. Predictive process models introduce a spatially autocorrelated covariate into parametric statistical approaches. The spatial process covariate can serve as a proxy to unmeasured factors affecting species distribution, such as dispersal or competition, and can account for sampling bias. Implemented in a Bayesian framework, the parameters of the spatial process are estimated concurrently with the conventional model coefficients, and associated uncertainties are propagated through to spatially explicit predictions. We hypothesize that SDMs incorporating a predictive process term will produce predictions with greater transferability than conventional approaches, and will more readily capture the species-climate relationship in an unbiased fashion. To test this, we fit conventional and spatial predictive process GLMs (Generalized Linear Models) to historic (1910-1940) vegetation data from the mountain ranges of California

  8. Determinants of rate of change in functional disability: An application of latent growth curve modeling.

    Science.gov (United States)

    Chen, Ya-Mei; Chen, Duan-Rung; Chiang, Tung-Liang; Tu, Yu-Kang; Yu, Hsiao-Wei

    2016-01-01

    Our aim was to identify disablement factors, including predisposing, intra-individual, and extra-individual factors, which predict the rate of change in general functional disability (GFD) in older adults. This study utilized the Taiwan Longitudinal Study on Aging Survey in 1996-2007 (N=3,186). Multiple-indicator latent growth curve modeling was used to examine how 12 disablement factors predicted the rate of change in GFD. GFD trajectories were modeled using Nagi's functional limitations, activities of daily living, and instrumental activities of daily living. Greater age (B=.025), female gender (B=.114), and greater numbers of comorbidities (B=.038) were associated with faster increase in GFD. Education (B=-.005) and participation in physically active leisure time activities (B=-.031) were associated with slower increase in GFD. Our findings add to the understanding of how disablement factors contribute to the rate of change in GFD. Predisposing factors played the main role. However, the factors we found to be associated with the rate of change in GFD in older adults were slightly different from the factors reported in the literature. Decreasing the number of comorbidities and increasing the level of physically active leisure time activity should be considered priorities for preventing disability as people age. PMID:26952373

  9. A study of consumers' perceptions and prediction of consumption patterns for generic health functional foods

    OpenAIRE

    Kang, Nam E; Kim, Ju Hyeon; Lee, Yeon Kyoung; Lee, Hye Young; Kim, Woo Kyoung

    2011-01-01

    The Korea Food and Drug Administration (KFDA) revised the Health Functional Food Act in 2008 and extended the form of health functional foods to general food types. Therefore, this study was performed to investigate consumers' perceptions of the expanded form of health functional food and to predict consumption patterns. For this study, 1,006 male and female adults aged 19 years and older were selected nationwide by multi-stage stratified random sampling and were surveyed in 1:1 interviews. T...

  10. Motor function predicts parent-reported musculoskeletal pain in children with cerebral palsy

    OpenAIRE

    Barney, Chantel C.; Krach, Linda E; Rivard, Patrick F; John L Belew; Symons, Frank J.

    2013-01-01

    BACKGROUND: The relationship between pain and motor function is not well understood, especially for children and adolescents with communication and motor impairments associated with cerebral palsy (CP).OBJECTIVES: To determine whether a predictive relationship between motor function and musculoskeletal pain exists in children with CP.METHODS: Following informed consent, caregivers of 34 pediatric patients with CP (mean [± SD] age 9.37±4.49 years; 80.0% male) completed pain- and function-relat...

  11. Stellar and HI Mass Functions Predicted by a Simple Preheating Galaxy Formation Model

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    According to the new preheating mechanism of galaxy formation suggested by Mo et al., we construct a simple model of formation of disk galaxies within the current paradigm of galaxy formation. It incorporates preheating, gas cooling, bulge formation and star formation. The predicted stellar and HI mass functions of galaxies are discussed and compared with the observations. It is found that our model can roughly match both the observed galaxy luminosity function and the observed HI-mass function.

  12. Less-structured time in children’s daily lives predicts self-directed executive functioning

    OpenAIRE

    JaneElizabethBarker; HannahR.Snyder

    2014-01-01

    Executive functions in childhood predict important life outcomes. Thus, there is great interest in attempts to improve executive functions early in life. Many interventions are led by trained adults, including structured training activities in the lab, and less-structured activities implemented in schools. Such programs have yielded gains in children’s externally-driven executive functioning, where they are instructed on what goal-directed actions to carry out and when. However, it is less cl...

  13. ACL-RSI and KOOS Measures Predict Normal Knee Function after ACL-SPORTS Training

    OpenAIRE

    White, Kathleen; Zeni, Joseph; Snyder-Mackler, Lynn

    2014-01-01

    Objectives: After anterior cruciate ligament reconstruction (ACLR) athletes commonly report increased fear of re-injury and below normal knee function. Implementing a post-operative training protocol (ACL-SPORTS Training) to improve patient perceived knee function, may improve short term outcomes after surgery. Identifying pre-training measures that predict normal knee function after training may allow us to determine who may respond to the treatment intervention. The purpose of this study wa...

  14. Early functional magnetic resonance imaging activations predict language outcome after stroke.

    Science.gov (United States)

    Saur, Dorothee; Ronneberger, Olaf; Kümmerer, Dorothee; Mader, Irina; Weiller, Cornelius; Klöppel, Stefan

    2010-04-01

    An accurate prediction of system-specific recovery after stroke is essential to provide rehabilitation therapy based on the individual needs. We explored the usefulness of functional magnetic resonance imaging scans from an auditory language comprehension experiment to predict individual language recovery in 21 aphasic stroke patients. Subjects with an at least moderate language impairment received extensive language testing 2 weeks and 6 months after left-hemispheric stroke. A multivariate machine learning technique was used to predict language outcome 6 months after stroke. In addition, we aimed to predict the degree of language improvement over 6 months. 76% of patients were correctly separated into those with good and bad language performance 6 months after stroke when based on functional magnetic resonance imaging data from language relevant areas. Accuracy further improved (86% correct assignments) when age and language score were entered alongside functional magnetic resonance imaging data into the fully automatic classifier. A similar accuracy was reached when predicting the degree of language improvement based on imaging, age and language performance. No prediction better than chance level was achieved when exploring the usefulness of diffusion weighted imaging as well as functional magnetic resonance imaging acquired two days after stroke. This study demonstrates the high potential of current machine learning techniques to predict system-specific clinical outcome even for a disease as heterogeneous as stroke. Best prediction of language recovery is achieved when the brain activation potential after system-specific stimulation is assessed in the second week post stroke. More intensive early rehabilitation could be provided for those with a predicted poor recovery and the extension to other systems, for example, motor and attention seems feasible. PMID:20299389

  15. Robust Predictive Functional Control for Flight Vehicles Based on Nonlinear Disturbance Observer

    Directory of Open Access Journals (Sweden)

    Yinhui Zhang

    2015-01-01

    Full Text Available A novel robust predictive functional control based on nonlinear disturbance observer is investigated in order to address the control system design for flight vehicles with significant uncertainties, external disturbances, and measurement noise. Firstly, the nonlinear longitudinal dynamics of the flight vehicle are transformed into linear-like state-space equations with state-dependent coefficient matrices. And then the lumped disturbances are considered in the linear structure predictive model of the predictive functional control to increase the precision of the predictive output and resolve the intractable mismatched disturbance problem. As the lumped disturbances cannot be derived or measured directly, the nonlinear disturbance observer is applied to estimate the lumped disturbances, which are then introduced to the predictive functional control to replace the unknown actual lumped disturbances. Consequently, the robust predictive functional control for the flight vehicle is proposed. Compared with the existing designs, the effectiveness and robustness of the proposed flight control are illustrated and validated in various simulation conditions.

  16. Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers.

    Directory of Open Access Journals (Sweden)

    Andrew T Kwon

    2011-12-01

    Full Text Available We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for capacity to direct selective reporter gene expression to differentiated C2C12 myotubes. A subset of 19 CRMs validated as functional in the assay. The rate of predictive success reveals striking limitations of computational regulatory sequence analysis methods for CRM discovery. Motif-based methods performed no better than predictions based only on sequence conservation. Analysis of the properties of the functional sequences relative to inactive sequences identifies nucleotide sequence composition can be an important characteristic to incorporate in future methods for improved predictive specificity. Muscle-related TFBSs predicted within the functional sequences display greater sequence conservation than non-TFBS flanking regions. Comparison with recent MyoD and histone modification ChIP-Seq data supports the validity of the functional regions.

  17. Present and future distributions of horseshoe crabs under predicted climate changes

    DEFF Research Database (Denmark)

    Funch, Peter; Obst, Matthias; Quevedo, Francisco;

    factors for the species distribution, quantify range shifts of the species in response to predicted climatic change, and obtain spatial predictions of suitable habitats under present and future climate scenarios. Suitable habitat was projected into marine protected areas in the region to better understand...... the potential of existing horseshoe crabs’ sanctuaries to accommodate the species in a changing climate........ gigas lives in sandy and shallow near-coast habitats, while C. rotundicauda mostly inhabits estuaries and mangroves. The third species T. tridentatus is living in shallow coastal zones from Malaysia to Japan. In order to improve our knowledge on current and future distribution of horseshoe crab...

  18. Changes in cognitive state alter human functional brain networks

    Directory of Open Access Journals (Sweden)

    Malaak Nasser Moussa

    2011-08-01

    Full Text Available The study of the brain as a whole system can be accomplished using network theory principles. Research has shown that human functional brain networks during a resting state exhibit small-world properties and high degree nodes, or hubs, localized to brain areas consistent with the default mode network (DMN. However, the study of brain networks across different tasks and or cognitive states has been inconclusive. Research in this field is important because the underpinnings of behavioral output are inherently dependent on whether or not brain networks are dynamic. This is the first comprehensive study to evaluate multiple network metrics at a voxel-wise resolution in the human brain at both the whole brain and regional level under various conditions: resting state, visual stimulation, and multisensory (auditory and visual stimulation. Our results show that despite global network stability, functional brain networks exhibit considerable task-induced changes in connectivity, efficiency, and community structure at the regional level.

  19. Predicting the Redshift 2 H-Alpha Luminosity Function Using [OIII] Emission Line Galaxies

    Science.gov (United States)

    Mehta, Vihang; Scarlata, Claudia; Colbert, James W.; Dai, Y. S.; Dressler, Alan; Henry, Alaina; Malkan, Matt; Rafelski, Marc; Siana, Brian; Teplitz, Harry I.; Bagley, Micaela; Beck, Melanie; Ross, Nathaniel R.; Rutkowski, Michael; Wang, Yun

    2015-01-01

    Upcoming space-based surveys such as Euclid and WFIRST-AFTA plan to measure Baryonic Acoustic Oscillations (BAOs) in order to study dark energy. These surveys will use IR slitless grism spectroscopy to measure redshifts of a large number of galaxies over a significant redshift range. In this paper, we use the WFC3 Infrared Spectroscopic Parallel Survey (WISP) to estimate the expected number of H-alpha emitters observable by these future surveys. WISP is an ongoing Hubble Space Telescope slitless spectroscopic survey, covering the 0.8 - 1.65 micrometers wavelength range and allowing the detection of H-alpha emitters up to z approximately equal to 1.5 and [OIII] emitters to z approximately equal to 2.3. We derive the H-alpha-[OIII] bivariate line luminosity function for WISP galaxies at z approximately equal to 1 using a maximum likelihood estimator that properly accounts for uncertainties in line luminosity measurement, and demonstrate how it can be used to derive the H-alpha luminosity function from exclusively fitting [OIII] data. Using the z approximately equal to 2 [OIII] line luminosity function, and assuming that the relation between H-alpha and [OIII] luminosity does not change significantly over the redshift range, we predict the H-alpha number counts at z approximately equal to 2 - the upper end of the redshift range of interest for the future surveys. For the redshift range 0.7 less than z less than 2, we expect approximately 3000 galaxies per sq deg for a flux limit of 3 x 10(exp -16) ergs per sec per sq cm (the proposed depth of Euclid galaxy redshift survey) and approximately 20,000 galaxies per sq deg for a flux limit of approximately 10(exp -16) ergs per sec per sq cm (the baseline depth of WFIRST galaxy redshift survey).

  20. Note: Work function change measurement via improved Anderson method

    International Nuclear Information System (INIS)

    We propose the modification to the Anderson method of work function change (Δϕ) measurements. In this technique, the kinetic energy of the probing electrons is already low enough for non-destructive investigation of delicate molecular systems. However, in our implementation, all electrodes including filament of the electron gun are polarized positively. As a consequence, electron bombardment of any elements of experimental system is eliminated. Our modification improves cleanliness of the ultra-high vacuum system. As an illustration of the solution capabilities, we present Δϕ of the Ag(100) surface induced by cobalt phthalocyanine layers

  1. Changes in the functions of undertakings in electricity supply

    International Nuclear Information System (INIS)

    For the electricity supply industry also it is necessary, by means of more intensive publicity work, to achieve the general realisation that neither new laws nor intervention of the state are required for dealing in the interests of the consumer with the problems arising, from great changes in all fields of business enterprise. It is more important for the electricity supply undertakings (EVU), by means of executive power and the administration of justice, to be put a position to carry out in the most efficient manner the functions entrusted to them by the Federal Government under the Power Supply Law and the energy programme. (orig.)

  2. Spatial and functional changes in recent urban development of Zagreb

    Directory of Open Access Journals (Sweden)

    Miroslav Sić

    2007-01-01

    Full Text Available This article discusses the urban development of Zagreb in the transition period. It analysesfour processes which have caused spatial and functional changes in the city’s developmentwithin its administrative limits. These are: the process of a new CBD establishment, expansionof hypermarkets and commercial centres, housing construction under new conditions andtransportation problems and solutions. Under the influence of these processes the spatiofunctionalstructure of the city becomes more and more complex. In this connection the cityhas started to have more influence on the urban region’s development.

  3. Spatial and functional changes in recent urban development of Zagreb

    Directory of Open Access Journals (Sweden)

    Miroslav Sić

    2007-12-01

    Full Text Available This article discusses the urban development of Zagreb in the transition period. It analyses four processes which have caused spatial and functional changes in the cityćs development within its administrative limits. These are: the process of a new CBD establishment, expansion of hypermarkets and commercial centres, housing construction under new conditions and transportation problems and solutions. Under the influence of these processes the spatiofunctional structure of the city becomes more and more complex. In this connection the city has started to have more influence on the urban regions development.

  4. Note: Work function change measurement via improved Anderson method

    Energy Technology Data Exchange (ETDEWEB)

    Sabik, A., E-mail: sabik@ifd.uni.wroc.pl; Gołek, F.; Antczak, G. [Institute of Experimental Physics, University of Wrocław, Wrocław (Poland)

    2015-05-15

    We propose the modification to the Anderson method of work function change (Δϕ) measurements. In this technique, the kinetic energy of the probing electrons is already low enough for non-destructive investigation of delicate molecular systems. However, in our implementation, all electrodes including filament of the electron gun are polarized positively. As a consequence, electron bombardment of any elements of experimental system is eliminated. Our modification improves cleanliness of the ultra-high vacuum system. As an illustration of the solution capabilities, we present Δϕ of the Ag(100) surface induced by cobalt phthalocyanine layers.

  5. Change of some coagulation function of overexposed persons

    International Nuclear Information System (INIS)

    TEG and platelet aggregation induced by ADP in 7 persons exposed to different doses were observed at different times after irradiation. TEG showed prominent prolongation of k and r + k values, and diminution of Ma and fibrinolysis rate after exposure. The maximum platelet aggregation percentage decreased in the 4 persons exposed to 0.6-3.5 Gy gamma rays. The changes of TEG and platelet aggregation function occurred earlier than that of platelet count. Apparently, TEG is one of the more useful tests providing basic data for the prognosis and the selection of therapeutic regime

  6. Changes in family functions in patients with secondary premature ejaculation

    Directory of Open Access Journals (Sweden)

    Mustafa Arı

    2011-06-01

    Full Text Available We aimed to inverstigate changes in family functions in patients with premature ejaculation.Materials and methods: In the present study, study group were randomly selected from Mustafa Kemal University Medical School Research and Training Hospital Urology Department outpatients clinic. Control group were selected among healthy volunteers. Totally 30 patients were included in the PE group and 30 healthy volunteers were included in the control group. Subjects were examined by the same psychiatrist. Beck Anxiety Inventory and Family Assessment Scale were applied to both groupsResults: Compared with the control group, premature ejaculation patients had significantly higher anxiety scores (p=0.001 and more deterioration in problem solving (p=0.001, communication (p=0.022, affective responsiveness (p=0.011, behavior control (p=0.032, and affective involvement in their families (p=0.011. There were no difference in terms of roles and general functions scores (p>0.05.Conclusion: It can be concluded that there is deterioration in family functions in patients with premature ejaculation, Therefore, approaches targeting family functions may be beneficial in the treatment of these patients.

  7. Prediction of color changes in acetaminophen solution using the time-temperature superposition principle.

    Science.gov (United States)

    Mochizuki, Koji; Takayama, Kozo

    2016-07-01

    A prediction method for color changes based on the time-temperature superposition principle (TTSP) was developed for acetaminophen solution. Color changes of acetaminophen solution are caused by the degradation of acetaminophen, such as hydrolysis and oxidation. In principle, the TTSP can be applied to only thermal aging. Therefore, the impact of oxidation on the color changes of acetaminophen solution was verified. The results of our experiment suggested that the oxidation products enhanced the color changes in acetaminophen solution. Next, the color changes of acetaminophen solution samples of the same head space volume after accelerated aging at various temperatures were investigated using the Commission Internationale de l'Eclairage (CIE) LAB color space (a*, b*, L* and ΔE*ab), following which the TTSP was adopted to kinetic analysis of the color changes. The apparent activation energies using the time-temperature shift factor of a*, b*, L* and ΔE*ab were calculated as 72.4, 69.2, 72.3 and 70.9 (kJ/mol), respectively, which are similar to the values for acetaminophen hydrolysis reported in the literature. The predicted values of a*, b*, L* and ΔE*ab at 40 °C were obtained by calculation using Arrhenius plots. A comparison between the experimental and predicted values for each color parameter revealed sufficiently high R(2) values (>0.98), suggesting the high reliability of the prediction. The kinetic analysis using TTSP was successfully applied to predicting the color changes under the controlled oxygen amount at any temperature and for any length of time. PMID:26559666

  8. Livestock Helminths in a Changing Climate: Approaches and Restrictions to Meaningful Predictions

    Directory of Open Access Journals (Sweden)

    Ross S. Davidson

    2012-03-01

    Full Text Available Climate change is a driving force for livestock parasite risk. This is especially true for helminths including the nematodes Haemonchus contortus, Teladorsagia circumcincta, Nematodirus battus, and the trematode Fasciola hepatica, since survival and development of free-living stages is chiefly affected by temperature and moisture. The paucity of long term predictions of helminth risk under climate change has driven us to explore optimal modelling approaches and identify current bottlenecks to generating meaningful predictions. We classify approaches as correlative or mechanistic, exploring their strengths and limitations. Climate is one aspect of a complex system and, at the farm level, husbandry has a dominant influence on helminth transmission. Continuing environmental change will necessitate the adoption of mitigation and adaptation strategies in husbandry. Long term predictive models need to have the architecture to incorporate these changes. Ultimately, an optimal modelling approach is likely to combine mechanistic processes and physiological thresholds with correlative bioclimatic modelling, incorporating changes in livestock husbandry and disease control. Irrespective of approach, the principal limitation to parasite predictions is the availability of active surveillance data and empirical data on physiological responses to climate variables. By combining improved empirical data and refined models with a broad view of the livestock system, robust projections of helminth risk can be developed.

  9. Livestock Helminths in a Changing Climate: Approaches and Restrictions to Meaningful Predictions.

    Science.gov (United States)

    Fox, Naomi J; Marion, Glenn; Davidson, Ross S; White, Piran C L; Hutchings, Michael R

    2012-01-01

    Climate change is a driving force for livestock parasite risk. This is especially true for helminths including the nematodes Haemonchus contortus, Teladorsagia circumcincta, Nematodirus battus, and the trematode Fasciola hepatica, since survival and development of free-living stages is chiefly affected by temperature and moisture. The paucity of long term predictions of helminth risk under climate change has driven us to explore optimal modelling approaches and identify current bottlenecks to generating meaningful predictions. We classify approaches as correlative or mechanistic, exploring their strengths and limitations. Climate is one aspect of a complex system and, at the farm level, husbandry has a dominant influence on helminth transmission. Continuing environmental change will necessitate the adoption of mitigation and adaptation strategies in husbandry. Long term predictive models need to have the architecture to incorporate these changes. Ultimately, an optimal modelling approach is likely to combine mechanistic processes and physiological thresholds with correlative bioclimatic modelling, incorporating changes in livestock husbandry and disease control. Irrespective of approach, the principal limitation to parasite predictions is the availability of active surveillance data and empirical data on physiological responses to climate variables. By combining improved empirical data and refined models with a broad view of the livestock system, robust projections of helminth risk can be developed. PMID:26486780

  10. Predicting changes in protein thermostability brought about by single- or multi-site mutations

    Directory of Open Access Journals (Sweden)

    Chu Xiaoyu

    2010-07-01

    Full Text Available Abstract Background An important aspect of protein design is the ability to predict changes in protein thermostability arising from single- or multi-site mutations. Protein thermostability is reflected in the change in free energy (ΔΔG of thermal denaturation. Results We have developed predictive software, Prethermut, based on machine learning methods, to predict the effect of single- or multi-site mutations on protein thermostability. The input vector of Prethermut is based on known structural changes and empirical measurements of changes in potential energy due to protein mutations. Using a 10-fold cross validation test on the M-dataset, consisting of 3366 mutants proteins from ProTherm, the classification accuracy of random forests and the regression accuracy of random forest regression were slightly better than support vector machines and support vector regression, whereas the overall accuracy of classification and the Pearson correlation coefficient of regression were 79.2% and 0.72, respectively. Prethermut performs better on proteins containing multi-site mutations than those with single mutations. Conclusions The performance of Prethermut indicates that it is a useful tool for predicting changes in protein thermostability brought about by single- or multi-site mutations and will be valuable in the rational design of proteins.

  11. Properties and prediction accuracy of a sigmoid function of time-determinate growth

    Directory of Open Access Journals (Sweden)

    Sedmák R

    2015-10-01

    Full Text Available The properties and short-term prediction accuracy of mathematical model of sigmoid time-determinate growth, denoted as “KM-function”, are presented. Comparative mathematical analysis of the function revealed that it is a model of asymmetrical sigmoid growth, which starts at zero size of an organism and terminates when it reaches its final size. The function assumes a finite length of the growth period and includes a parameter interpretable as the expected lifespan of the organism. Moreover, the possibility for growth curve inflexion at any age is possible, so the function can be used for modelling of S-shaped growth trajectories with various degree of asymmetry. These good theoretical predispositions for realistic growth predictions were empirically evaluated. The KM-function used in three and four-parameter forms was compared with three classical (Richards, Korf and Weibull growth functions employing two parameterisation methods - nonlinear least squares (NLS and Bayesian method. The evaluation was conducted on the basis of the tree diameter series obtained from stem analyses. The main empirical findings are: (i if the minimisation of the prediction bias is required, the KM-function in three-parameter form in connection with Bayes parameterisation can be recommended; (ii if the minimisation of root square error (RMSE is required, the best short-term prediction results for a particular dataset were obtained with four-parameter Weibull function employing NLS parameterisation; (iii moreover, three-parameter functions parameterised by Bayesian methods show a considerably smaller RMSE by 15-25% as well as smaller biases by 40-60% than four-parameter functions employing NLS. Overall, all analyses confirmed relative usefulness of the KM-function in comparison with classical growth functions, especially in connection with Bayesian parameterisation.

  12. Prediction of GPCR-G Protein Coupling Specificity Using Features of Sequences and Biological Functions

    Institute of Scientific and Technical Information of China (English)

    Toshihide Ono; Haretsugu Hishigaki

    2006-01-01

    Understanding the coupling specificity between G protein-coupled receptors (GPCRs) and specific classes of G proteins is important for further elucidation of receptor functions within a cell. Increasing information on GPCR sequences and the G protein family would facilitate prediction of the coupling properties of GPCRs. In this study, we describe a novel approach for predicting the coupling specificity between GPCRs and G proteins. This method uses not only GPCR sequences but also the functional knowledge generated by natural language processing, and can achieve 92.2% prediction accuracy by using the C4.5 algorithm.Furthermore, rules related to GPCR-G protein coupling are generated. The combination of sequence analysis and text mining improves the prediction accuracy for GPCR-G protein coupling specificity, and also provides clues for understanding GPCR signaling.

