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Sample records for extreme phenotype sampling

  1. Using Extreme Phenotype Sampling to Identify the Rare Causal Variants of Quantitative Traits in Association Studies

    OpenAIRE

    Li, Dalin; Lewinger, Juan Pablo; Gauderman, William J.; Murcray, Cassandra Elizabeth; Conti, David

    2011-01-01

    Variants identified in recent genome-wide association studies based on the common-disease common-variant hypothesis are far from fully explaining the hereditability of complex traits. Rare variants may, in part, explain some of the missing hereditability. Here, we explored the advantage of the extreme phenotype sampling in rare-variant analysis and refined this design framework for future large-scale association studies on quantitative traits. We first proposed a power calculation approach fo...

  2. EPS-LASSO: Test for High-Dimensional Regression Under Extreme Phenotype Sampling of Continuous Traits.

    Science.gov (United States)

    Xu, Chao; Fang, Jian; Shen, Hui; Wang, Yu-Ping; Deng, Hong-Wen

    2018-01-25

    Extreme phenotype sampling (EPS) is a broadly-used design to identify candidate genetic factors contributing to the variation of quantitative traits. By enriching the signals in extreme phenotypic samples, EPS can boost the association power compared to random sampling. Most existing statistical methods for EPS examine the genetic factors individually, despite many quantitative traits have multiple genetic factors underlying their variation. It is desirable to model the joint effects of genetic factors, which may increase the power and identify novel quantitative trait loci under EPS. The joint analysis of genetic data in high-dimensional situations requires specialized techniques, e.g., the least absolute shrinkage and selection operator (LASSO). Although there are extensive research and application related to LASSO, the statistical inference and testing for the sparse model under EPS remain unknown. We propose a novel sparse model (EPS-LASSO) with hypothesis test for high-dimensional regression under EPS based on a decorrelated score function. The comprehensive simulation shows EPS-LASSO outperforms existing methods with stable type I error and FDR control. EPS-LASSO can provide a consistent power for both low- and high-dimensional situations compared with the other methods dealing with high-dimensional situations. The power of EPS-LASSO is close to other low-dimensional methods when the causal effect sizes are small and is superior when the effects are large. Applying EPS-LASSO to a transcriptome-wide gene expression study for obesity reveals 10 significant body mass index associated genes. Our results indicate that EPS-LASSO is an effective method for EPS data analysis, which can account for correlated predictors. The source code is available at https://github.com/xu1912/EPSLASSO. hdeng2@tulane.edu. Supplementary data are available at Bioinformatics online. © The Author (2018). Published by Oxford University Press. All rights reserved. For Permissions, please

  3. Identification of extreme motor phenotypes in Huntington's disease.

    Science.gov (United States)

    Braisch, Ulrike; Hay, Birgit; Muche, Rainer; Rothenbacher, Dietrich; Landwehrmeyer, G Bernhard; Long, Jeffrey D; Orth, Michael

    2017-04-01

    The manifestation of motor signs in Huntington's disease (HD) has a well-known inverse relationship with HTT CAG repeat length, but the prediction is far from perfect. The probability of finding disease modifiers is enhanced in individuals with extreme HD phenotypes. We aimed to identify extreme HD motor phenotypes conditional on CAG and age, such as patients with very early or very late onset of motor manifestation. Retrospective data were available from 1,218 healthy controls and 9,743 HD participants with CAG repeats ≥40, and a total of about 30,000 visits. Boundaries (2.5% and 97.5% quantiles) for extreme motor phenotypes (UHDRS total motor score (TMS) and motor age-at-onset) were estimated using quantile regression for longitudinal data. More than 15% of HD participants had an extreme TMS phenotype for at least one visit. In contrast, only about 4% of participants were consistent TMS extremes at two or more visits. Data from healthy controls revealed an upper cut-off of 13 for the TMS representing the extreme of motor ratings for a normal aging population. In HD, boundaries of motor age-at-onset based on diagnostic confidence or derived from the TMS data cut-off in controls were similar. In summary, a UHDRS TMS of more than 13 in an individual carrying the HD mutation indicates a high likelihood of motor manifestations of HD irrespective of CAG repeat length or age. The identification of motor phenotype extremes can be useful in the search for disease modifiers, for example, genetic or environmental such as medication. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. Infill sampling criteria to locate extremes

    CSIR Research Space (South Africa)

    Watson, AG

    1995-07-01

    Full Text Available Three problem-dependent meanings for engineering ''extremes'' are motivated, established, and translated into formal geostatistical (model-based) criteria for designing infill sample networks. (I) Locate an area within the domain of interest where a...

  5. Sample size calculation in metabolic phenotyping studies.

    Science.gov (United States)

    Billoir, Elise; Navratil, Vincent; Blaise, Benjamin J

    2015-09-01

    The number of samples needed to identify significant effects is a key question in biomedical studies, with consequences on experimental designs, costs and potential discoveries. In metabolic phenotyping studies, sample size determination remains a complex step. This is due particularly to the multiple hypothesis-testing framework and the top-down hypothesis-free approach, with no a priori known metabolic target. Until now, there was no standard procedure available to address this purpose. In this review, we discuss sample size estimation procedures for metabolic phenotyping studies. We release an automated implementation of the Data-driven Sample size Determination (DSD) algorithm for MATLAB and GNU Octave. Original research concerning DSD was published elsewhere. DSD allows the determination of an optimized sample size in metabolic phenotyping studies. The procedure uses analytical data only from a small pilot cohort to generate an expanded data set. The statistical recoupling of variables procedure is used to identify metabolic variables, and their intensity distributions are estimated by Kernel smoothing or log-normal density fitting. Statistically significant metabolic variations are evaluated using the Benjamini-Yekutieli correction and processed for data sets of various sizes. Optimal sample size determination is achieved in a context of biomarker discovery (at least one statistically significant variation) or metabolic exploration (a maximum of statistically significant variations). DSD toolbox is encoded in MATLAB R2008A (Mathworks, Natick, MA) for Kernel and log-normal estimates, and in GNU Octave for log-normal estimates (Kernel density estimates are not robust enough in GNU octave). It is available at http://www.prabi.fr/redmine/projects/dsd/repository, with a tutorial at http://www.prabi.fr/redmine/projects/dsd/wiki. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  6. Sample Return Systems for Extreme Environments

    Data.gov (United States)

    National Aeronautics and Space Administration — In Phase I we were able to demonstrate that sample return missions utilizing high velocity penetrators (0.1- 1 km/s) could provide substantial new capabilities for...

  7. Sample Return Systems for Extreme Environments

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed work seeks to design, develop and test a hard impact penetrator/sampler that can withstand the hard impact and enable the sample to be returned to...

  8. The Autism Simplex Collection : an international, expertly phenotyped autism sample for genetic and phenotypic analyses

    OpenAIRE

    Buxbaum, Joseph D.; Bolshakova, Nadia; Brownfeld, Jessica M.; Anney, Richard J. L.; Bender, Patrick; Bernier, Raphael; Cook, Edwin H.; Coon, Hilary; Cuccaro, Michael L.; Freitag, Christine M.; Hallmayer, Joachim; Geschwind, Daniel H.; Klauck, Sabine M.; Nurnberger, John I.; Oliveira, Guiomar

    2014-01-01

    Background: There is an urgent need for expanding and enhancing autism spectrum disorder (ASD) samples, in order to better understand causes of ASD. Methods: In a unique public-private partnership, 13 sites with extensive experience in both the assessment and diagnosis of ASD embarked on an ambitious, 2-year program to collect samples for genetic and phenotypic research and begin analyses on these samples. The program was called The Autism Simplex Collection (TASC). TASC sample collection ...

  9. Extreme eigenvalues of sample covariance and correlation matrices

    DEFF Research Database (Denmark)

    Heiny, Johannes

    This thesis is concerned with asymptotic properties of the eigenvalues of high-dimensional sample covariance and correlation matrices under an infinite fourth moment of the entries. In the first part, we study the joint distributional convergence of the largest eigenvalues of the sample covariance...... matrix of a p-dimensional heavy-tailed time series when p converges to infinity together with the sample size n. We generalize the growth rates of p existing in the literature. Assuming a regular variation condition with tail index ... eigenvalues are essentially determined by the extreme order statistics from an array of iid random variables. The asymptotic behavior of the extreme eigenvalues is then derived routinely from classical extreme value theory. The resulting approximations are strikingly simple considering the high dimension...

