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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;

    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...

  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. Using Prediction Markets to Generate Probability Density Functions for Climate Change Risk Assessment

    Science.gov (United States)

    Boslough, M.

    2011-12-01

    Climate-related uncertainty is traditionally presented as an error bar, but it is becoming increasingly common to express it in terms of a probability density function (PDF). PDFs are a necessary component of probabilistic risk assessments, for which simple "best estimate" values are insufficient. Many groups have generated PDFs for climate sensitivity using a variety of methods. These PDFs are broadly consistent, but vary significantly in their details. One axiom of the verification and validation community is, "codes don't make predictions, people make predictions." This is a statement of the fact that subject domain experts generate results using assumptions within a range of epistemic uncertainty and interpret them according to their expert opinion. Different experts with different methods will arrive at different PDFs. For effective decision support, a single consensus PDF would be useful. We suggest that market methods can be used to aggregate an ensemble of opinions into a single distribution that expresses the consensus. Prediction markets have been shown to be highly successful at forecasting the outcome of events ranging from elections to box office returns. In prediction markets, traders can take a position on whether some future event will or will not occur. These positions are expressed as contracts that are traded in a double-action market that aggregates price, which can be interpreted as a consensus probability that the event will take place. Since climate sensitivity cannot directly be measured, it cannot be predicted. However, the changes in global mean surface temperature are a direct consequence of climate sensitivity, changes in forcing, and internal variability. Viable prediction markets require an undisputed event outcome on a specific date. Climate-related markets exist on Intrade.com, an online trading exchange. One such contract is titled "Global Temperature Anomaly for Dec 2011 to be greater than 0.65 Degrees C." Settlement is based

  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. Confirmation of linear system theory prediction: Changes in Herrnstein's k as a function of changes in reinforcer magnitude

    Science.gov (United States)

    McDowell, J. J; Wood, Helena M.

    1984-01-01

    Eight human subjects pressed a lever on a range of variable-interval schedules for 0.25¢ to 35.0¢ per reinforcement. Herrnstein's hyperbola described seven of the eight subjects' response-rate data well. For all subjects, the y-asymptote of the hyperbola increased with increasing reinforcer magnitude and its reciprocal was a linear function of the reciprocal of reinforcer magnitude. These results confirm predictions made by linear system theory; they contradict formal properties of Herrnstein's account and of six other mathematical accounts of single-alternative responding. PMID:16812366

  12. 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)

  13. 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

  14. Longitudinal Changes in Functional Brain Connectivity Predicts Conversion to Alzheimer's Disease.

    Science.gov (United States)

    Serra, Laura; Cercignani, Mara; Mastropasqua, Chiara; Torso, Mario; Spanò, Barbara; Makovac, Elena; Viola, Vanda; Giulietti, Giovanni; Marra, Camillo; Caltagirone, Carlo; Bozzali, Marco

    2016-01-01

    This longitudinal study investigates the modifications in structure and function occurring to typical Alzheimer's disease (AD) brains over a 2-year follow-up, from pre-dementia stages of disease, with the aim of identifying biomarkers of prognostic value. Thirty-one patients with amnestic mild cognitive impairment were recruited and followed-up with clinical, neuropsychological, and MRI assessments. Patients were retrospectively classified as AD Converters or Non-Converters, and the data compared between groups. Cross-sectional MRI data at baseline, assessing volume and functional connectivity abnormalities, confirmed previous findings, showing a more severe pattern of regional grey matter atrophy and default-mode network disconnection in Converters than in Non-Converters. Longitudinally, Converters showed more grey matter atrophy in the frontotemporal areas, accompanied by increased connectivity in the precuneus. Discriminant analysis revealed that functional connectivity of the precuneus within the default mode network at baseline is the parameter able to correctly classify patients in Converters and Non-Converters with high sensitivity, specificity, and accuracy.

  15. 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...

  16. 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

  17. 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....

  18. Confirmation of linear system theory prediction: Rate of change of Herrnstein's κ as a function of response-force requirement

    Science.gov (United States)

    McDowell, J. J; Wood, Helena M.

    1985-01-01

    Four human subjects worked on all combinations of five variable-interval schedules and five reinforcer magnitudes (¢/reinforcer) in each of two phases of the experiment. In one phase the force requirement on the operandum was low (1 or 11 N) and in the other it was high (25 or 146 N). Estimates of Herrnstein's κ were obtained at each reinforcer magnitude. The results were: (1) response rate was more sensitive to changes in reinforcement rate at the high than at the low force requirement, (2) κ increased from the beginning to the end of the magnitude range for all subjects at both force requirements, (3) the reciprocal of κ was a linear function of the reciprocal of reinforcer magnitude for seven of the eight data sets, and (4) the rate of change of κ was greater at the high than at the low force requirement by an order of magnitude or more. The second and third findings confirm predictions made by linear system theory, and replicate the results of an earlier experiment (McDowell & Wood, 1984). The fourth finding confirms a further prediction of the theory and supports the theory's interpretation of conflicting data on the constancy of Herrnstein's κ. PMID:16812408

  19. Can preoperative myocardial perfusion scintigraphy predict changes in left ventricular perfusion and function after coronary artery bypass graft surgery?

    DEFF Research Database (Denmark)

    Eckardt, Rozy; Kjeldsen, Bo Juel; Johansen, Allan;

    2012-01-01

    OBJECTIVESWe wanted to evaluate whether preoperative myocardial perfusion scintigraphy (MPS) could predict changes in cardiac symptoms and postoperative myocardial perfusion and left ventricular function after coronary artery bypass grafting (CABG).METHODSNinety-two patients with stable angina......%. Before CABG, one patient had normal perfusion; in the rest of them the defects were classified as follows: reversible (60%), partly reversible (27%) and irreversible (12%). Following CABG, 33% had normal perfusion; in the rest the defects were reversible in 29%, partly reversible in 12% and irreversible...... in 26%. Left ventricular ejection fraction (LVEF), which was normal before operation in 45%, improved in 40% of all patients. The increase in LVEF was not related to the preoperative pattern of perfusion defects. Of 30 patients with normalized perfusion after CABG, 29 (97%) had reversible defects...

  20. 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

    ://elastix.isi.uu.nl/), which was used for deformable registrations between inspiration phases and expiratory phases as well as calculation of Jacobian determinant images of Elekta XVI 4D-CBCT reconstructions. Approximately 3000 recorded XVI scans were available for this study group. The mean of the Jacobian determinant (MJD.......009 and DELTAFVCREL=- 0.008MLD+0.115; pMLD=0.002, respectively). Plots of DELTAFEV1 REL and DELTAFVCREL as a function of MLD are shown in the figure. Both plots show a declining tendency, indicating that higher MLD corresponds to larger decrease in clinically measured lung function tests. Spearman correlation...... coefficient between DELTAFEV1 REL and DELTAFVCREL versus mean lung dose were - 0.249 (p=0.003) and -0.252 (p=0.003), respectively. Conclusions: In this study it was possible to carry out the deformable registrations on the 4D-CBCT-scans, but for the current 4D-CBCTimage quality, it was not possible to show...

  1. Pons to Posterior Cingulate Functional Projections Predict Affective Processing Changes in the Elderly Following Eight Weeks of Meditation Training.

    Science.gov (United States)

    Shao, Robin; Keuper, Kati; Geng, Xiujuan; Lee, Tatia M C

    2016-08-01

    Evidence indicates meditation facilitates affective regulation and reduces negative affect. It also influences resting-state functional connectivity between affective networks and the posterior cingulate (PCC)/precuneus, regions critically implicated in self-referential processing. However, no longitudinal study employing active control group has examined the effect of meditation training on affective processing, PCC/precuneus connectivity, and their association. Here, we report that eight-week meditation, but not relaxation, training 'neutralized' affective processing of positive and negative stimuli in healthy elderly participants. Additionally, meditation versus relaxation training increased the positive connectivity between the PCC/precuneus and the pons, the direction of which was largely directed from the pons to the PCC/precuneus, as revealed by dynamic causal modeling. Further, changes in connectivity between the PCC/precuneus and pons predicted changes in affective processing after meditation training. These findings indicate meditation promotes self-referential affective regulation based on increased regulatory influence of the pons on PCC/precuneus, which new affective-processing strategy is employed across both resting state and when evaluating affective stimuli. Such insights have clinical implications on interventions on elderly individuals with affective disorders. PMID:27349456

  2. 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...

  3. 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....

  4. A new method of modelling early plasma creatinine changes predicts 1-year graft function after kidney transplantation

    DEFF Research Database (Denmark)

    Krogstrup, Nicoline V; Bibby, Bo Martin; Aulbjerg, Camilla;

    2016-01-01

    observational study of 100 kidney transplants we identified all p-cr measurements from the time of transplantation until 30 days post-transplant or last post-transplant dialysis, and correlated this with estimated glomerular filtration rate (eGFR) 1 year after transplantation. The initial changes in p-cr were...

  5. Prediction and inter-dependence of stock and change of soil quality, function and diversity at a national scale and implications for ecosystem services

    Science.gov (United States)

    Reynolds, B.; Emmett, B.; Spurgeon, D.; Rowe, E. C.; Mills, R.; Griffiths, R.; Jones, D.; Simfukwe, P.

    2011-12-01

    A soils monitoring programme which uses an ecosystem approach has been in place in Great Britain for 30 years.The findings from the latest survey in 2007 has been interpreted within a natural capital and ecosystem services context to assess the outcome of a range of policies to protect the natural environment and increase sustainability. Issues of interest included the impacts of declines in atmospheric deposition of acidity, nitrogen and metals, the benefits of agri-environment schemes and climate change on carbon storage in soils and soil biodiversity, and reduced fertiliser applications on eutrophication of soils and waters. Topsoil samples (0-15cm) were taken within 600 1km squares across the country stratified to cover all major habitat types. At the same time botanical surveys in permanent vegetation plots were recorded together with change in land use and management and stream and pond water quality and ecology. These data are used together with satellite images, digital cartography, and ancillary datasets to assess change in landcover for all of GB and upscaling of change data from the samples squares. Changes in topsoil were assessed in 1978, 1998 and again in 2007. An increase in pH but no change in soil carbon was observed between 1978 and 2007. Additional measures added in 1998 enabled a decline in Olsen-P,increase in C:N, decline in soil mesofauna diversity and decline in many metal concentrations to be identified over the last 10 years. In 2007, futher measurements were added to include carbon substrate utilisation, nitrogen mineralisation and bacterial diversity (fungi is in progress)enabling national maps to be created for the first time for these important soil parameters. Multi-variate statistics were used to explore the relationship between the different soil measures, the predictive capability of soil and vegetation type, and drivers of change to be identified. In addition, assigning measurements to specific functions which underpinned

  6. Myeloperoxidase levels predict executive function.

    Science.gov (United States)

    Haslacher, H; Perkmann, T; Lukas, I; Barth, A; Ponocny-Seliger, E; Michlmayr, M; Scheichenberger, V; Wagner, O; Winker, R

    2012-12-01

    The main purpose of the study was to investigate whether baseline myeloperoxidase (MPO) levels are associated with executive cognitive function in individuals with high physical activity. Baseline serum MPO levels of 56 elderly marathon runners and 58 controls were assessed by ELISA. Standardized tests were applied to survey domain-specific cognitive functions. Changes in brain morphology were visualized by magnetic resonance imaging (MRI). High baseline serum MPO levels correlated with worse outcome in tests assessing executive cognitive function in athletes but not in the control group (NAI maze test p<0.05, Trail Making Test ratio p<0.01). In control participants, subcortical white matter hyperintensities were associated with higher scores on the Geriatric Depression Scale (p<0.05), whereas athletes seem to be protected from this effect. During strenuous exercising, MPO as well as its educts may be elevated due to increased oxygen intake and excretion of pro-inflammatory mediators inducing host tissue damage via oxidative stress. This outweighs the potential benefits of physical activity on cognitive function.

  7. 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

  8. 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 ...

  9. 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…

  10. 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.

  11. Sivers function: SIDIS data, fits and predictions

    CERN Document Server

    Anselmino, M; D'Alesio, U; Kotzinian, A; Murgia, F; Prokudin, A

    2005-01-01

    The most recent data on the weighted transverse single spin asymmetry A_{UT}^{\\sin(\\phi_h-\\phi_S)} from HERMES and COMPASS collaborations are analysed within LO parton model; all transverse motions are taken into account. Extraction of the Sivers function for u and d quarks is performed. Based on the extracted Sivers functions, predictions for A_{UT}^{\\sin(\\phi_h-\\phi_S)} asymmetries at JLab are given; suggestions for further measurements at COMPASS, with a transversely polarized hydrogen target and selecting favourable kinematical ranges, are discussed. Predictions are also presented for Single Spin Asymmetries (SSA) in Drell-Yan processes at RHIC and GSI.

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

    Directory of Open Access Journals (Sweden)

    Shangkun Deng

    2014-01-01

    Full Text Available 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.

  13. 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...

  14. 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.

  15. 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...

  16. 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.

  17. 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: ...

  18. 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

  19. 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

  20. The predictability of molecular evolution during functional innovation.

    Science.gov (United States)

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

    2014-02-25

    Determining the molecular changes that give rise to functional innovations is a major unresolved problem in biology. The paucity of examples has served as a significant hindrance in furthering our understanding of this process. Here we used experimental evolution with the bacterium Escherichia coli to quantify the molecular changes underlying functional innovation in 68 independent instances ranging over 22 different metabolic functions. Using whole-genome sequencing, we show that the relative contribution of regulatory and structural mutations depends on the cellular context of the metabolic function. In addition, we find that regulatory mutations affect genes that act in pathways relevant to the novel function, whereas structural mutations affect genes that act in unrelated pathways. Finally, we use population genetic modeling to show that the relative contributions of regulatory and structural mutations during functional innovation may be affected by population size. These results provide a predictive framework for the molecular basis of evolutionary innovation, which is essential for anticipating future evolutionary trajectories in the face of rapid environmental change.

  1. 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...

  2. 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.  

  3. Spinal meningiomas: clinicoradiological factors predicting recurrence and functional outcome.

    Science.gov (United States)

    Maiti, Tanmoy K; Bir, Shyamal C; Patra, Devi Prasad; Kalakoti, Piyush; Guthikonda, Bharat; Nanda, Anil

    2016-08-01

    OBJECTIVE Spinal meningiomas are benign tumors with a wide spectrum of clinical and radiological features at presentation. The authors analyzed multiple clinicoradiological factors to predict recurrence and functional outcome in a cohort with a mean follow-up of more than 4 years. The authors also discuss the results of clinical studies regarding spinal meningiomas in the last 15 years. METHODS The authors retrospectively reviewed the clinical and radiological details of patients who underwent surgery for spinal tumors between 2001 and 2015 that were histopathologically confirmed as meningiomas. Demographic parameters, such as age, sex, race, and association with neurofibromatosis Type 2, were considered. Radiological parameters, such as tumor size, signal changes of spinal cord, spinal level, number of levels, location of tumor attachment, shape of tumor, and presence of dural tail/calcification, were noted. These factors were analyzed to predict recurrence and functional outcome. Furthermore, a pooled analysis was performed from 13 reports of spinal meningiomas in the last 15 years. RESULTS A total of 38 patients were included in this study. Male sex and tumors with radiological evidence of a dural tail were associated with an increased risk of recurrence at a mean follow-up of 51.2 months. Ventral or ventrolateral location, large tumors, T2 cord signal changes, and poor preoperative functional status were associated with poor functional outcome at 1-year follow-up. CONCLUSIONS Spine surgeons must be aware of the natural history and risk factors of spinal meningiomas to establish a prognosis for their patients.

  4. 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.

  5. 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.

  6. Prediction of the residual strength of clay using functional networks

    Institute of Scientific and Technical Information of China (English)

    S.Z. Khan; Shakti Suman; M. Pavani; S.K. Das

    2016-01-01

    Landslides are common natural hazards occurring in most parts of the world and have considerable adverse economic effects. Residual shear strength of clay is one of the most important factors in the determination of stability of slopes or landslides. This effect is more pronounced in sensitive clays which show large changes in shear strength from peak to residual states. This study analyses the prediction of the residual strength of clay based on a new prediction model, functional networks (FN) using data available in the literature. The performance of FN was compared with support vector machine (SVM) and artificial neural network (ANN) based on statistical parameters like correlation coefficient (R), Nash–Sutcliff coefficient of efficiency (E), absolute average error (AAE), maximum average error (MAE) and root mean square error (RMSE). Based on R and E parameters, FN is found to be a better prediction tool than ANN for the given data. However, the R and E values for FN are less than SVM. A prediction equation is presented that can be used by practicing geotechnical engineers. A sensitivity analysis is carried out to ascertain the importance of various inputs in the prediction of the output.

  7. 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.

  8. A Prediction Model of the Capillary Pressure J-Function

    Science.gov (United States)

    Xu, W. S.; Luo, P. Y.; Sun, L.; Lin, N.

    2016-01-01

    The capillary pressure J-function is a dimensionless measure of the capillary pressure of a fluid in a porous medium. The function was derived based on a capillary bundle model. However, the dependence of the J-function on the saturation Sw is not well understood. A prediction model for it is presented based on capillary pressure model, and the J-function prediction model is a power function instead of an exponential or polynomial function. Relative permeability is calculated with the J-function prediction model, resulting in an easier calculation and results that are more representative. PMID:27603701

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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...

  15. 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)

  16. 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...... multifunctional scope. The objective of increased agricultural multifunctionality has been included actively in EU agricultural policies which may be one of the drivers behind changes. However, from a functional point of view, these changes have are not precisely accounted for or quantified. The paper presents...

  17. Early executive function predicts reasoning development.

    Science.gov (United States)

    Richland, Lindsey E; Burchinal, Margaret R

    2013-01-01

    Analogical reasoning is a core cognitive skill that distinguishes humans from all other species and contributes to general fluid intelligence, creativity, and adaptive learning capacities. Yet its origins are not well understood. In the study reported here, we analyzed large-scale longitudinal data from the Study of Early Child Care and Youth Development to test predictors of growth in analogical-reasoning skill from third grade to adolescence. Our results suggest an integrative resolution to the theoretical debate regarding contributory factors arising from smaller-scale, cross-sectional experiments on analogy development. Children with greater executive-function skills (both composite and inhibitory control) and vocabulary knowledge in early elementary school displayed higher scores on a verbal analogies task at age 15 years, even after adjusting for key covariates. We posit that knowledge is a prerequisite to analogy performance, but strong executive-functioning resources during early childhood are related to long-term gains in fundamental reasoning skills.

  18. 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 ...

  19. 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.

  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. Model of local temperature changes in brain upon functional activation.

    Science.gov (United States)

    Collins, Christopher M; Smith, Michael B; Turner, Robert

    2004-12-01

    Experimental results for changes in brain temperature during functional activation show large variations. It is, therefore, desirable to develop a careful numerical model for such changes. Here, a three-dimensional model of temperature in the human head using the bioheat equation, which includes effects of metabolism, perfusion, and thermal conduction, is employed to examine potential temperature changes due to functional activation in brain. It is found that, depending on location in brain and corresponding baseline temperature relative to blood temperature, temperature may increase or decrease on activation and concomitant increases in perfusion and rate of metabolism. Changes in perfusion are generally seen to have a greater effect on temperature than are changes in metabolism, and hence active brain is predicted to approach blood temperature from its initial temperature. All calculated changes in temperature for reasonable physiological parameters have magnitudes <0.12 degrees C and are well within the range reported in recent experimental studies involving human subjects.

  2. Climate change damage functions in LCA

    DEFF Research Database (Denmark)

    Callesen, Ingeborg; Beier, Claus; Bagger Jørgensen, Rikke;

    , their properties, goods and services. In: Climate change 2007. Cambridge, Cambridge University Press, p. 211-272. [2] Mikkelsen TN, Beier C, et al. (2008) Experimental design of multifactor climate change experiments with elevated CO2, warming and drought – the CLIMAITE project. Functional Ecology, 22, 185-195. [3...

  3. Gesture Performance in Schizophrenia Predicts Functional Outcome After 6 Months

    Science.gov (United States)

    Walther, Sebastian; Eisenhardt, Sarah; Bohlhalter, Stephan; Vanbellingen, Tim; Müri, René; Strik, Werner; Stegmayer, Katharina

    2016-01-01

    The functional outcome of schizophrenia is heterogeneous and markers of the course are missing. Functional outcome is associated with social cognition and negative symptoms. Gesture performance and nonverbal social perception are critically impaired in schizophrenia. Here, we tested whether gesture performance or nonverbal social perception could predict functional outcome and the ability to adequately perform relevant skills of everyday function (functional capacity) after 6 months. In a naturalistic longitudinal study, 28 patients with schizophrenia completed tests of nonverbal communication at baseline and follow-up. In addition, functional outcome, social and occupational functioning, as well as functional capacity at follow-up were assessed. Gesture performance and nonverbal social perception at baseline predicted negative symptoms, functional outcome, and functional capacity at 6-month follow-up. Gesture performance predicted functional outcome beyond the baseline measure of functioning. Patients with gesture deficits at baseline had stable negative symptoms and experienced a decline in social functioning. While in patients without gesture deficits, negative symptom severity decreased and social functioning remained stable. Thus, a simple test of hand gesture performance at baseline may indicate favorable outcomes in short-term follow-up. The results further support the importance of nonverbal communication skills in subjects with schizophrenia. PMID:27566843

  4. Dopamine neurons share common response function for reward prediction error.

    Science.gov (United States)

    Eshel, Neir; Tian, Ju; Bukwich, Michael; Uchida, Naoshige

    2016-03-01

    Dopamine neurons are thought to signal reward prediction error, or the difference between actual and predicted reward. How dopamine neurons jointly encode this information, however, remains unclear. One possibility is that different neurons specialize in different aspects of prediction error; another is that each neuron calculates prediction error in the same way. We recorded from optogenetically identified dopamine neurons in the lateral ventral tegmental area (VTA) while mice performed classical conditioning tasks. Our tasks allowed us to determine the full prediction error functions of dopamine neurons and compare them to each other. We found marked homogeneity among individual dopamine neurons: their responses to both unexpected and expected rewards followed the same function, just scaled up or down. As a result, we were able to describe both individual and population responses using just two parameters. Such uniformity ensures robust information coding, allowing each dopamine neuron to contribute fully to the prediction error signal.