  13. Application of Excitation Function to the Prediction of RI Level Caused by Corona Discharge

    Institute of Scientific and Technical Information of China (English)

    ZHU Lingyu; JI Shengchang; HUI Sisi; GUO Jun; LI Yansong; FU Chenzhao

    2012-01-01

    Radio interference (RI), as an aftereffect of corona discharge, is an important research topic in the field of electromagnetic compatibility, where excitation function is applied broadly to the prediction of RI level. This paper presents the theory of excitation function method used in the RI level prediction. Then, some practical problems related to this method are discussed. The propagation procedure of corona current is solved by the phase-modal transformation, and the impedance matrix of multi transmission lines is calculated by a double logarithmic approximate model of Carson's Ground-Return impedance. At the same time, in order to calculate the RI level when total line corona is assumed, an analytical formula is deduced for integral operation. Based on the above solutions, an algorithm is presented and applied to the prediction of RI level of a practical overhead transmission line. Comparison of prediction and measurement results indicates that the algorithm proposed in this paper is effective and feasible.

  14. Key Technology of Predicting Dynamic Surface Subsidence Based on Knothe Time Function

    OpenAIRE

    Qing-Feng Hu; Xi-Min Cui; Guo Wang; Meng-Ru Wang; Yin-Xiao Ji; Wei Xue

    2011-01-01

    A method for calculating the parameter of Knothe time function was presented. The principle of predicting dynamic mining subsidence was discussed based to the relationship between the periodic fractures of main roof and surface subsidence. Pointed out there might be a section whose width was shorter than a mining unit when divided a workface into  equal mining elements, the section should be calculated specially in the algorithm. A model of predicting dynamic mining subsidence was made a...

  15. On the sensitivity of field reconstruction and prediction using Empirical Orthogonal Functions derived from gappy data

    OpenAIRE

    Taylor, Marc; Losch, Martin; Wenzel, Manfred; Schröter, Jens

    2013-01-01

    Empirical Orthogonal Function (EOF) Analysis is commonly used in the climate sciences and elsewhere to describe, reconstruct, and predict highly dimensional data fields. When data contain a high percentage of missing values (i.e. “gappy”), alternate approaches must be used in order to correctly derive EOFs. The aims of this paper are to assess the accuracy of several EOF approaches in the reconstruction and prediction of gappy data fields, using the Galapagos Archipelago as a case study examp...

  16. A Mixed QM/MM Scoring Function to Predict Protein-Ligand Binding Affinity

    OpenAIRE

    Hayik, Seth A.; Dunbrack, Roland; Merz, Kenneth M.

    2010-01-01

    Computational methods for predicting protein-ligand binding free energy continue to be popular as a potential cost-cutting method in the drug discovery process. However, accurate predictions are often difficult to make as estimates must be made for certain electronic and entropic terms in conventional force field based scoring functions. Mixed quantum mechanics/molecular mechanics (QM/MM) methods allow electronic effects for a small region of the protein to be calculated, treating the remaini...

  17. Woody plants and the prediction of climate-change impacts on bird diversity

    OpenAIRE

    Kissling, W. D.; Field, R.; Korntheuer, H.; Heyder, U.; Böhning-Gaese, K.

    2010-01-01

    Current methods of assessing climate-induced shifts of species distributions rarely account for species interactions and usually ignore potential differences in response times of interacting taxa to climate change. Here, we used species-richness data from 1005 breeding bird and 1417 woody plant species in Kenya and employed model-averaged coefficients from regression models and median climatic forecasts assembled across 15 climate-change scenarios to predict bird species richness under climat...

  18. Predicting Early Positive Change in Multisystemic Therapy with Youth Exhibiting Antisocial Behaviors

    OpenAIRE

    Tiernan, Kristine; Foster, Sharon L.; Cunningham, Phillippe B.; Brennan, Patricia; Whitmore, Elizabeth

    2014-01-01

    This study examined individual and family characteristics that predicted early positive change in the context of Multisystemic Therapy (MST). Families (n=185; 65% male; average youth age 15 years) receiving MST in community settings completed assessments at the outset of treatment and 6-12 weeks into treatment. Early positive changes in youth antisocial behavior were assessed using the caregiver report on the CBCL Externalizing Behaviors subscale and youth report on the Self-Report Delinquenc...

  19. Livestock Helminths in a Changing Climate: Approaches and Restrictions to Meaningful Predictions

    OpenAIRE

    Davidson, Ross S.; Piran C L White; Glenn Marion; Naomi J Fox; Hutchings, Michael R.

    2012-01-01

    Simple Summary Parasitic helminths represent one of the most pervasive challenges to livestock, and their intensity and distribution will be influenced by climate change. There is a need for long-term predictions to identify potential risks and highlight opportunities for control. We explore the approaches to modelling future helminth risk to livestock under climate change. One of the limitations to model creation is the lack of purpose driven data collection. We also conclude that models nee...

  20. Prospective prediction of post-radiation therapy lung function using quantitative lung scans and pulmonary function testing

    International Nuclear Information System (INIS)

    Surgeons have made use of quantitative perfusion lung scanning (QS) and forced expiratory volume in one second (FEV1) to predict a patient's ability to tolerate lung resection. In this study QS and FEV1 were used to predict prospectively pulmonary function following lung irradiation (XRT). Twenty-two patients have had QS and FEV1 determined before XRT and at planned intervals post-XRT. Serial determination of lung function post-XRT allows comment on the temporal nature of the XRT effect on lung function. Seventeen patients had QS and FEV1 determined at an interval of 2-6 months post-irradiation with a drop in the groups mean FEV1 from 1.91 to 1.87L. or 2% during that interval. In the interval from 6-12 months post-XRT, 13 patients had studies with the groups mean FEV1 dropping from 1.79 to 1.58L or 12% of the original. In the interval from 12-18 months, 6 patients had a decline in mean FEV1 from 1.73 to 1.56L. or 10% of the original. In 22 patients a predicted final FEV1 was compared with a measured value at an interval from XRT. Fourteen of these determinations were at intervals greater than 6 months from the start of XRT and 6 at intervals of greater than 1 year. FEV1 was seen to drop during the follow-up intervals toward the predicted value. In only 2 patients did the final FEV1 drop below the predicted FEV1 and never by more than 0.12L. (6%). In summary, a method for predicting post-XRT pulmonary function using QS and FEV1 is described. Serial follow-up revealed a latent period followed by a late phase where FEV1 fell toward, but not significantly below, the predicted value. Such a determination can be of value in formulating a treatment plan for patients with significantly diminished pulmonary function

  1. A Prediction Model for Functional Defects in System Testing using Six Sigma

    Directory of Open Access Journals (Sweden)

    Muhammad Dhiauddin Mohamed Suffian

    2011-09-01

    Full Text Available This research demonstrates the industry-centric approach of predicting defects and controlling them within system testing phase to prevent any escapees to the next testing level and later, to the end users. The importance of knowing total number of defects to be found at the start of system testing phase is a significant element in software engineering practices towards achieving zero known post release defects of the software released to users. Test defect prediction, particularly on functional defects serves as an initiative for test process improvement and optimization. Independent testing team able to discover as many defects as possible, determine when to stop testing, put comprehensive test coverage and ensuring all defects are contained within testing phase. Considering various prior efforts and approaches in building such prediction models, this research attempts to focus on formulating a mathematical model for specifically predicting functional test defects to be found in system testing phase before it is actually started. Six Sigma is chosen as the approach in building upthe mathematical model for predicting functional defects in system testing phase. Software projects are selected from those adopting V-Model software development process is the area of focus in which the software projects adopting this model are selected for the research. Analysis focuses on factors in phases prior to testing phase that have direct impact to the discovery of defect in system testing. The metrics in those phases which are significant to system testing defects are collected and analyzed statistically using multiple regression analysis. The proposed prediction model for functional defects in system testing is formulated using the best mathematical equation generated from the regression analysis, which is a combination of development and testing metrics. The proposed model is then validated to ensure it is fit for actual implementation. Control plan is

  2. Plant Functional Variability in Response to Late-Quaternary Climate Change Recorded in Ancient Packrat Middens

    Science.gov (United States)

    Holmgren, C. A.; Potts, D. L.

    2006-12-01

    Responses of plant functional traits to environmental variability are of enduring interest because they constrain organism performance and ecosystem function. However, most inferences regarding plant functional trait response to climatic variability have been limited to the modern period. To better understand plant functional response to long-term climate variability and how adjustments in leaf morphology may contribute to patterns of species establishment, persistence, or extirpation, we measured specific leaf area (SLA) from macrofossils preserved in ancient packrat middens collected along the Arizona/New Mexico border, USA. Our record spanned more than 32,000 years and included six woodland and Chihuahuan Desert species: Berberis cf. haematocarpa, Juniperus cf. coahuilensis, Juniperus osteosperma, Larrea tridentata, Prosopis glandulosa and Parthenium incanum. We predicted that regional climatic warming and drying since the late Pleistocene would result in intraspecific decreases in SLA. As predicted, SLA was positively correlated with midden age for three of the six species (L. tridentata, J. osteosperma, B. cf. haematocarpa). SLA was also negatively correlated with December (L. tridentata, J. cf. coahuilensis) or June (B. cf. haematocarpa, J. osteosperma) insolation. A unique record of vegetation community dynamics, plant macrofossils preserved in packrat middens also represent a rich and largely untapped source of information on long-term trends in species functional response to environmental change.

  3. Upset Prediction in Friction Welding Using Radial Basis Function Neural Network

    Directory of Open Access Journals (Sweden)

    Wei Liu

    2013-01-01

    Full Text Available This paper addresses the upset prediction problem of friction welded joints. Based on finite element simulations of inertia friction welding (IFW, a radial basis function (RBF neural network was developed initially to predict the final upset for a number of welding parameters. The predicted joint upset by the RBF neural network was compared to validated finite element simulations, producing an error of less than 8.16% which is reasonable. Furthermore, the effects of initial rotational speed and axial pressure on the upset were investigated in relation to energy conversion with the RBF neural network. The developed RBF neural network was also applied to linear friction welding (LFW and continuous drive friction welding (CDFW. The correlation coefficients of RBF prediction for LFW and CDFW were 0.963 and 0.998, respectively, which further suggest that an RBF neural network is an effective method for upset prediction of friction welded joints.

  4. Interoceptive awareness changes the posterior insula functional connectivity profile.

    Science.gov (United States)

    Kuehn, Esther; Mueller, Karsten; Lohmann, Gabriele; Schuetz-Bosbach, Simone

    2016-04-01

    Interoceptive awareness describes the ability to consciously perceive inner bodily signals, such as one's own heartbeat. The right anterior insula is assumed to mediate this ability. The role of the posterior insula, particularly posterior-to-anterior insula signal flows is less clear in this respect. We scanned 27 healthy people with either high or low interoceptive awareness using 3T fMRI, while they either monitored their own heartbeats, or external tones, respectively. We used a combination of network centrality and bivariate connectivity analyses to characterize changes in cortical signal flows between the posterior insula and the anterior insula during interoceptive awareness or exteroceptive awareness, respectively. We show that heartbeat monitoring was accompanied by reduced network centrality of the right posterior insula, and decreased functional connectivity strengths between the right posterior insula and the right mid and anterior insula. In addition, decreased signal flows between the right posterior insula and the bilateral anterior cingulate cortices, and the bilateral orbitofrontal cortices were observed during interoceptive awareness. Functional connectivity changes were only shown by people with high interoceptive awareness, and occurred specifically within the low-frequency range (i.e., own heartbeat. PMID:25613901

  5. Changes in lymphatic function after complex physical therapy for lymphedema.

    Science.gov (United States)

    Hwang, J H; Kwon, J Y; Lee, K W; Choi, J Y; Kim, B T; Lee, B B; Kim, D I

    1999-03-01

    Twenty-two extremities of 19 lymphedema patients (6 arms, 16 legs) were treated by 2 weeks of complex physical therapy (CPT) and self home maintenance therapy (bandage/wearing of elastic garment and exercise). In addition to the clinical response of volume reduction before and 3 months after CPT, we analyzed the functional changes of the peripheral lymphatic system by use of lymphoscintigraphy (LS). Before CPT, the main LS findings of lymphedema included dermal backflow (100%), absent or faintly visualized regional lymph nodes (95.5%), presence of collateral lymphatic vessels (68.2%), and no or barely visualized lymphatic vessels (27.3%). LS findings suggesting improved lymphatic function after CPT were a decrease in dermal backflow (72.7%), an increase in radioisotope uptake by lymphatic vessels (27.3%), and an increase in radioisotope uptake by lymph nodes (9.1%). 81.8% of limbs showed improved lymphoscintigraphic findings and no change in 9.1%. In the others (9.1%), LS findings appeared worse. There was, however, no correlation between LS "improvement" and the amount of limb volume reduction. PMID:10197323

  6. Changes in ventricular function during emotional stress and cold exposure

    International Nuclear Information System (INIS)

    Patients with cardiac disease frequently develop symptoms with emotional stress or cold exposure. To investigate the effects of these stresses in normal subjects, an ambulatory ventricular function monitor (VEST) (previously reported to measure EFs which correlate well with gamma camera measurements) was employed to record sequential 2 minute time activity curves from the left ventricles of 6 healthy men (ages 19-24) during a control period and during a 30 minute stress interview with a psychiatrist. Four of the subjects were also monitored in a cold room (10C) for 20 min. In addition to the left ventricular time-activity curve, heart rate (HR), and BP (cuff) were recorded. All subjects had increases in HR, BP and EF during the stress interview. Cold, however, produced decreases in HR and EF and an increase in BP. The results (mean +- SD) are tabulated. End-systolic and end-diastolic counts and hence volume decreased during the interview and increased during cold exposure. The results suggest that (1) ambulatory changes in ventricular function can be measured with the VEST, and (2) significant changes in cardiovascular physiology are seen in normal subjects during a stress interview and exposure to cold

  7. Changes in macrophage function modulated by the lipid environment.

    Science.gov (United States)

    Williams, Michael R; Cauvi, David M; Rivera, Isabel; Hawisher, Dennis; De Maio, Antonio

    2016-04-01

    Macrophages (Mφs) play a critical role in the defense against pathogens, orchestrating the inflammatory response during injury and maintaining tissue homeostasis. During these processes, macrophages encounter a variety of environmental conditions that are likely to change their gene expression pattern, which modulates their function. In this study, we found that murine Mφs displayed two different subpopulations characterized by differences in morphologies, expression of surface markers and phagocytic capacity under non-stimulated conditions. These two subpopulations could be recapitulated by changes in the culture conditions. Thus, Mφs grown in suspension in the presence of serum were highly phagocytic, whereas subtraction of serum resulted in rapid attachment and reduced phagocytic activity. The difference in phagocytosis between these subpopulations was correlated with the expression levels of FcγR. These two cell subpopulations also differed in their responses to LPS and the expression of surface markers, including CD14, CD86, scavenger receptor A1, TLR4 and low-density lipoprotein receptor. Moreover, we found that the lipid/cholesterol content in the culture medium mediated the differences between these two cell subpopulations. Thus, we described a mechanism that modulates Mφ function depending on the exposure to lipids within their surrounding microenvironment. PMID:26951856

  8. Prediction of postoperative pulmonary function following thoracic operations. Value of ventilation-perfusion scanning

    International Nuclear Information System (INIS)

    Surgical resection of lung cancer is frequently required in patients with severely impaired lung function resulting from chronic obstructive pulmonary disease. Twenty patients with obstructive lung disease and cancer (mean preoperative forced expiratory volume in 1 second [FEV1] . 1.73 L) were studied preoperatively and postoperatively by spirometry and radionuclide perfusion, single-breath ventilation, and washout techniques to test the ability of these methods to predict preoperatively the partial loss of lung function by the resection. Postoperative FEV1 and forced vital capacity (FVC) were accurately predicted by the formula: postoperative FEV1 (or FVC) . preoperative FEV1 X percent function of regions of lung not to be resected (r . 0.88 and 0.95, respectively). Ventilation and perfusion scans are equally effective in prediction. Washout data add to the sophistication of the method by permitting the qualitative evaluation of ventilation during tidal breathing. Criteria for patients requiring the study are suggested

  9. A GIS-model for predicting the impact of climate change on shore erosion in hydroelectric reservoirs

    International Nuclear Information System (INIS)

    Shoreline erosion affects inland lakes and hydroelectric reservoirs in several ways. This poster described a vector-based geographic information system (GIS) model designed to predict changes in shore zone geometry, top-of-bluff recession, and eroded sediment volumes. The model was designed for use in Manitoba Hydro's reservoirs in northern Manitoba, and simulated near-shore downcutting and bank recession caused by wind-generated waves. Parameters for the model included deep water wave energy, and water level fluctuations. Effective wave energy was seen as a function of the water level fluctuation range, wave conditions, and near-shore slope. The model was validated by field monitoring studies that included repeated shore zone transect surveys and sediment coring studies. Results of the study showed that the model provides a systematic method of predicting potential changes in erosion associated with climatic change. The volume and mass of eroded sediment predicted for the different modelling scenarios will be used as input data for future sedimentation models. tabs., figs

  10. Modeling and prediction of children’s growth data via functional principal component analysis

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    We use the functional principal component analysis(FPCA) to model and predict the weight growth in children.In particular,we examine how the approach can help discern growth patterns of underweight children relative to their normal counterparts,and whether a commonly used transformation to normality plays any constructive roles in a predictive model based on the FPCA.Our work supplements the conditional growth charts developed by Wei and He(2006) by constructing a predictive growth model based on a small number of principal components scores on individual’s past.

  11. Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasets.

    Science.gov (United States)

    Swanton, Charles; Larkin, James M; Gerlinger, Marco; Eklund, Aron C; Howell, Michael; Stamp, Gordon; Downward, Julian; Gore, Martin; Futreal, P Andrew; Escudier, Bernard; Andre, Fabrice; Albiges, Laurence; Beuselinck, Benoit; Oudard, Stephane; Hoffmann, Jens; Gyorffy, Balázs; Torrance, Chris J; Boehme, Karen A; Volkmer, Hansjuergen; Toschi, Luisella; Nicke, Barbara; Beck, Marlene; Szallasi, Zoltan

    2010-01-01

    The European Union multi-disciplinary Personalised RNA interference to Enhance the Delivery of Individualised Cytotoxic and Targeted therapeutics (PREDICT) consortium has recently initiated a framework to accelerate the development of predictive biomarkers of individual patient response to anti-cancer agents. The consortium focuses on the identification of reliable predictive biomarkers to approved agents with anti-angiogenic activity for which no reliable predictive biomarkers exist: sunitinib, a multi-targeted tyrosine kinase inhibitor and everolimus, a mammalian target of rapamycin (mTOR) pathway inhibitor. Through the analysis of tumor tissue derived from pre-operative renal cell carcinoma (RCC) clinical trials, the PREDICT consortium will use established and novel methods to integrate comprehensive tumor-derived genomic data with personalized tumor-derived small hairpin RNA and high-throughput small interfering RNA screens to identify and validate functionally important genomic or transcriptomic predictive biomarkers of individual drug response in patients. PREDICT's approach to predictive biomarker discovery differs from conventional associative learning approaches, which can be susceptible to the detection of chance associations that lead to overestimation of true clinical accuracy. These methods will identify molecular pathways important for survival and growth of RCC cells and particular targets suitable for therapeutic development. Importantly, our results may enable individualized treatment of RCC, reducing ineffective therapy in drug-resistant disease, leading to improved quality of life and higher cost efficiency, which in turn should broaden patient access to beneficial therapeutics, thereby enhancing clinical outcome and cancer survival. The consortium will also establish and consolidate a European network providing the technological and clinical platform for large-scale functional genomic biomarker discovery. Here we review our current understanding

  12. Predicting Climate Change using Response Theory: Global Averages and Spatial Patterns

    CERN Document Server

    Lucarini, Valerio; Ragone, Francesco

    2015-01-01

    The provision of accurate methods for predicting the climate response to anthropogenic and natural forcings is a key contemporary scientific challenge. Using a simplified and efficient open-source general circulation model of the atmosphere featuring O($10^5$) degrees of freedom, we show how it is possible to approach such a problem using nonequilibrium statistical mechanics. Response theory allows one to practically compute the time-dependent measure supported on the pullback attractor of the climate system, whose dynamics is non-autonomous as a result of time-dependent forcings. We propose a simple yet efficient method for predicting - at any lead time and in an ensemble sense - the change in climate properties resulting from increase in the concentration of CO$_2$ using test perturbation model runs. We assess strengths and limitations of the response theory in predicting the changes in the globally averaged values of surface temperature and of the yearly total precipitation, as well as their spatial patter...

  13. Cognitive biases to healthy and unhealthy food words predict change in BMI.

    Science.gov (United States)

    Calitri, Raff; Pothos, Emmanuel M; Tapper, Katy; Brunstrom, Jeffrey M; Rogers, Peter J

    2010-12-01

    The current study explored the predictive value of cognitive biases to food cues (assessed by emotional Stroop and dot probe tasks) on weight change over a 1-year period. This was a longitudinal study with undergraduate students (N = 102) living in shared student accommodation. After controlling for the effects of variables associated with weight (e.g., physical activity, stress, restrained eating, external eating, and emotional eating), no effects of cognitive bias were found with the dot probe. However, for the emotional Stroop, cognitive bias to unhealthy foods predicted an increase in BMI whereas cognitive bias to healthy foods was associated with a decrease in BMI. Results parallel findings in substance abuse research; cognitive biases appear to predict behavior change. Accordingly, future research should consider strategies for attentional retraining, encouraging individuals to reorient attention away from unhealthy eating cues. PMID:20379149

  14. Continental cichlid radiations: functional diversity reveals the role of changing ecological opportunity in the Neotropics.

    Science.gov (United States)

    Arbour, Jessica Hilary; López-Fernández, Hernán

    2016-08-17

    Adaptive radiations have been hypothesized to contribute broadly to the diversity of organisms. Models of adaptive radiation predict that ecological opportunity and ecological release, the availability of empty ecological niches and the response by adapting lineages to occupy them, respectively, drive patterns of phenotypic and lineage diversification. Adaptive radiations driven by 'ecological opportunity' are well established in island systems; it is less clear if ecological opportunity influences continent-wide diversification. We use Neotropical cichlid fishes to test if variation in rates of functional evolution is consistent with changing ecological opportunity. Across a functional morphological axis associated with ram-suction feeding traits, evolutionary rates declined through time as lineages diversified in South America. Evolutionary rates of ram-suction functional morphology also appear to have accelerated as cichlids colonized Central America and encountered renewed opportunity. Our results suggest that ecological opportunity may play an important role in shaping patterns of morphological diversity of even broadly distributed lineages like Neotropical cichlids. PMID:27512144

  15. Fat or lean: adjustment of endogenous energy stores to predictable and unpredictable changes in allostatic load

    Science.gov (United States)

    Schultner, Jannik; Kitaysky, Alexander S.; Welcker, Jorg; Hatch, Scott

    2013-01-01

    1. The ability to store energy endogenously is an important ecological mechanism that allows animals to buffer predictable and unpredictable variation in allostatic load. The secretion of glucocorticoids, which reflects changes in allostatic load, is suggested to play a major role in the adjustment of endogenous stores to these varying conditions.

  16. Predicting life-cycle adaptation of migratory birds to global climate change

    NARCIS (Netherlands)

    Coppack, T.; Both, C.

    2002-01-01

    Analyses of long-term data indicate that human-caused climatic changes are affecting bird phenology in directions consistent with theoretical predictions. Here, we report on recent trends in the timing of spring arrival and egg laying found within a western European Pied Flycatcher Ficedula hypoleuc

  17. The Predictive Utility of Hypnotizability: The Change in Suggestibility Produced by Hypnosis

    Science.gov (United States)

    Milling, Leonard S.; Coursen, Elizabeth L.; Shores, Jessica S.; Waszkiewicz, Jolanta A.