  10. Exome sequencing for gene discovery in lethal fetal disorders--harnessing the value of extreme phenotypes.

    Science.gov (United States)

    Filges, Isabel; Friedman, Jan M

    2015-10-01

    Massively parallel sequencing has revolutionized our understanding of Mendelian disorders, and many novel genes have been discovered to cause disease phenotypes when mutant. At the same time, next-generation sequencing approaches have enabled non-invasive prenatal testing of free fetal DNA in maternal blood. However, little attention has been paid to using whole exome and genome sequencing strategies for gene identification in fetal disorders that are lethal in utero, because they can appear to be sporadic and Mendelian inheritance may be missed. We present challenges and advantages of applying next-generation sequencing approaches to gene discovery in fetal malformation phenotypes and review recent successful discovery approaches. We discuss the implication and significance of recessive inheritance and cross-species phenotyping in fetal lethal conditions. Whole exome sequencing can be used in individual families with undiagnosed lethal congenital anomaly syndromes to discover causal mutations, provided that prior to data analysis, the fetal phenotype can be correlated to a particular developmental pathway in embryogenesis. Cross-species phenotyping allows providing further evidence for causality of discovered variants in genes involved in those extremely rare phenotypes and will increase our knowledge about normal and abnormal human developmental processes. Ultimately, families will benefit from the option of early prenatal diagnosis. © 2014 John Wiley & Sons, Ltd.

  11. Diagnosing phenotypes of single-sample individuals by edge biomarkers.

    Science.gov (United States)

    Zhang, Wanwei; Zeng, Tao; Liu, Xiaoping; Chen, Luonan

    2015-06-01

    Network or edge biomarkers are a reliable form to characterize phenotypes or diseases. However, obtaining edges or correlations between molecules for an individual requires measurement of multiple samples of that individual, which are generally unavailable in clinical practice. Thus, it is strongly demanded to diagnose a disease by edge or network biomarkers in one-sample-for-one-individual context. Here, we developed a new computational framework, EdgeBiomarker, to integrate edge and node biomarkers to diagnose phenotype of each single test sample. By applying the method to datasets of lung and breast cancer, it reveals new marker genes/gene-pairs and related sub-networks for distinguishing earlier and advanced cancer stages. Our method shows advantages over traditional methods: (i) edge biomarkers extracted from non-differentially expressed genes achieve better cross-validation accuracy of diagnosis than molecule or node biomarkers from differentially expressed genes, suggesting that certain pathogenic information is only present at the level of network and under-estimated by traditional methods; (ii) edge biomarkers categorize patients into low/high survival rate in a more reliable manner; (iii) edge biomarkers are significantly enriched in relevant biological functions or pathways, implying that the association changes in a network, rather than expression changes in individual molecules, tend to be causally related to cancer development. The new framework of edge biomarkers paves the way for diagnosing diseases and analyzing their molecular mechanisms by edges or networks in one-sample-for-one-individual basis. This also provides a powerful tool for precision medicine or big-data medicine. © The Author (2015). Published by Oxford University Press on behalf of Journal of Molecular Cell Biology, IBCB, SIBS, CAS. All rights reserved.

  12. Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition

    Directory of Open Access Journals (Sweden)

    Ramayo-Caldas Yuliaxis

    2012-10-01

    Full Text Available Abstract Background New advances in high-throughput technologies have allowed for the massive analysis of genomic data, providing new opportunities for the characterization of the transcriptome architectures. Recent studies in pigs have employed RNA-Seq to explore the transcriptome of different tissues in a reduced number of animals. The main goal of this study was the identification of differentially-expressed genes in the liver of Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition using RNA-Seq. Results The liver transcriptomes of two female groups (H and L with phenotypically extreme intramuscular fatty acid composition were sequenced using RNA-Seq. A total of 146 and 180 unannotated protein-coding genes were identified in intergenic regions for the L and H groups, respectively. In addition, a range of 5.8 to 7.3% of repetitive elements was found, with SINEs being the most abundant elements. The expression in liver of 186 (L and 270 (H lncRNAs was also detected. The higher reproducibility of the RNA-Seq data was validated by RT-qPCR and porcine expression microarrays, therefore showing a strong correlation between RT-qPCR and RNA-Seq data (ranking from 0.79 to 0.96, as well as between microarrays and RNA-Seq (r=0.72. A differential expression analysis between H and L animals identified 55 genes differentially-expressed between groups. Pathways analysis revealed that these genes belong to biological functions, canonical pathways and three gene networks related to lipid and fatty acid metabolism. In concordance with the phenotypic classification, the pathways analysis inferred that linolenic and arachidonic acids metabolism was altered between extreme individuals. In addition, a connection was observed among the top three networks, hence suggesting that these genes are interconnected and play an important role in lipid and fatty acid metabolism. Conclusions In the present study RNA-Seq was used

  13. Antarctic Climate Change: Extreme Events Disrupt Plastic Phenotypic Response in Adélie Penguins

    Science.gov (United States)

    Lescroël, Amélie; Ballard, Grant; Grémillet, David; Authier, Matthieu; Ainley, David G.

    2014-01-01

    In the context of predicted alteration of sea ice cover and increased frequency of extreme events, it is especially timely to investigate plasticity within Antarctic species responding to a key environmental aspect of their ecology: sea ice variability. Using 13 years of longitudinal data, we investigated the effect of sea ice concentration (SIC) on the foraging efficiency of Adélie penguins (Pygoscelis adeliae) breeding in the Ross Sea. A ‘natural experiment’ brought by the exceptional presence of giant icebergs during 5 consecutive years provided unprecedented habitat variation for testing the effects of extreme events on the relationship between SIC and foraging efficiency in this sea-ice dependent species. Significant levels of phenotypic plasticity were evident in response to changes in SIC in normal environmental conditions. Maximum foraging efficiency occurred at relatively low SIC, peaking at 6.1% and decreasing with higher SIC. The ‘natural experiment’ uncoupled efficiency levels from SIC variations. Our study suggests that lower summer SIC than currently observed would benefit the foraging performance of Adélie penguins in their southernmost breeding area. Importantly, it also provides evidence that extreme climatic events can disrupt response plasticity in a wild seabird population. This questions the predictive power of relationships built on past observations, when not only the average climatic conditions are changing but the frequency of extreme climatic anomalies is also on the rise. PMID:24489657

  14. Antarctic climate change: extreme events disrupt plastic phenotypic response in Adélie penguins.

    Directory of Open Access Journals (Sweden)

    Amélie Lescroël

    Full Text Available In the context of predicted alteration of sea ice cover and increased frequency of extreme events, it is especially timely to investigate plasticity within Antarctic species responding to a key environmental aspect of their ecology: sea ice variability. Using 13 years of longitudinal data, we investigated the effect of sea ice concentration (SIC on the foraging efficiency of Adélie penguins (Pygoscelis adeliae breeding in the Ross Sea. A 'natural experiment' brought by the exceptional presence of giant icebergs during 5 consecutive years provided unprecedented habitat variation for testing the effects of extreme events on the relationship between SIC and foraging efficiency in this sea-ice dependent species. Significant levels of phenotypic plasticity were evident in response to changes in SIC in normal environmental conditions. Maximum foraging efficiency occurred at relatively low SIC, peaking at 6.1% and decreasing with higher SIC. The 'natural experiment' uncoupled efficiency levels from SIC variations. Our study suggests that lower summer SIC than currently observed would benefit the foraging performance of Adélie penguins in their southernmost breeding area. Importantly, it also provides evidence that extreme climatic events can disrupt response plasticity in a wild seabird population. This questions the predictive power of relationships built on past observations, when not only the average climatic conditions are changing but the frequency of extreme climatic anomalies is also on the rise.

  15. Extreme Quantum Memory Advantage for Rare-Event Sampling

    Science.gov (United States)

    Aghamohammadi, Cina; Loomis, Samuel P.; Mahoney, John R.; Crutchfield, James P.