  5. Prediction-based estimating functions: Review and new developments

    DEFF Research Database (Denmark)

    Sørensen, Michael

    2011-01-01

    The general theory of prediction-based estimating functions for stochastic process models is reviewed and extended. Particular attention is given to optimal estimation, asymptotic theory and Gaussian processes. Several examples of applications are presented. In particular, partial observation...

  6. 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

  7. Supporting change processes in design: Complexity, prediction and reliability

    Energy Technology Data Exchange (ETDEWEB)

    Eckert, Claudia M. [Engineering Design Centre, University of Cambridge, Trumpington Street, Cambridge, CB2 1PZ (United Kingdom)]. E-mail: cme26@cam.ac.uk; Keller, Rene [Engineering Design Centre, University of Cambridge, Trumpington Street, Cambridge, CB2 1PZ (United Kingdom)]. E-mail: rk313@cam.ac.uk; Earl, Chris [Open University, Department of Design and Innovation, Walton Hall, Milton Keynes MK7 6AA (United Kingdom)]. E-mail: C.F.Earl@open.ac.uk; Clarkson, P. John [Engineering Design Centre, University of Cambridge, Trumpington Street, Cambridge, CB2 1PZ (United Kingdom)]. E-mail: pjc10@cam.ac.uk

    2006-12-15

    Change to existing products is fundamental to design processes. New products are often designed through change or modification to existing products. Specific parts or subsystems are changed to similar ones whilst others are directly reused. Design by modification applies particularly to safety critical products where the reuse of existing working parts and subsystems can reduce cost and risk. However change is rarely a matter of just reusing or modifying parts. Changing one part can propagate through the entire design leading to costly rework or jeopardising the integrity of the whole product. This paper characterises product change based on studies in the aerospace and automotive industry and introduces tools to aid designers in understanding the potential effects of change. Two ways of supporting designers are described: probabilistic prediction of the effects of change and visualisation of change propagation through product connectivities. Change propagation has uncertainties which are amplified by the choices designers make in practice as they implement change. Change prediction and visualisation is discussed with reference to complexity in three areas of product development: the structural backcloth of connectivities in the existing product (and its processes), the descriptions of the product used in design and the actions taken to carry out changes.

  8. 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.

  9. Community niche predicts the functioning of denitrifying bacterial assemblages

    NARCIS (Netherlands)

    Salles, Joana F.; Poly, Franck; Schmid, Bernhard; Le Roux, Xavier

    2009-01-01

    Predicting biodiversity effects on ecosystem functioning requires adequate evaluation of the mechanisms explaining why more diverse systems could perform better than less diverse ones. In this context, tackling functional diversity has become an important issue. Even though the aggregation of specie

  10. 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…

  11. 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

    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....... 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...

  12. 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.

  13. Predicting effects of environmental change on a migratory herbivore

    Science.gov (United States)

    Stillman, R A; Wood, K A; Gilkerson, Whelan; Elkinton, E; Black, J. M.; Ward, David H.; Petrie, M.

    2015-01-01

    Changes in climate, food abundance and disturbance from humans threaten the ability of species to successfully use stopover sites and migrate between non-breeding and breeding areas. To devise successful conservation strategies for migratory species we need to be able to predict how such changes will affect both individuals and populations. Such predictions should ideally be process-based, focusing on the mechanisms through which changes alter individual physiological state and behavior. In this study we use a process-based model to evaluate how Black Brant (Branta bernicla nigricans) foraging on common eelgrass (Zostera marina) at a stopover site (Humboldt Bay, USA), may be affected by changes in sea level, food abundance and disturbance. The model is individual-based, with empirically based parameters, and incorporates the immigration of birds into the site, tidal changes in availability of eelgrass, seasonal and depth-related changes in eelgrass biomass, foraging behavior and energetics of the birds, and their mass-dependent decisions to emigrate. The model is validated by comparing predictions to observations across a range of system properties including the time birds spent foraging, probability of birds emigrating, mean stopover duration, peak bird numbers, rates of mass gain and distribution of birds within the site: all 11 predictions were within 35% of the observed value, and 8 within 20%. The model predicted that the eelgrass within the site could potentially support up to five times as many birds as currently use the site. Future predictions indicated that the rate of mass gain and mean stopover duration were relatively insensitive to sea level rise over the next 100 years, primarily because eelgrass habitat could redistribute shoreward into intertidal mudflats within the site to compensate for higher sea levels. In contrast, the rate of mass gain and mean stopover duration were sensitive to changes in total eelgrass biomass and the percentage of time

  14. In vivo measurement of protein functional changes

    Directory of Open Access Journals (Sweden)

    Aili Wang, Zhicheng Zhang, Qinyi Zhao

    2009-01-01

    Full Text Available Conformational changes in proteins are fundamental to all biological functions. In protein science, the concept of protein flexibility is widely used to describe protein dynamics and thermodynamic properties that control protein conformational changes. In this study, we show that urea, which has strong sedative potency, can be administered to fish at high concentrations, and that protein functional changes related to anesthesia induction can be measured in vivo. Ctenopharyngodon idellus (the grass carp has two different types of N-methyl d-aspartate (NMDA receptors, urea-insensitive and urea-sensitive, which are responsible for the heat endurance of fish. The urea-sensitive NMDA receptor showed high protein flexibility, the gamma aminobutyric acid (GABA receptor showed less flexibility, and the protein that is responsible for ethanol anesthesia showed the lowest flexibility. The results suggest that an increase in protein flexibility underlies the fundamental biophysical mechanisms of volatile general anesthetics.

  15. 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 ...

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

    Science.gov (United States)

    Galbraith, Hector; DesRochers, David W; Brown, Stephen; Reed, J Michael

    2014-01-01

    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.

  17. 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.

  18. 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...

  19. Radial basis function network design for chaotic time series prediction

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Chang Yong; Kim, Taek Soo; Park, Sang Hui [Yonsei University, Seoul (Korea, Republic of); Choi, Yoon Ho [Kyonggi University, Suwon (Korea, Republic of)

    1996-04-01

    In this paper, radial basis function networks with two hidden layers, which employ the K-means clustering method and the hierarchical training, are proposed for improving the short-term predictability of chaotic time series. Furthermore the recursive training method of radial basis function network using the recursive modified Gram-Schmidt algorithm is proposed for the purpose. In addition, the radial basis function networks trained by the proposed training methods are compared with the X.D. He A Lapedes`s model and the radial basis function network by non-recursive training method. Through this comparison, an improved radial basis function network for predicting chaotic time series is presented. (author). 17 refs., 8 figs., 3 tabs.

  20. Climate-Induced Boreal Forest Change: Predictions versus Current Observations

    Science.gov (United States)

    Soja, Amber J.; Tchebakova, Nadezda M.; French, Nancy H. F.; Flannigan, Michael D.; Shugart, Herman H.; Stocks, Brian J.; Sukhinin, Anatoly I.; Parfenova, E. I.; Chapin, F. Stuart, III; Stackhouse, Paul W., Jr.

    2007-01-01

    For about three decades, there have been many predictions of the potential ecological response in boreal regions to the currently warmer conditions. In essence, a widespread, naturally occurring experiment has been conducted over time. In this paper, we describe previously modeled predictions of ecological change in boreal Alaska, Canada and Russia, and then we investigate potential evidence of current climate-induced change. For instance, ecological models have suggested that warming will induce the northern and upslope migration of the treeline and an alteration in the current mosaic structure of boreal forests. We present evidence of the migration of keystone ecosystems in the upland and lowland treeline of mountainous regions across southern Siberia. Ecological models have also predicted a moisture-stress-related dieback in white spruce trees in Alaska, and current investigations show that as temperatures increase, white spruce tree growth is declining. Additionally, it was suggested that increases in infestation and wildfire disturbance would be catalysts that precipitate the alteration of the current mosaic forest composition. In Siberia, five of the last seven years have resulted in extreme fire seasons, and extreme fire years have also been more frequent in both Alaska and Canada. In addition, Alaska has experienced extreme and geographically expansive multi-year outbreaks of the spruce beetle, which had been previously limited by the cold, moist environment. We suggest that there is substantial evidence throughout the circumboreal region to conclude that the biosphere within the boreal terrestrial environment has already responded to the transient effects of climate change. Additionally, temperature increases and warming-induced change are progressing faster than had been predicted in some regions, suggesting a potential non-linear rapid response to changes in climate, as opposed to the predicted slow linear response to climate change.

  1. 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.

  2. Predicting functional upstream open reading frames in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Kristiansson Erik

    2009-12-01

    Full Text Available Abstract Background Some upstream open reading frames (uORFs regulate gene expression (i.e., they are functional and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not yet fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of experimentally verified functional uORFs are needed. Unfortunately, wet-experiments to verify that uORFs are functional are expensive. Results In this paper, a new computational approach to predicting functional uORFs in the yeast Saccharomyces cerevisiae is presented. Our approach is based on inductive logic programming and makes use of a novel combination of knowledge about biological conservation, Gene Ontology annotations and genes' responses to different conditions. Our method results in a set of simple and informative hypotheses with an estimated sensitivity of 76%. The hypotheses predict 301 further genes to have 398 novel functional uORFs. Three (RPC11, TPK1, and FOL1 of these 301 genes have been hypothesised, following wet-experiments, by a related study to have functional uORFs. A comparison with another related study suggests that eleven of the predicted functional uORFs from genes LDB17, HEM3, CIN8, BCK2, PMC1, FAS1, APP1, ACC1, CKA2, SUR1, and ATH1 are strong candidates for wet-lab experimental studies. Conclusions Learning based prediction of functional uORFs can be done with a high sensitivity. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help to elucidate the regulatory roles of uORFs.

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

    NARCIS (Netherlands)

    Dormann, C.; Schweiger, O.; Arens, P.F.P.; Augenstein, I.; Aviron, S.; Bailey, D.; Baudry, J.; Billeter, R.; Bugter, R.J.F.; Bukacek, R.; Burel, F.; Cerny, M.; Cock, de R.; Blust, de G.; DeFilippi, R.; Diekotter, T.; Dirksen, J.; Durka, W.; Edwards, P.J.; Frenzel, M.; Hamersky, R.; Hendrickx, F.; Herzog, F.; Klotz, S.; Koolstra, B.J.H.; Lausch, A.; Coeur, Le D.; Liira, J.; Maelfait, J.P.; Opdam, P.; Roubalova, M.; Schermann, A.; Schermann, N.; Schmidt, T.; Smulders, M.J.M.; Speelmans, M.; Simova, P.; Verboom, J.; Wingerden, van W.K.R.E.; Zobel, M.

    2008-01-01

    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 chang

  4. 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.

  5. 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...

  6. Changes in Monocyte Functions of Astronauts

    Science.gov (United States)

    Kaur, I.; Simons, E.; Castro, V.; Ott, C. Mark; Pierson, Duane L.

    2004-01-01

    Monocyte cell numbers and functions, including phagocytosis, oxidative burst capacity, and degranulation and expression of related surface molecules, were studied in blood specimens from 25 astronauts and 9 healthy control subjects. Blood samples were obtained 10 days before a space flight, 3 hours after landing and 3 days after landing. The number of monocytes in astronauts did not change significantly among the three sample collection periods. Following space flight, the monocytes ability to phagocytize Escherichia coli, to exhibit an oxidative burst, and to degranulate was reduced as compared to monocytes from control subjects. These alterations in monocyte functions after space flight correlated with alterations in the expression of CD32 and CD64.

  7. 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/

  8. 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.

  9. Predictions of avian Plasmodium expansion under climate change

    Science.gov (United States)

    Loiseau, Claire; Harrigan, Ryan J.; Bichet, Coraline; Julliard, Romain; Garnier, Stéphane; Lendvai, Ádám Z.; Chastel, Olivier; Sorci, Gabriele

    2013-01-01

    Vector-borne diseases are particularly responsive to changing environmental conditions. Diurnal temperature variation has been identified as a particularly important factor for the development of malaria parasites within vectors. Here, we conducted a survey across France, screening populations of the house sparrow (Passer domesticus) for malaria (Plasmodium relictum). We investigated whether variation in remotely-sensed environmental variables accounted for the spatial variation observed in prevalence and parasitemia. While prevalence was highly correlated to diurnal temperature range and other measures of temperature variation, environmental conditions could not predict spatial variation in parasitemia. Based on our empirical data, we mapped malaria distribution under climate change scenarios and predicted that Plasmodium occurrence will spread to regions in northern France, and that prevalence levels are likely to increase in locations where transmission already occurs. Our findings, based on remote sensing tools coupled with empirical data suggest that climatic change will significantly alter transmission of malaria parasites. PMID:23350033

  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. 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.

  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. Perlite exposure and 4-year change in lung function.

    Science.gov (United States)

    Polatli, M; Erdinç, M; Erdinç, E; Okyay, E

    2001-07-01

    Perlite is a volcanic glass or amorphous aluminium silicate composed of 71-75% SiO(2). When heated to 800-1100 degrees C, it expands to form processed perlite, which has a low density, high surface area, and a low thermal conductivity. The objective was to determine the effect of perlite exposure on pulmonary function tests. Pulmonary function tests in conjunction with chest radiogram were carried out in 36 perlite-exposed workers and 22 unexposed office workers in 1992 and 1996. Respirable dust level exceeded permissible dust levels in work places in the 4 years under study. Transfer coefficient (K(CO)) decline was significant in nonsmoker perlite-exposed workers (n=9), and found to be 5.28+/-0.71 (predicted 4.32+/-0.11) and 3.84+/-0.96 (predicted 4.18+/-0.18) 1/min/mmHg, in 1992 and 1996, respectively (Pperlite workers and office workers showed significant obstruction to airflow in small airways with respect to predicted values and 4-year change in transfer factor (T(L), CO) was significant. Although predicted, 12-year perlite exposure did not lead to a decrease in mean pulmonary function test parameters, there was a tendency to a decline in T(L), CO in the 4-year study period, which may be due to high perlite dust levels. As early effects of perlite dust exposure may not be detected by spirometric measurements alone, the transfer coefficient should be added to spirometry.

  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 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.

  16. Predicting changes in the distribution and abundance of species under environmental change

    OpenAIRE

    Ehrlén, Johan; Morris, William F.

    2015-01-01

    Environmental changes are expected to alter both the distribution and the abundance of organisms. A disproportionate amount of past work has focused on distribution only, either documenting historical range shifts or predicting future occurrence patterns. However, simultaneous predictions of abundance and distribution across landscapes would be far more useful. To critically assess which approaches represent advances towards the goal of joint predictions of abundance and distribution, we revi...

  17. 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

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

    NARCIS (Netherlands)

    Radivojac, P.; Clark, W.T.; Oron, T.R.; Schnoes, A.M.; Wittkop, T.; Kourmpetis, Y.A.I.; Dijk, van A.D.J.; Friedberg, I.

    2013-01-01

    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

  19. 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.

  20. Caregiver Confidence: Does It Predict Changes in Disability among Elderly Home Care Recipients?

    Science.gov (United States)

    Li, Lydia W.; McLaughlin, Sara J.

    2012-01-01

    Purpose of the study: The primary aim of this investigation was to determine whether caregiver confidence in their care recipients' functional capabilities predicts changes in the performance of activities of daily living (ADL) among elderly home care recipients. A secondary aim was to explore how caregiver confidence and care recipient functional…

  1. 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.

  2. 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

  3. 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

  4. Climate change and predicted trend of fungal keratitis in Egypt.

    Science.gov (United States)

    Saad-Hussein, A; El-Mofty, H M; Hassanien, M A

    2011-06-01

    Rising rates of invasive fungal infections may be linked to global climate change. A study was made of the trend of ophthalmic fungal corneal keratitis in the greater Cairo area of Egypt and its association with climate records during the same period. Data on diagnosed cases of fungal keratitis were collected from records of ophthalmic departments of Cairo University hospital and atmospheric temperature and humidity for the greater Cairo area were obtained from online records. Statistical analysis showed a significant increase in the relative frequency of keratomycosis during 1997-2007. The rise correlated significantly with rises n min,mum temperature and the maximum atmospheric humidity in the greater Cairo area over the same period (after exclusion of the effect of the maximum atmos pheric temperature). The predicted increase in keratomycosis up to the year 2030 corresponds to predicted increases in CO2 emissions and surface temperature from climate change models for Egypt.

  5. 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

  6. 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.

  7. Detecting changes in functional linear models

    CERN Document Server

    Horvath, Lajos

    2011-01-01

    We observe two sequences of curve which are connected via an integral operator. Our model includes linear models as well as autoregressive models in Hilbert spaces. We wish to test the null hypothesis that the operator did not change during the observation period. Our method is based on projecting the observations onto a suitably chosen finite dimensional space. The testing procedure is based on functionals of the weighted residuals of the projections. Since the quadratic form is based on estimating the long-term covariance matrix of the residuals, we also provide some results on Bartlett-type estimators.

  8. 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.

  9. 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

  10. Plant functional group composition modifies the effects of precipitation change on grassland ecosystem function.

    Science.gov (United States)

    Fry, Ellen L; Manning, Pete; Allen, David G P; Hurst, Alex; Everwand, Georg; Rimmler, Martin; Power, Sally A

    2013-01-01

    Temperate grassland ecosystems face a future of precipitation change, which can alter community composition and ecosystem functions through reduced soil moisture and waterlogging. There is evidence that functionally diverse plant communities contain a wider range of water use and resource capture strategies, resulting in greater resistance of ecosystem function to precipitation change. To investigate this interaction between composition and precipitation change we performed a field experiment for three years in successional grassland in southern England. This consisted of two treatments. The first, precipitation change, simulated end of century predictions, and consisted of a summer drought phase alongside winter rainfall addition. The second, functional group identity, divided the plant community into three groups based on their functional traits- broadly described as perennials, caespitose grasses and annuals- and removed these groups in a factorial design. Ecosystem functions related to C, N and water cycling were measured regularly. Effects of functional groupidentity were apparent, with the dominant trend being that process rates were higher under control conditions where a range of perennial species were present. E.g. litter decomposition rates were significantly higher in plots containing several perennial species, the group with the highest average leaf N content. Process rates were also very strongly affected by the precipitation change treatmentwhen perennial plant species were dominant, but not where the community contained a high abundance of annual species and caespitose grasses. This contrasting response could be attributable to differing rooting patterns (shallower structures under annual plants, and deeper roots under perennials) and faster nutrient uptake in annuals compared to perennials. Our results indicate that precipitation change will have a smaller effect on key process rates in grasslandscontaining a range of perennial and annual species

  11. Plant functional group composition modifies the effects of precipitation change on grassland ecosystem function.

    Directory of Open Access Journals (Sweden)

    Ellen L Fry

    Full Text Available Temperate grassland ecosystems face a future of precipitation change, which can alter community composition and ecosystem functions through reduced soil moisture and waterlogging. There is evidence that functionally diverse plant communities contain a wider range of water use and resource capture strategies, resulting in greater resistance of ecosystem function to precipitation change. To investigate this interaction between composition and precipitation change we performed a field experiment for three years in successional grassland in southern England. This consisted of two treatments. The first, precipitation change, simulated end of century predictions, and consisted of a summer drought phase alongside winter rainfall addition. The second, functional group identity, divided the plant community into three groups based on their functional traits- broadly described as perennials, caespitose grasses and annuals- and removed these groups in a factorial design. Ecosystem functions related to C, N and water cycling were measured regularly. Effects of functional groupidentity were apparent, with the dominant trend being that process rates were higher under control conditions where a range of perennial species were present. E.g. litter decomposition rates were significantly higher in plots containing several perennial species, the group with the highest average leaf N content. Process rates were also very strongly affected by the precipitation change treatmentwhen perennial plant species were dominant, but not where the community contained a high abundance of annual species and caespitose grasses. This contrasting response could be attributable to differing rooting patterns (shallower structures under annual plants, and deeper roots under perennials and faster nutrient uptake in annuals compared to perennials. Our results indicate that precipitation change will have a smaller effect on key process rates in grasslandscontaining a range of perennial

  12. Water hammer prediction and control: the Green's function method

    Institute of Scientific and Technical Information of China (English)

    Li-Jun Xuan; Feng Mao; Jie-Zhi Wu

    2012-01-01

    By Green's function method we show that the water hammer (WH) can be analytically predicted for both laminar and turbulent flows (for the latter,with an eddy viscosity depending solely on the space coordinates),and thus its hazardous effect can be rationally controlled and minimized.To this end,we generalize a laminar water hammer equation of Wang et al.(J.Hydrodynamics,B2,51,1995)to include arbitrary initial condition and variable viscosity,and obtain its solution by Green's function method.The predicted characteristic WH behaviors by the solutions are in excellent agreement with both direct numerical simulation of the original governing equations and,by adjusting the eddy viscosity coefficient,experimentally measured turbulent flow data.Optimal WH control principle is thereby constructed and demonstrated.

  13. Plant functional traits predict green roof ecosystem services.

    Science.gov (United States)

    Lundholm, Jeremy; Tran, Stephanie; Gebert, Luke

    2015-02-17

    Plants make important contributions to the services provided by engineered ecosystems such as green roofs. Ecologists use plant species traits as generic predictors of geographical distribution, interactions with other species, and ecosystem functioning, but this approach has been little used to optimize engineered ecosystems. Four plant species traits (height, individual leaf area, specific leaf area, and leaf dry matter content) were evaluated as predictors of ecosystem properties and services in a modular green roof system planted with 21 species. Six indicators of ecosystem services, incorporating thermal, hydrological, water quality, and carbon sequestration functions, were predicted by the four plant traits directly or indirectly via their effects on aggregate ecosystem properties, including canopy density and albedo. Species average height and specific leaf area were the most useful traits, predicting several services via effects on canopy density or growth rate. This study demonstrates that easily measured plant traits can be used to select species to optimize green roof performance across multiple key services.

  14. 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.

  15. Predicting Species-environment Relationships with Functional Traits for the Understory Flora of Wisconsin

    Science.gov (United States)

    Ash, J.; Li, D.; Johnson, S.; Rogers, D. A.; Waller, D. M.