    2010-01-01

    Objective: The predictive utility of hypnotizability, conceptualized as the change in suggestibility produced by a hypnotic induction, was investigated in the suggested reduction of experimental pain. Method: One hundred and seventy-three participants were assessed for nonhypnotic imaginative suggestibility. Thereafter, participants experienced…

  18. Investigation of change of renal function following percutaneous nephrolithotomy

    International Nuclear Information System (INIS)

    The percutaneous removal of renal calculi is a relatively new technique which may significantly decrease the morbidity due to calculous disease of the upper urinary tract. Over two hundred such procedures have been performed in our institution over the last two years. The authors have designed a prospective study of fifty patients with non-obstructing calculi referred for percutaneous nephrolithotomy in order to determine if there is any functional change of the kidney secondary to the operation itself. Each patient is studied using a standard Tc99m DTPA renogram and computer assisted analysis both before and four to six weeks after surgery. In order to make the selection of regions of interest (ROIs) as reproducible as possible, the ROI of the entire kidney is selected on a frame early in the study, and later frames are used to outline the collecting system. Using subtractive techniques, the contribution of the cortex of the side to be operated upon to total cortical function is derived from the previously defined regions. Renogram curves are drawn for the entire kidney as well as renal cortex. The analysis post-operatively is performed using the same ROIs generated on the pre-operative study. To date, the authors have studied twenty patients pre-operatively and followed up seven. A small but consistent decrease in renal function is seen post-operatively in both the entire kidney and cortex. A statistical analysis of the study group will be performed after further follow up and data processing of more patients

  19. Changes of Cardiac Function During Ultradistance Trail Running.

    Science.gov (United States)

    Jouffroy, Romain; Caille, Vincent; Perrot, Stéphane; Vieillard-Baron, Antoine; Dubourg, Olivier; Mansencal, Nicolas

    2015-10-15

    Previous studies have noted reversible cardiac dysfunction during marathon races, but few data are available concerning ultradistance trail running. The aim of this study was to assess echocardiographic parameters during ultradistance trail running. We performed an observational study in 66 participants to the 80-km Ecotrail of Paris Ile de France. All subjects had echocardiographic examinations before the race and on arrival, and 28 of them underwent serial echocardiographic examinations during the race (21 and 53 km). A single experienced physician performed all echocardiographic examinations, and the same protocol was always used (conventional 2-dimensional and Doppler left ventricular parameters and longitudinal strain). All echocardiographic parameters of left ventricular (LV) systolic function were significantly decreased on arrival (p ≤0.002). A significant reduction of LV systolic function was observed in 48% of study subjects on arrival. No significant modification was observed at 21 or at 53 km, and only global longitudinal strain was significantly decreased (p = 0.0008). At arrival, mitral E/A ratio and average mitral tissue Doppler imaging e' wave were significantly decreased (p = 0.0001 and p = 0.0004, respectively), but these changes were observed from 21 km. In conclusion, ultradistance trail running can lead to abnormalities of LV systolic and diastolic functions in amateur runners. Diastolic dysfunction arises earlier than systolic dysfunction. Left ventricular systolic dysfunction occurred in 48% of the study subjects and was detected early by assessment of longitudinal strain. PMID:26294134

  20. UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.

    Science.gov (United States)

    Lua, Rhonald C; Wilson, Stephen J; Konecki, Daniel M; Wilkins, Angela D; Venner, Eric; Morgan, Daniel H; Lichtarge, Olivier

    2016-01-01

    The structure and function of proteins underlie most aspects of biology and their mutational perturbations often cause disease. To identify the molecular determinants of function as well as targets for drugs, it is central to characterize the important residues and how they cluster to form functional sites. The Evolutionary Trace (ET) achieves this by ranking the functional and structural importance of the protein sequence positions. ET uses evolutionary distances to estimate functional distances and correlates genotype variations with those in the fitness phenotype. Thus, ET ranks are worse for sequence positions that vary among evolutionarily closer homologs but better for positions that vary mostly among distant homologs. This approach identifies functional determinants, predicts function, guides the mutational redesign of functional and allosteric specificity, and interprets the action of coding sequence variations in proteins, people and populations. Now, the UET database offers pre-computed ET analyses for the protein structure databank, and on-the-fly analysis of any protein sequence. A web interface retrieves ET rankings of sequence positions and maps results to a structure to identify functionally important regions. This UET database integrates several ways of viewing the results on the protein sequence or structure and can be found at http://mammoth.bcm.tmc.edu/uet/. PMID:26590254

  1. Adaptation, plasticity, and extinction in a changing environment: towards a predictive theory.

    Directory of Open Access Journals (Sweden)

    Luis-Miguel Chevin

    Full Text Available Many species are experiencing sustained environmental change mainly due to human activities. The unusual rate and extent of anthropogenic alterations of the environment may exceed the capacity of developmental, genetic, and demographic mechanisms that populations have evolved to deal with environmental change. To begin to understand the limits to population persistence, we present a simple evolutionary model for the critical rate of environmental change beyond which a population must decline and go extinct. We use this model to highlight the major determinants of extinction risk in a changing environment, and identify research needs for improved predictions based on projected changes in environmental variables. Two key parameters relating the environment to population biology have not yet received sufficient attention. Phenotypic plasticity, the direct influence of environment on the development of individual phenotypes, is increasingly considered an important component of phenotypic change in the wild and should be incorporated in models of population persistence. Environmental sensitivity of selection, the change in the optimum phenotype with the environment, still crucially needs empirical assessment. We use environmental tolerance curves and other examples of ecological and evolutionary responses to climate change to illustrate how these mechanistic approaches can be developed for predictive purposes.

  2. Recursive Parameter Method for Computing the Predicting Function of the Multivariable ARMAX Model

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    New method for computing the predicting function of the ARMAX model is proposed. The proposed method constructs a set of schemes for recursively computing the parameters in predicting function of the ARMAX model. In contrast to the existing method, that only gives results for the special case of the ARX model, the method presented is suitable not only for an SISO system, but also for an MIMO system. For the SISO system, the method presented here is even more convenient than the exisiting ones.

  3. Functional-environmental assessment of Chernozems' technogenic changes in the Central-Chernozem Region of Russia

    Science.gov (United States)

    Deviatova, Tatiana; Jablonskikh, Lidiia; Alaeva, Liliia; Negrobova, Elena

    2015-04-01

    Long-term research revealed the significant changes in Chernozems of the recreational, urban, industrial and transport areas in the eastern part of the Central-Chernozem Region of Russia. They are reflected in the soil properties and regimes disturbances that determine their environmental functions. The level of the Chernozems' anthropogenic degradation is usually determined not only by their pollutants composition and quantity but by landscape, microclimatic, hydrological and soil features too. The Chernozems strongest degradation has been observed in the industrial zone and central part of Voronezh, and also in the 20-m zone of the highway "Don" with maximum technogenic input intensity and depth. The Chernozems' resistance to contamination is determined by their texture, organic matter content and quality, microbial activity and biochemical processes, pH and redox power. The level of the pollution impact on the organic substances decomposition can be evaluated according to the extracellular biological processes changes from their standard rates: 50% - very hazardous (ecotoxicological scale). The investigated soil types and subtypes have essentially different resistance to their contamination. In case of the gray forest soils already medium input of pollutants often results in irreversible changes in their biocenosis functions. In case of the leached Chernozems 50%-drop in their biological state occurs only at high levels of pollution. The developed criteria reflect the man-made ecosystems' soil principal changes and can be useful in prediction of their environmental functions.

  4. Connectome organization is related to longitudinal changes in general functioning, symptoms and IQ in chronic schizophrenia.

    Science.gov (United States)

    Collin, G; de Nijs, J; Hulshoff Pol, H E; Cahn, W; van den Heuvel, M P

    2016-06-01

    Emerging evidence suggests schizophrenia to involve widespread alterations in the macroscale wiring architecture of the human connectome. Recent findings of attenuated connectome alterations in unaffected siblings of schizophrenia patients suggest that altered connectome organization may relate to the vulnerability to develop the disorder, but whether it relates to progression of illness after disease onset is currently unknown. Here, we examined the interaction between connectome structure and longitudinal changes in general functioning, clinical symptoms and IQ in the 3years following MRI assessment in a group of chronically ill schizophrenia patients. Effects in patients were compared to associations between connectome organization and changes in subclinical symptoms and IQ in healthy controls and unaffected siblings of schizophrenia patients. Analyzing the patient sample revealed a relationship between structural connectivity-particularly among central 'brain hubs'-and progressive changes in general functioning (p=0.007), suggesting that more prominent impairments of hub connectivity may herald future functional decline. Our findings further indicate that affected local connectome organization relates to longitudinal increases in overall PANSS symptoms (p=0.013) and decreases in total IQ (p=0.003), independent of baseline symptoms and IQ. No significant associations were observed in controls and siblings, suggesting that the findings in patients represent effects of ongoing illness, as opposed to normal time-related changes. In all, our findings suggest connectome structure to have predictive value for the course of illness in schizophrenia. PMID:25843919

  5. Application of maximin correlation analysis to classifying protein environments for function prediction.

    Science.gov (United States)

    Lee, Taehoon; Min, Hyeyoung; Kim, Seung Jean; Yoon, Sungroh

    2010-09-17

    More and more protein structures are being discovered, but most of these still have little functional information. Based on the assumption that structural resemblance would lead to functional similarity, researchers computationally compare a new structure with functionally annotated structures, for high-throughput function prediction. The effectiveness of this approach depends critically upon the quality of comparison. In particular, robust classification often becomes difficult when a function class is an aggregate of multiple subclasses, as is the case with protein annotations. For such multiple-subclass classification problems, an optimal method termed the maximin correlation analysis (MCA) was proposed. However, MCA has never been applied to automated protein function prediction although MCA can minimize the misclassification risk in the correlation-based nearest neighbor classification, thus increasing classification accuracy. In this article, we apply MCA to classifying three-dimensional protein local environment data derived from a subset of the protein data bank (PDB). In our framework, the MCA-based classifier outperformed the compared alternatives by 7-19% and 6-27% in terms of average sensitivity and specificity, respectively. Given that correlation-based similarity measures have been widely used for mining protein data, we expect that MCA would be employed to enhance other types of automated function prediction methods. PMID:20719237

  6. Weaknesses in executive functioning predict the initiating of adolescents’ alcohol use

    Directory of Open Access Journals (Sweden)

    Margot Peeters

    2015-12-01

    Full Text Available Recently, it has been suggested that impairments in executive functioning might be risk factors for the onset of alcohol use rather than a result of heavy alcohol use. In the present study, we examined whether two aspects of executive functioning, working memory and response inhibition, predicted the first alcoholic drink and first binge drinking episode in young adolescents using discrete survival analyses. Adolescents were selected from several Dutch secondary schools including both mainstream and special education (externalizing behavioral problems. Participants were 534 adolescents between 12 and 14 years at baseline. Executive functioning and alcohol use were assessed four times over a period of two years. Working memory uniquely predicted the onset of first drink (p = .01 and first binge drinking episode (p = .04 while response inhibition only uniquely predicted the initiating of the first drink (p = .01. These results suggest that the association of executive functioning and alcohol consumption found in former studies cannot simply be interpreted as an effect of alcohol consumption, as weaknesses in executive functioning, found in alcohol naïve adolescents, predict the initiating of (binge drinking. Though, prolonged and heavy alcohol use might further weaken already existing deficiencies.

  7. Renographic indices for evaluation of changes in graft function

    International Nuclear Information System (INIS)

    Radionuclide renal diagnostic studies play an important role in assessing renal allograft function, especially in the early post-transplant period. In the past two decades various quantitative parameters have been derived from the radionuclide renogram to evaluate changes in perfusion and/or function of the kidney allograft. In this review article we discuss the quantitative parameters that have been used to assess graft condition, with emphasis on the early postoperative period. These quantitative methods are divided into parameters used for assessing renal graft perfusion and parameters used for evaluating parenchymal function. The blood flow in renal transplants can be quantified (a) by measuring the rate of activity appearance in the kidney graft, (b) by calculating the ratio of the integral activity under the transplanted kidney and arterial curves and (c) by calculating the renal vascular transit time. In this article we review a number of parenchymal uptake and excretion indices, such as the accumulation index, the graft uptake capacity at 2 and 10 min, the excretion index and the elimination index. The literature on these parameters shows that they have some practical disadvantages. In addition, values suffer from significant overlap when various graft pathologies coexist. A retrospective study was designed in our institution to evaluate the clinical usefulness of some of the frequently used previously published methods in which the graft function is quantitatively assessed in the early post-transplant period. The quantitative parameters studied which were reasonably reproducible in our hands included: global perfusion index (GPI), cortical perfusion index (CPI), vascular transit time, and the parenchymal parameters uptake capacity at 2 min (UC2) and elimination index (K3/20). The patient population in this study consisted of 43 patients with 157 technetium-99m mercaptylacetyltriglycine renograms. The perfusion indices GPI and CPI did not allow

  8. Renographic indices for evaluation of changes in graft function

    Energy Technology Data Exchange (ETDEWEB)

    El-Maghraby, T.A.F.; Eck-Smit, B.L.F. van; Pauwels, E.K.J. [Division of Nuclear Medicine, Department of Radiology, Leiden University Medical Centre, Leiden (Netherlands); Fijter, J.W. de [Department of Nephrology, Leiden University Medical Centre, Leiden (Netherlands); Zwinderman, A.H. [Department of Medical Statistics, Leiden University Medical Centre, Leiden (Netherlands); El-Haddad, S.I. [Department of Oncology and Nuclear Medicine, Cairo University (Egypt)

    1998-11-01

    Radionuclide renal diagnostic studies play an important role in assessing renal allograft function, especially in the early post-transplant period. In the past two decades various quantitative parameters have been derived from the radionuclide renogram to evaluate changes in perfusion and/or function of the kidney allograft. In this review article we discuss the quantitative parameters that have been used to assess graft condition, with emphasis on the early postoperative period. These quantitative methods are divided into parameters used for assessing renal graft perfusion and parameters used for evaluating parenchymal function. The blood flow in renal transplants can be quantified (a) by measuring the rate of activity appearance in the kidney graft, (b) by calculating the ratio of the integral activity under the transplanted kidney and arterial curves and (c) by calculating the renal vascular transit time. In this article we review a number of parenchymal uptake and excretion indices, such as the accumulation index, the graft uptake capacity at 2 and 10 min, the excretion index and the elimination index. The literature on these parameters shows that they have some practical disadvantages. In addition, values suffer from significant overlap when various graft pathologies coexist. A retrospective study was designed in our institution to evaluate the clinical usefulness of some of the frequently used previously published methods in which the graft function is quantitatively assessed in the early post-transplant period. The quantitative parameters studied which were reasonably reproducible in our hands included: global perfusion index (GPI), cortical perfusion index (CPI), vascular transit time, and the parenchymal parameters uptake capacity at 2 min (UC{sub 2}) and elimination index (K{sub 3/20}). The patient population in this study consisted of 43 patients with 157 technetium-99m mercaptylacetyltriglycine renograms. The perfusion indices GPI and CPI did not allow

  9. The predicted influence of climate change on lesser prairie-chicken reproductive parameters

    Science.gov (United States)

    Grisham, Blake A.; Boal, Clint W.; Haukos, David A.; Davis, Dawn M.; Boydston, Kathy K.; Dixon, Charles; Heck, Willard R.

    2013-01-01

    The Southern High Plains is anticipated to experience significant changes in temperature and precipitation due to climate change. These changes may influence the lesser prairie-chicken (Tympanuchus pallidicinctus) in positive or negative ways. We assessed the potential changes in clutch size, incubation start date, and nest survival for lesser prairie-chickens for the years 2050 and 2080 based on modeled predictions of climate change and reproductive data for lesser prairie-chickens from 2001–2011 on the Southern High Plains of Texas and New Mexico. We developed 9 a priori models to assess the relationship between reproductive parameters and biologically relevant weather conditions. We selected weather variable(s) with the most model support and then obtained future predicted values from climatewizard.org. We conducted 1,000 simulations using each reproductive parameter’s linear equation obtained from regression calculations, and the future predicted value for each weather variable to predict future reproductive parameter values for lesser prairie-chickens. There was a high degree of model uncertainty for each reproductive value. Winter temperature had the greatest effect size for all three parameters, suggesting a negative relationship between above-average winter temperature and reproductive output. The above-average winter temperatures are correlated to La Niña events, which negatively affect lesser prairie-chickens through resulting drought conditions. By 2050 and 2080, nest survival was predicted to be below levels considered viable for population persistence; however, our assessment did not consider annual survival of adults, chick survival, or the positive benefit of habitat management and conservation, which may ultimately offset the potentially negative effect of drought on nest survival.

  10. Translational research and functional changes in voiding function in older adults

    Science.gov (United States)

    Kullmann, F. Aura; Birder, Lori Ann; Andersson, Karl-Erik

    2016-01-01

    Synopsis This article describes a number of changes in lower urinary tract (LUT) function that occurs in the aging population as well as in animal models. Age-related LUT dysfunctions result from complex processes controlled by multiple genetic, epigenetic and environmental factors and accounts for high costs of healthcare. While the underlying factors that contribute to patient symptoms are not known, this article will discuss a number of risk factors that may play a role in age- related LUT dysfunction. In addition, while limited data is available using animal models of aging, there is evidence that many of the structural and functional changes observed in these studies appear to be similar to those observed in humans. A better understanding of factors and mechanisms underlying LUTS in the older population may lead to therapeutic interventions which may be used to reduce these dysfunctions. PMID:26476114

  11. Safety Performance Improvement for Nuclear Power Plants Using THOMAS and Accident Prediction Function

    International Nuclear Information System (INIS)

    The environments of nuclear industry are changed by incoming of digital technology. Until now, the nuclear power plant was adhering to analogue system in the large part of system. However the reliability of digital technology is increased, the adopting of digital technology is accelerated in the nuclear industry. It is not exception of the part of monitoring system. Digital based thermal hydraulics online monitoring advisory system of nuclear power plant, as called THOMAS, which is can be developed economically compared with existing monitoring system is used for the decision making tool in the accident condition. We selected the Ulchin 3 and 4 units which is the type of Korea Standard Nuclear Power Plant(KSNP) as reference plant. For nuclear power plants, EOPs (Emergency Operating Procedures) help operators to diagnose and analyze accidents. But it is very difficult that operators diagnose and analyze similar accidents with EOPs in a given short time. There are also possibilities to follow wrong procedures due to complex and extensive procedures. Therefore, it is important to develop a methodology for diagnosing accidents in a short time and reduction of human errors that made by complex signals and indicators. THOMAS has a function of decision making using influence diagram logic. The influence diagram logic is based on total probability and Bayesian theory. And also the accident modeling is based on emergency operating procedure(EOP). The final goal of this system is, in the accident situation, to present the success path to the operator for the recovery of system. In this paper, at first, we will deal briefly with total system of THOMAS. And then 3D visualized window and accident prediction function will be introduced in detail

  12. Predicting critical temperatures of iron(II) spin crossover materials: Density functional theory plus U approach

    International Nuclear Information System (INIS)

    A first-principles study of critical temperatures (Tc) of spin crossover (SCO) materials requires accurate description of the strongly correlated 3d electrons as well as much computational effort. This task is still a challenge for the widely used local density or generalized gradient approximations (LDA/GGA) and hybrid functionals. One remedy, termed density functional theory plus U (DFT+U) approach, introduces a Hubbard U term to deal with the localized electrons at marginal computational cost, while treats the delocalized electrons with LDA/GGA. Here, we employ the DFT+U approach to investigate the Tc of a pair of iron(II) SCO molecular crystals (α and β phase), where identical constituent molecules are packed in different ways. We first calculate the adiabatic high spin-low spin energy splitting ΔEHL and molecular vibrational frequencies in both spin states, then obtain the temperature dependent enthalpy and entropy changes (ΔH and ΔS), and finally extract Tc by exploiting the ΔH/T − T and ΔS − T relationships. The results are in agreement with experiment. Analysis of geometries and electronic structures shows that the local ligand field in the α phase is slightly weakened by the H-bondings involving the ligand atoms and the specific crystal packing style. We find that this effect is largely responsible for the difference in Tc of the two phases. This study shows the applicability of the DFT+U approach for predicting Tc of SCO materials, and provides a clear insight into the subtle influence of the crystal packing effects on SCO behavior

  13. Omega-6 and omega-3 fatty acids predict accelerated decline of peripheral nerve function in older persons.

    Science.gov (United States)

    Lauretani, F; Bandinelli, S; Bartali, B; Benedetta, B; Cherubini, A; Iorio, A D; Blè, A; Giacomini, V; Corsi, A M; Guralnik, J M; Ferrucci, L

    2007-07-01

    Pre-clinical studies suggest that both omega-6 and omega-3 fatty acids have beneficial effects on peripheral nerve function. Rats feed a diet rich in polyunsaturated fatty acids (PUFAs) showed modification of phospholipid fatty acid composition in nerve membranes and improvement of sciatic nerve conduction velocity (NCV). We tested the hypothesis that baseline plasma omega-6 and omega-3 fatty acids levels predict accelerated decline of peripheral nerve function. Changes between baseline and the 3-year follow-up in peripheral nerve function was assessed by standard surface ENG of the right peroneal nerve in 384 male and 443 female participants of the InCHIANTI study (age range: 24-97 years). Plasma concentrations of selected fatty acids assessed at baseline by gas chromatography. Independent of confounders, plasma omega-6 fatty acids and linoleic acid were significantly correlated with peroneal NCV at enrollment. Lower plasma PUFA, omega-6 fatty acids, linoleic acid, ratio omega-6/omega-3, arachidonic acid and docosahexanoic acid levels were significantly predicted a steeper decline in nerve function parameters over the 3-year follow-up. Low plasma omega-6 and omega-3 fatty acids levels were associated with accelerated decline of peripheral nerve function with aging. PMID:17594339

  14. Effort, Anhedonia, and Function in Schizophrenia: Reduced Effort Allocation Predicts Amotivation and Functional Impairment

    OpenAIRE

    Deanna M Barch; Treadway, Michael; Schoen, Nathan

    2014-01-01

    One of the most debilitating aspects of schizophrenia is an apparent of interest in or ability to exert effort for rewards. Such “negative symptoms” may prevent individuals from obtaining potentially beneficial outcomes in educational, occupational or social domains. In animal models, dopamine abnormalities decrease willingness to work for rewards, implicating DA function as a candidate substrate for negative symptoms given that schizophrenia involves dysregulation of the dopamine system. We ...

  15. Functional connectivity classification of autism identifies highly predictive brain features but falls short of biomarker standards

    OpenAIRE

    Mark Plitt; Kelly Anne Barnes; Alex Martin

    2015-01-01

    Objectives: Autism spectrum disorders (ASD) are diagnosed based on early-manifesting clinical symptoms, including markedly impaired social communication. We assessed the viability of resting-state functional MRI (rs-fMRI) connectivity measures as diagnostic biomarkers for ASD and investigated which connectivity features are predictive of a diagnosis. Methods: Rs-fMRI scans from 59 high functioning males with ASD and 59 age- and IQ-matched typically developing (TD) males were used to build ...

  16. Less-structured time in children's daily lives predicts self-directed executive functioning

    OpenAIRE

    Barker, Jane E.; Semenov, Andrei D.; Michaelson, Laura; Provan, Lindsay S.; Snyder, Hannah R.; Munakata, Yuko

    2014-01-01

    Executive functions (EFs) in childhood predict important life outcomes. Thus, there is great interest in attempts to improve EFs early in life. Many interventions are led by trained adults, including structured training activities in the lab, and less-structured activities implemented in schools. Such programs have yielded gains in children's externally-driven executive functioning, where they are instructed on what goal-directed actions to carry out and when. However, it is less clear how ch...

  17. Weaknesses in executive functioning predict the initiating of adolescents’ alcohol use.

    OpenAIRE

    Margot Peeters; Tim Janssen; Karin Monshouwer; Wouter Boendermaker; Thomas Pronk; Reinout Wiers; Wilma Vollebergh

    2015-01-01

    Recently, it has been suggested that impairments in executive functioning might be risk factors for the onset of alcohol use rather than a result of heavy alcohol use. In the present study, we examined whether two aspects of executive functioning, working memory and response inhibition, predicted the first alcoholic drink and first binge drinking episode in young adolescents using discrete survival analyses. Adolescents were selected from several Dutch secondary schools including both mainstr...

  18. Specific Measures of Executive Function Predict Cognitive Decline in Older Adults

    OpenAIRE

    Clark, Lindsay R.; Schiehser, Dawn M.; Weissberger, Gali H.; Salmon, David P.; Delis, Dean C.; Bondi, Mark W.

    2011-01-01

    Decline in executive function has been noted in the prodromal stage of Alzheimer’s disease (AD) and may presage more global cognitive declines. In this prospective longitudinal study, five measures of executive function were used to predict subsequent global cognitive decline in initially nondemented older adults. Of 71 participants, 15 demonstrated significant decline over a 1-year period on the Dementia Rating Scale (Mattis, 1988) and the remaining participants remained stable. In the year ...

  19. Computational RNomics:Structure identification and functional prediction of non-coding RNAs in silico

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The eukaryotic genome contains varying numbers of non-coding RNA(ncRNA) genes."Computational RNomics" takes a multidisciplinary approach,like information science,to resolve the structure and function of ncRNAs.Here,we review the main issues in "Computational RNomics" of data storage and management,ncRNA gene identification and characterization,ncRNA target identification and functional prediction,and we summarize the main methods and current content of "computational RNomics".