    2018-02-01

    We introduce a quantum algorithm for memory-efficient biased sampling of rare events generated by classical memoryful stochastic processes. Two efficiency metrics are used to compare quantum and classical resources for rare-event sampling. For a fixed stochastic process, the first is the classical-to-quantum ratio of required memory. We show for two example processes that there exists an infinite number of rare-event classes for which the memory ratio for sampling is larger than r , for any large real number r . Then, for a sequence of processes each labeled by an integer size N , we compare how the classical and quantum required memories scale with N . In this setting, since both memories can diverge as N →∞ , the efficiency metric tracks how fast they diverge. An extreme quantum memory advantage exists when the classical memory diverges in the limit N →∞ , but the quantum memory has a finite bound. We then show that finite-state Markov processes and spin chains exhibit memory advantage for sampling of almost all of their rare-event classes.

  16. Extreme Quantum Memory Advantage for Rare-Event Sampling

    Directory of Open Access Journals (Sweden)

    Cina Aghamohammadi

    2018-02-01

    Full Text Available We introduce a quantum algorithm for memory-efficient biased sampling of rare events generated by classical memoryful stochastic processes. Two efficiency metrics are used to compare quantum and classical resources for rare-event sampling. For a fixed stochastic process, the first is the classical-to-quantum ratio of required memory. We show for two example processes that there exists an infinite number of rare-event classes for which the memory ratio for sampling is larger than r, for any large real number r. Then, for a sequence of processes each labeled by an integer size N, we compare how the classical and quantum required memories scale with N. In this setting, since both memories can diverge as N→∞, the efficiency metric tracks how fast they diverge. An extreme quantum memory advantage exists when the classical memory diverges in the limit N→∞, but the quantum memory has a finite bound. We then show that finite-state Markov processes and spin chains exhibit memory advantage for sampling of almost all of their rare-event classes.

  17. Sample-Based Extreme Learning Machine with Missing Data

    Directory of Open Access Journals (Sweden)

    Hang Gao

    2015-01-01

    Full Text Available Extreme learning machine (ELM has been extensively studied in machine learning community during the last few decades due to its high efficiency and the unification of classification, regression, and so forth. Though bearing such merits, existing ELM algorithms cannot efficiently handle the issue of missing data, which is relatively common in practical applications. The problem of missing data is commonly handled by imputation (i.e., replacing missing values with substituted values according to available information. However, imputation methods are not always effective. In this paper, we propose a sample-based learning framework to address this issue. Based on this framework, we develop two sample-based ELM algorithms for classification and regression, respectively. Comprehensive experiments have been conducted in synthetic data sets, UCI benchmark data sets, and a real world fingerprint image data set. As indicated, without introducing extra computational complexity, the proposed algorithms do more accurate and stable learning than other state-of-the-art ones, especially in the case of higher missing ratio.

  18. Taxonomic analysis of extremely halophilic archaea isolated from 56-years-old dead sea brine samples.

    Science.gov (United States)

    Arahal, D R; Gutiérrez, M C; Volcani, B E; Ventosa, A

    2000-10-01

    A taxonomic study comprising both phenotypic and genotypic characterization, has been carried out on a total of 158 extremely halophilic aerobic archaeal strains. These strains were isolated from enrichments prepared from Dead Sea water samples dating from 1936 that were collected by B. E. Volcani for the demonstration of microbial life in the Dead Sea. The isolates were examined for 126 morphological, physiological, biochemical and nutritional tests. Numerical analysis of the data, by using the S(J) coefficient and UPGMA clustering method, showed that the isolates clustered into six phenons. Twenty-two out of the 158 strains used in this study were characterized previously (ARAHAL et al., 1996) and were placed into five phenotypic groups. The genotypic study included both the determination of the guanineplus-cytosine content of the DNA and DNA-DNA hybridization studies. For this purpose, representative strains from the six phenons were chosen. These groups were found to represent some members of three different genera - Haloarcula (phenons A, B, and C), Haloferax (phenons D and E) and Halobacterium (phenon F) - of the family Halobacteriaceae, some of them never reported to occur in the Dead Sea, such as Haloarcula hispanica, while Haloferax volcanii (phenons D and E) was described in the Dead Sea by studies carried out several decades later than Volcani's work.

  19. Advanced diabetic nephropathy with “Clean” eyes: An extreme phenotype

    Directory of Open Access Journals (Sweden)

    Debmalya Sanyal

    2018-01-01

    Full Text Available Introduction: It is generally accepted that renal and eye changes in diabetes are concordant. There are however a fair number of patients with diabetes who have end-stage renal disease (ESRD without any of the typical eye changes. The present study highlights the discordance between retinopathy and nephropathy and describes a series of patients of long-standing diabetes undergoing renal transplant who had little or no evidence of retinopathy. Methods: All patients with ESRD undergoing renal transplants underwent comprehensive fundus evaluation including dilated indirect ophthalmoscopy, slit lamp biomicroscopy, and fundus photography. The patients' age, gender, physical parameters (body mass index and blood pressure, duration of diabetes, glycosylated hemoglobin (HbA1c, albumin creatinine ratio, and presence of diabetic peripheral neuropathy (DPN were determined. Renal histopathology was reviewed, if available. Results: Five patients with diabetic nephropathy (DN underwent renal transplant and had no evidence of diabetic retinopathy (DR or up to two microaneurysms per fundus. All the patients were between 50 and 65 (mean ± standard deviation – 58.6 ± 4.67 years of age. The mean duration of diabetes was 16 ± 2.91 years. All had poor glycemic control with a mean HbA1c of 9.2 ± 0.837%. All had hypertension, macroalbuminuria, and DPN. Conclusion: There is a well-recognized association between retinopathy and nephropathy, in which nephropathy without retinopathy is rare but retinopathy without nephropathy is common. We have identified a subset of patients with kidney disease of sufficient severity to warrant renal transplant but who are protected from retinopathy. It is possible that there is an extreme phenotype of DN patients with unaffected eyes who carry genes protecting against DR.

  20. Extreme Environment Sampling System Deployment Mechanism, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Future Venus or Comet mission architectures may feature robotic sampling systems comprised of a Sampling Tool and Deployment Mechanism. Since 2005, Honeybee has been...

  1. Phenotypic variation in California populations of valley oak (Quercus lobata Née) sampled along elevational gradients

    Science.gov (United States)

    Ana L. Albarrán-Lara; Jessica W. Wright; Paul F. Gugger; Annette Delfino-Mix; Juan Manuel Peñaloza-Ramírez; Victoria L. Sork

    2015-01-01

    California oaks exhibit tremendous phenotypic variation throughout their range. This variation reflects phenotypic plasticity in tree response to local environmental conditions as well as genetic differences underlying those phenotypes. In this study, we analyze phenotypic variation in leaf traits for valley oak adults sampled along three elevational transects and in...

  2. The Structure of The Extended Psychosis Phenotype in Early Adolescence-A Cross-sample Replication

    NARCIS (Netherlands)

    Wigman, Johanna T. W.; Vollebergh, Wilma A. M.; Raaijmakers, Quinten A. W.; Iedema, Jurjen; van Dorsselaer, Saskia; Ormel, Johan; Verhulst, Frank C.; van Os, Jim

    The extended psychosis phenotype, or the expression of nonclinical positive psychotic experiences, is already prevalent in adolescence and has a dose-response risk relationship with later psychotic disorder. In 2 large adolescent general population samples (n = 5422 and n = 2230), prevalence and

  3. Prognosis of complicated clinical course of varicose veins of lower extremities on the basis of analysis of phenotypic characteristics of connective tissue dysplasia

    Directory of Open Access Journals (Sweden)

    Tsarev О.А.

    2015-12-01

    Full Text Available Aim: to identify the phenotypic characteristics of indeterminate connective tissue dysplasia, which help to predict the progression of varicose veins of lower extremities and disease recurrence after surgery. Material and Methods. The long-term results of surgical treatment of 60 patients with varicose veins of lower extremities in a 5-year period after phlebectomy were analyzed. The phenotypic characteristics of indeterminate connective tissue dysplasia were researched. 24 patients had recurrence of varicose veins of lower extremities associated with disease progression; 36 patients did not have recurrence of varicose veins of lower extremities. Results. All the patients demonstrated the signs of indeterminate connective tissue dysplasia, whereas their frequency was different. There were specified nine phenotypic characteristics of indeterminate connective tissue dysplasia, which were significantly more frequent for patients with recurrence of varicose vein disease of lower extremities: 1 postural abnormality, 2 flat foot, 3 skin pallor, 4 hyperextension of skin, 5 positive "wrist test", 6 positive "pollex test", 7 diastasis recti abdominis, 8 myopia, 9 hematomas which form quickly. Conclusion. The determined sum of phenotypic characters of indeterminate connective tissue dysplasia allows to predict progression of varicose vein disease of lower extremities, and offers new opportunities for improving the results of surgical treatment via developing special therapeutic measures aimed at improving lifestyle and dysplasia treatment.