    2015-12-01

    Understanding the processes that structure species' abundance patterns is a central problem in ecology, both for explaining current species' distributions and predicting future changes. Environmental gradients affect species' distribution patterns with these responses likely depending on species' functional traits. Thus, tracking shifts in species' traits can provide insight into the mechanisms by which species respond to dynamic environmental conditions. We examined how functional traits are associated with long-term changes in the distribution and abundance of understory plants in Wisconsin forests over the last 50+ years. We relied on detailed surveys and resurveys of the same Wisconsin forest plots, data on 12 functional traits, and site-level environmental variables including soil and climate conditions. We then related changes in the abundance of 293 species across a network of 249 sites to these environmental variables and explored whether functional traits served to predict these relationships using multilevel models. Species abundance patterns were strongly related to variation in environmental conditions among sites, but species appear to be responding to distinct sets of environmental variables. Functional traits only weakly predicted these species-environment relationships, limiting our ability to generalize these results to other systems. Nonetheless, understanding how traits interact with environmental gradients to structure species distribution patterns helps us to disentangle the drivers of ecological change across diverse landscapes.

  16. Advancing catchment hydrology to deal with predictions under change

    Directory of Open Access Journals (Sweden)

    U. Ehret

    2013-07-01

    Full Text Available Throughout its historical development, hydrology as an engineering discipline and earth science has relied strongly on the assumption of long-term stationary boundary conditions and system configurations, which allowed for simplified and sectoral descriptions of the dynamics of hydrological systems. However, in the face of rapid and extensive global changes (of climate, land use etc. which affect all parts of the hydrological cycle, the general validity of this assumption appears doubtful. Likewise, so does the application of hydrological concepts based on stationarity to questions of hydrological change. The reason is that transient system behaviours often develop through feedbacks between the system constituents, and with the environment, generating effects that could often be neglected under stationary conditions. In this context, the aim of this paper is to present and discuss paradigms and theories potentially helpful to advancing hydrology towards the goal of understanding and predicting hydrological systems under change. For the sake of brevity we focus on catchment hydrology. We begin with a discussion of the general nature of explanation in hydrology and briefly review the history of catchment hydrology. We then propose and discuss several perspectives on catchments: as complex dynamical systems, self-organizing systems, co-evolving systems and open dissipative thermodynamic systems. We discuss the benefits of comparative hydrology and of taking an information-theoretic view of catchments, including the flow of information from data to models to predictions. In summary, we suggest that the combination of these closely related perspectives can serve as a paradigm for the further development of catchment hydrology to address predictions under change.

  17. Achieving the Gaussian Rate-Distortion Function by Prediction

    CERN Document Server

    Zamir, Ram; Erez, Uri

    2007-01-01

    The "water-filling" solution for the quadratic rate-distortion function of a stationary Gaussian source is given in terms of its power spectrum. This formula naturally lends itself to a frequency domain "test-channel" realization. We provide an alternative time-domain realization for the rate-distortion function, based on linear prediction. This solution has some interesting implications, including the optimality at all distortion levels of pre/post filtered vector-quantized differential pulse code modulation (DPCM), and a duality relationship with decision-feedback equalization (DFE) for inter-symbol interference (ISI) channels.

  18. 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...

  19. 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...

  20. 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.

  1. Density functional theory predictions of isotropic hyperfine coupling constants.

    Science.gov (United States)

    Hermosilla, L; Calle, P; García de la Vega, J M; Sieiro, C

    2005-02-17

    The reliability of density functional theory (DFT) in the determination of the isotropic hyperfine coupling constants (hfccs) of the ground electronic states of organic and inorganic radicals is examined. Predictions using several DFT methods and 6-31G, TZVP, EPR-III and cc-pVQZ basis sets are made and compared to experimental values. The set of 75 radicals here studied was selected using a wide range of criteria. The systems studied are neutral, cationic, anionic; doublet, triplet, quartet; localized, and conjugated radicals, containing 1H, 9Be, 11B, 13C, 14N, 17O, 19F, 23Na, 25Mg, 27Al, 29Si, 31P, 33S, and 35Cl nuclei. The considered radicals provide 241 theoretical hfcc values, which are compared with 174 available experimental ones. The geometries of the studied systems are obtained by theoretical optimization using the same functional and basis set with which the hfccs were calculated. Regression analysis is used as a basic and appropriate methodology for this kind of comparative study. From this analysis, we conclude that DFT predictions of the hfccs are reliable for B3LYP/TZVP and B3LYP/EPR-III combinations. Both functional/basis set scheme are the more useful theoretical tools for predicting hfccs if compared to other much more expensive methods.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. Integrating Gene Ontology and Blast to predict gene functions

    Institute of Scientific and Technical Information of China (English)

    WANG Cheng-gang; MO Zhi-hong

    2007-01-01

    A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology (GO) annotations together. The operation system was based on Debian Linux 3.1, with Apache as the web server and Mysql database as the data storage system. FASTA files with GO annotations were taken as the sequence source for blast alignment, which were formatted by wu-formatdb program. The GoBlast system includes three Bioperl modules in Perl: a data input module, a data process module and a data output module. A GoBlast query starts with an amino acid or nucleotide sequence. It ends with an output in an html page, presenting high scoring gene products which are of a high homology to the queried sequence and listing associated GO terms beside respective gene poducts. A simple click on a GO term leads to the detailed explanation of the specific gene function. This avails gene function prediction by Blast. GoBlast can be a very useful tool for functional genome research and is available for free at http://bioq.org/goblast.

  7. 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.

  8. 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.

  9. 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

  10. 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

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

    DEFF Research Database (Denmark)

    Brander, Keith

    2010-01-01

    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......Environmental factors act on individual fishes directly and indirectly. The direct effects on rates and behaviour can be studied experimentally and in the field, particularly with the advent of ever smarter tags for tracking fishes and their environment. Indirect effects due to changes in food......, 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...

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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

    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...

  18. 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

  19. The Evolutionary Legacy of Diversification Predicts Ecosystem Function.

    Science.gov (United States)

    Yguel, Benjamin; Jactel, Hervé; Pearse, Ian S; Moen, Daniel; Winter, Marten; Hortal, Joaquin; Helmus, Matthew R; Kühn, Ingolf; Pavoine, Sandrine; Purschke, Oliver; Weiher, Evan; Violle, Cyrille; Ozinga, Wim; Brändle, Martin; Bartish, Igor; Prinzing, Andreas

    2016-10-01

    Theory suggests that the structure of evolutionary history represented in a species community may affect its functioning, but phylogenetic diversity metrics do not allow for the identification of major differences in this structure. Here we propose a new metric, ELDERness (for Evolutionary Legacy of DivERsity) to estimate evolutionary branching patterns within communities by fitting a polynomial function to lineage-through-time (LTT) plots. We illustrate how real and simulated community branching patterns can be more correctly described by ELDERness and can successfully predict ecosystem functioning. In particular, the evolutionary history of branching patterns can be encapsulated by the parameters of third-order polynomial functions and further measured through only two parameters, the "ELDERness surfaces." These parameters captured variation in productivity of a grassland community better than existing phylogenetic diversity or diversification metrics and independent of species richness or presence of nitrogen fixers. Specifically, communities with small ELDERness surfaces (constant accumulation of lineages through time in LTT plots) were more productive, consistent with increased productivity resulting from complementary lineages combined with niche filling within lineages. Overall, while existing phylogenetic diversity metrics remain useful in many contexts, we suggest that our ELDERness approach better enables testing hypotheses that relate complex patterns of macroevolutionary history represented in local communities to ecosystem functioning.

  20. Predicting Infrared Spectra of Nerve Agents Using Density Functional Theory

    Science.gov (United States)

    Zhang, Y.-P.; Wang, H.-T.; Zheng, W.-P.; Sun, C.; Bai, Y.; Guo, X.-D.; Sun, H.

    2016-09-01

    Vibration frequencies of four nerve agents and two simulators are calculated using B3LYP coupled with ten basis sets. To evaluate the accuracy of calculated spectra, root mean square error (RMSE) and weighted cross-correlation average (WCCA) are considered. The evaluation shows that B3LYP/6-311+g(d,p) performs best in predicting infrared spectra, and polarization functions are found to be more important than diffusion functions in spectra simulation. Moreover, B3LYP calculation underestimates frequencies related to the P atom. The WCCA metric derives 1.008 as a unique scaling factor for calculated frequencies. The results indicate that the WCCA metric can identify six agents based on calculated spectra.

  1. Predicting richness effects on ecosystem function in natural communities

    DEFF Research Database (Denmark)

    Dangles, Olivier; Crespo-Pérez, Verónica; Andino, Patricio;

    2011-01-01

    . Despite the increased complexity of experimental and theoretical studies on the biodiversity-ecosystem functioning (B-EF) relationship, a major challenge is to demonstrate whether the observed importance of biodiversity in controlled experimental systems also persists in nature. Due...... to their structural simplicity and their low levels of human impacts, extreme species-poor ecosystems may provide new insights into B-EF relationships in natural systems. We address this issue using shredder invertebrate communities and organic matter decomposition rates in 24 high-altitude (3200-3900 m) Neotropical...... among the three shredder species, indicating complementary resource use and/or facilitation. By integrating survey and experimental data in surface response analyses we found that observed B-EF patterns fit those predicted by a linear model that described litter decomposition rates as a function...

  2. Utility functions predict variance and skewness risk preferences in monkeys.

    Science.gov (United States)

    Genest, Wilfried; Stauffer, William R; Schultz, Wolfram

    2016-07-26

    Utility is the fundamental variable thought to underlie economic choices. In particular, utility functions are believed to reflect preferences toward risk, a key decision variable in many real-life situations. To assess the validity of utility representations, it is therefore important to examine risk preferences. In turn, this approach requires formal definitions of risk. A standard approach is to focus on the variance of reward distributions (variance-risk). In this study, we also examined a form of risk related to the skewness of reward distributions (skewness-risk). Thus, we tested the extent to which empirically derived utility functions predicted preferences for variance-risk and skewness-risk in macaques. The expected utilities calculated for various symmetrical and skewed gambles served to define formally the direction of stochastic dominance between gambles. In direct choices, the animals' preferences followed both second-order (variance) and third-order (skewness) stochastic dominance. Specifically, for gambles with different variance but identical expected values (EVs), the monkeys preferred high-variance gambles at low EVs and low-variance gambles at high EVs; in gambles with different skewness but identical EVs and variances, the animals preferred positively over symmetrical and negatively skewed gambles in a strongly transitive fashion. Thus, the utility functions predicted the animals' preferences for variance-risk and skewness-risk. Using these well-defined forms of risk, this study shows that monkeys' choices conform to the internal reward valuations suggested by their utility functions. This result implies a representation of utility in monkeys that accounts for both variance-risk and skewness-risk preferences.

  3. 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.

  4. 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.

  5. Predictive equations using regression analysis of pulmonary function for healthy children in Northeast China.

    Directory of Open Access Journals (Sweden)

    Ya-Nan Ma

    Full Text Available BACKGROUND: There have been few published studies on spirometric reference values for healthy children in China. We hypothesize that there would have been changes in lung function that would not have been precisely predicted by the existing spirometric reference equations. The objective of the study was to develop more accurate predictive equations for spirometric reference values for children aged 9 to 15 years in Northeast China. METHODOLOGY/PRINCIPAL FINDINGS: Spirometric measurements were obtained from 3,922 children, including 1,974 boys and 1,948 girls, who were randomly selected from five cities of Liaoning province, Northeast China, using the ATS (American Thoracic Society and ERS (European Respiratory Society standards. The data was then randomly split into a training subset containing 2078 cases and a validation subset containing 1844 cases. Predictive equations used multiple linear regression techniques with three predictor variables: height, age and weight. Model goodness of fit was examined using the coefficient of determination or the R(2 and adjusted R(2. The predicted values were compared with those obtained from the existing spirometric reference equations. The results showed the prediction equations using linear regression analysis performed well for most spirometric parameters. Paired t-tests were used to compare the predicted values obtained from the developed and existing spirometric reference equations based on the validation subset. The t-test for males was not statistically significant (p>0.01. The predictive accuracy of the developed equations was higher than the existing equations and the predictive ability of the model was also validated. CONCLUSION/SIGNIFICANCE: We developed prediction equations using linear regression analysis of spirometric parameters for children aged 9-15 years in Northeast China. These equations represent the first attempt at predicting lung function for Chinese children following the ATS

  6. 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

  7. 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.

  8. Selection, adaptation, and predictive information in changing environments

    Science.gov (United States)

    Feltgen, Quentin; Nemenman, Ilya

    2014-03-01

    Adaptation by means of natural selection is a key concept in evolutionary biology. Individuals better matched to the surrounding environment outcompete the others. This increases the fraction of the better adapted individuals in the population, and hence increases its collective fitness. Adaptation is also prominent on the physiological scale in neuroscience and cell biology. There each individual infers properties of the environment and changes to become individually better, improving the overall population as well. Traditionally, these two notions of adaption have been considered distinct. Here we argue that both types of adaptation result in the same population growth in a broad class of analytically tractable population dynamics models in temporally changing environments. In particular, both types of adaptation lead to subextensive corrections to the population growth rates. These corrections are nearly universal and are equal to the predictive information in the environment time series, which is also the characterization of the time series complexity. This work has been supported by the James S. McDonnell Foundation.

  9. Does obesity predict functional outcome in the dysvascular amputee?

    Science.gov (United States)

    Kalbaugh, Corey A; Taylor, Spence M; Kalbaugh, Brooke A; Halliday, Matthew; Daniel, Grace; Cass, Anna L; Blackhurst, Dawn W; Cull, David L; Langan, Eugene M; Carsten, Christopher G; York, John W; Snyder, Bruce A; Youkey, Jerry R

    2006-08-01

    Limited information is available concerning the effects of obesity on the functional outcomes of patients requiring major lower limb amputation because of peripheral arterial disease (PAD). The purpose of this study was to examine the predictive ability of body mass index (BMI) to determine functional outcome in the dysvascular amputee. To do this, 434 consecutive patients (mean age, 65.8 +/- 13.3, 59% male, 71.4% diabetic) undergoing major limb amputation (225 below-knee amputation, 27 through-knee amputation, 132 above-knee amputation, and 50 bilateral) as a complication of PAD from January 1998 through May 2004 were analyzed according to preoperative BMI. BMI was classified according to the four-group Center for Disease Control system: underweight, 0 to 18.4 kg/m2; normal, 18.5 to 24.9 kg/m2; overweight, 25 to 29.9 kg/m2; and obese, > or = 30 kg/m2. Outcome parameters measured included prosthetic usage, maintenance of ambulation, survival, and maintenance of independent living status. The chi2 test for association was used to examine prosthesis wear. Kaplan-Meier curves were constructed to assess maintenance of ambulation, survival, and maintenance of independent living status. Multivariate analysis using the multiple logistic regression model and a Cox proportional hazards model were used to predict variables independently associated with prosthetic use and ambulation, survival, and independence, respectively. Overall prosthetic usage and 36-month ambulation, survival, and independent living status for the entire cohort was 48.6 per cent, 42.8 per cent, 48.1 per cent, 72.3 per cent, and for patients with normal BMI was 41.5 per cent, 37.4 per cent, 45.6 per cent, and 69.5 per cent, respectively. There was no statistically significant difference in outcomes for overweight patients (59.2%, 50.7%, 52.5%, and 75%) or obese patients (51.8%, 46.2%, 49.7%, and 75%) when compared with normal patients. Although there were significantly poorer outcomes for underweight

  10. 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.

  11. 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.

  12. 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...

  13. 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

  14. 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

  15. 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...

  16. 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.

  17. 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. PMID:27242680

  18. 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

  19. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Beckendorf, V. [Centre Alexis Vautrin, Vandoeuvre-les Nancy (France); Hay, M. [Centre Val d`Aurelle, Montpellier (France); Rozan, R. [Centre Jean Perrin, Clermont-Ferrand (France); Lagrange, J.L. [Centre Antoine Lacassagne, Nice (France); N`Guyen, T. [Centre Jean Godinot, Reims (France); Giraud, B. [CCMI Commission de Cooperation Medicale Intercentres, Centre Hospitalier Univ. et Centre Jean Perrin, Clement-Ferrand (France)

    1996-01-01

    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).

  1. 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

  2. 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;

    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...

  3. 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

    OBJECTIVE: To investigate relations between predictors and outcomes, and especially to identify predictors influencing the time trend in recovery after mild traumatic brain injury. METHODS: We included 59 patients with mild head injury in a prospective study. They underwent comprehensive assessment...... 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....... 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....

  4. 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

  5. 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

  6. 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.

  7. 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...... 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...... 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....

  8. 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

  9. 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. ...

  10. 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

  11. 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...

  12. Comparing Predictions and Outcomes : Theory and Application to Income Changes

    NARCIS (Netherlands)

    Das, J.W.M.; Dominitz, J.; van Soest, A.H.O.

    1997-01-01

    Household surveys often elicit respondents' intentions or predictions of future outcomes. The survey questions may ask respondents to choose among a selection of (ordered) response categories. If panel data or repeated cross-sections are available, predictions may be compared with realized outcomes.

  13. PREDICTS: Projecting Responses of Ecological Diversity in Changing Terrestrial Systems

    Directory of Open Access Journals (Sweden)

    Georgina Mace

    2012-12-01

    Full Text Available The PREDICTS project (www.predicts.org.uk is a three-year NERC-funded project to model and predict at a global scale how local terrestrial diversity responds to human pressures such as land use, land cover, pollution, invasive species and infrastructure. PREDICTS is a collaboration between Imperial College London, the UNEP World Conservation Monitoring Centre, Microsoft Research Cambridge, UCL and the University of Sussex. In order to meet its aims, the project relies on extensive data describing the diversity and composition of biological communities at a local scale. Such data are collected on a vast scale through the committed efforts of field ecologists. If you have appropriate data that you would be willing to share with us, please get in touch (enquiries@predicts.org.uk. All contributions will be acknowledged appropriately and all data contributors will be included as co-authors on an open-access paper describing the database.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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...

  19. Functional identity and functional structure change through succession in a rocky intertidal marine herbivore assemblage.

    Science.gov (United States)

    Aguilera, Moisés A; Navarrete, Sergio A

    2012-01-01

    Despite the great interest in characterizing the functional structure and resilience of functional groups in natural communities, few studies have examined in which way the roles and relationships of coexisting species change during community succession, a fundamental and natural process that follows the release of new resources in terrestrial and aquatic ecosystems. Variation in algal traits that characterize different phases and stages of community succession on rocky shores are likely to influence the magnitude, direction of effects, and the level of redundancy and complementarity in the diverse assemblage of herbivores. Two separate field experiments were conducted to quantify per capita and population effects and the functional relationship (i.e., redundancy or complementarity) of four herbivore species found in central Chile during early and late algal succession. The first experiment examined grazer effects on the colonization and establishment of early-succession algal species. The second experiment examined effects on the late-successional, dominant corticated alga Mazzaella laminarioides. Complementary laboratory experiments with all species and under natural environmental conditions allowed us to further characterize the collective effects of these species. We found that, during early community succession, all herbivore species had similar effects on the ephemeral algae, ulvoids, but only during the phase of colonization. Once these algae were established, only a subset of the species was able to control their abundance. During late succession, only the keyhole limpet Fissurella crassa could control corticated Mazzaella. The functional relationships among these species changed dramatically from redundant effects on ephemeral algae during early colonization, to a more complementary role on established early-successional algae, to a dominant (i.e., keystone) effect on late succession. This study highlights that functional relationship within consumer

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. Stress induced changes in testis function.

    Science.gov (United States)

    López-Calderón, A; Ariznavarreta, C; González-Quijano, M I; Tresguerres, J A; Calderón, M D

    1991-01-01

    The mechanism through which chronic stress inhibits the hypothalamic-pituitary-testicular axis has been investigated. Chronic restraint stress decreases testosterone secretion, an effect that is associated with a decrease in plasma gonadotropin levels. In chronically stressed rats there was a decrease in hypothalamic luteinizing hormone-releasing hormone (LHRH) content and the response on plasma gonadotropins to LHRH administration was enhanced. Thus the inhibitory effect of chronic stress on plasma LH and FSH levels seems not to be due to a reduction in pituitary responsiveness to LHRH, but rather to a modification in LHRH secretion. It has been suggested that beta-endorphin might interfere with hypothalamic LHRH secretion during stress. Chronic immobilization did not modify hypothalamic beta-endorphin, while an increase in pituitary beta-endorphin secretion was observed. Since we cannot exclude that changes in beta-endorphin secreted by the pituitary or other opioids may play some role in the stress-induced decrease in LHRH secretion, the effect of naltrexone administration on plasma gonadotropin was studied in chronically stressed rats. Naltrexone treatment did not modify the decrease in plasma concentrations of LH or FSH. These findings suggest that the inhibitory effect of restraint on the testicular axis is exerted at hypothalamic level by some mechanism other than opioids. PMID:1958548

  6. 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.

  7. Aggressive behavior and change in salivary testosterone concentrations predict willingness to engage in a competitive task.

    Science.gov (United States)

    Carré, Justin M; McCormick, Cheryl M

    2008-08-01

    The current study investigated relationships among aggressive behavior, change in salivary testosterone concentrations, and willingness to engage in a competitive task. Thirty-eight male participants provided saliva samples before and after performing the Point Subtraction Aggression Paradigm (a laboratory measure that provides opportunity for aggressive and defensive behavior while working for reward; all three involve pressing specific response keys). Baseline testosterone concentrations were not associated with aggressive responding. However, aggressive responding (but not point reward or point protection responding) predicted the pre- to post-PSAP change in testosterone: Those with the highest aggressive responding had the largest percent increase in testosterone concentrations. Together, aggressive responding and change in testosterone predicted willingness to compete following the PSAP. Controlling for aggression, men who showed a rise in testosterone were more likely to choose to compete again (p=0.03) and controlling for testosterone change, men who showed the highest level of aggressive responding were more likely to choose the non-competitive task (p=0.02). These results indicate that situation-specific aggressive behavior and testosterone responsiveness are functionally relevant predictors of future social behavior.

  8. 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…

  9. Gradient radial basis function networks for nonlinear and nonstationary time series prediction.

    Science.gov (United States)

    Chng, E S; Chen, S; Mulgrew, B

    1996-01-01

    We present a method of modifying the structure of radial basis function (RBF) network to work with nonstationary series that exhibit homogeneous nonstationary behavior. In the original RBF network, the hidden node's function is to sense the trajectory of the time series and to respond when there is a strong correlation between the input pattern and the hidden node's center. This type of response, however, is highly sensitive to changes in the level and trend of the time series. To counter these effects, the hidden node's function is modified to one which detects and reacts to the gradient of the series. We call this new network the gradient RBF (GRBF) model. Single and multistep predictive performance for the Mackey-Glass chaotic time series were evaluated using the classical RBF and GRBF models. The simulation results for the series without and with a tine-varying mean confirm the superior performance of the GRBF predictor over the RBF predictor.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. Enhancing the Executive Functions of 3-Year-Olds in the Dimensional Change Card Sort Task

    Science.gov (United States)

    Perone, Sammy; Molitor, Stephen J.; Buss, Aaron T.; Spencer, John P.; Samuelson, Larissa K.