  20. On the adequacy of wall functions to predict condensation rates from steam-noncondensable gas mixtures

    International Nuclear Information System (INIS)

    Highlights: • Work investigates the effect of near-wall mesh resolution on CFD predictions. • Case study: turbulent condensation in the presence of noncondensable gases. • Wall functions largely underpredict condensation rates at boundary layer onset. • When boundary layer is developed, wall functions predictions are reasonable. • Prescribed wall functions must be compatible with prevailing flow regime. - Abstract: As one looks forward to applying CFD based methods to simulate turbulent flows in larger volumes up to containment scales, the mesh resolution, especially near the walls, becomes one of the main issues dictating the feasibility of the simulation. The wall-function approach is a natural choice to minimize the computational size of the problem and make it tractable. In the current investigation, we compare the wall-function to the fully resolved boundary layer approaches for the prediction of vapor condensation rates on cold walls in the presence of noncondensable gases. We simulate three sets of geometric configurations. The first two sets relate to domains which are small (height of 2 m) and medium (height 4.8 m), and for which experimental heat transfer data are available. In the third set, we look at a hypothetical large 2D rectangular domain in which the condenser height is comparable to that of typical NPP containments (20 m). In the developing region of the boundary layer, it is found that the wall function treatment leads to substantial deviations from the wall resolved approach and available experimental data. Further downstream, however, when the boundary layer is fully developed, the discrepancy is greatly reduced. It is therefore concluded that the wall-function formulation is able to provide predictions of condensation rates that are similar to wall-resolved treatments in simple forced flows for which fully developed boundary layers can be assumed over most of the domain. Care must however be exercised to ensure the chosen wall

  1. Personality and Community Prevention Teams: Dimensions of Team Leader and Member Personality Predicting Team Functioning

    OpenAIRE

    Feinberg, Mark E; Kim, Ji-Yeon; Greenberg, Mark T.

    2008-01-01

    The predictors and correlates of positive functioning among community prevention teams have been examined in a number of research studies; however, the role of personality has been neglected. In this study, we examined whether team member and leader personality dimensions assessed at the time of team formation predicted local prevention team functioning 2.5 – 3.5 years later. Participants were 159 prevention team members in 14 communities participating in the PROSPER study of prevention progr...

  2. AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation

    Directory of Open Access Journals (Sweden)

    Majid Masso

    2014-01-01

    Full Text Available The AUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins upon single residue substitutions, developed by combining structure-based features with trained statistical learning models. Three of the predictors evaluate changes to protein stability upon mutation, each complementing a distinct experimental approach. Two additional classifiers are available, one for predicting activity changes due to residue replacements and the other for determining the disease potential of mutations associated with nonsynonymous single nucleotide polymorphisms (nsSNPs in human proteins. These five command-line driven tools, as well as all the supporting programs, complement those that run our AUTO-MUTE web-based server. Nevertheless, all the codes have been rewritten and substantially altered for the new portable software, and they incorporate several new features based on user feedback. Included among these upgrades is the ability to perform three highly requested tasks: to run “big data” batch jobs; to generate predictions using modified protein data bank (PDB structures, and unpublished personal models prepared using standard PDB file formatting; and to utilize NMR structure files that contain multiple models.

  3. AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation.

    Science.gov (United States)

    Masso, Majid; Vaisman, Iosif I

    2014-01-01

    The AUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins upon single residue substitutions, developed by combining structure-based features with trained statistical learning models. Three of the predictors evaluate changes to protein stability upon mutation, each complementing a distinct experimental approach. Two additional classifiers are available, one for predicting activity changes due to residue replacements and the other for determining the disease potential of mutations associated with nonsynonymous single nucleotide polymorphisms (nsSNPs) in human proteins. These five command-line driven tools, as well as all the supporting programs, complement those that run our AUTO-MUTE web-based server. Nevertheless, all the codes have been rewritten and substantially altered for the new portable software, and they incorporate several new features based on user feedback. Included among these upgrades is the ability to perform three highly requested tasks: to run "big data" batch jobs; to generate predictions using modified protein data bank (PDB) structures, and unpublished personal models prepared using standard PDB file formatting; and to utilize NMR structure files that contain multiple models. PMID:25197272

  4. An Improved Optimal Slip Ratio Prediction considering Tyre Inflation Pressure Changes

    Directory of Open Access Journals (Sweden)

    Guoxing Li

    2015-01-01

    Full Text Available The prediction of optimal slip ratio is crucial to vehicle control systems. Many studies have verified there is a definitive impact of tyre pressure change on the optimal slip ratio. However, the existing method of optimal slip ratio prediction has not taken into account the influence of tyre pressure changes. By introducing a second-order factor, an improved optimal slip ratio prediction considering tyre inflation pressure is proposed in this paper. In order to verify and evaluate the performance of the improved prediction, a cosimulation platform is developed by using MATLAB/Simulink and CarSim software packages, achieving a comprehensive simulation study of vehicle braking performance cooperated with an ABS controller. The simulation results show that the braking distances and braking time under different tyre pressures and initial braking speeds are effectively shortened with the improved prediction of optimal slip ratio. When the tyre pressure is slightly lower than the nominal pressure, the difference of braking performances between original optimal slip ratio and improved optimal slip ratio is the most obvious.

  5. PROTS-RF: a robust model for predicting mutation-induced protein stability changes.

    Directory of Open Access Journals (Sweden)

    Yunqi Li

    Full Text Available The ability to improve protein thermostability via protein engineering is of great scientific interest and also has significant practical value. In this report we present PROTS-RF, a robust model based on the Random Forest algorithm capable of predicting thermostability changes induced by not only single-, but also double- or multiple-point mutations. The model is built using 41 features including evolutionary information, secondary structure, solvent accessibility and a set of fragment-based features. It achieves accuracies of 0.799,0.782, 0.787, and areas under receiver operating characteristic (ROC curves of 0.873, 0.868 and 0.862 for single-, double- and multiple- point mutation datasets, respectively. Contrary to previous suggestions, our results clearly demonstrate that a robust predictive model trained for predicting single point mutation induced thermostability changes can be capable of predicting double and multiple point mutations. It also shows high levels of robustness in the tests using hypothetical reverse mutations. We demonstrate that testing datasets created based on physical principles can be highly useful for testing the robustness of predictive models.

  6. Functional Task Test: 2. Spaceflight-Induced Cardiovascular Change and Recovery During NASA's Functional Task Test

    Science.gov (United States)

    Phillips, Tiffany; Arzeno, Natalia M.; Stenger, Michael; Lee, Stuart M. C.; Bloomberg, Jacob J.; Platts, Steven H.

    2011-01-01

    The overall objective of the functional task test (FTT) is to correlate spaceflight-induced physiological adaptations with changes in performance of high priority exploration mission-critical tasks. This presentation will focus on the recovery from fall/stand test (RFST), which measures the cardiovascular response to the transition from the prone posture (simulated fall) to standing in normal gravity, as well as heart rate (HR) during 11 functional tasks. As such, this test describes some aspects of spaceflight-induced cardiovascular deconditioning and the course of recovery in Space Shuttle and International Space Station (ISS) astronauts. The sensorimotor and neuromuscular components of the FTT are described in two separate abstracts: Functional Task Test 1 and 3.

  7. Physics-Based Predictions for Coherent Change Detection Using X-Band Synthetic Aperture Radar

    Directory of Open Access Journals (Sweden)

    Mark Preiss

    2005-12-01

    Full Text Available A theoretical model is developed to describe the interferometric coherency between pairs of SAR images of rough soil surfaces. The model is derived using a dyadic form for surface reflectivity in the Kirchhoff approximation. This permits the combination of Kirchhoff theory and spotlight synthetic aperture radar (SAR image formation theory. The resulting model is used to describe the interferometric coherency between pairs of SAR images of rough soil surfaces. The theoretical model is applied to SAR images formed before and after surface changes observed by a repeat-pass SAR system. The change in surface associated with a tyre track following vehicle passage is modelled and SAR coherency estimates are obtained. Predicted coherency distributions for both the change and no-change scenarios are used to estimate receiver operator curves for the detection of the changes using a high-resolution, X-band SAR system.

  8. Predicted climate change alters the indirect effect of predators on an ecosystem process.

    Science.gov (United States)

    Lensing, Janet R; Wise, David H

    2006-10-17

    Changes in rainfall predicted to occur with global climate change will likely alter rates of leaf-litter decomposition through direct effects on primary decomposers. In a field experiment replicated at two sites, we show that altered rainfall may also change how cascading trophic interactions initiated by arthropod predators in the leaf litter indirectly influence litter decomposition. On the drier site there was no interaction between rainfall and the indirect effect of predators on decomposition. In contrast, on the moister site spiders accelerated the disappearance rate of deciduous leaf litter under low rainfall, but had no, or possibly a negative, indirect effect under high rainfall. Thus, changes resulting from the more intense hydrological cycle expected to occur with climate change will likely influence how predators indirectly affect an essential ecosystem process. PMID:17023538

  9. Predicting ecosystem shifts requires new approaches that integrate the effects of climate change across entire systems.

    Science.gov (United States)

    Russell, Bayden D; Harley, Christopher D G; Wernberg, Thomas; Mieszkowska, Nova; Widdicombe, Stephen; Hall-Spencer, Jason M; Connell, Sean D

    2012-04-23

    Most studies that forecast the ecological consequences of climate change target a single species and a single life stage. Depending on climatic impacts on other life stages and on interacting species, however, the results from simple experiments may not translate into accurate predictions of future ecological change. Research needs to move beyond simple experimental studies and environmental envelope projections for single species towards identifying where ecosystem change is likely to occur and the drivers for this change. For this to happen, we advocate research directions that (i) identify the critical species within the target ecosystem, and the life stage(s) most susceptible to changing conditions and (ii) the key interactions between these species and components of their broader ecosystem. A combined approach using macroecology, experimentally derived data and modelling that incorporates energy budgets in life cycle models may identify critical abiotic conditions that disproportionately alter important ecological processes under forecasted climates. PMID:21900317

  10. The predictive skill of species distribution models for plankton in a changing climate.

    Science.gov (United States)

    Brun, Philipp; Kiørboe, Thomas; Licandro, Priscilla; Payne, Mark R

    2016-09-01

    Statistical species distribution models (SDMs) are increasingly used to project spatial relocations of marine taxa under future climate change scenarios. However, tests of their predictive skill in the real-world are rare. Here, we use data from the Continuous Plankton Recorder program, one of the longest running and most extensive marine biological monitoring programs, to investigate the reliability of predicted plankton distributions. We apply three commonly used SDMs to 20 representative plankton species, including copepods, diatoms, and dinoflagellates, all found in the North Atlantic and adjacent seas. We fit the models to decadal subsets of the full (1958-2012) dataset, and then use them to predict both forward and backward in time, comparing the model predictions against the corresponding observations. The probability of correctly predicting presence was low, peaking at 0.5 for copepods, and model skill typically did not outperform a null model assuming distributions to be constant in time. The predicted prevalence increasingly differed from the observed prevalence for predictions with more distance in time from their training dataset. More detailed investigations based on four focal species revealed that strong spatial variations in skill exist, with the least skill at the edges of the distributions, where prevalence is lowest. Furthermore, the scores of traditional single-value model performance metrics were contrasting and some implied overoptimistic conclusions about model skill. Plankton may be particularly challenging to model, due to its short life span and the dispersive effects of constant water movements on all spatial scales, however there are few other studies against which to compare these results. We conclude that rigorous model validation, including comparison against null models, is essential to assess the robustness of projections of marine planktonic species under climate change. PMID:27040720

  11. Mothers' depressive symptoms and children's cognitive and social agency: Predicting first-grade cognitive functioning.

    Science.gov (United States)

    Yan, Ni; Dix, Theodore

    2016-08-01

    Using data from the National Institute of Child Health and Human Development (NICHD) Study of Early Child Care and Youth Development (N = 1,364), the present study supports an agentic perspective; it demonstrates that mothers' depressive symptoms in infancy predict children's poor first-grade cognitive functioning because depressive symptoms predict children's low social and cognitive agency-low motivation to initiate social interaction and actively engage in activities. When mothers' depressive symptoms were high in infancy, children displayed poor first-grade cognitive functioning due to (a) tendencies to become socially withdrawn by 36 months and low in mastery motivation by 54 months and (b) tendencies for children's low agency to predict declines in mothers' sensitivity and cognitive stimulation. Findings suggest that mothers' depressive symptoms undermine cognitive development through bidirectional processes centered on children's low motivation to engage in social interaction and initiate and persist at everyday tasks. (PsycINFO Database Record PMID:27389834

  12. The study of radionuclide lung SPECT imaging for the prediction of residual lung function

    International Nuclear Information System (INIS)

    The authors reported the prediction of residual lung function before pulmonary lobectomy by he method of radionuclide lung perfusion tomographic study. 140 cases of pulmonary disease were proved by pathologic section or operation. Among them, there were 127 primary lung cancers, 11 benign lesions and 2 metastatic lung cancers. Comparative analyses were performed between the predicted expiratory volume (PFEV1) and the actual measured volume (FEV1) after operation in 87 cases of pulmonary lobectomy, and also the Q value before and after operation in 40 cases with pulmonary lobectomy. All showed significantly correlated results, P>0.05, r = 0.9925 in the former group and P>0.05, r = 0.865 in the latter group. The derivation of the formula and the method of calculation for the prediction of residual pulmonary function were described

  13. Composite motifs integrating multiple protein structures increase sensitivity for function prediction.

    Science.gov (United States)

    Chen, Brian Y; Bryant, Drew H; Cruess, Amanda E; Bylund, Joseph H; Fofanov, Viacheslav Y; Kristensen, David M; Kimmel, Marek; Lichtarge, Olivier; Kavraki, Lydia E

    2007-01-01

    The study of disease often hinges on the biological function of proteins, but determining protein function is a difficult experimental process. To minimize duplicated effort, algorithms for function prediction seek characteristics indicative of possible protein function. One approach is to identify substructural matches of geometric and chemical similarity between motifs representing known active sites and target protein structures with unknown function. In earlier work, statistically significant matches of certain effective motifs have identified functionally related active sites. Effective motifs must be carefully designed to maintain similarity to functionally related sites (sensitivity) and avoid incidental similarities to functionally unrelated protein geometry (specificity). Existing motif design techniques use the geometry of a single protein structure. Poor selection of this structure can limit motif effectiveness if the selected functional site lacks similarity to functionally related sites. To address this problem, this paper presents composite motifs, which combine structures of functionally related active sites to potentially increase sensitivity. Our experimentation compares the effectiveness of composite motifs with simple motifs designed from single protein structures. On six distinct families of functionally related proteins, leave-one-out testing showed that composite motifs had sensitivity comparable to the most sensitive of all simple motifs and specificity comparable to the average simple motif. On our data set, we observed that composite motifs simultaneously capture variations in active site conformation, diminish the problem of selecting motif structures, and enable the fusion of protein structures from diverse data sources. PMID:17951837

  14. Individual Differences in Executive Functioning Predict Preschoolers' Improvement from Theory-of-Mind Training

    Science.gov (United States)

    Benson, Jeannette E.; Sabbagh, Mark A.; Carlson, Stephanie M.; Zelazo, Philip David

    2013-01-01

    Twenty-four 3.5-year-old children who initially showed poor performance on false-belief tasks participated in a training protocol designed to promote performance on these tasks. Our aim was to determine whether the extent to which children benefited from training was predicted by their performance on a battery of executive functioning tasks.…

  15. Mothers' Predictions of Their Son's Executive Functioning Skills: Relations to Child Behavior Problems

    Science.gov (United States)

    Johnston, Charlotte

    2011-01-01

    This study examined mothers' ability to accurately predict their sons' performance on executive functioning tasks in relation to the child's behavior problems. One-hundred thirteen mothers and their 4-7 year old sons participated. From behind a one-way mirror, mothers watched their sons perform tasks assessing inhibition and planning skills.…

  16. Executive Functioning Predicts School Readiness and Success: Implications for Assessment and Intervention

    Science.gov (United States)

    Cantin, Rachelle H.; Mann, Trisha D.; Hund, Alycia M.

    2012-01-01

    In recent years, executive functioning (EF) has received increasing attention from researchers and practitioners focusing on how EF predicts important outcomes such as success at school and in life. For example, EF has been described as the single best predictor of school readiness (Blair & Razza, 2007). Moreover, EF has been implicated in…

  17. Multiple Sequence Alignments as Tools for Protein Structure and Function Prediction

    OpenAIRE

    2003-01-01

    Multiple sequence alignments have much to offer to the understanding of protein structure, evolution and function. We are developing approaches to use this information in predicting protein-binding specificity, intra-protein and protein-protein interactions, and in reconstructing protein interaction networks.

  18. Comparison of moments from the valence structure function with QCD predictions

    International Nuclear Information System (INIS)

    Moments (both ordinary and Nachtmann) of the nucleon valence structure function measured in high Q2 γFe scattering are presented, supplemented by data from deep inelastic eD scattering. These data seem to agree with QCD predictions for vector gluons. The QCD parameter Λ is found to be of the order 0.5 GeV. (Auth.)

  19. Identification of the best DFT functionals for a reliable prediction of lignin vibrational properties

    DEFF Research Database (Denmark)

    Barsberg, Soren

    2015-01-01

    set was used. B98, X3LYP and B97-1 were the overall best-performing functionals, and “fingerprint” band positions were predicted by single-factor scaling of harmonic frequencies to an average error of ±3 cm−1 by optimized scaling factors of 1.017, 1.021 and 1.016, respectively. Their performance using...

  20. Value of plasma ADMA in predicting cardiac structure and function of patients with chronic kidney diseases

    Institute of Scientific and Technical Information of China (English)

    叶建华

    2012-01-01

    Objective To explore the predicting value of plasma asymmetric dimethylarginine (ADMA) in cardiac structure and function of patients with chronic kidney diseases(CKD). Methods A total of 100 CKD patients were enrolled in this cross-sectional study. According to staging of the

  1. Functional MRI and the Wada test provide complementary information for predicting post-operative seizure control.

    Science.gov (United States)

    Killgore, W D; Glosser, G; Casasanto, D J; French, J A; Alsop, D C; Detre, J A

    1999-12-01

    Prediction of post-surgical seizure relief and potential cognitive deficits secondary to anterior temporal lobectomy (ATL) are important to pre-surgical planning. Although the intracarotid amobarbital test (IAT) is predictive of post-ATL seizure outcome, development of non-invasive and more precise means for determining post-ATL seizure relief are needed. We previously reported on a technique utilizing functional MRI (fMRI) to evaluate the relative functional adequacy of mesial temporal lobe structures in preparation for ATL. In the present study, we report follow-up outcome data on eight temporal lobe epilepsy (TLE) patients 1-year post-ATL who were evaluated pre-surgically using IAT and fMRI. Functional memory lateralization using fMRI predicted post-ATL seizure outcome as effectively as the IAT. In general, asymmetry of functional mTL activation favouring the non-epileptic hemisphere was associated with seizure-free status at 1-year follow-up. Moreover, when combined, fMRI and IAT provided complementary data that resulted in improved prediction of post-operative seizure control compared with either procedure alone. PMID:10627406

  2. Predicting protein function by machine learning on amino acid sequences - a critical evaluation

    NARCIS (Netherlands)

    Al-Shahib, A.; Breitling, R.; Gilbert, D.R.

    2007-01-01

    Al-Shahib A, Breitling R, Gilbert DR. Biomedical Informatics Signals and Systems Research Laboratory, Department of Electronic, Electrical and Computer Engineering, The University of Birmingham, Birmingham, UK. a.alshahib@bham.ac.uk BACKGROUND: Predicting the function of newly discovered proteins by

  3. Multiple Sequence Alignments as Tools for Protein Structure and Function Prediction

    Directory of Open Access Journals (Sweden)

    Alfonso Valencia

    2006-04-01

    Full Text Available Multiple sequence alignments have much to offer to the understanding of protein structure, evolution and function. We are developing approaches to use this information in predicting protein-binding specificity, intra-protein and protein-protein interactions, and in reconstructing protein interaction networks.

  4. Comparison of an Imaging Software and Manual Prediction of Soft Tissue Changes after Orthognathic Surgery

    Directory of Open Access Journals (Sweden)

    M. S. Ahmad Akhoundi

    2012-01-01

    Full Text Available Objective: Accurate prediction of the surgical outcome is important in treating dentofacial deformities. Visualized treatment objectives usually involve manual surgical simulation based on tracing of cephalometric radiographs. Recent technical advancements have led to the use of computer assisted imaging systems in treatment planning for orthognathic surgical cases. The purpose of this study was to examine and compare the ability and reliability of digitization using Dolphin Imaging Software with traditional manual techniques and to compare orthognathic prediction with actual outcomes.Materials and Methods: Forty patients consisting of 35 women and 5 men (32 class III and 8 class II with no previous surgery were evaluated by manual tracing and indirect digitization using Dolphin Imaging Software. Reliability of each method was assessed then the two techniques were compared using paired t test.Result: The nasal tip presented the least predicted error and higher reliability. The least accurate regions in vertical plane were subnasal and upper lip, and subnasal and pogonion in horizontal plane. There were no statistically significant differences between the predictions of groups with and without genioplasty.Conclusion: Computer-generated image prediction was suitable for patient education and communication. However, efforts are still needed to improve accuracy and reliability of the prediction program and to include changes in soft tissue tension and muscle strain.

  5. Changes of left ventricular function at exercise after lung resection

    International Nuclear Information System (INIS)

    To determine the effect of lung resection on left ventricular function, 29 surgical patients were examined by using a nuclear stethoscope as a non-invasive means for measuring ventricular function at exercise. Pre- and post-operative parameters were obtained at rest and exercise. At rest, postoperative stroke volume (SV), end-diastolic volume (EDV), ejection fraction (EF), and ejection rate (ER) were significantly decreased; heart rate (HR) was significantly increased; and both filling rate (FR) and cardiac output (CO) remained unchanged. At maximum exercise, postoperative EDV, SV, ER and FR were significantly decreased; and there was no significant difference in either HR or EF, resulting in a significantly decreased CO. A ratio of CO and FR at maximum exercise to at rest was significantly decreased after surgery, as compared with that before surgery. According to the number of lobe resection, similar findings for all parameters, except for EF, were observed in the group of two lobe or more resection (n=13); and only two parameters, ER and FR, had the same tendency as those mentioned above in the group of a single lobe resection (n=16). The age group of 60 years or less (n=14) had similar findings for all parameters. In the group of 65 years or more (n=10), resting HR after surgery was not different from that before surgery; and postoperative CO was significantly decreased at rest, but not different from preoperative value at maximum exercise. In conclusion, left ventricular function associated with lung resection is reflected by decreased EDV and SV resulting from reduced pre-load. These changes may be corrected at rest, but not corrected at maximum exercise, resulting in decreased CO. More noticeable decrease in EDV and SV seems to be associated with larger lung resection. In older patients, HR is not corrected well, resulting in a decrease in CO at rest. (N.K.)