  4. SAIL—a software system for sample and phenotype availability across biobanks and cohorts

    Science.gov (United States)

    Gostev, Mikhail; Fernandez-Banet, Julio; Rung, Johan; Dietrich, Joern; Prokopenko, Inga; Ripatti, Samuli; McCarthy, Mark I.; Brazma, Alvis; Krestyaninova, Maria

    2011-01-01

    Summary: The Sample avAILability system—SAIL—is a web based application for searching, browsing and annotating biological sample collections or biobank entries. By providing individual-level information on the availability of specific data types (phenotypes, genetic or genomic data) and samples within a collection, rather than the actual measurement data, resource integration can be facilitated. A flexible data structure enables the collection owners to provide descriptive information on their samples using existing or custom vocabularies. Users can query for the available samples by various parameters combining them via logical expressions. The system can be scaled to hold data from millions of samples with thousands of variables. Availability: SAIL is available under Aferro-GPL open source license: https://github.com/sail. Contact: gostev@ebi.ac.uk, support@simbioms.org Supplementary information: Supplementary data are available at Bioinformatics online and from http://www.simbioms.org. PMID:21169373

  5. SAIL--a software system for sample and phenotype availability across biobanks and cohorts.

    Science.gov (United States)

    Gostev, Mikhail; Fernandez-Banet, Julio; Rung, Johan; Dietrich, Joern; Prokopenko, Inga; Ripatti, Samuli; McCarthy, Mark I; Brazma, Alvis; Krestyaninova, Maria

    2011-02-15

    The Sample avAILability system-SAIL-is a web based application for searching, browsing and annotating biological sample collections or biobank entries. By providing individual-level information on the availability of specific data types (phenotypes, genetic or genomic data) and samples within a collection, rather than the actual measurement data, resource integration can be facilitated. A flexible data structure enables the collection owners to provide descriptive information on their samples using existing or custom vocabularies. Users can query for the available samples by various parameters combining them via logical expressions. The system can be scaled to hold data from millions of samples with thousands of variables. SAIL is available under Aferro-GPL open source license: https://github.com/sail.

  6. The Structure of The Extended Psychosis Phenotype in Early Adolescence—A Cross-sample Replication

    Science.gov (United States)

    Wigman, Johanna T. W.; Vollebergh, Wilma A. M.; Raaijmakers, Quinten A. W.; Iedema, Jurjen; van Dorsselaer, Saskia; Ormel, Johan; Verhulst, Frank C.; van Os, Jim

    2011-01-01

    The extended psychosis phenotype, or the expression of nonclinical positive psychotic experiences, is already prevalent in adolescence and has a dose-response risk relationship with later psychotic disorder. In 2 large adolescent general population samples (n = 5422 and n = 2230), prevalence and structure of the extended psychosis phenotype was investigated. Positive psychotic experiences, broadly defined, were reported by the majority of adolescents. Exploratory analysis with Structural Equation Modelling (Exploratory Factor Analysis followed by Confirmatory Factor Analysis [CFA]) in sample 1 suggested that psychotic experiences were best represented by 5 underlying dimensions; CFA in sample 2 provided a replication of this model. Dimensions were labeled Hallucinations, Delusions, Paranoia, Grandiosity, and Paranormal beliefs. Prevalences differed strongly, Hallucinations having the lowest and Paranoia having the highest rates. Girls reported more experiences on all dimensions, except Grandiosity, and from age 12 to 16 years rates increased. Hallucinations, Delusions, and Paranoia, but not Grandiosity and Paranormal beliefs, were associated with distress and general measures of psychopathology. Thus, only some of the dimensions of the extended psychosis phenotype in young people may represent a continuum with more severe psychopathology and predict later psychiatric disorder. PMID:20044595

  7. A genome-wide study reveals rare CNVs exclusive to extreme phenotypes of Alzheimer disease.

    Science.gov (United States)

    Rovelet-Lecrux, Anne; Legallic, Solenn; Wallon, David; Flaman, Jean-Michel; Martinaud, Olivier; Bombois, Stéphanie; Rollin-Sillaire, Adeline; Michon, Agnès; Le Ber, Isabelle; Pariente, Jérémie; Puel, Michèle; Paquet, Claire; Croisile, Bernard; Thomas-Antérion, Catherine; Vercelletto, Martine; Lévy, Richard; Frébourg, Thierry; Hannequin, Didier; Campion, Dominique

    2012-06-01

    Studying rare extreme forms of Alzheimer disease (AD) may prove to be a useful strategy in identifying new genes involved in monogenic determinism of AD. Amyloid precursor protein (APP), PSEN1, and PSEN2 mutations account for only 85% of autosomal dominant early-onset AD (ADEOAD) families. We hypothesised that rare copy number variants (CNVs) could be involved in ADEOAD families without mutations in known genes, as well as in rare sporadic young-onset AD cases. Using high-resolution array comparative genomic hybridisation, we assessed the presence of rare CNVs in 21 unrelated ADEOAD cases, having no alteration on known genes, and 12 sporadic AD cases, with an age of onset younger than 55 years. The analysis revealed the presence of 7 singleton CNVs (4 in ADEOAD and 3 in sporadic cases) absent in 1078 controls and 912 late-onset AD cases. Strikingly, 4 out of 7 rearrangements target genes (KLK6, SLC30A3, MEOX2, and FPR2) encoding proteins that are tightly related to amyloid-β peptide metabolism or signalling. Although these variants are individually rare and restricted to particular subgroups of patients, these findings support the causal role, in human pathology, of a set of genes coding for molecules suspected for a long time to modify Aβ metabolism or signalling, and for which animal or cellular models have already been developed.

  8. Gastric extremely well differentiated adenocarcinoma of gastric phenotype: as a gastric counterpart of adenoma malignum of the uterine cervix

    Directory of Open Access Journals (Sweden)

    Ae Lee Won

    2005-05-01

    Full Text Available Abstract Background Most of gastric adenocarcinoma can be simply diagnosed by microscopic examination of biopsy specimen. Rarely the structural and cellular atypia of tumor cells is too insignificant to discriminate from benign foveolar epithelium. Case presentation A 67-year-old male presented with a gastric mass incidentally found on the abdominal computed tomography (CT for routine medical examination. Gastric endoscopic examination revealed a huge fungating mass at the cardia and mucosal biopsy was performed. Microscopically the biopsy specimen showed proliferation of bland looking foveolar epithelia in the inflammatory background and diagnosed as foveolar epithelial hyperplasia. Because the clinical and endoscopic features of this patient were strongly suggestive of malignancy, the patient underwent radical total gastrectomy. The resected stomach revealed a huge fungating tumor at the cardia. The cut surface of the tumor was whitish gelatinous. Microscopically the tumor was sharply demarcated from surrounding mucosa and composed of very well formed glandular structures without significant cellular atypia, which invaded into the whole layer of the gastric wall. Tumor glands were occasionally complicated or dilated, and glandular lumina were filled with abundant mucin. Immunohistochemically the tumor cells revealed no overexpression of p53 protein but high Ki-67 labeling index. The tumor cells and intraluminal mucin were diffusely expressed MUC1 and MUC5AC and only focally expressed MUC2. On abdominal CT taken after 12 months demonstrated peritoneal carcinomatosis and multiple metastatic foci in the lung. Conclusion The clinicopathologic profiles of gastric extremely well differentiated adenocarcinoma of gastric phenotype include cardiac location, fungating gross type, very similar histology to foveolar epithelial hyperplasia, foveolar mucin phenotype, lack of p53 overexpressoin and high proliferative index.