    2015-01-01

    Executive functions enable flexible thinking, something young children are notoriously bad at. For instance, in the dimensional change card sort (DCCS) task, 3-year-olds can sort cards by one dimension (shape), but continue to sort by this dimension when asked to switch (to color). This study tests a prediction of a dynamic neural field model that…

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    (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...

  16. 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...

  17. 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.…

  18. 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.

  19. Fluctuating Electrocardiographic Changes Predict Poor Outcomes After Acute Subarachnoid Hemorrhage

    Science.gov (United States)

    Elsharkawy, Hesham; Abd-Elsayed, Alaa; El-Hadi, Sherif; Provencio, Javier; Tetzlaff, John

    2016-01-01

    Background: Electrocardiogram (ECG) abnormalities following aneurysmal subarachnoid hemorrhage (SAH) have been well documented. Evidence suggests that ECG changes and cardiac dysfunction worsen outcome. Determining which patients are at most risk is unclear but important to ascertain. Methods: We prospectively studied clinical markers, cardiac abnormalities, and clinical outcomes in 20 patients admitted within 48 hours of aneurysmal SAH. All patients had ECGs prior to surgical clipping, during the clipping surgery, and during the postoperative period. Results: The aneurysm was located in the anterior circulation in 17 patients (85%) and in the posterior circulation in 3 patients (15%). Abnormal ECG changes in patients with acute SAH were observed, with a total incidence rate of 65%. The incidence of T wave abnormalities was 53.8% among the patients with ECG changes, 46.2% had ST segment change, and 30.8% had QT interval prolongation. Of the 13 patients with ECG changes, 4 (30.8%) had fluctuating ECG abnormalities (an abnormality that presented and disappeared during the study period or changed in character). All 4 patients with fluctuating ECG changes had a poor outcome (100%) compared to 3 of the 9 patients (33.3%) patients with fixed abnormalities (Paneurysmal SAH. In our group, all the patients who had ECG changes that fluctuated from one abnormal change to another had a poor outcome. The etiology of this finding is not clear but may open the door to further study into the pathogenesis of cardiac changes in aneurysmal SAH. The clinical utility of the variability of ECG abnormalities needs to be validated in a larger cohort of patients with longer follow-up than was possible in this study.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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...

  7. Are Psychotherapeutic Changes Predictable? Comparison of a Chicago Counseling Center Project with a Penn Psychotherapy Project.

    Science.gov (United States)

    Luborsky, Lester; And Others

    1979-01-01

    Compared studies predicting outcomes of psychotherapy. Level of prediction success in both projects was modest. Particularly for the rated benefits score, the profile of variables showed similar levels of success between the projects. Successful predictions were based on adequacy of personality functioning, match on marital status, and length of…

  8. 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...

  9. 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...

  10. 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.

  11. 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.

  12. 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...

  13. Executive Function Predicts Artificial Language Learning in Children and Adults

    Science.gov (United States)

    Kapa, Leah Lynn

    2013-01-01

    Prior research has established an executive function advantage among bilinguals as compared to monolingual peers. These non-linguistic cognitive advantages are largely assumed to result from the experience of managing two linguistic systems. However, the possibility remains that the relationship between bilingualism and executive function is…

  14. 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.

  15. Can We Predict Types of Code Changes? An Empirical Analysis

    NARCIS (Netherlands)

    Giger, E.; Pinzger, M.; Gall, H.C.

    2012-01-01

    Preprint of paper published in: 9th IEEE Working Conference on Mining Software Repositories (MSR), 2-3 June 2012; doi:10.1109/MSR.2012.6224284 There exist many approaches that help in pointing developers to the change-prone parts of a software system. Although beneficial, they mostly fall short in

  16. 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...

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. Application of the Condensed Fukui Function to Predict Reactivity in Core–Shell Transition Metal Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Allison, Thomas C.; Tong, Yu ye J.

    2013-07-01

    Chemical reactivity descriptors are a powerful means for understanding reactivity in a wide variety of chemical compounds. These descriptors, rooted in density functional theory, have found broad application in organic chemical reactions, but have not been as widely applied for other classes of chemical species such as nanoparticles, which are the subject of this article. Specifically, we explore application of the Fukui function, the global hardness and softness, the local softness, and the dual descriptor to pure metallic and core–shell nanoparticles, with and without a CO molecule bound to the surface. We find that the Fukui function is useful in predicting and interpreting chemical reactivity, and that it correlates well with the results of the popular d-band center method. Differences in the Fukui function before and after bonding of a CO molecule to the surface of a nanoparticle reveal interesting information about the reactivity of the nanoparticle surface. The change in the Fukui function when an electric field is applied to the molecule is also considered. Though the results are generally good, some of the limitations of this approach become clear.

  2. 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 potential...... will decline. These levels of confidence seem unwarranted, since many processes are either absent from or poorly represented in the models used, data are sparse and, unlike terrestrial crop projections, there are no controlled experiments.This review discusses methodological issues that affect our...

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. 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...... of cerebral serotonin transmission to seasonal and other forms of environmental change imparts greater behavioral flexibility, at the expense of increased vulnerability to stress. This model may explain the somewhat higher prevalence of the s-allele in some human populations dwelling at geographic latitudes...

  8. 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…

  9. 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.

  10. 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.

  11. 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.

  12. Per capita interactions and stress tolerance drive stress-induced changes in biodiversity effects on ecosystem functions.

    Science.gov (United States)

    Baert, Jan M; Janssen, Colin R; Sabbe, Koen; De Laender, Frederik

    2016-01-01

    Environmental stress changes the relationship between biodiversity and ecosystem functions, but the underlying mechanisms are poorly understood. Because species interactions shape biodiversity-ecosystem functioning relationships, changes in per capita interactions under stress (as predicted by the stress gradient hypothesis) can be an important driver of stress-induced changes in these relationships. To test this hypothesis, we measure productivity in microalgae communities along a diversity and herbicide gradient. On the basis of additive partitioning and a mechanistic community model, we demonstrate that changes in per capita interactions do not explain effects of herbicide stress on the biodiversity-productivity relationship. Instead, assuming that the per capita interactions remain unaffected by stress, causing species densities to only change through differences in stress tolerance, suffices to predict the stress-induced changes in the biodiversity-productivity relationship and community composition. We discuss how our findings set the stage for developing theory on how environmental stress changes biodiversity effects on ecosystem functions. PMID:27534986

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    investigated endothelial dysfunction, risk factors, and progression of carotid intima-media thickness (cIMT) in late-middle-aged individuals at low to intermediate cardiovascular risk in a prospective study between 1997 and 2005. METHODS AND RESULTS: Brachial artery flow-mediated dilatation and cIMT were...... measured in 213 nonsmoking British civil servants recruited from a prospective cohort (Whitehall II study). Participants (age, 45 to 66 years) were free of clinical cardiovascular disease and diabetes mellitus. Risk factors and Framingham Risk Score were determined at baseline. cIMT was repeated 6...... to its impact on the evolution of the atherosclerotic substrate. Flow-mediated dilatation testing provides an integrated vascular measure that may aid the prediction of structural disease evolution and represents a potential short- to intermediate-term outcome measure for evaluation of preventive...

  14. 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.

  15. 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...

  16. 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.

  17. 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

  18. 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.

  19. In silico predicted structural and functional robustness of piscine steroidogenesis.

    Science.gov (United States)

    Hala, D; Huggett, D B

    2014-03-21

    Assessments of metabolic robustness or susceptibility are inherently dependent on quantitative descriptions of network structure and associated function. In this paper a stoichiometric model of piscine steroidogenesis was constructed and constrained with productions of selected steroid hormones. Structural and flux metrics of this in silico model were quantified by calculating extreme pathways and optimal flux distributions (using linear programming). Extreme pathway analysis showed progestin and corticosteroid synthesis reactions to be highly participant in extreme pathways. Furthermore, reaction participation in extreme pathways also fitted a power law distribution (degree exponent γ=2.3), which suggested that progestin and corticosteroid reactions act as 'hubs' capable of generating other functionally relevant pathways required to maintain steady-state functionality of the network. Analysis of cofactor usage (O2 and NADPH) showed progestin synthesis reactions to exhibit high robustness, whereas estrogen productions showed highest energetic demands with low associated robustness to maintain such demands. Linear programming calculated optimal flux distributions showed high heterogeneity of flux values with a near-random power law distribution (degree exponent γ≥2.7). Subsequently, network robustness was tested by assessing maintenance of metabolite flux-sum subject to targeted deletions of rank-ordered (low to high metric) extreme pathway participant and optimal flux reactions. Network robustness was susceptible to deletions of extreme pathway participant reactions, whereas minimal impact of high flux reaction deletion was observed. This analysis shows that the steroid network is susceptible to perturbation of structurally relevant (extreme pathway) reactions rather than those carrying high flux.

  20. Change in Depression Symptomatology and Cognitive Function in Twins

    DEFF Research Database (Denmark)

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

    2016-01-01

    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 of correla...... to detect any causal association between change in depressive symptomatology and cognitive decline in middle-aged and elderly people over a 10-year interval.......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...... 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...

  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. Does human presynaptic striatal dopamine function predict social conformity?

    Science.gov (United States)

    Stokes, Paul R A; Benecke, Aaf; Puraite, Julita; Bloomfield, Michael A P; Shotbolt, Paul; Reeves, Suzanne J; Lingford-Hughes, Anne R; Howes, Oliver; Egerton, Alice

    2014-03-01

    Socially desirable responding (SDR) is a personality trait which reflects either a tendency to present oneself in an overly positive manner to others, consistent with social conformity (impression management (IM)), or the tendency to view one's own behaviour in an overly positive light (self-deceptive enhancement (SDE)). Neurochemical imaging studies report an inverse relationship between SDR and dorsal striatal dopamine D₂/₃ receptor availability. This may reflect an association between SDR and D₂/₃ receptor expression, synaptic dopamine levels or a combination of the two. In this study, we used a [¹⁸F]-DOPA positron emission tomography (PET) image database to investigate whether SDR is associated with presynaptic dopamine function. Striatal [¹⁸F]-DOPA uptake, (k(i)(cer), min⁻¹), was determined in two independent healthy participant cohorts (n=27 and 19), by Patlak analysis using a cerebellar reference region. SDR was assessed using the revised Eysenck Personality Questionnaire (EPQ-R) Lie scale, and IM and SDE were measured using the Paulhus Deception Scales. No significant associations were detected between Lie, SDE or IM scores and striatal [¹⁸F]-DOPA k(i)(cer). These results indicate that presynaptic striatal dopamine function is not associated with social conformity and suggests that social conformity may be associated with striatal D₂/₃ receptor expression rather than with synaptic dopamine levels.

  3. 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.

  4. 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.

  5. Modelling land Use Change : Improving the prediction of future land use patterns

    NARCIS (Netherlands)

    de Nijs, A.C.M.

    2009-01-01

    Modelling land Use Change: Improving the prediction of future land use patterns. Man has been altering his living environment since prehistoric times and will continue to do so. It is predicted that by 2030 about 90,000 ha will be needed for residential developments in the Netherlands and 55,000 ha

  6. Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties.

    Science.gov (United States)

    Powell, Jeff R; Welsh, Allana; Hallin, Sara

    2015-07-01

    Microorganisms drive biogeochemical processes, but linking these processes to real changes in microbial communities under field conditions is not trivial. Here, we present a model-based approach to estimate independent contributions of microbial community shifts to ecosystem properties. The approach was tested empirically, using denitrification potential as our model process, in a spatial survey of arable land encompassing a range of edaphic conditions and two agricultural production systems. Soil nitrate was the most important single predictor of denitrification potential (the change in Akaike's information criterion, corrected for sample size, ΔAIC(c) = 20.29); however, the inclusion of biotic variables (particularly the evenness and size of denitrifier communities [ΔAIC(c) = 12.02], and the abundance of one denitrifier genotype [ΔAIC(c) = 18.04]) had a substantial effect on model precision, comparable to the inclusion of abiotic variables (biotic R2 = 0.28, abiotic R2 = 0.50, biotic + abiotic R2 = 0.76). This approach provides a valuable tool for explicitly linking microbial communities to ecosystem functioning. By making this link, we have demonstrated that including aspects of microbial community structure and diversity in biogeochemical models can improve predictions of nutrient cycling in ecosystems and enhance our understanding of ecosystem functionality.

  7. 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.

  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

    effect of amphiphiles, at concentrations often used in biological research, on the bilayer elastic response to a change in the hydrophobic length of an embedded protein. The effects of structurally diverse amphiphiles can be described by changes in a phenomenological bilayer spring constant (H......Many drugs are amphiphiles that, in addition to binding to a particular target protein, adsorb to cell membrane lipid bilayers and alter intrinsic bilayer physical properties (e. g., bilayer thickness, monolayer curvature, and elastic moduli). Such changes can modulate membrane protein function......-B) that summarizes the bilayer elastic properties, as sensed by a bilayer-spanning protein. Amphiphile-induced changes in H-B, measured using gA channels of a particular length, quantitatively predict changes in lifetime for channels of a different length-as well as changes in the inactivation of voltage...

  9. 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)

  10. Modified estimators for the change point in hazard function

    Science.gov (United States)

    Karasoy, Durdu; Kadilar, Cem

    2009-07-01

    We propose the consistent estimators for the change point in hazard function by improving the estimators in [A.P. Basu, J.K. Ghosh, S.N. Joshi, On estimating change point in a failure rate, in: S.S. Gupta, J.O. Berger (Eds.), Statistical Decision Theory and Related Topics IV, vol. 2, Springer-Verlag, 1988, pp. 239-252] and [H.T. Nguyen, G.S. Rogers, E.A. Walker, Estimation in change point hazard rate model, Biometrika 71 (1984) 299-304]. By a simulation study, we show that the proposed estimators are more efficient than the original estimators in many cases.

  11. 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.

  12. 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...

  13. 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.

  14. 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

  15. [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.

  16. [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

  17. Age-related changes in task related functional network connectivity.

    Directory of Open Access Journals (Sweden)

    Jason Steffener

    Full Text Available Aging has a multi-faceted impact on brain structure, brain function and cognitive task performance, but the interaction of these different age-related changes is largely unexplored. We hypothesize that age-related structural changes alter the functional connectivity within the brain, resulting in altered task performance during cognitive challenges. In this neuroimaging study, we used independent components analysis to identify spatial patterns of coordinated functional activity involved in the performance of a verbal delayed item recognition task from 75 healthy young and 37 healthy old adults. Strength of functional connectivity between spatial components was assessed for age group differences and related to speeded task performance. We then assessed whether age-related differences in global brain volume were associated with age-related differences in functional network connectivity. Both age groups used a series of spatial components during the verbal working memory task and the strength and distribution of functional network connectivity between these components differed across the age groups. Poorer task performance, i.e. slower speed with increasing memory load, in the old adults was associated with decreases in functional network connectivity between components comprised of the supplementary motor area and the middle cingulate and between the precuneus and the middle/superior frontal cortex. Advancing age also led to decreased brain volume; however, there was no evidence to support the hypothesis that age-related alterations in functional network connectivity were the result of global brain volume changes. These results suggest that age-related differences in the coordination of neural activity between brain regions partially underlie differences in cognitive performance.

  18. Predictive functional control based on fuzzy T-S model for HVAC systems temperature control

    Institute of Scientific and Technical Information of China (English)

    Hongli L(U); Lei JIA; Shulan KONG; Zhaosheng ZHANG

    2007-01-01

    In heating,ventilating and air-conditioning(HVAC)systems,there exist severe nonlinearity,time-varying nature,disturbances and uncertainties.A new predictive functional control based on Takagi-Sugeno(T-S)fuzzy model was proposed to control HVAC systems.The T-S fuzzy model of stabilized controlled process was obtained using the least squares method,then on the basis of global linear predictive model from T-S fuzzy model,the process was controlled by the predictive functional controller.Especially the feedback regulation part was developed to compensate uncertainties of fuzzy predictive model.Finally simulation test results in HVAC systems control applications showed that the proposed fuzzy model predictive functional control improves tracking effect and robustness.Compared with the conventional PID controller,this control strategy has the advantages of less overshoot and shorter setting time,etc.

  19. Dynamic Associations of Change in Physical Activity and Change in Cognitive Function: Coordinated Analyses of Four Longitudinal Studies

    Directory of Open Access Journals (Sweden)

    Magnus Lindwall

    2012-01-01

    Full Text Available The present study used a coordinated analyses approach to examine the association of physical activity and cognitive change in four longitudinal studies. A series of multilevel growth models with physical activity included both as a fixed (between-person and time-varying (within-person predictor of four domains of cognitive function (reasoning, memory, fluency, and semantic knowledge was used. Baseline physical activity predicted fluency, reasoning and memory in two studies. However, there was a consistent pattern of positive relationships between time-specific changes in physical activity and time-specific changes in cognition, controlling for expected linear trajectories over time, across all four studies. This pattern was most evident for the domains of reasoning and fluency.

  20. 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.

  1. 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...

  2. 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)

  3. 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.

  4. Applications of Displacement Transfer Functions to Deformed Shape Predictions of the GIII Swept-Wing Structure

    Science.gov (United States)

    Lung, Shun-Fat; Ko, William L.

    2016-01-01

    The displacement transfer functions (DTFs) were applied to the GIII swept wing for the deformed shape prediction. The calculated deformed shapes are very close to the correlated finite element results as well as the measured data. The convergence study showed that using 17 strain stations, the wing-tip displacement prediction error was 1.6 percent, and that there is no need to use a large number of strain stations for G-III wing shape predictions.

  5. 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...

  6. COMPASS: A computational model to predict changes in MMSE scores 24-months after initial assessment of Alzheimer’s disease

    Science.gov (United States)

    Zhu, Fan; Panwar, Bharat; Dodge, Hiroko H.; Li, Hongdong; Hampstead, Benjamin M.; Albin, Roger L.; Paulson, Henry L.; Guan, Yuanfang

    2016-01-01

    We present COMPASS, a COmputational Model to Predict the development of Alzheimer’s diSease Spectrum, to model Alzheimer’s disease (AD) progression. This was the best-performing method in recent crowdsourcing benchmark study, DREAM Alzheimer’s Disease Big Data challenge to predict changes in Mini-Mental State Examination (MMSE) scores over 24-months using standardized data. In the present study, we conducted three additional analyses beyond the DREAM challenge question to improve the clinical contribution of our approach, including: (1) adding pre-validated baseline cognitive composite scores of ADNI-MEM and ADNI-EF, (2) identifying subjects with significant declines in MMSE scores, and (3) incorporating SNPs of top 10 genes connected to APOE identified from functional-relationship network. For (1) above, we significantly improved predictive accuracy, especially for the Mild Cognitive Impairment (MCI) group. For (2), we achieved an area under ROC of 0.814 in predicting significant MMSE decline: our model has 100% precision at 5% recall, and 91% accuracy at 10% recall. For (3), “genetic only” model has Pearson’s correlation of 0.15 to predict progression in the MCI group. Even though addition of this limited genetic model to COMPASS did not improve prediction of progression of MCI group, the predictive ability of SNP information extended beyond well-known APOE allele. PMID:27703197

  7. 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.

  8. 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

    Mountain ecosystems will likely be affected by global warming during the 21st century, with substantial biodiversity loss predicted by species distribution models (SDMs). Depending on the geographic extent, elevation range, and spatial resolution of data used in making these models, different rates...... 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...

  9. 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.

  10. Predicting College Students' Positive Psychology Associated Traits with Executive Functioning Dimensions

    Science.gov (United States)

    Marshall, Seth

    2016-01-01

    More research is needed that investigates how positive psychology-associated traits are predicted by neurocognitive processes. Correspondingly, the purpose of this study was to ascertain how, and to what extent, four traits, namely, grit, optimism, positive affect, and life satisfaction were predicted by the executive functioning (EF) dimensions…

  11. 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…

  12. 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.

  13. Amygdala functional connectivity as a longitudinal biomarker of symptom changes in generalized anxiety

    Science.gov (United States)

    Makovac, Elena; Watson, David R.; Meeten, Frances; Garfinkel, Sarah N.; Cercignani, Mara; Critchley, Hugo D.

    2016-01-01

    Generalized anxiety disorder (GAD) is characterized by excessive worry, autonomic dysregulation and functional amygdala dysconnectivity, yet these illness markers have rarely been considered together, nor their interrelationship tested longitudinally. We hypothesized that an individual’s capacity for emotion regulation predicts longer-term changes in amygdala functional connectivity, supporting the modification of GAD core symptoms. Sixteen patients with GAD (14 women) and individually matched controls were studied at two time points separated by 1 year. Resting-state fMRI data and concurrent measurement of vagally mediated heart rate variability were obtained before and after the induction of perseverative cognition. A greater rise in levels of worry following the induction predicted a stronger reduction in connectivity between right amygdala and ventromedial prefrontal cortex, and enhanced coupling between left amygdala and ventral tegmental area at follow-up. Similarly, amplified physiological responses to the induction predicted increased connectivity between right amygdala and thalamus. Longitudinal shifts in a distinct set of functional connectivity scores were associated with concomitant changes in GAD symptomatology over the course of the year. Results highlight the prognostic value of indices of emotional dysregulation and emphasize the integral role of the amygdala as a critical hub in functional neural circuitry underlying the progression of GAD symptomatology. PMID:27369066

  14. 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.

  15. 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...

  16. 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...

  17. 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.

  18. Reversed optimality and predictive ecology : burrowing depth forecasts population change in a bivalve

    NARCIS (Netherlands)

    van Gils, Jan A.; Kraan, Casper; Dekinga, Anne; Koolhaas, Anita; Drent, Jan; de Goeij, Petra; Piersma, Theunis

    2009-01-01

    Optimality reasoning from behavioural ecology can be used as a tool to infer how animals perceive their environment. Using optimality principles in a 'reversed manner' may enable ecologists to predict changes in population size before such changes actually happen. Here we show that a behavioural ant

  19. 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

  20. Strong artificial selection in the wild results in predicted small evolutionary change

    NARCIS (Netherlands)

    Postma, E.; Visser, J.; Van Noordwijk, A.J.