  6. Metabolic and functional connectivity changes in mal de debarquement syndrome.

    Directory of Open Access Journals (Sweden)

    Yoon-Hee Cha

    Full Text Available BACKGROUND: Individuals with mal de debarquement syndrome (MdDS experience a chronic illusion of self-motion triggered by prolonged exposure to passive motion, such as from sea or air travel. The experience is one of rocking dizziness similar to when the individual was originally on the motion trigger such as a boat or airplane. MdDS represents a prolonged version of a normal phenomenon familiar to most individuals but which persists for months or years in others. It represents a natural example of the neuroplasticity of motion adaptation. However, the localization of where that motion adaptation occurs is unknown. Our goal was to localize metabolic and functional connectivity changes associated with persistent MdDS. METHODS: Twenty subjects with MdDS lasting a median duration of 17.5 months were compared to 20 normal controls with (18F FDG PET and resting state fMRI. Resting state metabolism and functional connectivity were calculated using age, grey matter volume, and mood and anxiety scores as nuisance covariates. RESULTS: MdDS subjects showed increased metabolism in the left entorhinal cortex and amygdala (z>3.3. Areas of relative hypometabolism included the left superior medial gyrus, left middle frontal gyrus, right amygdala, right insula, and clusters in the left superior, middle, and inferior temporal gyri. MdDS subjects showed increased connectivity between the entorhinal cortex/amygdala cluster and posterior visual and vestibular processing areas including middle temporal gyrus, motion sensitive area MT/V5, superior parietal lobule, and primary visual cortex, while showing decreased connectivity to multiple prefrontal areas. CONCLUSION: These data show an association between resting state metabolic activity and functional connectivity between the entorhinal cortex and amygdala in a human disorder of abnormal motion perception. We propose a model for how these biological substrates can allow a limited period of motion exposure to lead

  7. A Regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data

    Directory of Open Access Journals (Sweden)

    Ruzzo Walter L

    2006-03-01

    Full Text Available Abstract Background As a variety of functional genomic and proteomic techniques become available, there is an increasing need for functional analysis methodologies that integrate heterogeneous data sources. Methods In this paper, we address this issue by proposing a general framework for gene function prediction based on the k-nearest-neighbor (KNN algorithm. The choice of KNN is motivated by its simplicity, flexibility to incorporate different data types and adaptability to irregular feature spaces. A weakness of traditional KNN methods, especially when handling heterogeneous data, is that performance is subject to the often ad hoc choice of similarity metric. To address this weakness, we apply regression methods to infer a similarity metric as a weighted combination of a set of base similarity measures, which helps to locate the neighbors that are most likely to be in the same class as the target gene. We also suggest a novel voting scheme to generate confidence scores that estimate the accuracy of predictions. The method gracefully extends to multi-way classification problems. Results We apply this technique to gene function prediction according to three well-known Escherichia coli classification schemes suggested by biologists, using information derived from microarray and genome sequencing data. We demonstrate that our algorithm dramatically outperforms the naive KNN methods and is competitive with support vector machine (SVM algorithms for integrating heterogenous data. We also show that by combining different data sources, prediction accuracy can improve significantly. Conclusion Our extension of KNN with automatic feature weighting, multi-class prediction, and probabilistic inference, enhance prediction accuracy significantly while remaining efficient, intuitive and flexible. This general framework can also be applied to similar classification problems involving heterogeneous datasets.

  8. Predicting early positive change in multisystemic therapy with youth exhibiting antisocial behaviors.

    Science.gov (United States)

    Tiernan, Kristine; Foster, Sharon L; Cunningham, Phillippe B; Brennan, Patricia; Whitmore, Elizabeth

    2015-03-01

    This study examined individual and family characteristics that predicted early positive change in the context of Multisystemic Therapy (MST). Families (n = 185; 65% male; average youth age 15 years) receiving MST in community settings completed assessments at the outset of treatment and 6-12 weeks into treatment. Early positive changes in youth antisocial behavior were assessed using the caregiver report on the Child Behavior Checklist Externalizing Behaviors subscale and youth report on the Self-Report Delinquency Scale. Overall, families showed significant positive changes by 6-12 weeks into treatment; these early changes were maintained into midtreatment 6-12 weeks later. Families who exhibited clinically significant gains early in treatment were more likely to terminate treatment successfully compared with those who did not show these gains. Low youth internalizing behaviors and absence of youth drug use predicted early positive changes in MST. High levels of parental monitoring and low levels of affiliation with deviant peers (mechanisms known to be associated with MST success) were also associated with early positive change. PMID:24866967

  9. On the importance of paleoclimate modelling for improving predictions of future climate change

    Directory of Open Access Journals (Sweden)

    J. C. Hargreaves

    2009-12-01

    Full Text Available We use an ensemble of runs from the MIROC3.2 AGCM with slab-ocean to explore the extent to which mid-Holocene simulations are relevant to predictions of future climate change. The results are compared with similar analyses for the Last Glacial Maximum (LGM and pre-industrial control climate. We suggest that the paleoclimate epochs can provide some independent validation of the models that is also relevant for future predictions. Considering the paleoclimate epochs, we find that the stronger global forcing and hence larger climate change at the LGM makes this likely to be the more powerful one for estimating the large-scale changes that are anticipated due to anthropogenic forcing. The phenomena in the mid-Holocene simulations which are most strongly correlated with future changes (i.e., the mid to high northern latitude land temperature and monsoon precipitation do, however, coincide with areas where the LGM results are not correlated with future changes, and these are also areas where the paleodata indicate significant climate changes have occurred. Thus, these regions and phenomena for the mid-Holocene may be useful for model improvement and validation.

  10. Predicting Climate Change Using Response Theory: Global Averages and Spatial Patterns

    Science.gov (United States)

    Lucarini, Valerio; Ragone, Francesco; Lunkeit, Frank

    2016-04-01

    The provision of accurate methods for predicting the climate response to anthropogenic and natural forcings is a key contemporary scientific challenge. Using a simplified and efficient open-source general circulation model of the atmosphere featuring O(10^5 ) degrees of freedom, we show how it is possible to approach such a problem using nonequilibrium statistical mechanics. Response theory allows one to practically compute the time-dependent measure supported on the pullback attractor of the climate system, whose dynamics is non-autonomous as a result of time-dependent forcings. We propose a simple yet efficient method for predicting—at any lead time and in an ensemble sense—the change in climate properties resulting from increase in the concentration of CO_2 using test perturbation model runs. We assess strengths and limitations of the response theory in predicting the changes in the globally averaged values of surface temperature and of the yearly total precipitation, as well as in their spatial patterns. The quality of the predictions obtained for the surface temperature fields is rather good, while in the case of precipitation a good skill is observed only for the global average. We also show how it is possible to define accurately concepts like the inertia of the climate system or to predict when climate change is detectable given a scenario of forcing. Our analysis can be extended for dealing with more complex portfolios of forcings and can be adapted to treat, in principle, any climate observable. Our conclusion is that climate change is indeed a problem that can be effectively seen through a statistical mechanical lens, and that there is great potential for optimizing the current coordinated modelling exercises run for the preparation of the subsequent reports of the Intergovernmental Panel for Climate Change.

  11. Changes in household composition as determinant of changes in functional ability among old men and women

    DEFF Research Database (Denmark)

    Avlund, Kirsten; Due, Pernille; Holstein, Bjorn E;

    2002-01-01

    functional ability are described as 1) sustained good, 2) decreased, 3) improved, and 4) sustained poor, and changes in household composition as 1) sustained living alone, 2) from living with others to living alone, and 3) sustained living with others. Number of chronic diseases and home help were included......, 19/21% deteriorated, 3/6% improved, and 14/14% had sustained poor function. Among the women in need of help at age 75, those who lived alone/became alone had a higher risk of sustained need for help from age 75 to 80 compared to women who lived with others [adjusted OR=4.0 (1.3-12.2/4.4 (0...... participated in the NORA follow-up study of 75-80 year-old men and women in Jyväskylä, Finland (N=243), Göteborg, Sweden (N=226), and Glostrup, Denmark (N=274). Functional ability was measured by tiredness and need for help in Physical and Instrumental Activities of Daily Living (PADL and IADL). Changes in...

  12. miRNA-mediated functional changes through co-regulating function related genes.

    Directory of Open Access Journals (Sweden)

    Jie He

    Full Text Available BACKGROUND: MicroRNAs play important roles in various biological processes involving fairly complex mechanism. Analysis of genome-wide miRNA microarray demonstrate that a single miRNA can regulate hundreds of genes, but the regulative extent on most individual genes is surprisingly mild so that it is difficult to understand how a miRNA provokes detectable functional changes with such mild regulation. RESULTS: To explore the internal mechanism of miRNA-mediated regulation, we re-analyzed the data collected from genome-wide miRNA microarray with bioinformatics assay, and found that the transfection of miR-181b and miR-34a in Hela and HCT-116 tumor cells regulated large numbers of genes, among which, the genes related to cell growth and cell death demonstrated high Enrichment scores, suggesting that these miRNAs may be important in cell growth and cell death. MiR-181b induced changes in protein expression of most genes that were seemingly related to enhancing cell growth and decreasing cell death, while miR-34a mediated contrary changes of gene expression. Cell growth assays further confirmed this finding. In further study on miR-20b-mediated osteogenesis in hMSCs, miR-20b was found to enhance osteogenesis by activating BMPs/Runx2 signaling pathway in several stages by co-repressing of PPARγ, Bambi and Crim1. CONCLUSIONS: With its multi-target characteristics, miR-181b, miR-34a and miR-20b provoked detectable functional changes by co-regulating functionally-related gene groups or several genes in the same signaling pathway, and thus mild regulation from individual miRNA targeting genes could have contributed to an additive effect. This might also be one of the modes of miRNA-mediated gene regulation.

  13. Performance of the tau-dependent functionals in predicting the magnetic coupling of ionic antiferromagnetic insulators.

    Science.gov (United States)

    Ciofini, Ilaria; Illas, Francesc; Adamo, Carlo

    2004-02-22

    The performance of some kinetic energy density (tau) dependent functionals in predicting the effective Heisenberg exchange has been explored using the KNiF3 and K2NiF4 insulators as case examples. Our results show that this new generation of functionals represents an important improvement with respect to the current local and gradient corrected functionals yielding a semi-quantitative description of the antiferromagnetic coupling without the need of hybrid approaches thus avoiding the calculation of exact, Hartree-Fock exchange. This feature opens a wide field of application especially in solid state. PMID:15268545

  14. Performance of the τ-dependent functionals in predicting the magnetic coupling of ionic antiferromagnetic insulators

    Science.gov (United States)

    Ciofini, Ilaria; Illas, Francesc; Adamo, Carlo

    2004-02-01

    The performance of some kinetic energy density (τ) dependent functionals in predicting the effective Heisenberg exchange has been explored using the KNiF3 and K2NiF4 insulators as case examples. Our results show that this new generation of functionals represents an important improvement with respect to the current local and gradient corrected functionals yielding a semi-quantitative description of the antiferromagnetic coupling without the need of hybrid approaches thus avoiding the calculation of exact, Hartree-Fock exchange. This feature opens a wide field of application especially in solid state.

  15. Structure-Based Activity Prediction for an Enzyme of Unknown Function

    Energy Technology Data Exchange (ETDEWEB)

    Hermann,J.; Marti-Arbona, R.; Fedorov, A.; Fedorov, E.; Almo, S.; Shoichet, B.; Raushel, F.

    2007-01-01

    With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (10{sup 5} M{sup -1} s{sup -1}). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function.

  16. Modelling changes to electricity demand load duration curves as a consequence of predicted climate change for Australia

    International Nuclear Information System (INIS)

    In this paper, we describe a method for constructing regional electricity demand data sets at 30 min intervals, which are consistent with climate change scenarios. Specifically, we modify a commonly used linear regression model between regional electricity demand and climate to also describe intraday variability in demand so that regional load duration curves (LDCs) can be predicted. The model is evaluated for four different Australian states that are participants in the Australian National Electricity Market (NEM) and the resultant data sets are found to reproduce each state's LDCs with reasonable accuracy. We also apply the demand model to CSIRO's Mk 3 global climate model data sets that have been downscaled to 60 km resolution using CSIRO's conformal-cubic atmospheric model to estimate how LDCs change as a consequence of a 1 C increase in the average temperature of Australian state capital cities. These regional electricity demand data sets are then useful for economic modelling of electricity markets such as the NEM. (author)

  17. Pressure Prediction of Coal Slurry Transportation Pipeline Based on Particle Swarm Optimization Kernel Function Extreme Learning Machine

    Directory of Open Access Journals (Sweden)

    Xue-cun Yang

    2015-01-01

    Full Text Available For coal slurry pipeline blockage prediction problem, through the analysis of actual scene, it is determined that the pressure prediction from each measuring point is the premise of pipeline blockage prediction. Kernel function of support vector machine is introduced into extreme learning machine, the parameters are optimized by particle swarm algorithm, and blockage prediction method based on particle swarm optimization kernel function extreme learning machine (PSOKELM is put forward. The actual test data from HuangLing coal gangue power plant are used for simulation experiments and compared with support vector machine prediction model optimized by particle swarm algorithm (PSOSVM and kernel function extreme learning machine prediction model (KELM. The results prove that mean square error (MSE for the prediction model based on PSOKELM is 0.0038 and the correlation coefficient is 0.9955, which is superior to prediction model based on PSOSVM in speed and accuracy and superior to KELM prediction model in accuracy.

  18. On the applicability of hybrid functionals for predicting fundamental properties of metals

    Science.gov (United States)

    Gao, Weiwei; Abtew, Tesfaye A.; Cai, Tianyi; Sun, Yi-Yang; Zhang, Shengbai; Zhang, Peihong

    2016-05-01

    The repercussions of an inaccurate account of electronic states near the Fermi level by hybrid functionals in predicting several important metallic properties are investigated. The difficulties include a vanishing or severely suppressed density of states (DOS) at EF, significantly widened valence bandwidth, greatly enhanced electron-phonon (el-ph) deformation potentials, and an overestimate of magnetic moment in transition metals. The erroneously enhanced el-ph coupling calculated by hybrid functionals may lead to a false prediction of lattice instability. The main culprit of the problem comes from the simplistic treatment of the exchange functional rooted in the original Fock exchange energy. The use of a short-ranged Coulomb interaction alleviates some of the drawbacks but the fundamental issues remain unchanged.

  19. Thalamic functional connectivity predicts seizure laterality in individual TLE patients: Application of a biomarker development strategy

    Directory of Open Access Journals (Sweden)

    Daniel S. Barron

    2015-01-01

    No significant differences in functional connection strength in patient and control groups were observed with Mann-Whitney Tests (corrected for multiple comparisons. Notwithstanding the lack of group differences, individual patient difference scores (from control mean connection strength successfully predicted seizure onset zone as shown in ROC curves: discriminant analysis (two-dimensional predicted seizure onset zone with 85% sensitivity and 91% specificity; logistic regression (four-dimensional achieved 86% sensitivity and 100% specificity. The strongest markers in both analyses were left thalamo-hippocampal and right thalamo-entorhinal cortex functional connection strength. Thus, this study shows that thalamic functional connections are sensitive and specific markers of seizure onset laterality in individual temporal lobe epilepsy patients. This study also advances an overall strategy for the programmatic development of neuroimaging biomarkers in clinical and genetic populations: a disease model informed by coordinate-based meta-analysis was used to anatomically constrain individual patient analyses.

  20. Saccadic gain adaptation is predicted by the statistics of natural fluctuations in oculomotor function

    Directory of Open Access Journals (Sweden)

    Mark V Albert

    2012-12-01

    Full Text Available Due to multiple factors such as fatigue, muscle strengthening, and neural plasticity, the responsiveness of the motor apparatus to neural commands changes over time. To enable precise movements the nervous system must adapt to compensate for these changes. Recent models of motor adaptation derive from assumptions about the way the motor apparatus changes. Characterizing these changes is difficult because motor adaptation happens at the same time, masking most of the effects of ongoing changes. Here, we analyze eye movements of monkeys with lesions to the posterior cerebellar vermis that impair adaptation. Their fluctuations better reveal the underlying changes of the motor system over time. When these measured, unadapted changes are used to derive optimal motor adaptation rules the prediction precision significantly improves. Among three models that similarly fit single-day adaptation results, the model that also matches the temporal correlations of the nonadapting saccades most accurately predicts multiple day adaptation. Saccadic gain adaptation is well matched to the natural statistics of fluctuations of the oculomotor plant.

  1. Climate Change Policies for the XXIst Century: Mechanisms, Predictions and Recommendations

    CERN Document Server

    Khmelinskii, Igor

    2011-01-01

    Recent experimental works demonstrated that the Anthropogenic Global Warming (AGW) hypothesis, embodied in a series of Intergovernmental Panel on Climate Change (IPCC) global climate models, is erroneous. These works prove that atmospheric carbon dioxide contributes only very moderately to the observed warming, and that there is no climatic catastrophe in the making, independent on whether or not carbon dioxide emissions will be reduced. In view of these developments, we discuss climate predictions for the XXIst century. Based on the solar activity tendencies, a new Little Ice Age is predicted by the middle of this century, with significantly lower global temperatures. We also show that IPCC climate models can't produce any information regarding future climate, due to essential physical phenomena lacking in those, and that the current budget deficit in many EU countries is mainly caused by the policies promoting renewable energies and other AGW-motivated measures. In absence of any predictable adverse climate...

  2. Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome

    Directory of Open Access Journals (Sweden)

    McCarthy Fiona M

    2007-11-01

    Full Text Available Abstract Background The chicken genome was sequenced because of its phylogenetic position as a non-mammalian vertebrate, its use as a biomedical model especially to study embryology and development, its role as a source of human disease organisms and its importance as the major source of animal derived food protein. However, genomic sequence data is, in itself, of limited value; generally it is not equivalent to understanding biological function. The benefit of having a genome sequence is that it provides a basis for functional genomics. However, the sequence data currently available is poorly structurally and functionally annotated and many genes do not have standard nomenclature assigned. Results We analysed eight chicken tissues and improved the chicken genome structural annotation by providing experimental support for the in vivo expression of 7,809 computationally predicted proteins, including 30 chicken proteins that were only electronically predicted or hypothetical translations in human. To improve functional annotation (based on Gene Ontology, we mapped these identified proteins to their human and mouse orthologs and used this orthology to transfer Gene Ontology (GO functional annotations to the chicken proteins. The 8,213 orthology-based GO annotations that we produced represent an 8% increase in currently available chicken GO annotations. Orthologous chicken products were also assigned standardized nomenclature based on current chicken nomenclature guidelines. Conclusion We demonstrate the utility of high-throughput expression proteomics for rapid experimental structural annotation of a newly sequenced eukaryote genome. These experimentally-supported predicted proteins were further annotated by assigning the proteins with standardized nomenclature and functional annotation. This method is widely applicable to a diverse range of species. Moreover, information from one genome can be used to improve the annotation of other genomes and

  3. Pressure Prediction of Coal Slurry Transportation Pipeline Based on Particle Swarm Optimization Kernel Function Extreme Learning Machine

    OpenAIRE

    Xue-cun Yang; Xiao-ru Yan; Chun-feng Song

    2015-01-01

    For coal slurry pipeline blockage prediction problem, through the analysis of actual scene, it is determined that the pressure prediction from each measuring point is the premise of pipeline blockage prediction. Kernel function of support vector machine is introduced into extreme learning machine, the parameters are optimized by particle swarm algorithm, and blockage prediction method based on particle swarm optimization kernel function extreme learning machine (PSOKELM) is put forward. The a...

  4. Analysis of changes in pulmonary functions at rest following humidity changes

    OpenAIRE

    Kim, Jae Hyun; Hyong, In Hyouk

    2015-01-01

    [Purpose] The purpose of this study was to compare the effect of humidity changes on the values of pulmonary function at rest. [Subjects and Methods] This study was conducted with 30 young adults (9 males, 21 females; mean age 19.4 years). Participants’ mean height was 165.1 cm, and their mean weight was 60.2 kg. The experimental setting was a laboratory in which temperature was fixed at 25 °C. Using a humidifier, relative humidity was successively to adjusted 25%, 50%, and 90%, and pulmonary...

  5. Predicting functional divergence in protein evolution by site-specific rate shifts

    Science.gov (United States)

    Gaucher, Eric A.; Gu, Xun; Miyamoto, Michael M.; Benner, Steven A.

    2002-01-01

    Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.

  6. Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE.

    Science.gov (United States)

    Rhodius, Virgil A; Mutalik, Vivek K

    2010-02-16

    Sequenced bacterial genomes provide a wealth of information but little understanding of transcriptional regulatory circuits largely because accurate prediction of promoters is difficult. We examined two important issues for accurate promoter prediction: (1) the ability to predict promoter strength and (2) the sequence properties that distinguish between active and weak/inactive promoters. We addressed promoter prediction using natural core promoters recognized by the well-studied alternative sigma factor, Escherichia coli sigma(E), as a representative of group 4 sigmas, the largest sigma group. To evaluate the contribution of sequence to promoter strength and function, we used modular position weight matrix models comprised of each promoter motif and a penalty score for suboptimal motif location. We find that a combination of select modules is moderately predictive of promoter strength and that imposing minimal motif scores distinguished active from weak/inactive promoters. The combined -35/-10 score is the most important predictor of activity. Our models also identified key sequence features associated with active promoters. A conserved "AAC" motif in the -35 region is likely to be a general predictor of function for promoters recognized by group 4 sigmas. These results provide valuable insights into sequences that govern promoter strength, distinguish active and inactive promoters for the first time, and are applicable to both in vivo and in vitro measures of promoter strength. PMID:20133665

  7. Pulmonary Function Parameters Changes at Different Altitudes in Healthy Athletes

    Directory of Open Access Journals (Sweden)

    Vahid Ziaee

    2008-06-01

    It could be concluded that changes in some pulmonary ventilatory parameters were proportional to the magnitude of change in altitude during a high-altitude trek. These changes are significant at the beginning of ascending.

  8. Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold.

    Science.gov (United States)

    Zitnik, Marinka; Zupan, Blaž

    2014-01-01

    The development of effective methods for the characterization of gene functions that are able to combine diverse data sources in a sound and easily-extendible way is an important goal in computational biology. We have previously developed a general matrix factorization-based data fusion approach for gene function prediction. In this manuscript, we show that this data fusion approach can be applied to gene function prediction and that it can fuse various heterogeneous data sources, such as gene expression profiles, known protein annotations, interaction and literature data. The fusion is achieved by simultaneous matrix tri-factorization that shares matrix factors between sources. We demonstrate the effectiveness of the approach by evaluating its performance on predicting ontological annotations in slime mold D. discoideum and on recognizing proteins of baker's yeast S. cerevisiae that participate in the ribosome or are located in the cell membrane. Our approach achieves predictive performance comparable to that of the state-of-the-art kernel-based data fusion, but requires fewer data preprocessing steps. PMID:24297565

  9. Nonlinear modeling and predictive functional control of Hammerstein system with application to the turntable servo system

    Science.gov (United States)

    Zhang, Qian; Wang, Qunjing; Li, Guoli

    2016-05-01

    This article deals with the identification of nonlinear model and Nonlinear Predictive Functional Controller (NPFC) design based on the Hammerstein structure for the turntable servo system. As a mechanism with multi-mass rotational system, nonlinearities significantly influence the system operation, especially when the turntable is in the states of zero-crossing distortion or rapid acceleration/deceleration, etc. The field data from identification experiments are processed by Comprehensive Learning Particle Swarm Optimization (CLPSO). As a result, Hammerstein model can be derived to describe the input-output relationship globally, considering all the linear and nonlinear factors of the turntable system. Cross validation results demonstrate good correspondence between the real equipment and the identified model. In the second part of this manuscript, a nonlinear control strategy based on the genetic algorithm and predictive control is developed. The global nonlinear predictive controller is carried out by two steps: (i) build the linear predictive functional controller with state space equations for the linear subsystem of Hammerstein model, and (ii) optimize the global control variable by minimizing the cost function through genetic algorithm. On the basis of distinguish model for turntable and the effectiveness of NPFC, the good performance of tracking ability is achieved in the simulation results.

  10. Energy-loss function including damping and prediction of plasmon lifetime

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen-Truong, Hieu T., E-mail: ntthieu@hcmus.edu.vn

    2014-03-01

    Highlights: • We present an approach to take damping into account of the energy loss function. • We calculate the electron inelastic mean free path for Al, Si, Cu, and Au. • We predict the values of damping and lifetime at low energies. • Influence of damping is significant in the low-energy region. • The damping value is not only energy dependent but also material dependent. - Abstract: An approach to include plasmon damping in the energy-loss function is described within the dielectric theory. Use of the energy-loss function included damping for calculating the electron inelastic mean free path yields results in good agreement with the experimental data and other theoretical results at medium–high energies. At a few eV above the Fermi energy, the present results are entirely consistent with those obtained from other measurements for Au. Also, a simple way to predict the values of damping and lifetime at low energies is described. Two values of lifetime for an electron with energy (above the Fermi energy) of 5 eV in Al and 6 eV in Au are predicted to be 2.18 fs and 1.70 fs, respectively. These predicted values are in reasonable agreement with those estimated from other measurements at the corresponding energies: 2.16 ± 0.22 fs in Al, and 1.91 ± 0.32 fs in Au.

  11. Electrocardiographic Changes Improve Risk Prediction in Asymptomatic Persons Age 65 Years or Above Without Cardiovascular Disease

    DEFF Research Database (Denmark)

    Jørgensen, Peter Godsk; Jensen, Jan S; Marott, Jacob L;

    2014-01-01

    BACKGROUND: Risk prediction in elderly patients is increasingly relevant due to longer life expectancy. OBJECTIVES: This study sought to examine whether electrocardiographic (ECG) changes provide prognostic information incremental to current risk models and to the conventional risk factors. METHODS......: In all, 6,991 participants from the Copenhagen Heart Study attending an examination at age ≥65 years were included. ECG changes were defined as Q waves, ST-segment depression, T-wave changes, ventricular conduction defects, and left ventricular hypertrophy based on the Minnesota code. The primary...... endpoint was fatal cardiovascular disease (CVD) event and the secondary was fatal or nonfatal CVD event. In our study, 2,236 fatal CVD and 3,849 fatal or nonfatal CVD events occurred during a median of 11.9 and 9.8 years of follow-up. RESULTS: ECG changes were frequently present (30.6%) and associated with...