  9. Limit theory for the sample autocorrelations and extremes of a GARCH (1,1) process

    NARCIS (Netherlands)

    Mikosch, T; Starica, C

    2000-01-01

    The asymptotic theory for the sample autocorrelations and extremes of a GARCH(I, 1) process is provided. Special attention is given to the case when the sum of the ARCH and GARCH parameters is close to 1, that is, when one is close to an infinite Variance marginal distribution. This situation has

  10. Unmanned Aerial System (UAS)-based phenotyping of soybean using multi-sensor data fusion and extreme learning machine

    Science.gov (United States)

    Maimaitijiang, Maitiniyazi; Ghulam, Abduwasit; Sidike, Paheding; Hartling, Sean; Maimaitiyiming, Matthew; Peterson, Kyle; Shavers, Ethan; Fishman, Jack; Peterson, Jim; Kadam, Suhas; Burken, Joel; Fritschi, Felix

    2017-12-01

    Estimating crop biophysical and biochemical parameters with high accuracy at low-cost is imperative for high-throughput phenotyping in precision agriculture. Although fusion of data from multiple sensors is a common application in remote sensing, less is known on the contribution of low-cost RGB, multispectral and thermal sensors to rapid crop phenotyping. This is due to the fact that (1) simultaneous collection of multi-sensor data using satellites are rare and (2) multi-sensor data collected during a single flight have not been accessible until recent developments in Unmanned Aerial Systems (UASs) and UAS-friendly sensors that allow efficient information fusion. The objective of this study was to evaluate the power of high spatial resolution RGB, multispectral and thermal data fusion to estimate soybean (Glycine max) biochemical parameters including chlorophyll content and nitrogen concentration, and biophysical parameters including Leaf Area Index (LAI), above ground fresh and dry biomass. Multiple low-cost sensors integrated on UASs were used to collect RGB, multispectral, and thermal images throughout the growing season at a site established near Columbia, Missouri, USA. From these images, vegetation indices were extracted, a Crop Surface Model (CSM) was advanced, and a model to extract the vegetation fraction was developed. Then, spectral indices/features were combined to model and predict crop biophysical and biochemical parameters using Partial Least Squares Regression (PLSR), Support Vector Regression (SVR), and Extreme Learning Machine based Regression (ELR) techniques. Results showed that: (1) For biochemical variable estimation, multispectral and thermal data fusion provided the best estimate for nitrogen concentration and chlorophyll (Chl) a content (RMSE of 9.9% and 17.1%, respectively) and RGB color information based indices and multispectral data fusion exhibited the largest RMSE 22.6%; the highest accuracy for Chl a + b content estimation was

  11. Cherenkov radiation effects on counting efficiency in extremely quenched liquid scintillation samples

    International Nuclear Information System (INIS)

    Grau Carles, A.; Grau Malonda, A.; Rodriguez Barquero, L.

    1993-01-01

    The CIEMAT/NIST tracer method has successfully standardized nuclides with diverse quench values and decay schemes in liquid scintillation counting. However, the counting efficiency is computed inaccurately for extremely quenched samples. This article shows that when samples are extremely quenched, the counting efficiency in high-energy beta-ray nuclides depends principally on the Cherenkov effect. A new technique is described for quench determination, which makes the measurement of counting efficiency possible when scintillation counting approaches zero. A new efficiency computation model for pure beta-ray nuclides is also described. The results of the model are tested experimentally for 89 Sr, 90 Y, 36 Cl and 204 Tl nuclides with independence of the quench level. (orig.)

  12. Genomic Selection Using Extreme Phenotypes and Pre-Selection of SNPs in Large Yellow Croaker (Larimichthys crocea).

    Science.gov (United States)

    Dong, Linsong; Xiao, Shijun; Chen, Junwei; Wan, Liang; Wang, Zhiyong

    2016-10-01

    Genomic selection (GS) is an effective method to improve predictive accuracies of genetic values. However, high cost in genotyping will limit the application of this technology in some species. Therefore, it is necessary to find some methods to reduce the genotyping costs in genomic selection. Large yellow croaker is one of the most commercially important marine fish species in southeast China and Eastern Asia. In this study, genotyping-by-sequencing was used to construct the libraries for the NGS sequencing and find 29,748 SNPs in the genome. Two traits, eviscerated weight (EW) and the ratio between eviscerated weight and whole body weight (REW), were chosen to study. Two strategies to reduce the costs were proposed as follows: selecting extreme phenotypes (EP) for genotyping in reference population or pre-selecting SNPs to construct low-density marker panels in candidates. Three methods of pre-selection of SNPs, i.e., pre-selecting SNPs by absolute effects (SE), by single marker analysis (SMA), and by fixed intervals of sequence number (EL), were studied. The results showed that using EP was a feasible method to save the genotyping costs in reference population. Heritability did not seem to have obvious influences on the predictive abilities estimated by EP. Using SMA was the most feasible method to save the genotyping costs in candidates. In addition, the combination of EP and SMA in genomic selection also showed good results, especially for trait of REW. We also described how to apply the new methods in genomic selection and compared the genotyping costs before and after using the new methods. Our study may not only offer a reference for aquatic genomic breeding but also offer a reference for genomic prediction in other species including livestock and plants, etc.

  13. Manipulation of Samples at Extreme Temperatures for Fast in-situ Synchrotron Measurements

    Energy Technology Data Exchange (ETDEWEB)

    Weber, Richard [Materials Development, Inc., Arlington Heights, IL (United States)

    2016-04-22

    An aerodynamic sample levitation system with laser beam heating was integrated with the APS beamlines 6 ID-D, 11 ID-C and 20 BM-B. The new capability enables in-situ measurements of structure and XANES at extreme temperatures (300-3500 °C) and in conditions that completely avoid contact with container surfaces. In addition to maintaining a high degree of sample purity, the use of aerodynamic levitation enables deep supercooling and greatly enhanced glass formation from a wide variety of melts and liquids. Development and integration of controlled extreme sample environments and new measurement techniques is an important aspect of beamline operations and user support. Processing and solidifying liquids is a critical value-adding step in manufacturing semiconductors, optical materials, metals and in the operation of many energy conversion devices. Understanding structural evolution is of fundamental importance in condensed materials, geology, and biology. The new capability provides unique possibilities for materials research and helps to develop and maintain a competitive materials manufacturing and energy utilization industry. Test samples were used to demonstrate key features of the capability including experiments on hot crystalline materials, liquids at temperatures from about 500 to 3500 °C. The use of controlled atmospheres using redox gas mixtures enabled in-situ changes in the oxidation states of cations in melts. Significant innovations in this work were: (i) Use of redox gas mixtures to adjust the oxidation state of cations in-situ (ii) Operation with a fully enclosed system suitable for work with nuclear fuel materials (iii) Making high quality high energy in-situ x-ray diffraction measurements (iv) Making high quality in-situ XANES measurements (v) Publishing high impact results (vi) Developing independent funding for the research on nuclear materials This SBIR project work led to a commercial instrument product for the niche market of processing and

  14. Power and sample size calculations in the presence of phenotype errors for case/control genetic association studies

    Directory of Open Access Journals (Sweden)

    Finch Stephen J

    2005-04-01

    Full Text Available Abstract Background Phenotype error causes reduction in power to detect genetic association. We present a quantification of phenotype error, also known as diagnostic error, on power and sample size calculations for case-control genetic association studies between a marker locus and a disease phenotype. We consider the classic Pearson chi-square test for independence as our test of genetic association. To determine asymptotic power analytically, we compute the distribution's non-centrality parameter, which is a function of the case and control sample sizes, genotype frequencies, disease prevalence, and phenotype misclassification probabilities. We derive the non-centrality parameter in the presence of phenotype errors and equivalent formulas for misclassification cost (the percentage increase in minimum sample size needed to maintain constant asymptotic power at a fixed significance level for each percentage increase in a given misclassification parameter. We use a linear Taylor Series approximation for the cost of phenotype misclassification to determine lower bounds for the relative costs of misclassifying a true affected (respectively, unaffected as a control (respectively, case. Power is verified by computer simulation. Results Our major findings are that: (i the median absolute difference between analytic power with our method and simulation power was 0.001 and the absolute difference was no larger than 0.011; (ii as the disease prevalence approaches 0, the cost of misclassifying a unaffected as a case becomes infinitely large while the cost of misclassifying an affected as a control approaches 0. Conclusion Our work enables researchers to specifically quantify power loss and minimum sample size requirements in the presence of phenotype errors, thereby allowing for more realistic study design. For most diseases of current interest, verifying that cases are correctly classified is of paramount importance.