    2007-01-01

    Estimates of genetic variation and selection allow for quantitative predictions of evolutionary change, at least in controlled laboratory experiments. Natural populations are, however, different in many ways, and natural selection on heritable traits does not always result in phenotypic change. To t

  1. Changes in pulmonary function after definitive radiotherapy for NSCLC

    DEFF Research Database (Denmark)

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

    2015-01-01

    a negative impact on FVC. Long-term FEV1 and FVC were analyzed using linear regression. Treatment year and V60 had a significant impact on loss of FEV1. V60 had a significant impact on FVC changes. CONCLUSION: In this study, early PF change reached a plateau at 6months after the start of radiotherapy......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......, they were tested as covariates in multivariable analysis. RESULTS: Early PF change was quantified at six months after the start of radiotherapy. Smoking status and increasing V60 was associated with a significant decrease in PF, whereas smoking was protective. In addition, neoadjuvant chemotherapy had...

  2. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

    Directory of Open Access Journals (Sweden)

    Christopher Y Park

    Full Text Available A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g. machine learning that predict protein function have been developed to address this question. These methods generally build from existing annotations of genes to pathways and thus are often unable to identify additional genes participating in processes that are not already well studied. Many of these processes are well studied in some organism, but not necessarily in an investigator's organism of interest. Sequence-based search methods (e.g. BLAST have been used to transfer such annotation information between organisms. We demonstrate that functional genomics can complement traditional sequence similarity to improve the transfer of gene annotations between organisms. Our method transfers annotations only when functionally appropriate as determined by genomic data and can be used with any prediction algorithm to combine transferred gene function knowledge with organism-specific high-throughput data to enable accurate function prediction. We show that diverse state-of-art machine learning algorithms leveraging functional knowledge transfer (FKT dramatically improve their accuracy in predicting gene-pathway membership, particularly for processes with little experimental knowledge in an organism. We also show that our method compares favorably to annotation transfer by sequence similarity. Next, we deploy FKT with state-of-the-art SVM classifier to predict novel genes to 11,000 biological processes across six diverse organisms and expand the coverage of accurate function predictions to processes that are often ignored because of a dearth of annotated genes in an organism. Finally, we perform in vivo experimental investigation in Danio rerio and confirm the regulatory role of our top predicted novel gene, wnt5b, in leftward cell migration during heart development. FKT is immediately applicable to many bioinformatics

  3. Emotion-Induced Topological Changes in Functional Brain Networks.

    Science.gov (United States)

    Park, Chang-Hyun; Lee, Hae-Kook; Kweon, Yong-Sil; Lee, Chung Tai; Kim, Ki-Tae; Kim, Young-Joo; Lee, Kyoung-Uk

    2016-01-01

    In facial expression perception, a distributed network is activated according to stimulus context. We proposed that an interaction between brain activation and stimulus context in response to facial expressions could signify a pattern of interactivity across the whole brain network beyond the face processing network. Functional magnetic resonance imaging data were acquired for 19 young healthy subjects who were exposed to either emotionally neutral or negative facial expressions. We constructed group-wise functional brain networks for 12 face processing areas [bilateral inferior occipital gyri (IOG), fusiform gyri (FG), superior temporal sulci (STS), amygdalae (AMG), inferior frontal gyri (IFG), and orbitofrontal cortices (OFC)] and for 73 whole brain areas, based on partial correlation of mean activation across subjects. We compared the topological properties of the networks with respect to functional distance-based measures, global and local efficiency, between the two types of face stimulus. In both face processing and whole brain networks, global efficiency was lower and local efficiency was higher for negative faces relative to neutral faces, indicating that network topology differed according to stimulus context. Particularly in the face processing network, emotion-induced changes in network topology were attributable to interactions between core (bilateral IOG, FG, and STS) and extended (bilateral AMG, IFG, and OFC) systems. These results suggest that changes in brain activation patterns in response to emotional face stimuli could be revealed as changes in the topological properties of functional brain networks for the whole brain as well as for face processing areas.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. Predicting accurate fluorescent spectra for high molecular weight polycyclic aromatic hydrocarbons using density functional theory

    Science.gov (United States)

    Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.

    2016-10-01

    The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.

  9. Gene-specific function prediction for non-synonymous mutations in monogenic diabetes genes.

    Directory of Open Access Journals (Sweden)

    Quan Li

    Full Text Available The rapid progress of genomic technologies has been providing new opportunities to address the need of maturity-onset diabetes of the young (MODY molecular diagnosis. However, whether a new mutation causes MODY can be questionable. A number of in silico methods have been developed to predict functional effects of rare human mutations. The purpose of this study is to compare the performance of different bioinformatics methods in the functional prediction of nonsynonymous mutations in each MODY gene, and provides reference matrices to assist the molecular diagnosis of MODY. Our study showed that the prediction scores by different methods of the diabetes mutations were highly correlated, but were more complimentary than replacement to each other. The available in silico methods for the prediction of diabetes mutations had varied performances across different genes. Applying gene-specific thresholds defined by this study may be able to increase the performance of in silico prediction of disease-causing mutations.

  10. 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.)

  11. 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....

  12. 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/.

  13. 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.

  14. 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...

  15. 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.

  16. Which Moral Foundations Predict Willingness to Make Lifestyle Changes to Avert Climate Change in the USA?

    Science.gov (United States)

    Dickinson, Janis L.; McLeod, Poppy; Bloomfield, Robert; Allred, Shorna

    2016-01-01

    Jonathan Haidt’s Moral Foundations Theory identifies five moral axes that can influence human motivation to take action on vital problems like climate change. The theory focuses on five moral foundations, including compassion, fairness, purity, authority, and ingroup loyalty; these have been found to differ between liberals and conservatives as well as Democrats and Republicans. Here we show, based on the Cornell National Social Survey (USA), that valuations of compassion and fairness were strong, positive predictors of willingness to act on climate change, whereas purity had a non-significant tendency in the positive direction (p = 0.07). Ingroup loyalty and authority were not supported as important predictor variables using model selection (ΔAICc__). Compassion and fairness were more highly valued by liberals, whereas purity, authority, and in-group loyalty were more highly valued by conservatives. As in previous studies, participants who were younger, more liberal, and reported greater belief in climate change, also showed increased willingness to act on climate change. Our research supports the potential importance of moral foundations as drivers of intentions with respect to climate change action, and suggests that compassion, fairness, and to a lesser extent, purity, are potential moral pathways for personal action on climate change in the USA. PMID:27760207

  17. 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

  18. Quantifying the evolutionary divergence of protein structures: the role of function change and function conservation.

    Science.gov (United States)

    Pascual-García, Alberto; Abia, David; Méndez, Raúl; Nido, Gonzalo S; Bastolla, Ugo

    2010-01-01

    The molecular clock hypothesis, stating that protein sequences diverge in evolution by accumulating amino acid substitutions at an almost constant rate, played a major role in the development of molecular evolution and boosted quantitative theories of evolutionary change. These studies were extended to protein structures by the seminal paper by Chothia and Lesk, which established the approximate proportionality between structure and sequence divergence. Here we analyse how function influences the relationship between sequence and structure divergence, studying four large superfamilies of evolutionarily related proteins: globins, aldolases, P-loop and NADP-binding. We introduce the contact divergence, which is more consistent with sequence divergence than previously used structure divergence measures. Our main findings are: (1) Small structure and sequence divergences are proportional, consistent with the molecular clock. Approximate validity of the clock is also supported by the analysis of the clustering coefficient of structure similarity networks. (2) Functional constraints strongly limit the structure divergence of proteins performing the same function and may allow to identify incomplete or wrong functional annotations. (3) The rate of structure versus sequence divergence is larger for proteins performing different functions than for proteins performing the same function. We conjecture that this acceleration is due to positive selection for new functions. Accelerations in structure divergence are also suggested by the analysis of the clustering coefficient. (4) For low sequence identity, structural diversity explodes. We conjecture that this explosion is related to functional diversification. (5) Large indels are almost always associated with function changes.

  19. Towards virtual surgery in oral cancer to predict postoperative oral functions preoperatively

    NARCIS (Netherlands)

    Alphen, M.J.A.; Kreeft, A.M.; Heijden, van der F.; Smeele, L.E.; Balm, A.J.M.

    2013-01-01

    Our aim was to develop a dynamic virtual model of the oral cavity and oropharynx so that we could incorporate patient-specific factors into the prediction of functional loss after advanced resections for oral cancer. After a virtual resection, functional consequences can be assessed, and a more subs

  20. 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

  1. 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.

  2. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

    Science.gov (United States)

    Shameer, Khader; Tripathi, Lokesh P; Kalari, Krishna R; Dudley, Joel T; Sowdhamini, Ramanathan

    2016-09-01

    Accurate assessment of genetic variation in human DNA sequencing studies remains a nontrivial challenge in clinical genomics and genome informatics. Ascribing functional roles and/or clinical significances to single nucleotide variants identified from a next-generation sequencing study is an important step in genome interpretation. Experimental characterization of all the observed functional variants is yet impractical; thus, the prediction of functional and/or regulatory impacts of the various mutations using in silico approaches is an important step toward the identification of functionally significant or clinically actionable variants. The relationships between genotypes and the expressed phenotypes are multilayered and biologically complex; such relationships present numerous challenges and at the same time offer various opportunities for the design of in silico variant assessment strategies. Over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants in the protein coding regions. In this review, we provide an overview of the bioinformatics resources for the prediction, annotation and visualization of coding single nucleotide variants. We discuss the currently available approaches and major challenges from the perspective of protein sequence, structure, function and interactions that require consideration when interpreting the impact of putatively functional variants. We also discuss the relevance of incorporating integrated workflows for predicting the biomedical impact of the functionally important variations encoded in a genome, exome or transcriptome. Finally, we propose a framework to classify variant assessment approaches and strategies for incorporation of variant assessment within electronic health records.

  3. Structural and Functional Changes With the Aging Kidney.

    Science.gov (United States)

    Denic, Aleksandar; Glassock, Richard J; Rule, Andrew D

    2016-01-01

    Senescence or normal physiologic aging portrays the expected age-related changes in the kidney as compared to a disease that occurs in some but not all individuals. The microanatomical structural changes of the kidney with older age include a decreased number of functional glomeruli from an increased prevalence of nephrosclerosis (arteriosclerosis, glomerulosclerosis, and tubular atrophy with interstitial fibrosis), and to some extent, compensatory hypertrophy of remaining nephrons. Among the macroanatomical structural changes, older age associates with smaller cortical volume, larger medullary volume until middle age, and larger and more numerous kidney cysts. Among carefully screened healthy kidney donors, glomerular filtration rate (GFR) declines at a rate of 6.3 mL/min/1.73 m(2) per decade. There is reason to be concerned that the elderly are being misdiagnosed with CKD. Besides this expected kidney function decline, the lowest risk of mortality is at a GFR of ≥75 mL/min/1.73 m(2) for age kidney functional reserve when they do actually develop CKD, and they are at higher risk for acute kidney injury.

  4. Prediction of Reagents Needs Using Radial Basis Function in Teaching Hospital

    Directory of Open Access Journals (Sweden)

    Indrabayu

    2015-08-01

    Full Text Available A robust reagents prediction is able to support the service improvement in laboratories. In this paper, Radial Basis Function Networks (RBFN method with (3, Q, 1 architecture is used to predict two types of reagents needs, i.e. SD Bioline HBsAg and SD Bioline Anti HCV. Data of reagents from 2012 - 2013 are used as training data, whereas 2014 data are used as comparative data for the prediction result. In RBFN training, the best condition obtained when the spread value is 4 with RMSE 1.63E-06 for both types of reagents. The prediction results with RBFN methods reached 99% with correlation value of 0.99 for each reagents. RBFN method shows better prediction result compared to BPNN method with prediction of 92%.

  5. Protein distance constraints predicted by neural networks and probability density functions

    DEFF Research Database (Denmark)

    Lund, Ole; Frimand, Kenneth; Gorodkin, Jan;

    1997-01-01

    We predict interatomic C-α distances by two independent data driven methods. The first method uses statistically derived probability distributions of the pairwise distance between two amino acids, whilst the latter method consists of a neural network prediction approach equipped with windows taking....... The predictions are based on a data set derived using a new threshold similarity. We show that distances in proteins are predicted more accurately by neural networks than by probability density functions. We show that the accuracy of the predictions can be further increased by using sequence profiles. A threading...... the context of the two residues into account. These two methods are used to predict whether distances in independent test sets were above or below given thresholds. We investigate which distance thresholds produce the most information-rich constraints and, in turn, the optimal performance of the two methods...

  6. Functional connectivity changes in second language vocabulary learning.

    Science.gov (United States)

    Ghazi Saidi, Ladan; Perlbarg, Vincent; Marrelec, Guillaume; Pélégrini-Issac, Mélani; Benali, Habib; Ansaldo, Ana-Inés

    2013-01-01

    Functional connectivity changes in the language network (Price, 2010), and in a control network involved in second language (L2) processing (Abutalebi & Green, 2007) were examined in a group of Persian (L1) speakers learning French (L2) words. Measures of network integration that characterize the global integrative state of a network (Marrelec, Bellec et al., 2008) were gathered, in the shallow and consolidation phases of L2 vocabulary learning. Functional connectivity remained unchanged across learning phases for L1, whereas total, between- and within-network integration levels decreased as proficiency for L2 increased. The results of this study provide the first functional connectivity evidence regarding the dynamic role of the language processing and cognitive control networks in L2 learning (Abutalebi, Cappa, & Perani, 2005; Altarriba & Heredia, 2008; Leonard et al., 2011; Parker-Jones et al., 2011). Thus, increased proficiency results in a higher degree of automaticity and lower cognitive effort (Segalowitz & Hulstijn, 2005).

  7. 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

  8. 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

  9. 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.

  10. 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

    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......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...

  11. Predicting demographically sustainable rates of adaptation: can great tit breeding time keep pace with climate change?

    Science.gov (United States)

    Gienapp, Phillip; Lof, Marjolein; Reed, Thomas E; McNamara, John; Verhulst, Simon; Visser, Marcel E

    2013-01-19

    Populations need to adapt to sustained climate change, which requires micro-evolutionary change in the long term. A key question is how the rate of this micro-evolutionary change compares with the rate of environmental change, given that theoretically there is a 'critical rate of environmental change' beyond which increased maladaptation leads to population extinction. Here, we parametrize two closely related models to predict this critical rate using data from a long-term study of great tits (Parus major). We used stochastic dynamic programming to predict changes in optimal breeding time under three different climate scenarios. Using these results we parametrized two theoretical models to predict critical rates. Results from both models agreed qualitatively in that even 'mild' rates of climate change would be close to these critical rates with respect to great tit breeding time, while for scenarios close to the upper limit of IPCC climate projections the calculated critical rates would be clearly exceeded with possible consequences for population persistence. We therefore tentatively conclude that micro-evolution, together with plasticity, would rescue only the population from mild rates of climate change, although the models make many simplifying assumptions that remain to be tested.

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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...

  18. 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...

  19. 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.

  20. 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.

  1. Incremental multivariable predictive functional control and its application in a gas fractionation unit

    Institute of Scientific and Technical Information of China (English)

    施惠元; 苏成利; 曹江涛; 李平; 宋英莉; 李宁波

    2015-01-01

    The control of gas fractionation unit (GFU) in petroleum industry is very difficult due to multivariable characteristics and a large time delay. PID controllers are still applied in most industry processes. However, the traditional PID control has been proven not sufficient and capable for this particular petro-chemical process. In this work, an incremental multivariable predictive functional control (IMPFC) algorithm was proposed with less online computation, great precision and fast response. An incremental transfer function matrix model was set up through the step-response data, and predictive outputs were deduced with the theory of single-value optimization. The results show that the method can optimize the incremental control variable and reject the constraint of the incremental control variable with the positional predictive functional control algorithm, and thereby making the control variable smoother. The predictive output error and future set-point were approximated by a polynomial, which can overcome the problem under the model mismatch and make the predictive outputs track the reference trajectory. Then, the design of incremental multivariable predictive functional control was studied. Simulation and application results show that the proposed control strategy is effective and feasible to improve control performance and robustness of process.

  2. Assessing conservation relevance of organism-environment relations using predicted changes in response variables

    Science.gov (United States)

    Gutzwiller, Kevin J.; Barrow, Wylie C.; White, Joseph D.; Johnson-Randall, Lori; Cade, Brian S.; Zygo, Lisa M.

    2010-01-01

    1. Organism–environment models are used widely in conservation. The degree to which they are useful for informing conservation decisions – the conservation relevance of these relations – is important because lack of relevance may lead to misapplication of scarce conservation resources or failure to resolve important conservation dilemmas. Even when models perform well based on model fit and predictive ability, conservation relevance of associations may not be clear without also knowing the magnitude and variability of predicted changes in response variables. 2. We introduce a method for evaluating the conservation relevance of organism–environment relations that employs confidence intervals for predicted changes in response variables. The confidence intervals are compared to a preselected magnitude of change that marks a threshold (trigger) for conservation action. To demonstrate the approach, we used a case study from the Chihuahuan Desert involving relations between avian richness and broad-scale patterns of shrubland. We considered relations for three winters and two spatial extents (1- and 2-km-radius areas) and compared predicted changes in richness to three thresholds (10%, 20% and 30% change). For each threshold, we examined 48 relations. 3. The method identified seven, four and zero conservation-relevant changes in mean richness for the 10%, 20% and 30% thresholds respectively. These changes were associated with major (20%) changes in shrubland cover, mean patch size, the coefficient of variation for patch size, or edge density but not with major changes in shrubland patch density. The relative rarity of conservation-relevant changes indicated that, overall, the relations had little practical value for informing conservation decisions about avian richness. 4. The approach we illustrate is appropriate for various response and predictor variables measured at any temporal or spatial scale. The method is broadly applicable across ecological

  3. Changes in salivary estradiol predict changes in women's preferences for vocal masculinity.

    Science.gov (United States)

    Pisanski, Katarzyna; Hahn, Amanda C; Fisher, Claire I; DeBruine, Lisa M; Feinberg, David R; Jones, Benedict C

    2014-08-01

    Although many studies have reported that women's preferences for masculine physical characteristics in men change systematically during the menstrual cycle, the hormonal mechanisms underpinning these changes are currently poorly understood. Previous studies investigating the relationships between measured hormone levels and women's masculinity preferences tested only judgments of men's facial attractiveness. Results of these studies suggested that preferences for masculine characteristics in men's faces were related to either women's estradiol or testosterone levels. To investigate the hormonal correlates of within-woman variation in masculinity preferences further, here we measured 62 women's salivary estradiol, progesterone, and testosterone levels and their preferences for masculine characteristics in men's voices in five weekly test sessions. Multilevel modeling of these data showed that changes in salivary estradiol were the best predictor of changes in women's preferences for vocal masculinity. These results complement other recent research implicating estradiol in women's mate preferences, attention to courtship signals, sexual motivation, and sexual strategies, and are the first to link women's voice preferences directly to measured hormone levels.

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

    DEFF Research Database (Denmark)

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

    . 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...... 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....

  5. Functional traits predict drought performance and distribution of Mediterranean woody species

    Science.gov (United States)

    Lopez-Iglesias, Bárbara; Villar, Rafael; Poorter, Lourens

    2014-04-01

    Water availability is one of the key environmental factors that affect plant establishment and distribution. In many regions water availability will decline with climate change, exposing small seedlings to a greater likelihood of drought. In this study, 17 leaves, stem, root, and whole-plant traits of ten woody Mediterranean species were measured under favourable growing conditions and seedling drought survival was evaluated during a simulated dry-down episode. The aims of this study were: i) to assess drought survival of different species, ii) to analyse which functional traits predict drought survival time, and iii) to explain species distribution in the field, based on species drought survival and drought strategies. Drought survival time varied ten-fold across species, from 19 to 192 days. Across species, drought survival was positively related to the rooting depth per leaf area, i.e., the ability to acquire water from deeper soil layers while reducing transpiring leaf area. Drought survival time was negatively related to species ability to grow quickly, as indicated by high relative growth and net assimilation rates. Drought survival also explained species distribution in the field. It was found that species were sorted along a continuum, ranging between two contrasting species functional extremes based on functional traits and drought performance. One extreme consisted of acquisitive fast-growing deciduous species, with thin, soft metabolically active leaves, with high resource use and vulnerability to drought. The opposite extreme consisted of conservative slow-growing evergreen species with sclerophyllous leaves, deep roots, a low transpiring area, and low water use, resulting in high drought survival and drought tolerance. The results show that these drought strategies shape species distribution in this Mediterranean area.

  6. 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).

  7. 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

    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...

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. Alternative growth functions for predicting body, carcass, and breast weight in ducks: Lomolino equation and extreme value function.

    Science.gov (United States)

    Faridi, A; Murawska, D; Golian, A; Mottaghitalab, M; Gitoee, A; Lopez, S; France, J

    2014-04-01

    In this study, 2 alternative growth functions, the Lomolino and the extreme value function (EVF), are introduced and their ability to predict body, carcass, and breast weight in ducks evaluated. A comparative study was carried out of these equations with standard growth functions: Gompertz, exponential, Richards, and generalized Michaelis-Menten. Goodness of fit of the functions was evaluated using R(2), mean square error, Akaike information criterion, and Bayesian information criterion, whereas bias factor, accuracy factor, Durbin-Watson statistic, and number of runs of sign were the criteria used for analysis of residuals. Results showed that predictive performance of all functions was acceptable, though the Richards and exponential equations failed to converge in a few cases for both male and female ducks. Based on goodness-of-fit statistics, the Richards, Gompertz, and EVF were the best equations whereas the worst fits to the data were obtained with the exponential. Analysis of residuals indicated that, for the different traits investigated, the least biased and the most accurate equations were the Gompertz, EVF, Richards, and generalized Michaelis-Menten, whereas the exponential was the most biased and least accurate. Based on the Durbin-Watson statistic, all models generally behaved well and only the exponential showed evidence of autocorrelation for all 3 traits investigated. Results showed that with all functions, estimated final weights of males were higher than females for the body, carcass, and breast weight profiles. The alternative functions introduced here have desirable advantages including flexibility and a low number of parameters. However, because this is probably the first study to apply these functions to predict growth patterns in poultry or other animals, further analysis of these new models is suggested.