  12. Do preoperative pulmonary function indices predict morbidity after coronary artery bypass surgery?

    Directory of Open Access Journals (Sweden)

    Mahdi Najafi

    2015-01-01

    Full Text Available Context: The reported prevalence of chronic obstructive pulmonary disease (COPD varies among different groups of cardiac surgical patients. Moreover, the prognostic value of preoperative COPD in outcome prediction is controversial. Aims: The present study assessed the morbidity in the different levels of COPD severity and the role of pulmonary function indices in predicting morbidity in patients undergoing coronary artery bypass graft (CABG. Settings and Design: Patients who were candidates for isolated CABG with cardiopulmonary bypass who were recruited for Tehran Heart Center-Coronary Outcome Measurement Study. Methods: Based on spirometry findings, diagnosis of COPD was considered based on Global Initiative for Chronic Obstructive Lung Disease category as forced expiratory volume in 1 s [FEV1]/forced vital capacity 75% predicted, mild (FEV1 60-75% predicted, moderate (FEV1 50-59% predicted, severe (FEV1<50% predicted. The preoperative pulmonary function indices were assessed as predictors, and postoperative morbidity was considered the surgical outcome. Results: This study included 566 consecutive patients. Patients with and without COPD were similar regarding baseline characteristics and clinical data. Hypertension, recent myocardial infarction, and low ejection fraction were higher in patients with different degrees of COPD than the control group while male gender was more frequent in control patients than the others. Restrictive lung disease and current cigarette smoking did not have any significant impact on postoperative complications. We found a borderline P = 0.057 with respect to respiratory failure among different patients of COPD severity so that 14.1% patients in control group, 23.5% in mild, 23.4% in moderate, and 21.9% in severe COPD categories developed respiratory failure after CABG surgery. Conclusion: Among post-CABG complications, patients with different levels of COPD based on STS definition, more frequently developed

  13. Predicting short-term weight loss using four leading health behavior change theories

    OpenAIRE

    Barata José T; Minderico Cláudia S; Martins Sandra S; Branco Teresa L; Teixeira Pedro J; Palmeira António L; Serpa Sidónio O; Sardinha Luís B

    2007-01-01

    Abstract Background This study was conceived to analyze how exercise and weight management psychosocial variables, derived from several health behavior change theories, predict weight change in a short-term intervention. The theories under analysis were the Social Cognitive Theory, the Transtheoretical Model, the Theory of Planned Behavior, and Self-Determination Theory. Methods Subjects were 142 overweight and obese women (BMI = 30.2 ± 3.7 kg/m2; age = 38.3 ± 5.8y), participating in a 16-wee...

  14. Prediction of pressure induced structural phase transitions and internal mode frequency changes in solid N2+

    International Nuclear Information System (INIS)

    A rhombohedral distortion of the Pm3n structure is introduced which shows that a low temperature phase transition occurs from P42/mnm into the R3c calcite structure at P approx. = 19.2 kbar with a volume change of 0.125 cm3/mole. This transition agrees with recent Raman scattering measurements. Another transition from R3c into R3m is predicted at P approx. = 67.5 kbar, with a volume change of 0.1 cm3/mole. The pressure dependence of the intramolecular mode frequencies for the R3c structure is in reasonably good agreement with the two main branches observed experimentally

  15. Weight suppression predicts weight change over 5 years in bulimia nervosa

    OpenAIRE

    Herzog, David B.; Thomas, J. Graham; Kass, Andrea E.; Eddy, Kamryn T.; Franko, Debra L.; Lowe, Michael R.

    2010-01-01

    Recent studies suggest that weight suppression (WS), defined as the discrepancy between current and highest past weight, predicts short-term weight gain in bulimia nervosa (BN) during treatment. The current study was designed to build on this preliminary work by examining the relation between WS and long-term weight change in BN. Treatmentseeking women (N=97) with DSM-IV BN participated in a naturalistic longitudinal follow-up study of eating disorders. At intake, height and weight were measu...

  16. Developing predictive insight into changing water systems: use-inspired hydrologic science for the Anthropocene

    OpenAIRE

    Thompson, S. E.; Sivapalan, M.; C. J. Harman; V. Srinivasan; M. R. Hipsey; Reed, P.; Montanari, A.; G. Blöschl

    2013-01-01

    Globally, many different kinds of water resources management issues call for policy- and infrastructure-based responses. Yet responsible decision-making about water resources management raises a fundamental challenge for hydrologists: making predictions about water resources on decadal- to century-long timescales. Obtaining insight into hydrologic futures over 100 yr timescales forces researchers to address internal and exogenous changes in the properties of hydrologic systems....

  17. Imperfect predictability and mutual fund dynamics. How managers use predictors in changing systematic risk.

    OpenAIRE

    Amisano, Gianni; Savona, Roberto

    2008-01-01

    Suppose a fund manager uses predictors in changing port-folio allocations over time. How does predictability translate into portfolio decisions? To answer this question we derive a new model within the Bayesian framework, where managers are assumed to modulate the systematic risk in part by observing how the benchmark returns are related to some set of imperfect predictors, and in part on the basis of their own information set. In this portfolio allocation process, managers concern themselves...

  18. Predicting the change of child’s behavior problems : sociodemographic and maternal parenting stress factors

    OpenAIRE

    Viduolienė, Evelina

    2013-01-01

    Purpose - evaluate 1) whether child's externalizing problems increase or decrease within 12 months period; 2) the change of externalizing problems with respect to child gender and age, and 3) which maternal parenting stress factors and family sociodemographic characteristics can predict the increase and decrease of child's externalizing problems. Design/methodology/approach' participants were evaluated 2 times (with the interval of 12 months) with the Parenting Stress Index (Abidin, 1990) ...

  19. PREDICTING THE CHANGE OF CHILD’S BEHAVIOR PROBLEMS: SOCIODEMOGRAPHIC AND MATERNAL PARENTING STRESS FACTORS

    OpenAIRE

    Evelina Viduoliene

    2013-01-01

    Purpose: evaluate 1) whether child’s externalizing problems increase or decrease within 12 months period; 2) the change of externalizing problems with respect to child gender and age, and 3) which maternal parenting stress factors and family sociodemographic characteristics can predict the increase and decrease of child’s externalizing problems. Design/methodology/approach: participants were evaluated 2 times (with the interval of 12 months) with the Parenting Stress Index (Abidin, 1990) a...

  20. Organizational Changes to Thyroid Regulation in Alligator mississippiensis: Evidence for Predictive Adaptive Responses

    OpenAIRE

    Boggs, Ashley S. P.; Lowers, Russell H.; Cloy-McCoy, Jessica A.; Guillette, Louis J.

    2013-01-01

    During embryonic development, organisms are sensitive to changes in thyroid hormone signaling which can reset the hypothalamic-pituitary-thyroid axis. It has been hypothesized that this developmental programming is a ‘predictive adaptive response’, a physiological adjustment in accordance with the embryonic environment that will best aid an individual's survival in a similar postnatal environment. When the embryonic environment is a poor predictor of the external environment, the developmenta...

  1. Cognitive biases to healthy and unhealthy food words predict change in BMI

    OpenAIRE

    Calitri, R.; Pothos, E. M.; Tapper, K; Brunstrom, J M; Rogers, P J

    2010-01-01

    The current study explored the predictive value of cognitive biases to food cues (assessed by emotional Stroop and dot probe tasks) on weight change over a 1-year period. This was a longitudinal study with undergraduate students (N = 102) living in shared student accommodation. After controlling for the effects of variables associated with weight (e.g., physical activity, stress, restrained eating, external eating, and emotional eating), no effects of cognitive bias were found with the dot pr...

  2. Predictive value and rate of change of blood pressure throughout adolescence : a Belgian prospective study

    OpenAIRE

    Saint-Remy, Annie; Rorive, Georges

    1991-01-01

    We performed a prospective study on the natural course of blood pressure throughout adolescence. The major goals were to assess the predictive value of a high blood pressure level at the age of 12 years and the feasibilty of developing a screening test for the early detection of young subjects at risk of developing chronic hypertension. By measuring the relationship between the initial level and subsequent changes in blood pressure, we looked for a phenomenon previously demonstrated in adults...

  3. Availability of preoperative anxiety scale as a predictive factor for hemodynamic changes during induction of anesthesia

    OpenAIRE

    Kim, Won-Sung; Byeon, Gyeong-Jo; Song, Bong-Jae; Lee, Hyeon Jeong

    2010-01-01

    Background The current study evaluated whether the level of preoperative anxiety assessed by the state-trait anxiety inventory (STAI) affects cardiovascular response during anesthetic induction. Furthermore, we evaluated the utility of the preoperative anxiety scale as a predictive factor for hemodynamic changes. Methods One hundred twenty patients who were scheduled to undergo elective surgery under general anesthesia were enrolled in this prospective study. The patients were asked to fill o...

  4. New Approaches for Crop Genetic Adaptation to the Abiotic Stresses Predicted with Climate Change

    OpenAIRE

    Robert Redden

    2013-01-01

    Extreme climatic variation is predicted with climate change this century. In many cropping regions, the crop environment will tend to be warmer with more irregular rainfall and spikes in stress levels will be more severe. The challenge is not only to raise agricultural production for an expanding population, but to achieve this under more adverse environmental conditions. It is now possible to systematically explore the genetic variation in historic local landraces by using GPS locators and w...

  5. Probing Functional Changes in Exocyst Configuration with Monoclonal Antibodies.

    Science.gov (United States)

    Inamdar, Shivangi M; Hsu, Shu-Chan; Yeaman, Charles

    2016-01-01

    Spatial regulation of exocytosis relies on the exocyst, a hetero-octameric protein complex that tethers vesicles to fusion sites at the plasma membrane. Nevertheless, our understanding of mechanisms regulating exocyst assembly/disassembly, localization, and function are incomplete. Here, we have exploited a panel of anti-Sec6 monoclonal antibodies (mAbs) to probe possible configurational changes accompanying transitions in exocyst function in epithelial MDCK cells. Sec6 is quantitatively associated with Sec8 in high molecular weight complexes, as shown by gel filtration and co-immunoprecipitation studies. We mapped epitopes recognized by more than 20 distinct mAbs to one of six Sec6 segments. Surprisingly, mAbs that bound epitopes in each segment labeled distinct subcellular structures. In general, antibodies to epitopes in N-terminal domains labeled Sec6 in either cytosolic or nuclear pools, whereas those that bound epitopes in C-terminal domains labeled membrane-associated Sec6. In this latter group, we identified antibodies that labeled distinct Sec6 populations at the apical junctional complex, desmosomes, endoplasmic reticulum and vimentin-type intermediate filaments. That each antibody was specific was verified by both Sec6 RNAi and competition with fusion proteins containing each domain. Comparison of non-polarized and polarized cells revealed that many Sec6 epitopes either redistribute or become concealed during epithelial polarization. Transitions in exocyst configurations may be regulated in part by the actions of Ral GTPases, because the exposure of Sec6 C-terminal domain epitopes at the plasma membrane is significantly reduced upon RalA RNAi. To determine whether spatio-temporal changes in epitope accessibility was correlated with differential stability of interactions between Sec6 and other exocyst subunits, we quantified relative amounts of each subunit that co-immunoprecipitated with Sec6 when antibodies to N-terminal or C-terminal epitopes were used

  6. Prediction equations for pulmonary function values in healthy children in Mashhad city, North East Iran

    Directory of Open Access Journals (Sweden)

    Syad Saleh Tabatabaie

    2014-01-01

    Full Text Available Background: Pulmonary function tests (PFTs are used in assessing physiological to clinical status of the respiratory system, which is expressed as a percentage of predicted values. Predicted PFTs values are varies in different ethnics. Predicted PFTs values were studied in a sample of Iranian children. Materials and Methods: Prediction equations for PFTs were derived from urban children in the city of Mashhad (northeast Iran. Regression analysis using height and age as independent variables was applied to provide predicted values for both sexes. PFT values were measured in 414 healthy children (192 boy and 222 female, aged 4-10 years. Forced vital capacity (FVC, forced expiratory volume in one second (FEV 1 , maximal mid-expiratory flow (MMEF, peak expiratory flow (PEF, MEF at 75%, 50% and 25% of the FVC (MEF 75 , MEF 50 and MEF 25 respectively were measured. Results: There were positive correlations between each pulmonary function variable with height and age. The largest positive correlations were found for FVC (r = 0.712, P < 0.0001 and FEV 1 (r = 0.642, P < 0.0001 in boys and girls respectively with height and for PEF (0.698, P < 0.0001 and MEF (r = 0.624, P < 0.0001 with age. Comparison of PFTs derived from the equations of the present study showed significant differences with those of several previous studies (P < 0.001 for most cases. Conclusion: A set of PFT reference values and prediction equations for both sexes has been derived using relatively large, healthy, Iranian children for the first time, which the generated results were differ from several prediction equations.

  7. Music-induced changes in functional cerebral asymmetries.

    Science.gov (United States)

    Hausmann, Markus; Hodgetts, Sophie; Eerola, Tuomas

    2016-04-01

    After decades of research, it remains unclear whether emotion lateralization occurs because one hemisphere is dominant for processing the emotional content of the stimuli, or whether emotional stimuli activate lateralised networks associated with the subjective emotional experience. By using emotion-induction procedures, we investigated the effect of listening to happy and sad music on three well-established lateralization tasks. In a prestudy, Mozart's piano sonata (K. 448) and Beethoven's Moonlight Sonata were rated as the most happy and sad excerpts, respectively. Participants listened to either one emotional excerpt, or sat in silence before completing an emotional chimeric faces task (Experiment 1), visual line bisection task (Experiment 2) and a dichotic listening task (Experiment 3 and 4). Listening to happy music resulted in a reduced right hemispheric bias in facial emotion recognition (Experiment 1) and visuospatial attention (Experiment 2) and increased left hemispheric bias in language lateralization (Experiments 3 and 4). Although Experiments 1-3 revealed an increased positive emotional state after listening to happy music, mediation analyses revealed that the effect on hemispheric asymmetries was not mediated by music-induced emotional changes. The direct effect of music listening on lateralization was investigated in Experiment 4 in which tempo of the happy excerpt was manipulated by controlling for other acoustic features. However, the results of Experiment 4 made it rather unlikely that tempo is the critical cue accounting for the effects. We conclude that listening to music can affect functional cerebral asymmetries in well-established emotional and cognitive laterality tasks, independent of music-induced changes in the emotion state. PMID:26970942

  8. National Scale Prediction of Soil Carbon Sequestration under Scenarios of Climate Change

    Science.gov (United States)

    Izaurralde, R. C.; Thomson, A. M.; Potter, S. R.; Atwood, J. D.; Williams, J. R.

    2006-12-01

    Carbon sequestration in agricultural soils is gaining momentum as a tool to mitigate the rate of increase of atmospheric CO2. Researchers from the Pacific Northwest National Laboratory, Texas A&M University, and USDA-NRCS used the EPIC model to develop national-scale predictions of soil carbon sequestration with adoption of no till (NT) under scenarios of climate change. In its current form, the EPIC model simulates soil C changes resulting from heterotrophic respiration and wind / water erosion. Representative modeling units were created to capture the climate, soil, and management variability at the 8-digit hydrologic unit (USGS classification) watershed scale. The soils selected represented at least 70% of the variability within each watershed. This resulted in 7,540 representative modeling units for 1,412 watersheds. Each watershed was assigned a major crop system: corn, soybean, spring wheat, winter wheat, cotton, hay, alfalfa, corn-soybean rotation or wheat-fallow rotation based on information from the National Resource Inventory. Each representative farm was simulated with conventional tillage and no tillage, and with and without irrigation. Climate change scenarios for two future periods (2015-2045 and 2045-2075) were selected from GCM model runs using the IPCC SRES scenarios of A2 and B2 from the UK Hadley Center (HadCM3) and US DOE PCM (PCM) models. Changes in mean and standard deviation of monthly temperature and precipitation were extracted from gridded files and applied to baseline climate (1960-1990) for each of the 1,412 modeled watersheds. Modeled crop yields were validated against historical USDA NASS county yields (1960-1990). The HadCM3 model predicted the most severe changes in climate parameters. Overall, there would be little difference between the A2 and B2 scenarios. Carbon offsets were calculated as the difference in soil C change between conventional and no till. Overall, C offsets during the first 30-y period (513 Tg C) are predicted to

  9. Predicting objective function weights from patient anatomy in prostate IMRT treatment planning

    International Nuclear Information System (INIS)

    Purpose: Intensity-modulated radiation therapy (IMRT) treatment planning typically combines multiple criteria into a single objective function by taking a weighted sum. The authors propose a statistical model that predicts objective function weights from patient anatomy for prostate IMRT treatment planning. This study provides a proof of concept for geometry-driven weight determination. Methods: A previously developed inverse optimization method (IOM) was used to generate optimal objective function weights for 24 patients using their historical treatment plans (i.e., dose distributions). These IOM weights were around 1% for each of the femoral heads, while bladder and rectum weights varied greatly between patients. A regression model was developed to predict a patient's rectum weight using the ratio of the overlap volume of the rectum and bladder with the planning target volume at a 1 cm expansion as the independent variable. The femoral head weights were fixed to 1% each and the bladder weight was calculated as one minus the rectum and femoral head weights. The model was validated using leave-one-out cross validation. Objective values and dose distributions generated through inverse planning using the predicted weights were compared to those generated using the original IOM weights, as well as an average of the IOM weights across all patients. Results: The IOM weight vectors were on average six times closer to the predicted weight vectors than to the average weight vector, usingl2 distance. Likewise, the bladder and rectum objective values achieved by the predicted weights were more similar to the objective values achieved by the IOM weights. The difference in objective value performance between the predicted and average weights was statistically significant according to a one-sided sign test. For all patients, the difference in rectum V54.3 Gy, rectum V70.0 Gy, bladder V54.3 Gy, and bladder V70.0 Gy values between the dose distributions generated by the predicted

  10. Scenario Simulation and the Prediction of Land Use and Land Cover Change in Beijing, China

    Directory of Open Access Journals (Sweden)

    Huiran Han

    2015-04-01

    Full Text Available Land use and land cover (LULC models are essential for analyzing LULC change and predicting land use requirements and are valuable for guiding reasonable land use planning and management. However, each LULC model has its own advantages and constraints. In this paper, we explore the characteristics of LULC change and simulate future land use demand by combining a CLUE-S model with a Markov model to deal with some shortcomings of existing LULC models. Using Beijing as a case study, we describe the related driving factors from land-adaptive variables, regional spatial variables and socio-economic variables and then simulate future land use scenarios from 2010 to 2020, which include a development scenario (natural development and rapid development and protection scenarios (ecological and cultivated land protection. The results indicate good consistency between predicted results and actual land use situations according to a Kappa statistic. The conversion of cultivated land to urban built-up land will form the primary features of LULC change in the future. The prediction for land use demand shows the differences under different scenarios. At higher elevations, the geographical environment limits the expansion of urban built-up land, but the conversion of cultivated land to built-up land in mountainous areas will be more prevalent by 2020; Beijing, however, still faces the most pressure in terms of ecological and cultivated land protection.

  11. Predicting short-term weight loss using four leading health behavior change theories

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    Barata José T

    2007-04-01

    Full Text Available Abstract Background This study was conceived to analyze how exercise and weight management psychosocial variables, derived from several health behavior change theories, predict weight change in a short-term intervention. The theories under analysis were the Social Cognitive Theory, the Transtheoretical Model, the Theory of Planned Behavior, and Self-Determination Theory. Methods Subjects were 142 overweight and obese women (BMI = 30.2 ± 3.7 kg/m2; age = 38.3 ± 5.8y, participating in a 16-week University-based weight control program. Body weight and a comprehensive psychometric battery were assessed at baseline and at program's end. Results Weight decreased significantly (-3.6 ± 3.4%, p Conclusion The present models were able to predict 20–30% of variance in short-term weight loss and changes in weight management self-efficacy accounted for a large share of the predictive power. As expected from previous studies, exercise variables were only moderately associated with short-term outcomes; they are expected to play a larger explanatory role in longer-term results.

  12. Striatal structure and function predict individual biases in learning to avoid pain

    Science.gov (United States)

    Eldar, Eran; Hauser, Tobias U.; Dayan, Peter; Dolan, Raymond J.

    2016-01-01

    Pain is an elemental inducer of avoidance. Here, we demonstrate that people differ in how they learn to avoid pain, with some individuals refraining from actions that resulted in painful outcomes, whereas others favor actions that helped prevent pain. These individual biases were best explained by differences in learning from outcome prediction errors and were associated with distinct forms of striatal responses to painful outcomes. Specifically, striatal responses to pain were modulated in a manner consistent with an aversive prediction error in individuals who learned predominantly from pain, whereas in individuals who learned predominantly from success in preventing pain, modulation was consistent with an appetitive prediction error. In contrast, striatal responses to success in preventing pain were consistent with an appetitive prediction error in both groups. Furthermore, variation in striatal structure, encompassing the region where pain prediction errors were expressed, predicted participants’ predominant mode of learning, suggesting the observed learning biases may reflect stable individual traits. These results reveal functional and structural neural components underlying individual differences in avoidance learning, which may be important contributors to psychiatric disorders involving pathological harm avoidance behavior. PMID:27071092

  13. Integration of relational and hierarchical network information for protein function prediction

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    Jiang Xiaoyu

    2008-08-01

    Full Text Available Abstract Background In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions. Results We propose a probabilistic framework to integrate information in relational data, in the form of a protein-protein interaction network, and a hierarchically structured database of terms, in the form of the GO database, for the purpose of protein function prediction. At the heart of our framework is a factorization of local neighborhood information in the protein-protein interaction network across successive ancestral terms in the GO hierarchy. We introduce a classifier within this framework, with computationally efficient implementation, that produces GO-term predictions that naturally obey a hierarchical 'true-path' consistency from root to leaves, without the need for further post-processing. Conclusion A cross-validation study, using data from the yeast Saccharomyces cerevisiae, shows our method offers substantial improvements over both standard 'guilt-by-association' (i.e., Nearest-Neighbor and more refined Markov random field methods, whether in their original form or when post-processed to artificially impose 'true-path' consistency. Further analysis of the results indicates that these improvements are associated with increased predictive capabilities (i.e., increased

  14. Functional MRI neurofeedback training on connectivity between two regions induces long-lasting changes in intrinsic functional network

    OpenAIRE

    Megumi, Fukuda; Yamashita, Ayumu; Kawato, Mitsuo; Imamizu, Hiroshi

    2015-01-01

    Motor or perceptual learning is known to influence functional connectivity between brain regions and induce short-term changes in the intrinsic functional networks revealed as correlations in slow blood-oxygen-level dependent (BOLD) signal fluctuations. However, no cause-and-effect relationship has been elucidated between a specific change in connectivity and a long-term change in global networks. Here, we examine the hypothesis that functional connectivity (i.e., temporal correlation between...

  15. Pre-operative Tei Index does not predict left ventricular function immediately after mitral valve repair

    Directory of Open Access Journals (Sweden)

    Chirojit Mukherjee

    2012-01-01

    Full Text Available Echocardiographic assessment of systolic left ventricular (LV function in patients with severe mitral regurgitation (MR undergoing mitral valve (MV repair can be challenging because the measurement of ejection fraction (EF or fractional area change (FAC in pathological states is of questionable value. The aim of our study was to evaluate the usefulness of the pre-operative Tei Index in predicting left ventricular EF or FAC immediately after MV repair. One hundred and thirty patients undergoing MV repair with sinus rhythm pre- and post-operatively were enrolled in this prospective study. Twenty-six patients were excluded due to absence of sinus rhythm post-operatively. Standard transesophageal examination(IE 33,Philips,Netherlands was performed before and after cardiopulmonary bypass according to the guidelines of the ASE/SCA. FAC was determined in the transgastric midpapillary short-axis view. LV EF was measured in the midesophageal four- and two-chamber view. For calculation of the Tei Index, the deep transgastric and the midesophageal four-chamber view were used. Statistical analysis was performed with SPSS 17.0. values are expressed as mean with standard deviation. LV FAC and EF decreased significantly after MV repair (FAC: 56±12% vs. 50±14%, P<0.001; EF: 58±11 vs. 50±12Έ P<0.001. The Tei Index decreased from 0.66±0.23 before MV repair to 0.41±0.19 afterwards (P<0.001. No relationship between pre-operative Tei Index and post-operative FAC or post-operative EF were found (FAC: r=−0.061, P=0.554; EF: r=−0.29, P=0.771. Conclusion: Pre-operative Tei Index is not a good predictor for post-operative FAC and EF in patients undergoing MV repair.