  15. Comparison of duplex PCR and phenotypic analysis in differentiating Candida dubliniensis from Candida albicans from oral samples.

    Science.gov (United States)

    Sampath, Asanga; Weerasekera, Manjula; Dilhari, Ayomi; Gunasekara, Chinthika; Bulugahapitiya, Uditha; Fernando, Neluka; Samaranayake, Lakshman

    2017-12-01

    Candida dubliniensis shares a wide range of phenotypic characteristics with Candida albicans including a common trait called germ tube positivity. Hence, laboratory differentiation of these two species is cumbersome. Duplex PCR analyses for C. albicans and C. dubliniensis was performed directly on DNA extracted from a total of 122 germ tube positive isolates derived from 100 concentrated oral rinse samples from a random cohort of diabetics attending a clinic in Sri Lanka. These results were confirmed by DNA sequencing of internal transcribed spacer (ITS) region of rDNA of the yeasts. Performance efficacy of duplex PCR was then compared with phenotypic identification using a standard battery of phenotypic tests. Of the 122 germ tube positive isolates three were identified by duplex PCR as C. dubliniensis and the remainder as C. albicans. On the contrary, when the standard phenotypic tests, sugar assimilation and chlamydospore formation, were used to differentiate the two species 13 germ tube positive isolates were erroneously identified as C. dubliniensis. Duplex PCR was found to be rapid, sensitive and more specific than phenotypic identification methods in discriminating C. dubliniensis from C. albicans. This is also the first report on the oral carriage of C. dubliniensis in a Sri Lankan population.

  16. Optimization of multi-channel neutron focusing guides for extreme sample environments

    International Nuclear Information System (INIS)

    Di Julio, D D; Lelièvre-Berna, E; Andersen, K H; Bentley, P M; Courtois, P

    2014-01-01

    In this work, we present and discuss simulation results for the design of multichannel neutron focusing guides for extreme sample environments. A single focusing guide consists of any number of supermirror-coated curved outer channels surrounding a central channel. Furthermore, a guide is separated into two sections in order to allow for extension into a sample environment. The performance of a guide is evaluated through a Monte-Carlo ray tracing simulation which is further coupled to an optimization algorithm in order to find the best possible guide for a given situation. A number of population-based algorithms have been investigated for this purpose. These include particle-swarm optimization, artificial bee colony, and differential evolution. The performance of each algorithm and preliminary results of the design of a multi-channel neutron focusing guide using these methods are described. We found that a three-channel focusing guide offered the best performance, with a gain factor of 2.4 compared to no focusing guide, for the design scenario investigated in this work.

  17. THE ELM SURVEY. I. A COMPLETE SAMPLE OF EXTREMELY LOW-MASS WHITE DWARFS

    International Nuclear Information System (INIS)

    Brown, Warren R.; Kilic, Mukremin; Kenyon, Scott J.; Prieto, Carlos Allende

    2010-01-01

    We analyze radial velocity observations of the 12 extremely low-mass (ELM), with ≤0.25 M sun , white dwarfs (WDs) in the MMT Hypervelocity Star Survey. Eleven of the twelve WDs are binaries with orbital periods shorter than 14 hr; the one non-variable WD is possibly a pole-on system among our non-kinematically selected targets. Our sample is unique: it is complete in a well-defined range of apparent magnitude and color. The orbital mass functions imply that the unseen companions are most likely other WDs, although neutron star companions cannot be excluded. Six of the eleven systems with orbital solutions will merge within a Hubble time due to the loss of angular momentum through gravitational wave radiation. The quickest merger is J0923+3028, a g = 15.7 ELM WD binary with a 1.08 hr orbital period and a ≤130 Myr merger time. The chance of a supernova Ia event among our ELM WDs is only 1%-7%, however. Three binary systems (J0755+4906, J1233+1602, and J2119-0018) have extreme mass ratios and will most likely form stable mass-transfer AM CVn systems. Two of these objects, SDSS J1233+1602 and J2119-0018, are the lowest surface gravity WDs ever found; both show Ca II absorption likely from accretion of circumbinary material. We predict that at least one of our WDs is an eclipsing detached double WD system, important for constraining helium core WD models.

  18. Evaluation of a lateral flow-based technology card for blood typing using a simplified protocol in a model of extreme blood sampling conditions.

    Science.gov (United States)

    Clavier, Benoît; Pouget, Thomas; Sailliol, Anne

    2018-02-01

    Life-threatening situations requiring blood transfusion under extreme conditions or in remote and austere locations, such as the battlefield or in traffic accidents, would benefit from reliable blood typing practices that are easily understood by a nonscientist or nonlaboratory technician and provide quick results. A simplified protocol was developed for the lateral flow-based device MDmulticard ABO-D-Rh subgroups-K. Its performance was compared to a reference method (PK7300, Beckman Coulter) in native blood samples from donors. The method was tested on blood samples stressed in vitro as a model of hemorrhage cases (through hemodilution using physiologic serum) and dehydration (through hemoconcentration by removing an aliquot of plasma after centrifugation), respectively. A total of 146 tests were performed on 52 samples; 126 in the hemodilution group (42 for each native, diluted 1/2, and diluted 1/4 samples) and 20 in the hemoconcentration group (10 for each native and 10% concentrated samples). Hematocrit in the tested samples ranged from 9.8% to 57.6% while hemoglobin levels ranged from 3.2 to 20.1 g/dL. The phenotype profile detected with the MDmulticard using the simplified protocol resulted in 22 A, seven B, 20 O, and three AB, of which nine were D- and five were Kell positive. No discrepancies were found with respect to the results obtained with the reference method. The simplified protocol for MDmulticard use could be considered a reliable method for blood typing in extreme environment or emergency situations, worsened by red blood cell dilution or concentration. © 2017 AABB.

  19. Phenotypic and genotypic evaluation of 18 Nocardia isolates from human clinical samples in Mexico.

    Science.gov (United States)

    Sánchez-Herrera, K; Sandoval, H; Couble, A; Mouniee, D; Ramírez-Durán, N; Uzcategui de Morillo, M; Serrano, J A; Bergeron, E; Boiron, P; Rodríguez-Nava, V

    2012-03-01

    Mexico has the largest number of clinical cases of actinomycetoma in North and South America. Species originally identified by less specific methods have been recently reclassified as other known species or as new species. To assess, by 16S rRNA gene sequencing and phenotypic methods, the species distribution of 18 human clinical isolates originally identified as N. brasiliensis, some of them isolated between 1947 and 1959 in Mexico City. Clinical isolates came from the Hospital General, "Dr. Manuel Gea Gonzalez", and Instituto Nacional de Diagnóstico y Referencia Epidemiológica (INDRE) in Mexico, D.F. The strains used in this study included 15 clinical strains isolated between 1947 and 1959 that were originally identified as N. brasiliensis and three more strains obtained in 2007 identified as Nocardia spp. The isolates were identified genotypically by sequencing the 16S rRNA gene, and their phenotypic profiles were obtained with the API Coryne(®) system. Antibiotic susceptibility patterns were tested according to the protocol of the Comité de l'antibiogramme de la Société française de microbiologie[4]. According to 16S rRNA gene, sequencing were identified among 18 human clinical isolates as Nocardia farcinica (n=11) and Nocardia brasiliensis (n=7). A high number of the strains were susceptible to the majority of the antibiotics tested. The phenotypic profiles of the strains were quite uniform for N. farcinica and some variability was observed for N. brasiliensis strains. N. farcinica was the most prevalent species identified. Modern methodologies should be applied in clinical laboratories to accurately identify etiological agents. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  20. A Unique Sample of Extreme-BCG Clusters at 0.2 < z < 0.5

    Science.gov (United States)

    Garmire, Gordon

    2017-09-01

    The recently-discovered Phoenix cluster harbors the most extreme BCG in the known universe. Despite the cluster's high mass and X-ray luminosity, it was consistently identified by surveys as an isolated AGN, due to the bright central point source and the compact cool core. Armed with hindsight, we have undertaken an all-sky survey based on archival X-ray, OIR, and radio data to identify other similarly-extreme systems that were likewise missed. A pilot study demonstrated that this strategy works, leading to the discovery of a new, massive cluster at z 0.2 which was missed by previous X-ray surveys due to the presence of a bright central QSO. We propose here to observe 6 new clusters from our complete northern-sky survey, which harbor some of the most extreme central galaxies known.