  13. 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.

  14. 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.

  15. Functional Activities Questionnaire items that best discriminate and predict progression from clinically normal to mild cognitive impairment

    Science.gov (United States)

    Marshall, Gad A.; Zoller, Amy S.; Lorius, Natacha; Amariglio, Rebecca E.; Locascio, Joseph J.; Johnson, Keith A.; Sperling, Reisa A.; Rentz, Dorene M.

    2015-01-01

    Background Impairment in instrumental activities of daily living (IADL) emerges in the transition from mild cognitive impairment (MCI) to Alzheimer’s disease (AD) dementia. Some IADL scales are sensitive to early deficits in MCI, but none have been validated for detecting subtle functional changes in clinically normal (CN) elderly at risk for AD. Methods Data from 624 subjects participating in the Alzheimer’s Disease Neuroimaging Initiative and 524 subjects participating in the Massachusetts Alzheimer’s Disease Research Center, which are two large cohorts including CN elderly and MCI subjects, were used to determine which Functional Activities Questionnaire items best discriminate between and predict progression from CN to MCI. Results We found that “Remembering appointments” and “assembling tax records” best discriminated between CN and MCI subjects, while worse performance on “paying attention and understanding a TV program”, “paying bills/balancing checkbook”, and “heating water and turning off the stove” predicted greater hazard of progressing from a diagnosis of CN to MCI. Conclusions These results demonstrate that certain questions are especially sensitive in detecting the earliest functional changes in CN elderly at risk for AD. As the field moves toward earlier intervention in preclinical AD, it is important to determine which IADL changes can be detected at that stage and track decline over time. PMID:26017560

  16. 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

  17. 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.

  18. 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

  19. Inter-individual differences in the experience of negative emotion predict variations in functional brain architecture.

    Science.gov (United States)

    Petrican, Raluca; Saverino, Cristina; Shayna Rosenbaum, R; Grady, Cheryl

    2015-12-01

    Current evidence suggests that two spatially distinct neuroanatomical networks, the dorsal attention network (DAN) and the default mode network (DMN), support externally and internally oriented cognition, respectively, and are functionally regulated by a third, frontoparietal control network (FPC). Interactions among these networks contribute to normal variations in cognitive functioning and to the aberrant affective profiles present in certain clinical conditions, such as major depression. Nevertheless, their links to non-clinical variations in affective functioning are still poorly understood. To address this issue, we used fMRI to measure the intrinsic functional interactions among these networks in a sample of predominantly younger women (N=162) from the Human Connectome Project. Consistent with the previously documented dichotomous motivational orientations (i.e., withdrawal versus approach) associated with sadness versus anger, we hypothesized that greater sadness would predict greater DMN (rather than DAN) functional dominance, whereas greater anger would predict the opposite. Overall, there was evidence of greater DAN (rather than DMN) functional dominance, but this pattern was modulated by current experience of specific negative emotions, as well as subclinical depressive and anxiety symptoms. Thus, greater levels of currently experienced sadness and subclinical depression independently predicted weaker DAN functional dominance (i.e., weaker DAN-FPC functional connectivity), likely reflecting reduced goal-directed attention towards the external perceptual environment. Complementarily, greater levels of currently experienced anger and subclinical anxiety predicted greater DAN functional dominance (i.e., greater DAN-FPC functional connectivity and, for anxiety only, also weaker DMN-FPC coupling). Our findings suggest that distinct affective states and subclinical mood symptoms have dissociable neural signatures, reflective of the symbiotic relationship

  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. 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...

  2. 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...

  3. 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.

  4. 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.

  5. [Effects of sampling plot number on tree species distribution prediction under climate change].

    Science.gov (United States)

    Liang, Yu; He, Hong-Shi; Wu, Zhi-Wei; Li, Xiao-Na; Luo, Xu

    2013-05-01

    Based on the neutral landscapes under different degrees of landscape fragmentation, this paper studied the effects of sampling plot number on the prediction of tree species distribution at landscape scale under climate change. The tree species distribution was predicted by the coupled modeling approach which linked an ecosystem process model with a forest landscape model, and three contingent scenarios and one reference scenario of sampling plot numbers were assumed. The differences between the three scenarios and the reference scenario under different degrees of landscape fragmentation were tested. The results indicated that the effects of sampling plot number on the prediction of tree species distribution depended on the tree species life history attributes. For the generalist species, the prediction of their distribution at landscape scale needed more plots. Except for the extreme specialist, landscape fragmentation degree also affected the effects of sampling plot number on the prediction. With the increase of simulation period, the effects of sampling plot number on the prediction of tree species distribution at landscape scale could be changed. For generalist species, more plots are needed for the long-term simulation.

  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. 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.

  8. 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.

  9. 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...... patients and 15,220 matched-control subjects. Data on number of days per year on sick leave, unemployment, and disability pension were collected from central registries over a 5-year observation period from 2002–2007. Differences in number of days with occupational impairments between and within groups...

  10. 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...... patients and 15,220 matched-control subjects. Data on number of days per year on sick leave, unemployment, and disability pension were collected from central registries over a 5-year observation period from 2002–2007. Differences in number of days with occupational impairments between and within groups...

  11. 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

  12. 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.

  13. 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...

  14. 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

  15. Burrowing Behavior of a Deposit Feeding Bivalve Predicts Change in Intertidal Ecosystem State

    NARCIS (Netherlands)

    Compton, T.J.; Bodnar, W.; Koolhaas, A.; Dekinga, A.; Holthuijsen, S.; Ten Horn, J.; McSweeney, N.; van Gils, J.A.; Piersma, T,

    2016-01-01

    Behavior has a predictive power that is often underutilized as a tool for signaling ecological change. The burrowing behavior of the deposit feeding bivalve Macoma balthica reflects a typical food-safety trade-off. The choice to live close to the sediment surface comes at a risk of predation and is

  16. Burrowing behavior of a deposit feeding bivalve predicts change in intertidal ecosystem state

    NARCIS (Netherlands)

    Compton, Tanya J.; Bodnar, Wanda; Koolhaas, Anita; Dekinga, Anne; Holthuijsen, Sander; ten Horn, Job; McSweeney, Niamh; van Gils, Jan; Piersma, Theunis

    2016-01-01

    Behavior has a predictive power that is often underutilized as a tool for signaling ecological change. The burrowing behavior of the deposit feeding bivalve Macoma balthica reflects a typical food-safety trade-off. The choice to live close to the sediment surface comes at a risk of predation and is

  17. 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.

  18. 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

  19. 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…

  20. Prediction of the Functional Performance of Machined Components Based on Surface Topography: State of the Art

    Science.gov (United States)

    Grzesik, Wit

    2016-10-01

    This survey overviews the functional performance of manufactured components produced by typical finishing machining operations in terms of their topographical characteristics. Surface topographies were characterized using both profile (2D) and 3D (areal) surface roughness parameters. The prediction of typical functional properties such as fatigue, friction, wear, bonding and corrosion is discussed based on appropriate surface roughness parameters. Some examples of real 3D surface topographies produced with desired functional characteristics are provided. This survey highlights technological possibilities of producing surfaces with enhanced functional properties by machining processes.

  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. 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.

  3. 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.

  4. 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

  5. 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.

  6. An integrative approach to ortholog prediction for disease-focused and other functional studies

    Directory of Open Access Journals (Sweden)

    Perrimon Norbert

    2011-08-01

    Full Text Available Abstract Background Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the functions of orthologs in other species. Several tools for predicting orthologous gene relationships are available. However, these tools can give different results and identification of predicted orthologs is not always straightforward. Results We report a simple but effective tool, the Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT; http://www.flyrnai.org/diopt, for rapid identification of orthologs. DIOPT integrates existing approaches, facilitating rapid identification of orthologs among human, mouse, zebrafish, C. elegans, Drosophila, and S. cerevisiae. As compared to individual tools, DIOPT shows increased sensitivity with only a modest decrease in specificity. Moreover, the flexibility built into the DIOPT graphical user interface allows researchers with different goals to appropriately 'cast a wide net' or limit results to highest confidence predictions. DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. This helps users identify the most appropriate matches among multiple possible orthologs. To facilitate using model organisms for functional analysis of human disease-associated genes, we used DIOPT to predict high-confidence orthologs of disease genes in Online Mendelian Inheritance in Man (OMIM and genes in genome-wide association study (GWAS data sets. The results are accessible through the DIOPT diseases and traits query tool (DIOPT-DIST; http://www.flyrnai.org/diopt-dist. Conclusions DIOPT and DIOPT-DIST are useful resources for researchers working with model organisms, especially those who are interested in exploiting model organisms such as Drosophila to study the functions of human disease genes.

  7. Organization of intrinsic functional brain connectivity predicts decisions to reciprocate social behavior.

    Science.gov (United States)

    Cáceda, Ricardo; James, G Andrew; Gutman, David A; Kilts, Clinton D

    2015-10-01

    Reciprocation of trust exchanges is central to the development of interpersonal relationships and societal well-being. Understanding how humans make pro-social and self-centered decisions in dyadic interactions and how to predict these choices has been an area of great interest in social neuroscience. A functional magnetic resonance imaging (fMRI) based technology with potential clinical application is the study of resting state brain connectivity. We tested if resting state connectivity may predict choice behavior in a social context. Twenty-nine healthy adults underwent resting state fMRI before performing the Trust Game, a two person monetary exchange game. We assessed the ability of patterns of resting-state functional brain organization, demographic characteristics and a measure of moral development, the Defining Issues Test (DIT-2), to predict individuals' decisions to reciprocate money during the Trust Game. Subjects reciprocated in 74.9% of the trials. Independent component analysis identified canonical resting-state networks. Increased functional connectivity between the salience (bilateral insula/anterior cingulate) and central executive (dorsolateral prefrontal cortex/ posterior parietal cortex) networks significantly predicted the choice to reciprocate pro-social behavior (R(2) = 0.20, p = 0.015). Stepwise linear regression analysis showed that functional connectivity between these two networks (p = 0.002), age (p = 0.007) and DIT-2 personal interest schema score (p = 0.032) significantly predicted reciprocity behavior (R(2) = 0.498, p = 0.001). Intrinsic functional connectivity between neural networks in conjunction with other individual characteristics may be a valuable tool for predicting performance during social interactions. Future replication and temporal extension of these findings may bolster the understanding of decision making in clinical, financial and marketing settings. PMID:26166191

  8. 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...

  9. 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

  10. 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 ...

  11. 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 ...

  12. 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".

  13. On the adequacy of wall functions to predict condensation rates from steam-noncondensable gas mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Dehbi, A., E-mail: abdel.dehbi@psi.ch

    2013-12-15

    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

  14. 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...

  15. Sexual selection predicts advancement of avian spring migration in response to climate change

    DEFF Research Database (Denmark)

    Spottiswoode, Claire N; Tøttrup, Anders P; Coppack, Timothy

    2006-01-01

    suggest that sexual selection could help to understand this variation, since early spring arrival of males is favoured by female choice. Climate change could weaken the strength of natural selection opposing sexual selection for early migration, which would predict greatest advancement in species...... with stronger female choice. We test this hypothesis comparatively by investigating the degree of long-term change in spring passage at two ringing stations in northern Europe in relation to a synthetic estimate of the strength of female choice, composed of degree of extra-pair paternity, relative testes size...... in the timing of first-arriving individuals, suggesting that selection has not only acted on protandrous males. These results suggest that sexual selection may have an impact on the responses of organisms to climate change, and knowledge of a species' mating system might help to inform attempts at predicting...

  16. Using Wannier functions to improve solid band gap predictions in density functional theory

    Science.gov (United States)

    Ma, Jie; Wang, Lin-Wang

    2016-04-01

    Enforcing a straight-line condition of the total energy upon removal/addition of fractional electrons on eigen states has been successfully applied to atoms and molecules for calculating ionization potentials and electron affinities, but fails for solids due to the extended nature of the eigen orbitals. Here we have extended the straight-line condition to the removal/addition of fractional electrons on Wannier functions constructed within the occupied/unoccupied subspaces. It removes the self-interaction energies of those Wannier functions, and yields accurate band gaps for solids compared to experiments. It does not have any adjustable parameters and the computational cost is at the DFT level. This method can also work for molecules, providing eigen energies in good agreement with experimental ionization potentials and electron affinities. Our approach can be viewed as an alternative approach of the standard LDA+U procedure.

  17. 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 ...

  18. 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

  19. Integrating protein-protein interactions and text mining for protein function prediction

    Directory of Open Access Journals (Sweden)

    Leser Ulf

    2008-07-01

    Full Text Available Abstract Background Functional annotation of proteins remains a challenging task. Currently the scientific literature serves as the main source for yet uncurated functional annotations, but curation work is slow and expensive. Automatic techniques that support this work are still lacking reliability. We developed a method to identify conserved protein interaction graphs and to predict missing protein functions from orthologs in these graphs. To enhance the precision of the results, we furthermore implemented a procedure that validates all predictions based on findings reported in the literature. Results Using this procedure, more than 80% of the GO annotations for proteins with highly conserved orthologs that are available in UniProtKb/Swiss-Prot could be verified automatically. For a subset of proteins we predicted new GO annotations that were not available in UniProtKb/Swiss-Prot. All predictions were correct (100% precision according to the verifications from a trained curator. Conclusion Our method of integrating CCSs and literature mining is thus a highly reliable approach to predict GO annotations for weakly characterized proteins with orthologs.

  20. 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.

  1. 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

  2. Local network topology in human protein interaction data predicts functional association.

    Directory of Open Access Journals (Sweden)

    Hua Li

    Full Text Available The use of high-throughput techniques to generate large volumes of protein-protein interaction (PPI data has increased the need for methods that systematically and automatically suggest functional relationships among proteins. In a yeast PPI network, previous work has shown that the local connection topology, particularly for two proteins sharing an unusually large number of neighbors, can predict functional association. In this study we improved the prediction scheme by developing a new algorithm and applied it on a human PPI network to make a genome-wide functional inference. We used the new algorithm to measure and reduce the influence of hub proteins on detecting function-associated protein pairs. We used the annotations of the Gene Ontology (GO and the Kyoto Encyclopedia of Genes and Genomes (KEGG as benchmarks to compare and evaluate the function relevance. The application of our algorithms to human PPI data yielded 4,233 significant functional associations among 1,754 proteins. Further functional comparisons between them allowed us to assign 466 KEGG pathway annotations to 274 proteins and 123 GO annotations to 114 proteins with estimated false discovery rates of <21% for KEGG and <30% for GO. We clustered 1,729 proteins by their functional associations and made functional inferences from detailed analysis on one subcluster highly enriched in the TGF-beta signaling pathway (P<10(-50. Analysis of another four subclusters also suggested potential new players in six signaling pathways worthy of further experimental investigations. Our study gives clear insight into the common neighbor-based prediction scheme and provides a reliable method for large-scale functional annotation in this post-genomic era.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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

    BACKGROUND: Today large scale genome sequencing technologies are uncovering an increasing amount of new genes and proteins, which remain uncharacterized. Experimental procedures for protein function prediction are low throughput by nature and thus can't be used to keep up with the rate at which n...

  8. Exposure-response functions for (or versus?) the prediction of annoyance in specific situations

    NARCIS (Netherlands)

    Janssen, S.A.; Vos, H.

    2012-01-01

    Based on data from many surveys, exposure-response functions have been derived to describe the average expected annoyance response at a certain noise level. These have been used to define acceptable levels of environmental noise for separate noise sources. However, the prediction of the annoyance re

  9. 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.)

  10. 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

  11. Endothelial function predicts the development of renal damage after combined nephrectomy and myocardial infarction

    NARCIS (Netherlands)

    Ochodnicky, Peter; de Zeeuw, Dick; Henning, Robert H.; Kluppel, C. Alex; van Dokkum, Richard P. E.

    2006-01-01

    It was demonstrated that individual renal endothelial dilatory function of the healthy rat predicts susceptibility to subsequent renal damage induced by 5/6 nephrectomy. In addition, it is reported that myocardial infarction (MI) that was performed upon unilateral nephrectomy (UNx) induced highly va

  12. Can Functional Capacity Tests Predict Future Work Capacity in Patients With Whiplash-Associated Disorders?

    NARCIS (Netherlands)

    Trippolini, Maurizio A.; Dijkstra, Pieter U.; Cote, Pierre; Scholz-Odermatt, Stefan M.; Geertzen, J.H.B.; Reneman, Michiel F.

    2014-01-01

    Objective: To determine whether functional capacity evaluation (FCE) tests predict future work capacity (WC) of patients with whiplash-associated disorders (WADs) grades I and II who did not regain full WC 6 to 12 weeks after injury. Design: Prospective cohort study. Setting: Rehabilitation center.

  13. Prediction of human protein function from post-translational modifications and localization features

    DEFF Research Database (Denmark)

    Jensen, Lars Juhl; Gupta, Ramneek; Blom, Nikolaj;

    2002-01-01

    a number of functional attributes that are more directly related to the linear sequence of amino acids, and hence easier to predict, than protein structure. These attributes include features associated with post-translational modifications and protein sorting, but also much simpler aspects...

  14. 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

  15. 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

  16. 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

  17. Can we predict the direction of marine primary production change under global warming?

    Science.gov (United States)

    Taucher, J.; Oschlies, A.

    2011-01-01

    A global Earth System model is employed to investigate the role of direct temperature effects in the response of marine ecosystems to climate change. While model configurations with and without consideration of explicit temperature effects can reproduce observed current biogeochemical tracer distributions and estimated carbon export about equally well, carbon flow through the model ecosystem reveals strong temperature sensitivities. Depending on whether biological processes are assumed temperature sensitive or not, simulated marine net primary production (NPP) increases or decreases under projected climate change driven by a business-as-usual CO2 emission scenario for the 21st century. This suggests that indirect temperature effects such as changes in the supply of nutrients and light are not the only relevant factors to be considered when modeling the response of marine ecosystems to climate change. A better understanding of direct temperature effects on marine ecosystems is required before even the direction of change in NPP can be reliably predicted.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. USGS "iCoast - Did the Coast Change?" Project: Crowd-Tagging Aerial Photographs to Improve Coastal Change Prediction Models

    Science.gov (United States)

    Liu, S. B.; Poore, B. S.; Plant, N. G.; Stockdon, H. F.; Morgan, K.; Snell, R.

    2014-12-01

    The U.S. Geological Survey (USGS) has been acquiring oblique aerial photographs of the coast before and after major storms since 1995 and has amassed a database of over 140,000 photographs of the Gulf, Atlantic, and Pacific coasts. USGS coastal scientists use these photographs to document and characterize coastal change caused by storms. The images can also be used to evaluate the accuracy of predictive models of coastal erosion. However, the USGS does not have the personnel to manually analyze all of the photographs taken after a storm. Also, computers cannot yet automatically identify damages and geomorphic changes to the coast from the oblique aerial photographs. There is a high public interest in accessing the limited number of pre- and post-storm photographic pairs the USGS is currently able to share. Recent federal policies that encourage open data and open innovation initiatives have resulted in many federal agencies developing new ways of using citizen science and crowdsourcing techniques to share data and collaborate with the public to accomplish large tasks. The USGS launched a crowdsourcing application in June 2014 called "iCoast - Did the Coast Change?" (http://coastal.er.usgs.gov/icoast) to allow citizens to help USGS scientists identify changes to the coast by comparing USGS aerial photographs taken before and after storms, and then selecting pre-defined tags like "dune scarp" and "sand on road." The tags are accompanied by text definitions and pictorial examples of these coastal morphology terms and serve to informally and passively educate users about coastal hazards. The iCoast application facilitates greater citizen awareness of coastal change and is an educational resource for teachers and students interested in learning about coastal vulnerability. We expect that the citizen observations from iCoast will assist with probabilistic model development to produce more accurate predictions of coastal vulnerability.

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

    Directory of Open Access Journals (Sweden)

    Jane Elizabeth Barker

    2014-06-01

    Full Text Available 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 clear how children’s experiences relate to their development of self-directed executive functioning, where they must determine on their own what goal-directed actions to carry out and when. We hypothesized that time spent in less-structured activities would give children opportunities to practice self-directed executive functioning, and lead to benefits. To investigate this possibility, we collected information from parents about their 6-7 year-old children’s daily, annual, and typical schedules. We categorized children’s activities as structured or less-structured based on categorization schemes from prior studies on child leisure time use. We assessed children’s self-directed executive functioning using a well-established verbal fluency task, in which children generate members of a category and can decide on their own when to switch from one subcategory to another. The more time that children spent in less-structured activities, the better their self-directed executive functioning. The opposite was true of structured activities, which predicted poorer self-directed executive functioning. These relationships were robust (holding across increasingly strict classifications of structured and less-structured time and specific (time use did not predict externally-driven executive functioning. We discuss implications, caveats, and ways in which potential interpretations can be distinguished in future work, to advance an understanding of this fundamental

  4. Tools for Consumer Rights Protection in the Prediction of Electronic Virtual Market and Technological Changes

    Directory of Open Access Journals (Sweden)

    Mikuláš Gangur

    2014-05-01

    Full Text Available Electronic virtual markets can serve as an alternative tool for collecting information that is spread among numerous experts. This is the principal market functionality from the operators’ point of view. On the other hand it is profits that are the main interest of the market participants. What they expect from the market is liquidity as high as possible and the opportunity for unrestricted trading. Both the operator and the electronic market participant can be considered consumers of this particular market with reference to the requirements for the accuracy of its outputs but also for the market liquidity. Both the above mentioned groups of consumers (the operators and the participants themselves expect protection of their specific consumer rights, i.e. securing the two above mentioned functionalities of the market. These functionalities of the electronic market are, however, influenced by many factors, among others by participants’ activity. The article deals with the motivation tools that may improve the quality of the prediction market. In the prediction electronic virtual market there may be situations in which the commonly used tools for increasing business activities described in the published literature are not significantly effective. For such situations we suggest a new type of motivation incentive consisting in penalizing the individual market participants whose funds are not placed in the market. The functionality of the proposed motivation incentive is presented on the example of the existing data gained from the electronic virtual prediction market which is actively operated.

  5. Predicting recovery of cognitive function soon after stroke: differential modeling of logarithmic and linear regression.