  16. Trait-mediated assembly processes predict successional changes in community diversity of tropical forests

    OpenAIRE

    Lasky, Jesse R.; Uriarte, María; Boukili, Vanessa K.; Chazdon, Robin L.

    2014-01-01

    The assembly of ecological communities results from multiple mechanisms acting concurrently. Disentangling their relative importance represents a major challenge. Our study quantifies the relative importance of four trait-mediated mechanisms and associated changes in functional diversity over succession. We leverage the rapid community assembly in tropical successional forests and the rich information in functional trait data and spatially explicit long-term tree demographic data. Trait corre...

  17. Risk factors and prediction for functional and chronic inflammatory bowel diseases in infants

    Directory of Open Access Journals (Sweden)

    Marushko RV

    2014-03-01

    Full Text Available Objective — to determine mainly significant risk factors and prediction for development of functional bowel disease and chronic non-ulcerative non-specific colitis in infants. Materials and methods. Retrospective studies were conducted using the method of questioning parents and analysis of medical records of 344 infants in the age from 6 months to 3 years of life, including 134 infants with functional constipation (FC , 64 infants with functional diarrhea (FD and 146 children with chronic non-specific not-ulcerative colitis (CNNC. The control group included 50 healthy children of similar age and gender. In groups of children retrospectively determined the frequency of risk factors. To compare the data between different groups was used analysis of Pearson c2 criteria and relative risks (relative risk, RR with 95% confidence intervals. Prediction for the development of FC, FD and CNNC was applied the method of discriminant function analysis based on the analysis of 51 essential marks. Results. Mathematical analysis of risk factors for bowel diseases allowed to identify the most important of them, in particular, family history of diseases of the digestive system, including bowel disease, complications during pregnancy and at birth disorders, women chronic extragenital diseases, chronic diseases of women characterized by prolonged exposure in the body to opportunistic or pathogenic bacteria, nutritional and feeding disorders, high infection index and history of infectious diseases. Revealed by the discriminant function analysis significant risk factors, represent their important role in the development of functional bowel disorders and chronic non-specific non-ulcerative colitis. Conclusions. Identifying the risk factors for the development and application of prediction algorithm for functional bowel diseases and chronic non-specific non-ulcerative colitis is enable to develop the effective treatment and preventive measures to reduce the

  18. Prediction and extension of curves of distillation of vacuum residue using probability functions

    Science.gov (United States)

    León, A. Y.; Riaño, P. A.; Laverde, D.

    2016-02-01

    The use of the probability functions for the prediction of crude distillation curves has been implemented in different characterization studies for refining processes. The study of four functions of probability (Weibull extreme, Weibull, Kumaraswamy and Riazi), was analyzed in this work for the fitting of curves of distillation of vacuum residue. After analysing the experimental data was selected the Weibull extreme function as the best prediction function, the fitting capability of the best function was validated considering as criterions of estimation the AIC (Akaike Information Criterion), BIC (Bayesian information Criterion), and correlation coefficient R2. To cover a wide range of composition were selected fifty-five (55) vacuum residue derived from different hydrocarbon mixture. The parameters of the probability function Weibull Extreme were adjusted from simple measure properties such as Conradson Carbon Residue (CCR), and compositional analysis SARA (saturates, aromatics, resins and asphaltenes). The proposed method is an appropriate tool to describe the tendency of distillation curves and offers a practical approach in terms of classification of vacuum residues.

  19. Assessing physiological responses of dune forest functional groups to changing water availability: from Tropics to Mediterranean.

    Science.gov (United States)

    Antunes, Cristina; Lo Cascio, Mauro; Correia, Otília; Vieira, Simone; Cruz Diaz Barradas, Maria; Zunzunegui, Maria; Ramos, Margarida; João Pereira, Maria; Máguas, Cristina

    2014-05-01

    Alterations in water availability are important to vegetation as can produce dramatic changes in plant communities, on physiological performance or survival of plant species. Particularly, groundwater lowering and surface water diversions will affect vulnerable coastal dune forests, ecosystems particularly sensitive to groundwater limitation. Reduction of water tables can prevent the plants from having access to one of their key water sources and inevitably affect groundwater-dependent species. The additional impact of drought due to climatic change on groundwater-dependent ecosystems has become of increasing concern since it aggravates groundwater reduction impacts with consequent uncertainties about how vegetation will respond over the short and long term. Sand dune plant communities encompass a diverse number of species that differ widely in root depth, tolerance to drought and capacity to shift between seasonal varying water sources. Plant functional groups may be affected by water distribution and availability differently. The high ecological diversity of sand dune forests, characterized by sandy soils, well or poorly drained, poor in nutrients and with different levels of salinity, can occur in different climatic regions of the globe. Such is the case of Tropical, Meso-mediterranean and Mediterranean areas, where future climate change is predicted to change water availability. Analyses of the relative natural abundances of stable isotopes of carbon (13C/12C) and oxygen (18O/16O) have been used across a wide range of scales, contributing to our understanding of plant ecology and interactions. This approach can show important temporal and spatial changes in utilization of different water sources by vegetation. Accordingly, the core idea of this work is to evaluate, along a climatic gradient, the responses and capacity of different coastal plant communities to adapt to changing water availability. This large-climatic-scale study, covering Brazil, Portugal and

  20. Soil Erosion Prediction Based on Land Use Changes (A Case in Neka Watershed

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    Karim Solaimani

    2009-01-01

    Full Text Available Problem statement: Land use change has transformed a vast part of the natural landscapes of the developing world for the last 50 years. Land is a fundamental factor of production and though much of the course of human history, it has been tightly coupled with economic growth. Soil erosion by water is one of the most important land degradation processes in the Mediterranean basins. The unplanned land use change within and near a fast growing agricultural land in Neka River Basin, led to an accelerated erosion of soil in the area. Approach: This study aims to find the relationships between land use pattern, erosion and the sediment yield in the study area. The land use coefficient (Xa has applied in the model of Erosion Potential Method (EPM to forecast the effect of the land type to reduce the erosion. Land cover and land use change was projected for the next decade using topography, geology, land use maps and remote sensing data of the study area. Results: The results of this study indicated that the total sediment yield of the study area has notably decreased to 89.24% after an appropriate land use/cover alteration. The estimated special erosion for the Southern Neka Basin is about 144465.1 m3 km-2 where after management policy is predicted 15542.9 m3 km-2 year?1, therefore the total difference for the study area has estimated about 128922.2 m3 km-2 year-1. Conclusion: The land use changes assessed among the different land cover classes. It is important to mention that conducting of the present study a very severe land cover changes taken place as the result of agricultural land development. These changes in land cover led to the forest degradation of the study area. Relationship between land-use changes and agricultural growth offered a more robust prediction of soil erosion in Neka watershed.

  1. Morphological and functional changes in the vertebral column with increasing aquatic adaptation in crocodylomorphs.

    Science.gov (United States)

    Molnar, Julia L; Pierce, Stephanie E; Bhullar, Bhart-Anjan S; Turner, Alan H; Hutchinson, John R

    2015-11-01

    The lineage leading to modern Crocodylia has undergone dramatic evolutionary changes in morphology, ecology and locomotion over the past 200+ Myr. These functional innovations may be explained in part by morphological changes in the axial skeleton, which is an integral part of the vertebrate locomotor system. Our objective was to estimate changes in osteological range of motion (RoM) and intervertebral joint stiffness of thoracic and lumbar vertebrae with increasing aquatic adaptation in crocodylomorphs. Using three-dimensional virtual models and morphometrics, we compared the modern crocodile Crocodylus to five extinct crocodylomorphs: Terrestrisuchus, Protosuchus, Pelagosaurus, Steneosaurus and Metriorhynchus, which span the spectrum from terrestrial to fully aquatic. In Crocodylus, we also experimentally measured changes in trunk flexibility with sequential removal of osteoderms and soft tissues. Our results for the more aquatic species matched our predictions fairly well, but those for the more terrestrial early crocodylomorphs did not. A likely explanation for this lack of correspondence is the influence of other axial structures, particularly the rigid series of dorsal osteoderms in early crocodylomorphs. The most important structures for determining RoM and stiffness of the trunk in Crocodylus were different in dorsoventral versus mediolateral bending, suggesting that changes in osteoderm and rib morphology over crocodylomorph evolution would have affected movements in some directions more than others. PMID:26716001

  2. Use of triangular membership function for prediction of compressive strength of concrete containing nanosilica

    Directory of Open Access Journals (Sweden)

    Sakshi Gupta

    2015-12-01

    Full Text Available In this paper, application of fuzzy logic technique using triangular membership function for developing models for predicting compressive strength of concrete with partial replacement of cement with nanosilica has been carried out. For this, the data have been taken from various literatures and help in optimizing the constituents available and reducing cost and efforts in studying design to develop mixes by predefining suitable range for experimenting. The use of nanostructured materials in concrete can add many benefits that are directly related to the durability of various cementitious materials, besides the fact that it is possible to reduce the quantities of cement in the composite. Successful prediction by the model indicates that fuzzy logic could be a useful modelling tool for engineers and research scientists in the area of cement and concrete. Compressive strength values of concrete can be predicted in fuzzy logic models without attempting any experiments in a quite short period of time with tiny error rates.

  3. Prediction

    OpenAIRE

    Woollard, W.J.

    2006-01-01

    In this chapter we will look at the ways in which you can use ICT in the classroom to support hypothesis and prediction and how modern technology is enabling: pattern seeking, extrapolation and interpolation to meet the challenges of the information explosion of the 21st century.

  4. The more things change, the more they stay the same? When is trait variability important for stability of ecosystem function in a changing environment.

    Science.gov (United States)

    Wright, Justin P; Ames, Gregory M; Mitchell, Rachel M

    2016-05-19

    The importance of intraspecific trait variability for community dynamics and ecosystem functioning has been underappreciated. There are theoretical reasons for predicting that species that differ in intraspecific trait variability will also differ in their effects on ecosystem functioning, particularly in variable environments. We discuss whether species with greater trait variability are likely to exhibit greater temporal stability in their population dynamics, and under which conditions this might lead to stability in ecosystem functioning. Resolving this requires us to consider several questions. First, are species with high levels of variation for one trait equally variable in others? In particular, is variability in response and effects traits typically correlated? Second, what is the relative contribution of local adaptation and phenotypic plasticity to trait variability? If local adaptation dominates, then stability in function requires one of two conditions: (i) individuals of appropriate phenotypes present in the environment at high enough frequencies to allow for populations to respond rapidly to the changing environment, and (ii) high levels of dispersal and gene flow. While we currently lack sufficient information on the causes and distribution of variability in functional traits, filling in these key data gaps should increase our ability to predict how changing biodiversity will alter ecosystem functioning. PMID:27114574

  5. Observed and predicted effects of climate change on species abundance in protected areas

    Science.gov (United States)

    Johnston, Alison; Ausden, Malcolm; Dodd, Andrew M.; Bradbury, Richard B.; Chamberlain, Dan E.; Jiguet, Frédéric; Thomas, Chris D.; Cook, Aonghais S. C. P.; Newson, Stuart E.; Ockendon, Nancy; Rehfisch, Mark M.; Roos, Staffan; Thaxter, Chris B.; Brown, Andy; Crick, Humphrey Q. P.; Douse, Andrew; McCall, Rob A.; Pontier, Helen; Stroud, David A.; Cadiou, Bernard; Crowe, Olivia; Deceuninck, Bernard; Hornman, Menno; Pearce-Higgins, James W.

    2013-12-01

    The dynamic nature and diversity of species' responses to climate change poses significant difficulties for developing robust, long-term conservation strategies. One key question is whether existing protected area networks will remain effective in a changing climate. To test this, we developed statistical models that link climate to the abundance of internationally important bird populations in northwestern Europe. Spatial climate-abundance models were able to predict 56% of the variation in recent 30-year population trends. Using these models, future climate change resulting in 4.0°C global warming was projected to cause declines of at least 25% for more than half of the internationally important populations considered. Nonetheless, most EU Special Protection Areas in the UK were projected to retain species in sufficient abundances to maintain their legal status, and generally sites that are important now were projected to be important in the future. The biological and legal resilience of this network of protected areas is derived from the capacity for turnover in the important species at each site as species' distributions and abundances alter in response to climate. Current protected areas are therefore predicted to remain important for future conservation in a changing climate.

  6. Predicting the impact of climate change on threatened species in UK waters.

    Directory of Open Access Journals (Sweden)

    Miranda C Jones

    Full Text Available Global climate change is affecting the distribution of marine species and is thought to represent a threat to biodiversity. Previous studies project expansion of species range for some species and local extinction elsewhere under climate change. Such range shifts raise concern for species whose long-term persistence is already threatened by other human disturbances such as fishing. However, few studies have attempted to assess the effects of future climate change on threatened vertebrate marine species using a multi-model approach. There has also been a recent surge of interest in climate change impacts on protected areas. This study applies three species distribution models and two sets of climate model projections to explore the potential impacts of climate change on marine species by 2050. A set of species in the North Sea, including seven threatened and ten major commercial species were used as a case study. Changes in habitat suitability in selected candidate protected areas around the UK under future climatic scenarios were assessed for these species. Moreover, change in the degree of overlap between commercial and threatened species ranges was calculated as a proxy of the potential threat posed by overfishing through bycatch. The ensemble projections suggest northward shifts in species at an average rate of 27 km per decade, resulting in small average changes in range overlap between threatened and commercially exploited species. Furthermore, the adverse consequences of climate change on the habitat suitability of protected areas were projected to be small. Although the models show large variation in the predicted consequences of climate change, the multi-model approach helps identify the potential risk of increased exposure to human stressors of critically endangered species such as common skate (Dipturus batis and angelshark (Squatina squatina.

  7. Predicting the effect of missense mutations on protein function: analysis with Bayesian networks

    Directory of Open Access Journals (Sweden)

    Care Matthew A

    2006-09-01

    Full Text Available Abstract Background A number of methods that use both protein structural and evolutionary information are available to predict the functional consequences of missense mutations. However, many of these methods break down if either one of the two types of data are missing. Furthermore, there is a lack of rigorous assessment of how important the different factors are to prediction. Results Here we use Bayesian networks to predict whether or not a missense mutation will affect the function of the protein. Bayesian networks provide a concise representation for inferring models from data, and are known to generalise well to new data. More importantly, they can handle the noisy, incomplete and uncertain nature of biological data. Our Bayesian network achieved comparable performance with previous machine learning methods. The predictive performance of learned model structures was no better than a naïve Bayes classifier. However, analysis of the posterior distribution of model structures allows biologically meaningful interpretation of relationships between the input variables. Conclusion The ability of the Bayesian network to make predictions when only structural or evolutionary data was observed allowed us to conclude that structural information is a significantly better predictor of the functional consequences of a missense mutation than evolutionary information, for the dataset used. Analysis of the posterior distribution of model structures revealed that the top three strongest connections with the class node all involved structural nodes. With this in mind, we derived a simplified Bayesian network that used just these three structural descriptors, with comparable performance to that of an all node network.

  8. Does Perceived Racial Discrimination Predict Changes in Psychological Distress and Substance Use over Time? An Examination among Black Emerging Adults

    Science.gov (United States)

    Hurd, Noelle M.; Varner, Fatima A.; Caldwell, Cleopatra H.; Zimmerman, Marc A.

    2014-01-01

    We assessed whether perceived discrimination predicted changes in psychological distress and substance use over time and whether psychological distress and substance use predicted change in perceived discrimination over time. We also assessed whether associations between these constructs varied by gender. Our sample included 607 Black emerging…

  9. Predicting functional sites with an automated algorithm suitable for heterogeneous datasets

    Directory of Open Access Journals (Sweden)

    Livesay Dennis R

    2005-05-01

    Full Text Available Abstract Background In a previous report (La et al., Proteins, 2005, we have demonstrated that the identification of phylogenetic motifs, protein sequence fragments conserving the overall familial phylogeny, represent a promising approach for sequence/function annotation. Across a structurally and functionally heterogeneous dataset, phylogenetic motifs have been demonstrated to correspond to a wide variety of functional site archetypes, including those defined by surface loops, active site clefts, and less exposed regions. However, in our original demonstration of the technique, phylogenetic motif identification is dependent upon a manually determined similarity threshold, prohibiting large-scale application of the technique. Results In this report, we present an algorithmic approach that determines thresholds without human subjectivity. The approach relies on significant raw data preprocessing to improve signal detection. Subsequently, Partition Around Medoids Clustering (PAMC of the similarity scores assesses sequence fragments where functional annotation remains in question. The accuracy of the approach is confirmed through comparisons to our previous (manual results and structural analyses. Triosephosphate isomerase and arginyl-tRNA synthetase are discussed as exemplar cases. A quantitative functional site prediction assessment algorithm indicates that the phylogenetic motif predictions, which require sequence information only, are nearly as good as those from evolutionary trace methods that do incorporate structure. Conclusion The automated threshold detection algorithm has been incorporated into MINER, our web-based phylogenetic motif identification server. MINER is freely available on the web at http://www.pmap.csupomona.edu/MINER/. Pre-calculated functional site predictions of the COG database and an implementation of the threshold detection algorithm, in the R statistical language, can also be accessed at the website.

  10. Role of competition in vegetation change: evolutionarily stable strategy analysis as a means for predicting change in vegetation distributions

    Science.gov (United States)

    Farrior, C.

    2015-12-01

    One of the clearest differences among major vegetation types is allocation to woody biomass. Whether and to what extent plants invest in this long-lived tissue has a major impact on carbon storage and can have important feedbacks to the rising CO2 in the atmosphere. Wood is a multifaceted structure. It can allow plants to escape from ground fires, the pressure of herbivores, and perhaps most importantly competition with other plants for light. Understanding the result of this final pressure requires an incorporation of individual-based interactions among plants. This can be a particularly difficult because of both high computational demands and errors in implementation and understanding of such complex models. We have made progress on both difficulties for understanding allocation to woody biomass among trees in forests. Across gradients in resource availability within forests, we find a significant influence of individual-based competition on dominant plant allocation to woody biomass. In model predictions and observed differences among forests globally major tradeoffs occur in allocation to woody biomass versus allocation to fine roots. This is driven by shifting importance of individual-based competition for light versus shared resources belowground, in particular water and nitrogen. Moving beyond forests to biome boundaries, transitions between grassland, savanna, and forest we see again that competition can play an important role. In these zones of rapid change however, population dynamics is not as simple as a steady-state closed-canopy forest. Disturbance dynamics including response to fire and drought stress are also important pressures on dominant plant strategies. Here I show progress in incorporating disturbance dynamics with individual based competition to predict and understand dominant plant strategies including allocation to woody biomass. Results indicate that the influence of competition varies with disturbance regime. With stochastic disturbance

  11. Changes in vascular plant functional types drive carbon cycling in peatlands

    Science.gov (United States)

    Zeh, Lilli; Bragazza, Luca; Erhagen, Björn; Limpens, Juul; Kalbitz, Karsten

    2016-04-01

    Northern peatlands store a large organic carbon (C) pool that is highly exposed to future environmental changes with consequent risk of releasing enormous amounts of C. Biotic changes in plant community structure and species abundance might have an even stronger impact on soil organic C dynamics in peatlands than the direct effects of abiotic changes. Therefore, a sound understanding of the impact of vegetation dynamics on C cycling will help to better predict the response of peatlands to environmental changes. Here, we aimed to assess the role of plant functional types (PFTs) in affecting peat decomposition in relation to climate warming. To this aim, we selected two peatlands at different altitude (i.e. 1300 and 1700 m asl) on the south-eastern Alps of Italy. The two sites represent a contrast in temperature, overall vascular plant biomass and relative ericoids abundance, with the highest biomass and ericoids occurrence at the low latitude. Within the sites we selected 20 plots of similar microtopographical position and general vegetation type (hummocks). All plots contained both graminoids and ericoids and had a 100% cover of Sphagnum mosses. The plots were subjected to four treatments (control, and three clipping treatments) in which we selectively removed aboveground biomass of ericoids, graminoids or both to explore the contribution of the different PFTs for soil respiration (n=5) and peat chemistry. Peat chemical composition was determined by the analysis of C and N and their stable isotopes in association with pyrolysis GC/MS. Soil respiration was measured after clipping with a Licor system. Preliminary findings suggest that peat decomposition pathway and rate depend on plant species composition and particularly on differences in root activity between PFTs. Finally, this study underlines the importance of biotic drivers to predict the effects of future environmental changes on peatland C cycling.

  12. Applications of Kalman filters based on non-linear functions to numerical weather predictions

    Directory of Open Access Journals (Sweden)

    G. Galanis

    2006-10-01

    Full Text Available This paper investigates the use of non-linear functions in classical Kalman filter algorithms on the improvement of regional weather forecasts. The main aim is the implementation of non linear polynomial mappings in a usual linear Kalman filter in order to simulate better non linear problems in numerical weather prediction. In addition, the optimal order of the polynomials applied for such a filter is identified. This work is based on observations and corresponding numerical weather predictions of two meteorological parameters characterized by essential differences in their evolution in time, namely, air temperature and wind speed. It is shown that in both cases, a polynomial of low order is adequate for eliminating any systematic error, while higher order functions lead to instabilities in the filtered results having, at the same time, trivial contribution to the sensitivity of the filter. It is further demonstrated that the filter is independent of the time period and the geographic location of application.

  13. Key Technology of Predicting Dynamic Surface Subsidence Based on Knothe Time Function

    Directory of Open Access Journals (Sweden)

    Qing-Feng Hu

    2011-07-01

    Full Text Available A method for calculating the parameter of Knothe time function was presented. The principle of predicting dynamic mining subsidence was discussed based to the relationship between the periodic fractures of main roof and surface subsidence. Pointed out there might be a section whose width was shorter than a mining unit when divided a workface into  equal mining elements, the section should be calculated specially in the algorithm. A model of predicting dynamic mining subsidence was made according to the Knothe time function and probability integral method. A model how to divide a workface and two coordinate transformation models among three coordinates also were made. An algorithm step of the dynamic prediction model for multi-face mining was designed and implemented. And the algorithm was tested by nine measured subsidence data in different times of some mine 1176 east face, the result showed that the prediction results agreed well with the observation data, and the feasibility and effectiveness of the algorithm were demonstrated. Finally, the process of surface subsidence and deformation of 1176 east face was back analyzed.

  14. A noise level prediction method based on electro-mechanical frequency response function for capacitors.

    Directory of Open Access Journals (Sweden)

    Lingyu Zhu

    Full Text Available The capacitors in high-voltage direct-current (HVDC converter stations radiate a lot of audible noise which can reach higher than 100 dB. The existing noise level prediction methods are not satisfying enough. In this paper, a new noise level prediction method is proposed based on a frequency response function considering both electrical and mechanical characteristics of capacitors. The electro-mechanical frequency response function (EMFRF is defined as the frequency domain quotient of the vibration response and the squared capacitor voltage, and it is obtained from impulse current experiment. Under given excitations, the vibration response of the capacitor tank is the product of EMFRF and the square of the given capacitor voltage in frequency domain, and the radiated audible noise is calculated by structure acoustic coupling formulas. The noise level under the same excitations is also measured in laboratory, and the results are compared with the prediction. The comparison proves that the noise prediction method is effective.

  15. Pulmonary Function Measures Predict Mortality Differently in Idiopathic Pulmonary Fibrosis versus Combined Pulmonary Fibrosis and Emphysema

    OpenAIRE

    Schmidt, Shelley L.; Nambiar, Anoop M.; Tayob, Nabihah; Sundaram, Baskaran; Han, MeiLan K.; Gross, Barry H.; Kazerooni, Ella A.; Chughtai, Aamer R.; Lagstein, Amir; Myers, Jeffrey L.; Murray, Susan; Toews, Galen B.; Martinez, Fernando J; Flaherty, Kevin R.

    2010-01-01

    The composite physiologic index(CPI) was derived to represent the extent of fibrosis on high resolution computed tomography, adjusting for emphysema in patients with idiopathic pulmonary fibrosis(IPF). We hypothesized longitudinal change in CPI would better predict mortality than forced expiratory volume in 1 second(FEV1), forced vital capacity(FVC), or diffusing capacity for carbon monoxide(DLCO) in all patients with IPF, and especially in those with combined pulmonary fibrosis and emphysema...