  1. Evaluation of limited sampling models for prediction of oral midazolam AUC for CYP3A phenotyping and drug interaction studies.

    Science.gov (United States)

    Mueller, Silke C; Drewelow, Bernd

    2013-05-01

    The area under the concentration-time curve (AUC) after oral midazolam administration is commonly used for cytochrome P450 (CYP) 3A phenotyping studies. The aim of this investigation was to evaluate a limited sampling strategy for the prediction of AUC with oral midazolam. A total of 288 concentration-time profiles from 123 healthy volunteers who participated in four previously performed drug interaction studies with intense sampling after a single oral dose of 7.5 mg midazolam were available for evaluation. Of these, 45 profiles served for model building, which was performed by stepwise multiple linear regression, and the remaining 243 datasets served for validation. Mean prediction error (MPE), mean absolute error (MAE) and root mean squared error (RMSE) were calculated to determine bias and precision The one- to four-sampling point models with the best coefficient of correlation were the one-sampling point model (8 h; r (2) = 0.84), the two-sampling point model (0.5 and 8 h; r (2) = 0.93), the three-sampling point model (0.5, 2, and 8 h; r (2) = 0.96), and the four-sampling point model (0.5,1, 2, and 8 h; r (2) = 0.97). However, the one- and two-sampling point models were unable to predict the midazolam AUC due to unacceptable bias and precision. Only the four-sampling point model predicted the very low and very high midazolam AUC of the validation dataset with acceptable precision and bias. The four-sampling point model was also able to predict the geometric mean ratio of the treatment phase over the baseline (with 90 % confidence interval) results of three drug interaction studies in the categories of strong, moderate, and mild induction, as well as no interaction. A four-sampling point limited sampling strategy to predict the oral midazolam AUC for CYP3A phenotyping is proposed. The one-, two- and three-sampling point models were not able to predict midazolam AUC accurately.

  2. Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus

    Science.gov (United States)

    Jacquemont, Sébastien; Reymond, Alexandre; Zufferey, Flore; Harewood, Louise; Walters, Robin G.; Kutalik, Zoltán; Martinet, Danielle; Shen, Yiping; Valsesia, Armand; Beckmann, Noam D.; Thorleifsson, Gudmar; Belfiore, Marco; Bouquillon, Sonia; Campion, Dominique; De Leeuw, Nicole; De Vries, Bert B. A.; Esko, Tõnu; Fernandez, Bridget A.; Fernández-Aranda, Fernando; Fernández-Real, José Manuel; Gratacòs, Mònica; Guilmatre, Audrey; Hoyer, Juliane; Jarvelin, Marjo-Riitta; Kooy, Frank R.; Kurg, Ants; Le Caignec, Cédric; Männik, Katrin; Platt, Orah S.; Sanlaville, Damien; Van Haelst, Mieke M.; Villatoro Gomez, Sergi; Walha, Faida; Wu, Bai-Lin; Yu, Yongguo; Aboura, Azzedine; Addor, Marie-Claude; Alembik, Yves; Antonarakis, Stylianos E.; Arveiler, Benoît; Barth, Magalie; Bednarek, Nathalie; Béna, Frédérique; Bergmann, Sven; Beri, Mylène; Bernardini, Laura; Blaumeiser, Bettina; Bonneau, Dominique; Bottani, Armand; Boute, Odile; Brunner, Han G.; Cailley, Dorothée; Callier, Patrick; Chiesa, Jean; Chrast, Jacqueline; Coin, Lachlan; Coutton, Charles; Cuisset, Jean-Marie; Cuvellier, Jean-Christophe; David, Albert; De Freminville, Bénédicte; Delobel, Bruno; Delrue, Marie-Ange; Demeer, Bénédicte; Descamps, Dominique; Didelot, Gérard; Dieterich, Klaus; Disciglio, Vittoria; Doco-Fenzy, Martine; Drunat, Séverine; Duban-Bedu, Bénédicte; Dubourg, Christèle; El-Sayed Moustafa, Julia S.; Elliott, Paul; Faas, Brigitte H. W.; Faivre, Laurence; Faudet, Anne; Fellmann, Florence; Ferrarini, Alessandra; Fisher, Richard; Flori, Elisabeth; Forer, Lukas; Gaillard, Dominique; Gerard, Marion; Gieger, Christian; Gimelli, Stefania; Gimelli, Giorgio; Grabe, Hans J.; Guichet, Agnès; Guillin, Olivier; Hartikainen, Anna-Liisa; Heron, Délphine; Hippolyte, Loyse; Holder, Muriel; Homuth, Georg; Isidor, Bertrand; Jaillard, Sylvie; Jaros, Zdenek; Jiménez-Murcia, Susana; Joly Helas, Géraldine; Jonveaux, Philippe; Kaksonen, Satu; Keren, Boris; Kloss-Brandstätter, Anita; Knoers, Nine V. A. M.; Koolen, David A.; Kroisel, Peter M.; Kronenberg, Florian; Labalme, Audrey; Landais, Emilie; Lapi, Elisabetta; Layet, Valérie; Legallic, Solenn; Leheup, Bruno; Leube, Barbara; Lewis, Suzanne; Lucas, Josette; Macdermot, Kay D.; Magnusson, Pall; Marshall, Christian R.; Mathieu-Dramard, Michèle; Mccarthy, Mark I.; Meitinger, Thomas; Antonietta Mencarelli, Maria; Merla, Giuseppe; Moerman, Alexandre; Mooser, Vincent; Morice-Picard, Fanny; Mucciolo, Mafalda; Nauck, Matthias; Coumba Ndiaye, Ndeye; Nordgren, Ann; Pasquier, Laurent; Petit, Florence; Pfundt, Rolph; Plessis, Ghislaine; Rajcan-Separovic, Evica; Paolo Ramelli, Gian; Rauch, Anita; Ravazzolo, Roberto; Reis, Andre; Renieri, Alessandra; Richart, Cristobal; Ried, Janina S.; Rieubland, Claudine; Roberts, Wendy; Roetzer, Katharina M.; Rooryck, Caroline; Rossi, Massimiliano; Saemundsen, Evald; Satre, Véronique; Schurmann, Claudia; Sigurdsson, Engilbert; Stavropoulos, Dimitri J.; Stefansson, Hreinn; Tengström, Carola; Thorsteinsdóttir, Unnur; Tinahones, Francisco J.; Touraine, Renaud; Vallée, Louis; Van Binsbergen, Ellen; Van Der Aa, Nathalie; Vincent-Delorme, Catherine; Visvikis-Siest, Sophie; Vollenweider, Peter; Völzke, Henry; Vulto-Van Silfhout, Anneke T.; Waeber, Gérard; Wallgren-Pettersson, Carina; Witwicki, Robert M.; Zwolinksi, Simon; Andrieux, Joris; Estivill, Xavier; Gusella, James F.; Gustafsson, Omar; Metspalu, Andres; Scherer, Stephen W.; Stefansson, Kari; Blakemore, Alexandra I. F.; Beckmann, Jacques S.; Froguel, Philippe

    2011-01-01

    Both underweight and obesity have been associated with increased mortality1,2. Underweight, defined as body mass index (BMI) ≤ 18,5 kg/m2 in adults 3 and ≤ −2 standard deviations (SD) in children4,5, is the main sign of a series of heterogeneous clinical conditions such as failure to thrive (FTT) 6–8, feeding and eating disorder and/or anorexia nervosa9,10. In contrast to obesity, few genetic variants underlying these clinical conditions have been reported 11, 12. We previously demonstrated that hemizygosity of a ~600 kb region on the short arm of chromosome 16 (chr16:29.5–30.1Mb), causes a highly-penetrant form of obesity often associated with hyperphagia and intellectual disabilities13. Here we show that the corresponding reciprocal duplication is associated with underweight. We identified 138 (132 novel cases) duplication carriers (108 unrelated carriers) from over 95,000 individuals clinically-referred for developmental or intellectual disabilities (DD/ID), psychiatric disorders or recruited from population-based cohorts. These carriers show significantly reduced postnatal weight (mean Z-score −0.6; p=4.4×10−4) and BMI (mean Z-score −0.5; p=2.0×10−3). In particular, half of the boys younger than 5 years are underweight with a probable diagnosis of FTT, while adult duplication carriers have an 8.7-fold (p=5.9×10−11; CI_95=[4.5–16.6]) increased risk of being clinically underweight. We observe a significant trend towards increased severity in males, as well as a depletion of male carriers among non-medically ascertained cases. These features are associated with an unusually high frequency of selective and restrictive feeding behaviours and a significant reduction in head circumference (mean Z-score −0.9; p=7.8×10−6). Each of the observed phenotypes is the converse of one reported in carriers of deletions at this locus, correlating with changes in transcript levels for genes mapping within the duplication but not within flanking