    Directory of Open Access Journals (Sweden)

    Makoto Suzuki

    Full Text Available Cognitive disorders in the acute stage of stroke are common and are important independent predictors of adverse outcome in the long term. Despite the impact of cognitive disorders on both patients and their families, it is still difficult to predict the extent or duration of cognitive impairments. The objective of the present study was, therefore, to provide data on predicting the recovery of cognitive function soon after stroke by differential modeling with logarithmic and linear regression. This study included two rounds of data collection comprising 57 stroke patients enrolled in the first round for the purpose of identifying the time course of cognitive recovery in the early-phase group data, and 43 stroke patients in the second round for the purpose of ensuring that the correlation of the early-phase group data applied to the prediction of each individual's degree of cognitive recovery. In the first round, Mini-Mental State Examination (MMSE scores were assessed 3 times during hospitalization, and the scores were regressed on the logarithm and linear of time. In the second round, calculations of MMSE scores were made for the first two scoring times after admission to tailor the structures of logarithmic and linear regression formulae to fit an individual's degree of functional recovery. The time course of early-phase recovery for cognitive functions resembled both logarithmic and linear functions. However, MMSE scores sampled at two baseline points based on logarithmic regression modeling could estimate prediction of cognitive recovery more accurately than could linear regression modeling (logarithmic modeling, R(2 = 0.676, P<0.0001; linear regression modeling, R(2 = 0.598, P<0.0001. Logarithmic modeling based on MMSE scores could accurately predict the recovery of cognitive function soon after the occurrence of stroke. This logarithmic modeling with mathematical procedures is simple enough to be adopted in daily clinical practice.

  6. Serial Change in Cervical Length for the Prediction of Emergency Cesarean Section in Placenta Previa.

    Directory of Open Access Journals (Sweden)

    Jae Eun Shin

    Full Text Available To evaluate whether serial change in cervical length (CL over time can be a predictor for emergency cesarean section (CS in patients with placenta previa.This was a retrospective cohort study of patients with placenta previa between January 2010 and November 2014. All women were offered serial measurement of CL by transvaginal ultrasound at 19 to 23 weeks (CL1, 24 to 28 weeks (CL2, 29 to 31 weeks (CL3, and 32 to 34 weeks (CL4. We compared clinical characteristics, serial change in CL, and outcomes between the emergency CS group (case group and elective CS group (control group. The predictive value of change in CL for emergency CS was evaluated.A total of 93 women were evaluated; 31 had emergency CS due to massive vaginal bleeding. CL tended to decrease with advancing gestational age in each group. Until 29-31 weeks, CL showed no significant differences between the two groups, but after that, CL in the emergency CS group decreased abruptly, even though CL in the elective CS group continued to gradually decrease. On multivariate analysis to determine risk factors, only admissions for bleeding (odds ratio, 34.710; 95% CI, 5.239-229.973 and change in CL (odds ratio, 3.522; 95% CI, 1.210-10.253 were significantly associated with emergency CS. Analysis of the receiver operating characteristic curve showed that change in CL could be the predictor of emergency CS (area under the curve 0.734, p < 0.001, with optimal cutoff for predicting emergency cesarean delivery of 6.0 mm.Previous admission for vaginal bleeding and change in CL are independent predictors of emergency CS in placenta previa. Women with change in CL more than 6 mm between the second and third trimester are at high risk of emergency CS in placenta previa. Single measurements of short CL at the second or third trimester do not seem to predict emergency CS.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Extracting the Sivers function from polarized SIDIS data and making predictions

    CERN Document Server

    Anselmino, M; D'Alesio, U; Kotzinian, A; Murgia, F; Prokudin, A

    2005-01-01

    The most recent data on the weighted transverse single spin asymmetry $A_{UT}^{\\sin(\\phi_h-\\phi_S)}$ from HERMES and COMPASS collaborations are analysed within LO parton model with unintegrated parton distribution and fragmentation functions; all transverse motions are taken into account, with exact kinematics, in the elementary interactions. The overall quality of the data is such that, for the first time, a rather well constrained extraction of the Sivers function for $u$ and $d$ quarks is possible and is performed. Comparisons with models are made. Based on the extracted Sivers functions, predictions for $A_{UT}^{\\sin(\\phi_h-\\phi_S)}$ asymmetries at JLab are given; suggestions for further measurements at COMPASS, with a transversely polarized hydrogen target and selecting favourable kinematical ranges, are discussed. Predictions are also presented for Single Spin Asymmetries (SSA) in Drell-Yan processes at RHIC and GSI.

  14. PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics

    Directory of Open Access Journals (Sweden)

    Rychlewski Leszek

    2006-02-01

    Full Text Available Abstract Background The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB. Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity. Results Here we present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0, for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes. Conclusion We suggest that the structure-based prediction of an EC number should be conducted having the different similarity score cutoff for different protein folds. Moreover, performing the annotation using two different algorithms can reduce the rate of false positive assignments. We believe, that the presented web-based repository will help to decrease the number of protein structures that have functions marked as "unknown" in the PDB file. Availability http://paradox.harvard.edu/PDB-UF and http://bioinfo.pl/PDB-UF

  15. Architectural analysis and predicted functional capability of the human latissimus dorsi muscle.

    Science.gov (United States)

    Gerling, Michael E; Brown, Stephen H M

    2013-08-01

    The latissimus dorsi is primarily considered a muscle with actions at the shoulder, despite its widespread attachments at the spine. There is some dispute regarding the potential contribution of this muscle to lumbar spine function. The architectural design of a muscle is one of the most accurate predictors of muscle function; however, detailed architectural data on the latissimus dorsi muscle are limited. Therefore, the aim of this study was to quantify the architectural properties of the latissimus dorsi muscle and model mechanical function in light of these new data. One latissimus dorsi muscle was removed from each of 12 human cadavers, separated into regions, and micro-dissected for quantification of fascicle length, sarcomere length, and physiological cross-sectional area. From these data, sarcomere length operating ranges were modelled to determine the force-length characteristics of latissimus dorsi across the spine and shoulder ranges of motion. The physiological cross-sectional area of latissimus dorsi was 5.6±0.5 cm2 and normalized fascicle length was 26.4±1.0 cm, indicating that this muscle is designed to produce a moderate amount of force over a large range of lengths. Measured sarcomere length in the post-mortem neutral spine posture was nearly optimal at 2.69±0.06 μm. Across spine range of motion, biomechanical modelling predicted latissimus dorsi acts across both the ascending and descending limbs of the force-length curve during lateral bend, and primarily at or near the plateau region (where maximum force generation is possible) during flexion/extension and axial twist. Across shoulder range of motion, latissimus dorsi acts primarily on the plateau region and descending limbs of the force length curve during both flexion/extension and abduction/adduction. These data provide novel insights into the ability of the latissimus dorsi muscle to generate force and change length throughout the spine and shoulder ranges of motion. In addition, these

  16. 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...

  17. 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)

  18. 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

  19. Protein Function Prediction Based on Active Semi-sup ervised Learning

    Institute of Scientific and Technical Information of China (English)

    WANG Xuesong,CHENG Yuhu; LI Lijing

    2016-01-01

    In our study, the active learning and semi-supervised learning methods are comprehensively used for label delivery of proteins with known functions in Protein-protein interaction (PPI) network so as to predict the func-tions of unknown proteins. Because the real PPI network is generally observed with overlapping protein nodes with multiple functions, the mislabeling of overlapping protein may result in accumulation of prediction errors. For this reason, prior to executing the label delivery process of semi-supervised learning, the adjacency matrix is used to detect overlapping proteins. As the topological structure description of interactive relation between proteins, PPI network is observed with party hub protein nodes that play an important role, in co-expression with its neighborhood. Therefore, to reduce the manual labeling cost, party hub proteins most beneficial for improvement of prediction ac-curacy are selected for class labeling and the labeled party hub proteins are added into the labeled sample set for semi-supervised learning later. As the experimental results of real yeast PPI network show, the proposed algorithm can achieve high prediction accuracy with few labeled samples.

  20. 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

  1. 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.

  2. 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.

  3. Tire Changes, Fresh Air, and Yellow Flags: Challenges in Predictive Analytics for Professional Racing.

    Science.gov (United States)

    Tulabandhula, Theja; Rudin, Cynthia

    2014-06-01

    Our goal is to design a prediction and decision system for real-time use during a professional car race. In designing a knowledge discovery process for racing, we faced several challenges that were overcome only when domain knowledge of racing was carefully infused within statistical modeling techniques. In this article, we describe how we leveraged expert knowledge of the domain to produce a real-time decision system for tire changes within a race. Our forecasts have the potential to impact how racing teams can optimize strategy by making tire-change decisions to benefit their rank position. Our work significantly expands previous research on sports analytics, as it is the only work on analytical methods for within-race prediction and decision making for professional car racing.

  4. Filaggrin genotype in ichthyosis vulgaris predicts abnormalities in epidermal structure and function.

    Science.gov (United States)

    Gruber, Robert; Elias, Peter M; Crumrine, Debra; Lin, Tzu-Kai; Brandner, Johanna M; Hachem, Jean-Pierre; Presland, Richard B; Fleckman, Philip; Janecke, Andreas R; Sandilands, Aileen; McLean, W H Irwin; Fritsch, Peter O; Mildner, Michael; Tschachler, Erwin; Schmuth, Matthias

    2011-05-01

    Although it is widely accepted that filaggrin (FLG) deficiency contributes to an abnormal barrier function in ichthyosis vulgaris and atopic dermatitis, the pathomechanism of how FLG deficiency provokes a barrier abnormality in humans is unknown. We report here that the presence of FLG mutations in Caucasians predicts dose-dependent alterations in epidermal permeability barrier function. Although FLG is an intracellular protein, the barrier abnormality occurred solely via a paracellular route in affected stratum corneum. Abnormal barrier function correlated with alterations in keratin filament organization (perinuclear retraction), impaired loading of lamellar body contents, followed by nonuniform extracellular distribution of secreted organelle contents, and abnormalities in lamellar bilayer architecture. In addition, we observed reductions in corneodesmosome density and tight junction protein expression. Thus, FLG deficiency provokes alterations in keratinocyte architecture that influence epidermal functions localizing to the extracellular matrix. These results clarify how FLG mutations impair epidermal permeability barrier function.

  5. Predicting objective function weights from patient anatomy in prostate IMRT treatment planning

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Taewoo, E-mail: taewoo.lee@utoronto.ca; Hammad, Muhannad [Department of Mechanical and Industrial Engineering, University of Toronto, 5 King' s College Road, Toronto, Ontario M5S 3G8 (Canada); Chan, Timothy C. Y. [Department of Mechanical and Industrial Engineering, University of Toronto, 5 King' s College Road, Toronto, Ontario M5S 3G8 (Canada); Techna Institute for the Advancement of Technology for Health, 124-100 College Street, Toronto, Ontario M5G 1P5 (Canada); Craig, Tim [Radiation Medicine Program, UHN Princess Margaret Cancer Centre, 610 University Avenue, Toronto, Ontario M5T 2M9 (Canada); 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 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)

    2013-12-15

    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, usingl{sub 2} 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

  6. 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

  7. 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) ...

  8. 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...

  9. 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....

  10. 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...

  11. 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...

  12. Change ratio of hemoglobin has predictive value for upper gastrointestinal bleeding

    Science.gov (United States)

    Tomizawa, Minoru; Shinozaki, Fuminobu; Hasegawa, Rumiko; Shirai, Yoshinori; Motoyoshi, Yasufumi; Sugiyama, Takao; Yamamoto, Shigenori; Ishige, Naoki

    2016-01-01

    The present study aimed to identify novel predictors of upper gastrointestinal (GI) bleeding by assessing change ratios of blood test variables. Records of 1,023 patients (431 men and 592 women) who underwent endoscopy between October 2014 and September 2015 at the National Hospital Organization Shimoshizu Hospital (Yotsukaido, Japan) were retrospectively analyzed. Patients whose blood test variables for the time-point of endoscopy and three months previously were available were enrolled and subsequently categorized into a group with and another one without upper GI bleeding (n=32 and 84, respectively), and the respective change ratios were calculated for each group. One-way analysis of variance revealed that in patients with upper GI bleeding, change ratios of white blood cell count and alkaline phosphatase were significantly higher than those in patients without, while change ratios of hemoglobin (Hb), total protein and albumin were significantly reduced. Logistic regression analysis demonstrated that the change ratio of Hb was significantly correlated with upper GI bleeding. Receiver-operator characteristic analysis revealed that an 18.7% reduction of Hb was the threshold value for the prediction of upper GI bleeding. In conclusion, the present study revealed that a ≥18.7% reduction in Hb over three months has predictive value for upper GI bleeding.

  13. Integration of relational and hierarchical network information for protein function prediction

    Directory of Open Access Journals (Sweden)

    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. 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.

  15. Predicting short-term weight loss using four leading health behavior change theories

    Directory of Open Access Journals (Sweden)

    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.

  16. Predicting species distribution and abundance responses to climate change : why it is essential to include biotic interactions across trophic levels

    NARCIS (Netherlands)

    Van der Putten, Wim H.; Macel, Mirka; Visser, Marcel E.

    2010-01-01

    Current predictions on species responses to climate change strongly rely on projecting altered environmental conditions on species distributions. However, it is increasingly acknowledged that climate change also influences species interactions. We review and synthesize literature information on biot

  17. Predicting species distribution and abundance responses to climate change: why it is essential to include biotic interactions across trophic levels

    NARCIS (Netherlands)

    Putten, van der W.H.; Macel, M.; Visser, de M.

    2010-01-01

    Current predictions on species responses to climate change strongly rely on projecting altered environmental conditions on species distributions. However, it is increasingly acknowledged that climate change also influences species interactions. We review and synthesize literature information on biot

  18. Evaluation of a patient-specific cost function to predict the influence of foot path on the knee adduction torque during gait.

    Science.gov (United States)

    Fregly, Benjamin J; Reinbolt, Jeffery A; Chmielewski, Terese L

    2008-02-01

    A large external knee adduction torque during gait has been correlated with the progression of knee osteoarthritis (OA). Though foot path changes (e.g. toeing out) can reduce the adduction torque, no method currently exists to predict whether an optimal foot path exists for a specific patient. This study evaluates a patient-specific optimization cost function to predict how foot path changes influence both adduction torque peaks. Video motion and ground reaction data were collected from a patient with knee OA performing normal, toe out, and wide stance gait. Joint and inertial parameters in a dynamic, 27 degree-of-freedom, full-body gait model were calibrated to the patient's normal gait data. The model was then used in gait optimizations that predicted how the patient's adduction torque peaks would change due to changes in foot path. The cost function tracked the patient's normal gait data using weight factors calibrated to toe out gait and tested using wide stance gait. For both gait motions, the same cost function weights predicted the change in both adduction torque peaks to within 7% error. With further development, this approach may eventually permit the design of patient-specific rehabilitation procedures such as an optimal foot path for patients with knee OA.

  19. 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.

  20. 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

  1. 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.

  2. Longitudinal changes of cardiac structure and function in CKD (CASCADE study).

    Science.gov (United States)

    Cai, Qi-Zhe; Lu, Xiu-Zhang; Lu, Ye; Wang, Angela Yee-Moon

    2014-07-01

    Little is known regarding the natural longitudinal changes in cardiac structure and function in CKD. We hypothesized that baseline CKD stage is associated with progressive worsening in cardiac structure and function. We conducted a prospective longitudinal study, recruiting 300 patients with stages 3-5 CKD from a major regional tertiary center and university teaching hospital in Hong Kong. Baseline CKD stages were studied in relation to natural longitudinal changes in echocardiographic and tissue Doppler imaging-derived parameters. Over 1 year, the prevalence of left ventricular (LV) hypertrophy increased from 40.3% to 48.9%, median left atrial volume index increased 4.8 (interquartile range [IQR], 2.1, 7.7) ml/m(2) (Pcardiac structure and function and predicted greater longitudinal progression in LV mass index (odds ratio [OR], 3.02; 95% confidence interval [95% CI], 1.39 to 6.58), volume index (OR, 2.58; 95% CI, 1.18 to 5.62), and left atrial volume index (OR, 2.61; 95% CI, 1.20 to 5.69) and worse diastolic dysfunction grade (OR, 3.17; 95% CI, 1.16 to 8.69) compared with stage 3a in the fully adjusted analysis. In conclusion, more advanced CKD at baseline may be associated with larger longitudinal increases in LV mass and volume and greater deterioration in diastolic function.

  3. 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...

  4. Estimation of accuracies and expected genetic change from selection for selection indexes that use multiple-trait predictions of breeding values.

    Science.gov (United States)

    Barwick, S A; Tier, B; Swan, A A; Henzell, A L

    2013-10-01

    Procedures are described for estimating selection index accuracies for individual animals and expected genetic change from selection for the general case where indexes of EBVs predict an aggregate breeding objective of traits that may or may not have been measured. Index accuracies for the breeding objective are shown to take an important general form, being able to be expressed as the product of the accuracy of the index function of true breeding values and the accuracy with which that function predicts the breeding objective. When the accuracies of the individual EBVs of the index are known, prediction error variances (PEVs) and covariances (PECs) for the EBVs within animal are able to be well approximated, and index accuracies and expected genetic change from selection estimated with high accuracy. The procedures are suited to routine use in estimating index accuracies in genetic evaluation, and for providing important information, without additional modelling, on the directions in which a population will move under selection.

  5. 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...

  6. Ecological prediction with nonlinear multivariate time-frequency functional data models

    Science.gov (United States)

    Yang, Wen-Hsi; Wikle, Christopher K.; Holan, Scott H.; Wildhaber, Mark L.

    2013-01-01

    Time-frequency analysis has become a fundamental component of many scientific inquiries. Due to improvements in technology, the amount of high-frequency signals that are collected for ecological and other scientific processes is increasing at a dramatic rate. In order to facilitate the use of these data in ecological prediction, we introduce a class of nonlinear multivariate time-frequency functional models that can identify important features of each signal as well as the interaction of signals corresponding to the response variable of interest. Our methodology is of independent interest and utilizes stochastic search variable selection to improve model selection and performs model averaging to enhance prediction. We illustrate the effectiveness of our approach through simulation and by application to predicting spawning success of shovelnose sturgeon in the Lower Missouri River.

  7. 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.

  8. Risk predicting of macropore flow using pedotransfer functions, textural maps and modeling

    DEFF Research Database (Denmark)

    Iversen, Bo Vangsø; Børgesen, Christen Duus; Lægdsmand, Mette;

    2011-01-01

    using combinations of different soil physical parameters. The neural network was able to develop reasonably accurate PTFs predicting log[k(−1)], whereas the prediction of log(Ks) was less accurate. Using the distributed data of the hydraulic properties derived from the PTFs, outputs of water flow...... of this study were first to develop pedotransfer functions (PTFs) predicting near-saturated [k(−1)] and saturated (Ks) hydraulic conductivity using simple soil parameters as predictors and second to use this information and a newly developed rasterbased soil property map of Denmark to identify risk areas...... for macropore flow. The data set was based on hydraulic measurements on large, undisturbed soil columns from different localities in Denmark. Unsaturated [k(h)] and saturated hydraulic conductivity were measured in the laboratory; k(−1) representing the hydraulic conductivity of the soil matrix...

  9. Electrode Wear Prediction in Milling Electrical Discharge Machining Based on Radial Basis Function Neural Network

    Institute of Scientific and Technical Information of China (English)

    HUANG He; BAI Ji-cheng; LU Ze-sheng; GUO Yong-feng

    2009-01-01

    Milling electrical discharge machining (EDM) enables the machining of complex cavities using cylindrical or tubular electrodes. To ensure acceptable machining accuracy the process requires some methods of compensating for electrode wear. Due to the complexity and random nature of the process, existing methods of compensating for such wear usually involve off-line prediction. This paper discusses an innovative model of electrode wear prediction for milling EDM based upon a radial basis function (RBF) network. Data gained from an orthogonal experiment were used to provide training samples for the RBF network. The model established was used to forecast the electrode wear, making it possible to calculate the real-time tool wear in the milling EDM process and, to lay the foundations for dynamic compensation of the electrode wear on-line. This paper demonstrates that by using this model prediction errors can be controlled within 8%.

  10. 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

  11. Soil Erosion Prediction Based on Land Use Changes (A Case in Neka Watershed

    Directory of Open Access Journals (Sweden)

    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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. Does postsystolic motion or shortening predict recovery of myocardial function after primary percutanous coronary intervention?

    DEFF Research Database (Denmark)

    Terkelsen, Christian Juhl; Poulsen, Steen Hvitfeldt; Nørgaard, Bjarne Linde;

    2007-01-01

    or shortening appears more frequently in the acute phase in myocardial segments with impaired systolic function compared with normally functioning segments. However, presence of postsystolic contraction is not associated with improvement in strain or wall-motion score at follow-up, and does not seem......OBJECTIVE: The purpose of the study was to evaluate whether presence of postsystolic motion or shortening defined by Doppler tissue imaging may predict recovery of regional myocardial function in patients with ST-elevation myocardial infarction. METHODS: Echocardiography was performed a few hours......); and normal myocardial function in the acute phase (type E, n = 759). RESULTS: There were no differences among type A, B, C, and D segments with regard to the proportion presenting postsystolic tissue velocity equal to or greater than 1.0 cm/s (0.52, 0.54, 0.60, and 0.47, respectively, P = .20...

  20. 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.

  1. 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

  2. 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...

  3. 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...

  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. 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...

  6. 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...

  7. 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

  8. 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

    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...... 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...... of developing an automatic warning system for tail damage outbreaks, with activity level showing promising results for being monitored automatically. Encouraging results have been found so far for the development of an automatic warning system; however, there is a need for further investigation and development...

  9. 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

  10. Dual-orthogonal radial basis function networks for nonlinear time series prediction.

    Science.gov (United States)

    Hong, X; Billings, Steve A.

    1998-04-01

    A new structure of Radial Basis Function (RBF) neural network called the Dual-orthogonal RBF Network (DRBF) is introduced for nonlinear time series prediction. The hidden nodes of a conventional RBF network compare the Euclidean distance between the network input vector and the centres, and the node responses are radially symmetrical. But in time series prediction where the system input vectors are lagged system outputs, which are usually highly correlated, the Euclidean distance measure may not be appropriate. The DRBF network modifies the distance metric by introducing a classification function which is based on the estimation data set. Training the DRBF networks consists of two stages. Learning the classification related basis functions and the important input nodes, followed by selecting the regressors and learning the weights of the hidden nodes. In both cases, a forward Orthogonal Least Squares (OLS) selection procedure is applied, initially to select the important input nodes and then to select the important centres. Simulation results of single-step and multi-step ahead predictions over a test data set are included to demonstrate the effectiveness of the new approach.