  16. Can tail damage outbreaks in the pig be predicted by behavioural change?

    DEFF Research Database (Denmark)

    Larsen, Mona Lilian Vestbjerg; Andersen, Heidi Mai-Lis; Pedersen, Lene Juul

    2016-01-01

    Tail biting, resulting in outbreaks of tail damage in pigs, is a multifactorial welfare and economic problem which is usually partly prevented through tail docking. According to European Union legislation, tail docking is not allowed on a routine basis; thus there is a need for alternative...... preventive methods. One strategy is the surveillance of the pigs' behaviour for known preceding indicators of tail damage, which makes it possible to predict a tail damage outbreak and prevent it in proper time. This review discusses the existing literature on behavioural changes observed prior to a tail...... damage outbreak. Behaviours found to change prior to an outbreak include increased activity level, increased performance of enrichment object manipulation, and a changed proportion of tail posture with more tails between the legs. Monitoring these types of behaviours is also discussed for the purpose of...

  17. Fast Spatial Prediction from Inhomogeneously Sampled Data Based on Generalized Random Fields with Gibbs Energy Functionals

    CERN Document Server

    Hristopulos, D T

    2006-01-01

    An explicit optimal linear spatial predictor is derived. The spatial correlations are imposed by means of Gibbs energy functionals with explicit coupling coefficients instead of covariance matrices. The model inference process is based on physically identifiable constraints corresponding to distinct terms of the energy functional. The proposed predictor is compared with the geostatistical linear optimal filter (kriging) using simulated data. The agreement between the two methods is excellent. The proposed framework allows a unified approach to the problems of parameter inference, spatial prediction and simulation of spatial random fields.

  18. Large-Deformation Displacement Transfer Functions for Shape Predictions of Highly Flexible Slender Aerospace Structures

    Science.gov (United States)

    Ko, William L.; Fleischer, Van Tran

    2013-01-01

    Large deformation displacement transfer functions were formulated for deformed shape predictions of highly flexible slender structures like aircraft wings. In the formulation, the embedded beam (depth wise cross section of structure along the surface strain sensing line) was first evenly discretized into multiple small domains, with surface strain sensing stations located at the domain junctures. Thus, the surface strain (bending strains) variation within each domain could be expressed with linear of nonlinear function. Such piecewise approach enabled piecewise integrations of the embedded beam curvature equations [classical (Eulerian), physical (Lagrangian), and shifted curvature equations] to yield closed form slope and deflection equations in recursive forms.

  19. Multiclass Support Vector Machine-Based Lesion Mapping Predicts Functional Outcome in Ischemic Stroke Patients

    OpenAIRE

    Forkert, Nils Daniel; Verleger, Tobias; Cheng, Bastian; Thomalla, Götz; Hilgetag, Claus C.; Fiehler, Jens

    2015-01-01

    Purpose The aim of this study was to investigate if ischemic stroke final infarction volume and location can be used to predict the associated functional outcome using a multi-class support vector machine (SVM). Material and Methods Sixty-eight follow-up MR FLAIR datasets of ischemic stroke patients with known modified Rankin Scale (mRS) functional outcome after 30 days were used. The infarct regions were segmented and used to calculate the percentage of lesioned voxels in the predefined MNI,...

  20. Bilirubin binding with liver cystatin induced structural and functional changes.

    Science.gov (United States)

    Mustafa, Mir Faisal; Bano, Bilqees

    2014-05-01

    Cysteine proteinases and their inhibitors play a significant role in the proteolytic environment of the cells. Inhibitors of cysteine proteinases regulate the activity of these enzymes helping in checking the degdration activity of cathepsins. The bilirubin secreated by liver cells can bind to cystatin present in the liver resulting in its functional inactivation, which may further lead to the increase in cathepsins level causing liver cirrhosis. In case of some pathophysiological conditions excess bilirubin gets accumulated e.g. in presence of Fasciola hepatica (liver fluke) in mammals and humans, leading to liver cirrhosis and possibly jaundice or normal blockade of bile duct causing increased level of bilirubin in blood. Protease-cystatin imbalance causes disease progression. In the present study, Bilirubin (BR) and liver cystatin interaction was studied to explore the cystatin inactivation and structural alteration. The binding interaction was studied by UV-absorption, FT-IR and fluorescence spectroscopy. The quenching of protein fluorescence confirmed the binding of BR with buffalo liver cystatin (BLC). Stern-Volmer analysis of BR-BLC system indicates the presence of static component in the quenching mechanism and the number of binding sites to be close to 1. The fluorescence data proved that the fluorescence quenching of liver cystatin by BR was the result of BR-cystatin complex formation. FTIR analysis of BR-Cystatin complex revealed change in the secondary structure due to perturbation in the microenvironment further confirmed by the decreased caseinolytic activity of BLC against papain. Fluorescence measurements also revealed quenching of fluorescence and shift in peak at different time intervals and at varying pH values. Photo-illumination of BR-cystatin complex causes change in the surrounding environment of liver cystatin as indicated by red-shift. The binding constant for BR-BLC complex was found to be 9.279 × 10(4) M(-1). The cystatin binding with

  1. Emotion Regulation Predicts Pain and Functioning in Children With Juvenile Idiopathic Arthritis: An Electronic Diary Study

    OpenAIRE

    Connelly, Mark; Bromberg, Maggie H.; Anthony, Kelly K; Gil, Karen M.; Franks, Lindsey; Schanberg, Laura E

    2011-01-01

    Objectives This study utilized e-diaries to evaluate whether components of emotion regulation predict daily pain and function in children with juvenile idiopathic arthritis (JIA). Methods 43 children ages 8–17 years and their caregivers provided baseline reports of child emotion regulation. Children then completed thrice daily e-diary assessments of emotion, pain, and activity involvement for 28 days. E-diary ratings of negative and positive emotions were used to calculate emotion variability...

  2. Stability of executive function and predictions to adaptive behavior from middle childhood to pre-adolescence

    OpenAIRE

    Madeline eHarms; Vivian eZayas; Andrew eMeltzoff; Stephanie eCarlson

    2014-01-01

    The shift from childhood to adolescence is characterized by rapid remodeling of the brain and increased risk-taking behaviors. Current theories hypothesize that developmental enhancements in sensitivity to affective environmental cues in adolescence may undermine executive function (EF) and increase the likelihood of problematic behaviors. In the current study, we examined the extent to which EF in childhood predicts EF in early adolescence. We also tested whether individual differences in ne...

  3. Support Vector Machines for Predicting Membrane Protein Types by Using Functional Domain Composition

    OpenAIRE

    Cai, Yu-Dong; Zhou, Guo-Ping; Chou, Kuo-Chen

    2003-01-01

    Membrane proteins are generally classified into the following five types: 1), type I membrane protein; 2), type II membrane protein; 3), multipass transmembrane proteins; 4), lipid chain-anchored membrane proteins; and 5), GPI-anchored membrane proteins. In this article, based on the concept of using the functional domain composition to define a protein, the Support Vector Machine algorithm is developed for predicting the membrane protein type. High success rates are obtained by both the self...

  4. Structure-Functional Study of Tyrosine and Methionine Dipeptides: An Approach to Antioxidant Activity Prediction

    OpenAIRE

    Anna Torkova; Olga Koroleva; Ekaterina Khrameeva; Tatyana Fedorova; Mikhail Tsentalovich

    2015-01-01

    Quantum chemical methods allow screening and prediction of peptide antioxidant activity on the basis of known experimental data. It can be used to design the selective proteolysis of protein sources in order to obtain products with antioxidant activity. Molecular geometry and electronic descriptors of redox-active amino acids, as well as tyrosine and methionine-containing dipeptides, were studied by Density Functional Theory method. The calculated data was used to reveal several descriptors r...

  5. Prediction of the adhesive behavior of bio-inspired functionally graded materials against rough surfaces

    OpenAIRE

    Chen Peijian; Peng Juan; Zhao Yucheng; Gao Feng

    2014-01-01

    Roughness effect and adhesion properties are important characteristics to be accessed in the development of functionally graded materials for biological and biomimetic applications, particularly for the hierarchical composition in biomimetic gecko robot. A multi-asperities adhesion model to predict the adhesive forces is presented in this work. The effect of surface roughness and graded material properties, which significantly alter the adhesive strength between contact bodies, can be simulta...

  6. LRR Conservation Mapping to Predict Functional Sites within Protein Leucine-Rich Repeat Domains

    OpenAIRE

    Helft, Laura; Reddy, Vignyan; Chen, Xiyang; Koller, Teresa; Federici, Luca; Fernández-Recio, Juan; Gupta, Rishabh; Bent, Andrew

    2011-01-01

    Computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. Contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. Leucine-rich repeats (LRRs) are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. We devised Repeat Conservation Mapping (RCM...

  7. Predicting Functional Independence Measure Scores During Rehabilitation with Wearable Inertial Sensors

    OpenAIRE

    Sprint, Gina; Cook, Diane J.; Weeks, Douglas L.; Borisov, Vladimir

    2015-01-01

    Evaluating patient progress and making discharge decisions regarding inpatient medical rehabilitation rely upon standard clinical assessments administered by trained clinicians. Wearable inertial sensors can offer more objective measures of patient movement and progress. We undertook a study to investigate the contribution of wearable sensor data to predict discharge functional independence measure (FIM) scores for 20 patients at an inpatient rehabilitation facility. The FIM utilizes a 7-poin...

  8. IGFBP2 is a biomarker for predicting longitudinal deterioration in renal function in type 2 diabetes

    OpenAIRE

    Narayanan, Ram P; Fu, Bo; Heald, Adrian H; Siddals, Kirk W.; Oliver, Robert L.; Hudson, Julie E; Payton, Antony; Anderson, Simon G; White, Anne; Ollier, William E R; Gibson, J Martin

    2012-01-01

    Objective Insulin-like growth factors are implicated in the development of diabetic nephropathy. IGF-binding protein 2 (IGFBP2) and IGF2 are expressed in the kidney, but their associations with diabetic nephropathy are unclear. We therefore tested the hypothesis that circulating levels of IGF2 and IGFBP2 predict longitudinal renal function in individuals with type 2 diabetes. Design and methods IGFBP2 and IGF2 measurements were performed in 436 individuals (263 males) with type 2 diabetes. Li...

  9. A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction

    Directory of Open Access Journals (Sweden)

    Wang Renxiao

    2010-04-01

    Full Text Available Abstract Background Current scoring functions are not very successful in protein-ligand binding affinity prediction albeit their popularity in structure-based drug designs. Here, we propose a general knowledge-guided scoring (KGS strategy to tackle this problem. Our KGS strategy computes the binding constant of a given protein-ligand complex based on the known binding constant of an appropriate reference complex. A good training set that includes a sufficient number of protein-ligand complexes with known binding data needs to be supplied for finding the reference complex. The reference complex is required to share a similar pattern of key protein-ligand interactions to that of the complex of interest. Thus, some uncertain factors in protein-ligand binding may cancel out, resulting in a more accurate prediction of absolute binding constants. Results In our study, an automatic algorithm was developed for summarizing key protein-ligand interactions as a pharmacophore model and identifying the reference complex with a maximal similarity to the query complex. Our KGS strategy was evaluated in combination with two scoring functions (X-Score and PLP on three test sets, containing 112 HIV protease complexes, 44 carbonic anhydrase complexes, and 73 trypsin complexes, respectively. Our results obtained on crystal structures as well as computer-generated docking poses indicated that application of the KGS strategy produced more accurate predictions especially when X-Score or PLP alone did not perform well. Conclusions Compared to other targeted scoring functions, our KGS strategy does not require any re-parameterization or modification on current scoring methods, and its application is not tied to certain systems. The effectiveness of our KGS strategy is in theory proportional to the ever-increasing knowledge of experimental protein-ligand binding data. Our KGS strategy may serve as a more practical remedy for current scoring functions to improve their

  10. A trading-space-for-time approach to probabilistic continuous streamflow predictions in a changing climate

    Directory of Open Access Journals (Sweden)

    R. Singh

    2011-07-01

    Full Text Available Understanding the implications of potential future climatic conditions for hydrologic services and hazards is a crucial and current science question. The common approach to this problem is to force a hydrologic model, calibrated on historical data or using a priori parameter estimates, with future scenarios of precipitation and temperature. Recent studies suggest that the climatic regime of the calibration period is reflected in the resulting parameter estimates and that the model performance can be negatively impacted if the climate for which projections are made is significantly different from that during calibration. We address this issue by introducing a framework for probabilistic streamflow predictions in a changing climate wherein we quantify the impact of climate on model parameters. The strategy extends a regionalization approach (used for predictions in ungauged basins by trading space-for-time to account for potential parameter variability in a future climate that is beyond the historically observed one. The developed methodology was tested in five US watersheds located in dry to wet climates using synthetic climate scenarios generated by increasing the historical mean temperature from 0 to 8 °C and by changing historical mean precipitation from −30 % to +40 % of the historical values. Validation on historical data shows that changed parameters perform better if future streamflow differs from historical by more than 25 %. We found that the thresholds of climate change after which the streamflow projections using adjusted parameters were significantly different from those using fixed parameters were 0 to 2 °C for temperature change and −10 % to 20 % for precipitation change depending upon the aridity of the watershed. Adjusted parameter sets simulate a more extreme watershed response for both high and low flows.

  11. COMBINING CLIMATE MODEL PREDICTIONS, HYDROLOGICAL MODELING, AND ECOLOGICAL NICHE MODELING ALGORITHMS TO PREDICT THE IMPACTS OF CLIMATE CHANGE ON AQUATIC BIODIVERSITY

    Science.gov (United States)

    The results of this research will provide a broad taxonomic and regional assessment of the impacts of climate change on aquatic species in the United States by producing predictions of current and future habitat quality for aquatic taxa based on multiple climate change scen...

  12. Functional traits predict relationship between plant abundance dynamic and long-term climate warming

    OpenAIRE

    Soudzilovskaia, Nadejda A; Elumeeva, Tatiana G.; Onipchenko, Vladimir G.; Shidakov, Islam I.; Salpagarova, Fatima S.; Khubiev, Anzor B.; Tekeev, Dzhamal K.; Cornelissen, Johannes H. C.

    2013-01-01

    Although the response of the Plant Kingdom to climate change is acknowledged as one of the fundamental feedback mechanisms of environmental changes on the Earth, until now, the response of plant species to in situ climate warming has been described at the level of a few fixed plant functional types (i.e. grasses, forbs, shrubs etc.). This approach is very coarse and inflexible. Here, we show that plant functional traits (i.e., plant features) can be used as predictors of vegetation response t...

  13. Exercise Ventilatory Inefficiency Adds to Lung Function in Predicting Mortality in COPD.

    Science.gov (United States)

    Neder, J Alberto; Alharbi, Abdullah; Berton, Danilo C; Alencar, Maria Clara N; Arbex, Flavio F; Hirai, Daniel M; Webb, Katherine A; O'Donnell, Denis E

    2016-08-01

    Severity of resting functional impairment only partially predicts the increased risk of death in chronic obstructive pulmonary disease (COPD). Increased ventilation during exercise is associated with markers of disease progression and poor prognosis, including emphysema extension and pulmonary vascular impairment. Whether excess exercise ventilation would add to resting lung function in predicting mortality in COPD, however, is currently unknown. After an incremental cardiopulmonary exercise test, 288 patients (forced expiratory volume in one second ranging from 18% to 148% predicted) were followed for a median (interquartile range) of 57 (47) months. Increases in the lowest (nadir) ventilation to CO2 output (VCO2) ratio determined excess exercise ventilation. Seventy-seven patients (26.7%) died during follow-up: 30/77 (38.9%) deaths were due to respiratory causes. Deceased patients were older, leaner, had a greater co-morbidity burden (Charlson Index) and reported more daily life dyspnea. Moreover, they had poorer lung function and exercise tolerance (p 34 was associated with IC/TLC ≤ 0.34 or IC/TLC ≤ 0.31 for all-cause and respiratory mortality, respectively (p COPD severity. Physiological abnormalities beyond traditional airway dysfunction and lung mechanics are relevant in determining the course of the disease. PMID:27077955

  14. Climate change and peripheral populations: predictions for a relict Mediterranean viper

    Directory of Open Access Journals (Sweden)

    José C. Brito

    2011-06-01

    Full Text Available Ecological niche-based models were developed in peripheral populations of Vipera latastei North Africa to: 1 identify environmental factors related to species occurrence; 2 identify present suitable areas; 3 estimate future areas according to forecasted scenarios of climate change; and 4 quantify habitat suitability changes between present and future climatic scenarios. Field observations were combined with environmental factors to derive an ensemble of predictions of species occurrence. The resulting models were projected to the future North African environmental scenarios. Species occurrence was most related to precipitation variation. Present suitable habitats were fragmented and ranged from coastal to mountain habitats, and the overall fragmented range suggests a relict distribution from wider past ranges. Future projections suggest a progressive decrease in suitable areas. The relationship with precipitation supports the current unsuitability of most North Africa for the species and predicts future increased extinction risk. Monitoring of population trends and full protection of mountain forests are key-targets for long-term conservation of African populations of this viper. Predicted trends may give indications about other peripheral populations of Palearctic vertebrates in North Africa which should be assessed in detail.

  15. Predictions of Actions and Their Justifications in False-Belief Tasks: The Role of Executive Function

    Directory of Open Access Journals (Sweden)

    Putko Adam

    2014-12-01

    Full Text Available The main objective of this study was to examine whether children’s ability to justify their action predictions in terms of mental states is related, in a similar way as the ability to predict actions, to such aspects of executive function (EF as executive control and working memory. An additional objective was to check whether the frequency of different types of justifications made by children in false-belief tasks is associated with aforementioned aspects of EF, as well as language. The study included 59 children aged 3-4 years. The ability to predict actions and to justify these predictions was measured with false-belief tasks. Luria’s hand-game was used to assess executive control, and the Counting and Labelling dual-task was used to assess working memory capacity. Language development was controlled using an embedded syntax test. It was found that executive control was a significant predictor of the children’s ability to justify their action predictions in terms of mental states, even when age and language were taken into account. Results also indicated a relationship between the type of justification in the false-belief task and language development. With the development of language children gradually cease to justify their action predictions in terms of current location, and they tend to construct irrelevant justifications before they begin to refer to beliefs. Data suggest that executive control, in contrast to language, is a factor which affects the development of the children’s ability to justify their action predictions only in its later phase, during a shift from irrelevant to correct justifications.

  16. Functional changes of dendritic cells in hypersensivity reactions to amoxicillin

    Directory of Open Access Journals (Sweden)

    C.M.F. Lima

    2010-10-01

    Full Text Available A better understanding of dendritic cell (DC involvement in responses to haptenic drugs is needed, because it represents a possible approach to the development of an in vitro test, which could identify patients prone to drug allergies. There are two main DC subsets: plasmacytoid DC (pDC and myeloid DC (mDC. β-lactams form hapten-carrier conjugates and may provide a suitable model to study DC behavior in drug allergy reactions. It has been demonstrated that drugs interact differently with DC in drug allergic and non-allergic patients, but there are no studies regarding these subsets. Our aim was to assess the functional changes of mDC and pDC harvested from an amoxicillin-hypersensitive 32-year-old woman who experienced a severe maculopapular exanthema as reflected in interleukin-6 (IL-6 production after stimulation with this drug and penicillin. We also aim to demonstrate, for the first time, the feasibility of this method for dendritic cell isolation followed by in vitro stimulation for studies of drug allergy physiopathology. DC were harvested using a double Percoll density gradient, which generates a basophil-depleted cell (BDC suspension. Further, pDC were isolated by blood DC antigen 4-positive magnetic selection and gravity filtration through magnetized columns. After stimulation with amoxicillin, penicillin and positive and negative controls, IL-6 production was measured by ELISA. A positive dose-response curve for IL-6 after stimulation with amoxicillin and penicillin was observed for pDC, but not for mDC or BDC suspension. These preliminary results demonstrate the feasibility of this methodology to expand the knowledge of the effect of dendritic cell activation by drug allergens.

  17. Functional changes of human quadriceps muscle injured by eccentric exercise

    Directory of Open Access Journals (Sweden)

    F.V. Serrão

    2003-06-01

    Full Text Available The present study evaluated functional changes of quadriceps muscle after injury induced by eccentric exercise. Maximal isometric torque of quadriceps and the surface electromyography (root mean square, RMS, and median frequency, MDF of the vastus medialis oblique (VMO and vastus lateralis (VL muscles were examined before, immediately after and during the first 7 days after injury. Serum creatine kinase (CK levels and magnetic resonance imaging (MRI were used to identify muscle injury. The subject was used as her own control and percent refers to pre-injury data. Experiments were carried out with a sedentary 23-year-old female. Injury was induced by 4 bouts of 15 maximal isokinetic eccentric contractions (angular velocity of 5º/s; range of motion from 40º to 110º of knee flexion. The isometric torque of the quadriceps (knee at 90º flexion decreased 52% immediately after eccentric exercise and recovered on the 5th day. The highest reduction of RMS occurred on the 2nd day after injury in both VL (63% and VMO (66% and only VL recovered to the pre-injury level on the 7th day. Immediately after injury, the MDF decreased by 5 and 3% (VMO and VL, respectively and recovered one day later. Serum CK levels increased by 109% on the 2nd day and were still increased by 32% on the 7th day. MRI showed large areas of injury especially in the deep region of quadriceps. In conclusion, eccentric exercise decreased the isometric torque and electromyographic signals of quadriceps muscle, which were recovered in one week, despite the muscle regeneration signals.

  18. Improved Serum Leptin and Ghrelin Following Bariatric Surgery Predict Better Postoperative Cognitive Function

    OpenAIRE

    Alosco, Michael L.; Spitznagel, Mary Beth; Strain, Gladys; Devlin, Michael; Cohen, Ronald; Crosby, Ross D.; Mitchell, James E; Gunstad, John

    2015-01-01

    Background and Purpose Bariatric surgery is associated with improved cognitive function, but the mechanisms underlying these gains remain poorly understood. Disturbed leptin and ghrelin systems are common in obese individuals and are associated with impaired cognitive function in other samples. Bariatric surgery has been shown to improve serum leptin and ghrelin levels, and these changes may underlie postoperative cognitive improvements. Methods Eighty-four patients completed a computerized c...

  19. Predicting impacts of climate change on medicinal asclepiads of Pakistan using Maxent modeling

    Science.gov (United States)

    Khanum, Rizwana; Mumtaz, A. S.; Kumar, Sunil

    2013-05-01

    Maximum entropy (Maxent) modeling was used to predict the potential climatic niches of three medicinally important Asclepiad species: Pentatropis spiralis, Tylophora hirsuta, and Vincetoxicum arnottianum. All three species are members of the Asclepiad plant family, yet they differ in ecological requirements, biogeographic importance, and conservation value. Occurrence data were collected from herbarium specimens held in major herbaria of Pakistan and two years (2010 and 2011) of field surveys. The Maxent model performed better than random for the three species with an average test AUC value of 0.74 for P. spiralis, 0.84 for V. arnottianum, and 0.59 for T. hirsuta. Under the future climate change scenario, the Maxent model predicted habitat gains for P. spiralis in southern Punjab and Balochistan, and loss of habitat in south-eastern Sindh. Vincetoxicum arnottianum as well as T. hirsuta would gain habitat in upper Peaks of northern parts of Pakistan. T. hirsuta is predicted to lose most of the habitats in northern Punjab and in parches from lower peaks of Galliat, Zhob, Qalat etc. The predictive modeling approach presented here may be applied to other rare Asclepiad species, especially those under constant extinction threat.

  20. Emotional attentional control predicts changes in diurnal cortisol secretion following exposure to a prolonged psychosocial stressor.

    Science.gov (United States)

    Lenaert, Bert; Barry, Tom J; Schruers, Koen; Vervliet, Bram; Hermans, Dirk

    2016-01-01

    Hypothalamic-pituitary-adrenal (HPA) axis irregularities have been associated with several psychological disorders. Hence, the identification of individual difference variables that predict variations in HPA-axis activity represents an important challenge for psychiatric research. We investigated whether self-reported attentional control in emotionally demanding situations prospectively predicted changes in diurnal salivary cortisol secretion following exposure to a prolonged psychosocial stressor. Low ability to voluntarily control attention has previously been associated with anxiety and depressive symptomatology. Attentional control was assessed using the Emotional Attentional Control Scale. In students who were preparing for academic examination, salivary cortisol was assessed before (time 1) and after (time 2) examination. Results showed that lower levels of self-reported emotional attentional control at time 1 (N=90) predicted higher absolute diurnal cortisol secretion and a slower decline in cortisol throughout the day at time 2 (N=71). Difficulty controlling attention during emotional experiences may lead to chronic HPA-axis hyperactivity after prolonged exposure to stress. These results indicate that screening for individual differences may foster prediction of HPA-axis disturbances, paving the way for targeted disorder prevention. PMID:26539967