  11. A New Mathematical Model for Flank Wear Prediction Using Functional Data Analysis Methodology

    Directory of Open Access Journals (Sweden)

    Sonja Jozić

    2014-01-01

    Full Text Available This paper presents a new approach improving the reliability of flank wear prediction during the end milling process. In the present work, prediction of flank wear has been achieved by using cutting parameters and force signals as the sensitive carriers of information about the machining process. A series of experiments were conducted to establish the relationship between flank wear and cutting force components as well as the cutting parameters such as cutting speed, feed per tooth, and radial depth of cut. In order to be able to predict flank wear a new linear regression mathematical model has been developed by utilizing functional data analysis methodology. Regression coefficients of the model are in the form of time dependent functions that have been determined through the use of functional data analysis methodology. The mathematical model has been developed by means of applied cutting parameters and measured cutting forces components during the end milling of workpiece made of 42CrMo4 steel. The efficiency and flexibility of the developed model have been verified by comparing it with the separate experimental data set.

  12. 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

  13. 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...

  14. 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

  15. 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

    of 122 tree species from different functional types (FT). We then explored projections of future distributions under one climate scenario for 2080, considering two alternative dispersal assumptions: no dispersal and unlimited dispersal. The species-rich broadleaved deciduous group appeared to play a key......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...... role in the future of different European regions. Temperate areas were projected to lose both species richness and functional diversity due to the loss of broadleaved deciduous trees. These were projected to migrate to boreal forests, thereby increasing their species richness and functional diversity...

  16. 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.

  17. 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...

  18. 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.

  19. 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

  20. Changes in cystic fibrosis airway microbial community associated with a severe decline in lung function.

    Directory of Open Access Journals (Sweden)

    Patrizia Paganin

    Full Text Available Cystic fibrosis (CF is a genetic disease resulting in chronic polymicrobial infections of the airways and progressive decline in lung function. To gain insight into the underlying causes of severe lung diseases, we aimed at comparing the airway microbiota detected in sputum of CF patients with stable lung function (S versus those with a substantial decline in lung function (SD. Microbiota composition was investigated by using culture-based and culture-independent methods, and by performing multivariate and statistical analyses. Culture-based methods identified some microbial species associated with a worse lung function, i.e. Pseudomonas aeruginosa, Rothia mucilaginosa, Streptococcus pneumoniae and Candida albicans, but only the presence of S. pneumoniae and R. mucilaginosa was found to be associated with increased severe decline in forced expiratory volume in 1 second (FEV1. Terminal-Restriction Fragment Length Polymorphism (T-RFLP analysis revealed a higher bacterial diversity than that detected by culture-based methods. Molecular signatures with a statistically significant odds ratio for SD status were detected, and classified as Pseudomonas, Burkholderia and Shewanella, while for other Terminal Restriction Fragments (T-RFs no species assignation was achieved. The analysis of T-RFLP data using ecological biodiversity indices showed reduced Evenness in SD patients compared to S ones, suggesting an impaired ecology of the bacterial community in SD patients. Statistically significant differences of the ecological biodiversity indices among the three sub-groups of FEV1 (normal/mild vs moderate vs severe were also found, suggesting that the patients with moderate lung disease experienced changes in the airway assembly of taxa. Overall, changes in CF airway microbial community associated with a severe lung function decline were detected, allowing us to define some discriminatory species as well as some discriminatory T-RFs that represent good

  1. Lung Function in Preteenaged Canadian School Children: Comparison with Two Standard Prediction Equations and Examination of the Effect of Weight

    Directory of Open Access Journals (Sweden)

    Judith A Leech

    1996-01-01

    Full Text Available OBJECTIVES: To compare prediction curves for forced vital capacity (FVC in children from a large population sample with the standard prediction curves currently in clinical use. A secondary objective was to assess the contribution of weight to the prediction of lung function in preteenagers.

  2. Using quantitative breath sound measurements to predict lung function following resection

    Directory of Open Access Journals (Sweden)

    Keus Leendert

    2010-10-01

    Full Text Available Abstract Background Predicting postoperative lung function is important for estimating the risk of complications and long-term disability after pulmonary resection. We investigated the capability of vibration response imaging (VRI as an alternative to lung scintigraphy for prediction of postoperative lung function in patients with intrathoracic malignancies. Methods Eighty-five patients with intrathoracic malignancies, considered candidates for lung resection, were prospectively studied. The projected postoperative (ppo lung function was calculated using: perfusion scintigraphy, ventilation scintigraphy, and VRI. Two sets of assessments made: one for lobectomy and one for pneumonectomy. Clinical concordance was defined as both methods agreeing that either a patient was or was not a surgical candidate based on a ppoFEV1% and ppoDLCO% > 40%. Results Limits of agreement between scintigraphy and VRI for ppo following lobectomy were -16.47% to 15.08% (mean difference = -0.70%;95%CI = -2.51% to 1.12% and for pneumonectomy were -23.79% to 19.04% (mean difference = -2.38%;95%CI = -4.69% to -0.07%. Clinical concordance between VRI and scintigraphy was 73% for pneumonectomy and 98% for lobectomy. For patients who had surgery and postoperative lung function testing (n = 31, ppoFEV1% using scintigraphic methods correlated with measured postoperative values better than projections using VRI, (adjusted R2 = 0.32 scintigraphy; 0.20 VRI, however the difference between methods failed to reach statistical significance. Limits of agreement between measured FEV1% postoperatively and ppoFEV1% based on perfusion scintigraphy were -16.86% to 23.73% (mean difference = 3.44%;95%CI = -0.29% to 7.16%; based on VRI were -19.56% to 28.99% (mean difference = 4.72%;95%CI = 0.27% to 9.17%. Conclusions Further investigation of VRI as an alternative to lung scintigraphy for prediction of postoperative lung function is warranted.

  3. Thalamic functional connectivity predicts seizure laterality in individual TLE patients: Application of a biomarker development strategy

    Science.gov (United States)

    Barron, Daniel S.; Fox, Peter T.; Pardoe, Heath; Lancaster, Jack; Price, Larry R.; Blackmon, Karen; Berry, Kristen; Cavazos, Jose E.; Kuzniecky, Ruben; Devinsky, Orrin; Thesen, Thomas

    2014-01-01

    Noninvasive markers of brain function could yield biomarkers in many neurological disorders. Disease models constrained by coordinate-based meta-analysis are likely to increase this yield. Here, we evaluate a thalamic model of temporal lobe epilepsy that we proposed in a coordinate-based meta-analysis and extended in a diffusion tractography study of an independent patient population. Specifically, we evaluated whether thalamic functional connectivity (resting-state fMRI-BOLD) with temporal lobe areas can predict seizure onset laterality, as established with intracranial EEG. Twenty-four lesional and non-lesional temporal lobe epilepsy patients were studied. 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. PMID:25610790

  4. 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.

  5. Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction

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    Fofanov Viacheslav Y

    2010-05-01

    Full Text Available Abstract Background Structural variations caused by a wide range of physico-chemical and biological sources directly influence the function of a protein. For enzymatic proteins, the structure and chemistry of the catalytic binding site residues can be loosely defined as a substructure of the protein. Comparative analysis of drug-receptor substructures across and within species has been used for lead evaluation. Substructure-level similarity between the binding sites of functionally similar proteins has also been used to identify instances of convergent evolution among proteins. In functionally homologous protein families, shared chemistry and geometry at catalytic sites provide a common, local point of comparison among proteins that may differ significantly at the sequence, fold, or domain topology levels. Results This paper describes two key results that can be used separately or in combination for protein function analysis. The Family-wise Analysis of SubStructural Templates (FASST method uses all-against-all substructure comparison to determine Substructural Clusters (SCs. SCs characterize the binding site substructural variation within a protein family. In this paper we focus on examples of automatically determined SCs that can be linked to phylogenetic distance between family members, segregation by conformation, and organization by homology among convergent protein lineages. The Motif Ensemble Statistical Hypothesis (MESH framework constructs a representative motif for each protein cluster among the SCs determined by FASST to build motif ensembles that are shown through a series of function prediction experiments to improve the function prediction power of existing motifs. Conclusions FASST contributes a critical feedback and assessment step to existing binding site substructure identification methods and can be used for the thorough investigation of structure-function relationships. The application of MESH allows for an automated

  6. Continuously Growing Rodent Molars Result from a Predictable Quantitative Evolutionary Change over 50 Million Years

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    Vagan Tapaltsyan

    2015-05-01

    Full Text Available The fossil record is widely informative about evolution, but fossils are not systematically used to study the evolution of stem-cell-driven renewal. Here, we examined evolution of the continuous growth (hypselodonty of rodent molar teeth, which is fuelled by the presence of dental stem cells. We studied occurrences of 3,500 North American rodent fossils, ranging from 50 million years ago (mya to 2 mya. We examined changes in molar height to determine whether evolution of hypselodonty shows distinct patterns in the fossil record, and we found that hypselodont taxa emerged through intermediate forms of increasing crown height. Next, we designed a Markov simulation model, which replicated molar height increases throughout the Cenozoic and, moreover, evolution of hypselodonty. Thus, by extension, the retention of the adult stem cell niche appears to be a predictable quantitative rather than a stochastic qualitative process. Our analyses predict that hypselodonty will eventually become the dominant phenotype.

  7. Opposing Patterns of Seasonal Change in Functional and Phylogenetic Diversity of Tadpole Assemblages

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    Strauß, Axel; Guilhaumon, François; Randrianiaina, Roger Daniel; Wollenberg Valero, Katharina C.; Vences, Miguel; Glos, Julian

    2016-01-01

    Assemblages that are exposed to recurring temporal environmental changes can show changes in their ecological properties. These can be expressed by differences in diversity and assembly rules. Both can be identified using two measures of diversity: functional (FD) and phylogenetic diversity (PD). Frog communities are understudied in this regard, especially during the tadpole life stage. We utilised tadpole assemblages from Madagascan rainforest streams to test predictions of seasonal changes on diversity and assemblage composition and on diversity measures. From the warm-wet to the cool-dry season, species richness (SR) of tadpole assemblages decreased. Also FD and PD decreased, but FD less and PD more than expected by chance. During the dry season, tadpole assemblages were characterised by functional redundancy (among assemblages—with increasing SR), high FD (compared to a null model), and low PD (phylogenetic clustering; compared to a null model). Although mutually contradictory at first glance, these results indicate competition as tadpole community assembly driving force. This is true during the limiting cool-dry season but not during the more suitable warm-wet season. We thereby show that assembly rules can strongly depend on season, that comparing FD and PD can reveal such forces, that FD and PD are not interchangeable, and that conclusions on assembly rules based on FD alone are critical. PMID:27014867

  8. Bilirubin binding with liver cystatin induced structural and functional changes.

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    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

  9. Can tail damage outbreaks in the pig be predicted by behavioural change?

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    Larsen, Mona Lilian Vestbjerg; Andersen, Heidi Mai-Lis; Pedersen, Lene Juul

    2016-03-01

    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 developing an automatic warning system for tail damage outbreaks, with activity level showing promising results for being monitored automatically. Encouraging results have been found so far for the development of an automatic warning system; however, there is a need for further investigation and development, starting with the description of the temporal development of the predictive behaviour in relation to tail damage outbreaks. PMID:26831153

  10. Land use change and prediction in the Baimahe Basin using GIS and CA-Markov model

    International Nuclear Information System (INIS)

    Using ArcGIS and IDRISI, land use dynamics and Shannon entropy information were applied in this paper to analyze the quantity and structure change in the Baimahe Basin from 1996 to 2008. A CA-Markov model was applied to predict the land use patterns in 2020. Results showed that farmland, forest and construction land are the dominant land use types in the Baimahe Basin. From 1996 to 2008, areas of farmland and forest decreased and other land use types increased, with construction land increasing the most. The prediction results showed that the changes in land use patterns from 2008 to 2020 would be the same with those from 1996 to 2008. Main changes are the transiting out of farmland and forest and the transiting in of construction land. The order degree of the whole basin goes on decreasing. Measures of farmland protection and grain for green projects should be adopted to enhance the stability of land use system in the Baimahe Basin in order to promote regional sustainable development

  11. Meditation-induced changes in high-frequency heart rate variability predict smoking outcomes

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    Daniel J. Libby

    2012-03-01

    Full Text Available Background: High-frequency heart rate variability (HF-HRV is a measure of parasympathetic nervous system output that has been associated with enhanced self-regulation. Low resting levels of HF-HRV are associated with nicotine dependence and blunted stress-related changes in HF-HRV are associated with decreased ability to resist smoking. Meditation has been shown to increase HF-HRV. However, it is unknown whether tonic levels of HF-HRV or acute changes in HF-HRV during meditation predict treatment responses in addictive behaviors such as smoking cessation. Purpose: To investigate the relationship between HF-HRV and subsequent smoking outcomes. Methods: HF-HRV during resting baseline and during mindfulness meditation was measured within two weeks of completing a 4-week smoking cessation intervention in a sample of 31 community participants. Self-report measures of smoking were obtained at a follow up 17-weeks after the initiation of treatment. Results: Regression analyses indicated that individuals exhibiting acute increases in HF-HRV from resting baseline to meditation smoked fewer cigarettes at follow-up than those who exhibited acute decreases in HF-HRV (b=-4.94, p=.009. Conclusion: Acute changes in HF-HRV in response to meditation may be a useful tool to predict smoking cessation treatment response.

  12. Switch region for pathogenic structural change in conformational disease and its prediction.

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    Xin Liu

    Full Text Available Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1 influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1 it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2 it provides an ideal target for clinical treatment.

  13. FFPred 3: feature-based function prediction for all Gene Ontology domains.

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    Cozzetto, Domenico; Minneci, Federico; Currant, Hannah; Jones, David T

    2016-01-01

    Predicting protein function has been a major goal of bioinformatics for several decades, and it has gained fresh momentum thanks to recent community-wide blind tests aimed at benchmarking available tools on a genomic scale. Sequence-based predictors, especially those performing homology-based transfers, remain the most popular but increasing understanding of their limitations has stimulated the development of complementary approaches, which mostly exploit machine learning. Here we present FFPred 3, which is intended for assigning Gene Ontology terms to human protein chains, when homology with characterized proteins can provide little aid. Predictions are made by scanning the input sequences against an array of Support Vector Machines (SVMs), each examining the relationship between protein function and biophysical attributes describing secondary structure, transmembrane helices, intrinsically disordered regions, signal peptides and other motifs. This update features a larger SVM library that extends its coverage to the cellular component sub-ontology for the first time, prompted by the establishment of a dedicated evaluation category within the Critical Assessment of Functional Annotation. The effectiveness of this approach is demonstrated through benchmarking experiments, and its usefulness is illustrated by analysing the potential functional consequences of alternative splicing in human and their relationship to patterns of biological features. PMID:27561554

  14. Functional changes of human quadriceps muscle injured by eccentric exercise

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    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.

  15. Functional changes of dendritic cells in hypersensivity reactions to amoxicillin

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    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.

  16. Predicting climate change effects on surface soil organic carbon of Louisiana, USA.

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    Zhong, Biao; Xu, Yi Jun

    2014-10-01

    This study aimed to assess the degree of potential temperature and precipitation change as predicted by the HadCM3 (Hadley Centre Coupled Model, version 3) climate model for Louisiana, and to investigate the effects of potential climate change on surface soil organic carbon (SOC) across Louisiana using the Rothamsted Carbon Model (RothC) and GIS techniques at the watershed scale. Climate data sets at a grid cell of 0.5° × 0.5° for the entire state of Louisiana were collected from the HadCM3 model output for three climate change scenarios: B2, A2, and A1F1, that represent low, higher, and even higher greenhouse gas emissions, respectively. Geo-referenced datasets including USDA-NRCS Soil Geographic Database (STATSGO), USGS Land Cover Dataset (NLCD), and the Louisiana watershed boundary data were gathered for SOC calculation at the watershed scale. A soil carbon turnover model, RothC, was used to simulate monthly changes in SOC from 2001 to 2100 under the projected temperature and precipitation changes. The simulated SOC changes in 253 watersheds from three time periods, 2001-2010, 2041-2050, and 2091-2100, were tested for the influence of the land covers and emissions scenarios using SAS PROC GLIMMIX and PDMIX800 macro to separate Tukey-Kramer (p change from 30.7 t/ha in 2001 to 25.4, 26.6, and 27.0 t/ha in 2100, respectively. Annual SOC changes will be significantly different among the land cover classes including evergreen forest, mixed forest, deciduous forest, small grains, row crops, and pasture/hay (p < 0.0001), emissions scenarios (p < 0.0001), and their interactions (p < 0.0001).

  17. Prediction of individual clinical scores in patients with Parkinson's disease using resting-state functional magnetic resonance imaging.

    Science.gov (United States)

    Hou, YanBing; Luo, ChunYan; Yang, Jing; Ou, RuWei; Song, Wei; Wei, QianQian; Cao, Bei; Zhao, Bi; Wu, Ying; Shang, Hui-Fang; Gong, QiYong

    2016-07-15

    Neuroimaging holds the promise that it may one day aid the clinical assessment. However, the vast majority of studies using resting-state functional magnetic resonance imaging (fMRI) have reported average differences between Parkinson's disease (PD) patients and healthy controls, which do not permit inferences at the level of individuals. This study was to develop a model for the prediction of PD illness severity ratings from individual fMRI brain scan. The resting-state fMRI scans were obtained from 84 patients with PD and the Unified Parkinson's Disease Rating Scale-III (UPDRS-III) scores were obtained before scanning. The RVR method was used to predict clinical scores (UPDRS-III) from fMRI scans. The application of RVR to whole-brain resting-state fMRI data allowed prediction of UPDRS-III scores with statistically significant accuracy (correlation=0.35, P-value=0.001; mean sum of squares=222.17, P-value=0.002). This prediction was informed strongly by negative weight areas including prefrontal lobe and medial occipital lobe, and positive weight areas including medial parietal lobe. It was suggested that fMRI scans contained sufficient information about neurobiological change in patients with PD to permit accurate prediction about illness severity, on an individual subject basis. Our results provided preliminary evidence, as proof-of-concept, to support that fMRI might be possible to be a clinically useful quantitative assessment aid in PD at individual level. This may enable clinicians to target those uncooperative patients and machines to replace human for a more efficient use of health care resources. PMID:27288771

  18. Predicting Nitrogen Loading in Streams Under Climate Change Scenarios in the Continental United States.

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    Sinha, E.; Michalak, A. M.

    2014-12-01

    Human actions have doubled the amount of nitrogen in the terrestrial biosphere. Although nitrogen application in the form of fertilizers increases food production, excess nitrogen can be harmful to the environment and to human well-being. Excess nitrogen in streams is transported into downstream water bodies, which leads to increased eutrophication and associated problems such as harmful algal blooms and/or hypoxic conditions. The amount of nitrogen exported to streams depends on several factors, including nitrogen input to the watershed, land use, and precipitation. Previous studies have developed models for predicting nitrate load using stream discharge, in order to estimate the contribution of various factors to total nitrogen load, to identify strategies for reducing nitrogen load, and to assess future changes in nitrogen load resulting from anticipated changes in precipitation patterns. Applying these models to estimate future nitrogen loads thus requires running a rainfall-runoff model driven by climate model predictions before nitrogen loading can, in turn, be estimated, thereby compounding uncertainties. In this study, we present a statistical modeling approach that circumvents this two-step process by estimating nitrogen loading directly from precipitation predictions that can be obtained from climate model outputs. The proposed model uses net anthropogenic nitrogen input (NANI), land use type, and precipitation as input parameters. Preliminary results show that the model explains greater than 65% of the variance in the observed annual log transformed nitrogen loads across various catchments throughout the United States. The model is applied to the watersheds comprising the Mississippi river basin to identify the spatial distribution of the sources of nitrogen loading and the inter-annual variation in nitrogen loads under current conditions. Additionally, the model is used to examine changes in magnitude and spatial patterns of nitrogen loading for

  19. Recent improvements in prediction of protein structure by global optimization of a potential energy function

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    Pillardy, Jarosław; Czaplewski, Cezary; Liwo, Adam; Lee, Jooyoung; Ripoll, Daniel R.; Kaźmierkiewicz, Rajmund; Ołdziej, Stanisław; Wedemeyer, William J.; Gibson, Kenneth D.; Arnautova, Yelena A.; Saunders, Jeff; Ye, Yuan-Jie; Scheraga, Harold A.

    2001-01-01

    Recent improvements of a hierarchical ab initio or de novo approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic α-helical protein of 70 residues was predicted to within 4.3 Å α-carbon (Cα) rms deviation (rmsd) whereas, for other α-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 Å Cα rmsd. Whereas β structures can now be predicted with the new procedure, the success rate for α/β- and β-proteins is lower than that for α-proteins at present. For the β portions of α/β structures, the Cα rmsd's are less than 6.0 Å for contiguous fragments of 30–40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a Cα rmsd less than 6.0 Å. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence. PMID:11226239

  20. Changing housework, changing health? A longitudinal analysis of how changes in housework are associated with functional somatic symptoms

    Science.gov (United States)

    Landstedt, Evelina; Harryson, Lisa; Hammarström, Anne

    2016-01-01

    Aim The aim of this study was to analyse how changes in housework over the course of adulthood are related to somatic health in Swedish men and women. Methods Data were drawn from 2 waves of the Northern Swedish Cohort Study, response rate 94.3%, N=1,001. A subsample of cohabiting individuals was selected (n=328 women, 300 men). Outcome variable was functional somatic symptoms (FSS) at age 42. Associations were assessed in multivariate general linear models with adjustment for confounders and somatic health at age 30. Results Housework is primarily performed by women, and women's responsibility for and performance of housework increased from ages 30 to 42. These changes were associated with elevated levels of FSS at age 42 in women. Men reported considerably lower responsibility for and performed less housework compared with women, the load of housework for men does not change substantially from ages 30 to 42 and no associations with FSS were identified. Conclusions The gendered division of housework means that women are particularly exposed to a heavy workload. Women's responsibility for and performance of housework increase between ages 30 and 42 and this threatens to be embodied in the form FSS. We conclude that housework should be considered an important source of stress in addition to that from waged work and that a deeper understanding of the links between housework and health requires a gender theoretical analysis. PMID:27369590