  3. Multivariate genetic analysis of atopy phenotypes in a selected sample of twins

    DEFF Research Database (Denmark)

    Thomsen, S F; Ulrik, C S; Kyvik, K O

    2006-01-01

    traits were estimated and latent factor models of genetic and environmental effects were fitted to the observed data using maximum likelihood methods. RESULTS: The various phenotypic correlations between wheeze, rhinitis, AHR and posSPT were all significant and ranged between 0.50 and 0.86. Traits......BACKGROUND: Atopic traits often co-occur and this can potentially be caused by common aetiological relationships between traits, i.e. a common genetic or a common environmental background. OBJECTIVE: To estimate to what extent the same genetic and environmental factors influence wheeze, rhinitis...... that showed highest genetic correlations were wheeze-rhinitis (rho(A)=0.95), wheeze-AHR (rho(A)=0.85) and rhinitis-posSPT (rho(A)=0.92), whereas lower genetic correlations were observed for rhinitis-AHR (rho(A)=0.43) and AHR-posSPT (rho(A)=0.59). Traits with a high degree of environmental sharing were...

  4. Weighted Moments Estimators of the Parameters for the Extreme Value Distribution Based on the Multiply Type II Censored Sample

    Directory of Open Access Journals (Sweden)

    Jong-Wuu Wu

    2013-01-01

    Full Text Available We propose the weighted moments estimators (WMEs of the location and scale parameters for the extreme value distribution based on the multiply type II censored sample. Simulated mean squared errors (MSEs of best linear unbiased estimator (BLUE and exact MSEs of WMEs are compared to study the behavior of different estimation methods. The results show the best estimator among the WMEs and BLUE under different combinations of censoring schemes.

  5. Identification of Candida albicans and Candida dubliniensis Species Isolated from Bronchoalveolar Lavage Samples Using Genotypic and Phenotypic Methods

    Directory of Open Access Journals (Sweden)

    Sahar Kianipour

    2018-01-01

    Full Text Available Background: Candida dubliniensis is a newly diagnosed species very similar to Candida albicans phenotypically and first discovered in the mouth of people with AIDS in 1995. Among the different phenotypic and genotypic methods, a cost-effective method should be selected which makes it possible to differentiate these similar species. Materials and Methods: Polymerase chain reaction (PCR-restriction fragment length polymorphism with MspI enzyme and the Duplex-PCR method were done by DNA extraction using boiling. The sequencing of the amplified ribosomal region was used to confirm the C. dubliniensis species. Direct examination and colony count of the yeasts were applied for bronchoalveolar lavage (BAL samples and the growth rate of the yeasts were studied at 45°C. To understand the ability formation of chlamydoconidia in yeast isolates, they were separately cultured on the sunflower seed agar, wheat flour agar, and corn meal agar media. Results: Fifty-nine (49.2% yeast colonies were identified from the total of 120 BAL specimens. Twenty-nine isolated yeasts; including 17 (58.6% of C. albicans/dubliniensis complex and 12 (41.4% of nonalbicans isolates produced pseudohypha or blastoconidia in direct smear with a mean colony count of 42000 CFU/mL. C. albicans with the frequency of 15 (42.9% were the most common isolated yeasts, whereas C. dubliniensis was identified in two nonHIV patients. Conclusion: Sequencing of the replicated gene fragment is the best method for identifying the yeasts, but the determination of the species by phenotypic methods such as the creation of chlamydoconidia in sunflower seeds agar and wheat flour agar media can be cost-effective, have sensitivity and acceptable quality.

  6. Identification of Candida albicans and Candida dubliniensis Species Isolated from Bronchoalveolar Lavage Samples Using Genotypic and Phenotypic Methods.

    Science.gov (United States)

    Kianipour, Sahar; Ardestani, Mohammad Emami; Dehghan, Parvin

    2018-01-01

    Candida dubliniensis is a newly diagnosed species very similar to Candida albicans phenotypically and first discovered in the mouth of people with AIDS in 1995. Among the different phenotypic and genotypic methods, a cost-effective method should be selected which makes it possible to differentiate these similar species. Polymerase chain reaction (PCR)-restriction fragment length polymorphism with MspI enzyme and the Duplex-PCR method were done by DNA extraction using boiling. The sequencing of the amplified ribosomal region was used to confirm the C. dubliniensis species. Direct examination and colony count of the yeasts were applied for bronchoalveolar lavage (BAL) samples and the growth rate of the yeasts were studied at 45°C. To understand the ability formation of chlamydoconidia in yeast isolates, they were separately cultured on the sunflower seed agar, wheat flour agar, and corn meal agar media. Fifty-nine (49.2%) yeast colonies were identified from the total of 120 BAL specimens. Twenty-nine isolated yeasts; including 17 (58.6%) of C. albicans / dubliniensis complex and 12 (41.4%) of nonalbicans isolates produced pseudohypha or blastoconidia in direct smear with a mean colony count of 42000 CFU/mL. C. albicans with the frequency of 15 (42.9%) were the most common isolated yeasts, whereas C. dubliniensis was identified in two nonHIV patients. Sequencing of the replicated gene fragment is the best method for identifying the yeasts, but the determination of the species by phenotypic methods such as the creation of chlamydoconidia in sunflower seeds agar and wheat flour agar media can be cost-effective, have sensitivity and acceptable quality.

  7. A random sampling approach for robust estimation of tissue-to-plasma ratio from extremely sparse data.

    Science.gov (United States)

    Chu, Hui-May; Ette, Ene I

    2005-09-02

    his study was performed to develop a new nonparametric approach for the estimation of robust tissue-to-plasma ratio from extremely sparsely sampled paired data (ie, one sample each from plasma and tissue per subject). Tissue-to-plasma ratio was estimated from paired/unpaired experimental data using independent time points approach, area under the curve (AUC) values calculated with the naïve data averaging approach, and AUC values calculated using sampling based approaches (eg, the pseudoprofile-based bootstrap [PpbB] approach and the random sampling approach [our proposed approach]). The random sampling approach involves the use of a 2-phase algorithm. The convergence of the sampling/resampling approaches was investigated, as well as the robustness of the estimates produced by different approaches. To evaluate the latter, new data sets were generated by introducing outlier(s) into the real data set. One to 2 concentration values were inflated by 10% to 40% from their original values to produce the outliers. Tissue-to-plasma ratios computed using the independent time points approach varied between 0 and 50 across time points. The ratio obtained from AUC values acquired using the naive data averaging approach was not associated with any measure of uncertainty or variability. Calculating the ratio without regard to pairing yielded poorer estimates. The random sampling and pseudoprofile-based bootstrap approaches yielded tissue-to-plasma ratios with uncertainty and variability. However, the random sampling approach, because of the 2-phase nature of its algorithm, yielded more robust estimates and required fewer replications. Therefore, a 2-phase random sampling approach is proposed for the robust estimation of tissue-to-plasma ratio from extremely sparsely sampled data.

  8. On the assessment of extremely low breakdown probabilities by an inverse sampling procedure [gaseous insulation

    DEFF Research Database (Denmark)

    Thyregod, Poul; Vibholm, Svend

    1991-01-01

    the flashover probability function and the corresponding distribution of first breakdown voltages under the inverse sampling procedure, and show how this relation may be utilized to assess the single-shot flashover probability corresponding to the observed average first breakdown voltage. Since the procedure......First breakdown voltages obtained under the inverse sampling procedure assuming a double exponential flashover probability function are discussed. An inverse sampling procedure commences the voltage application at a very low level, followed by applications at stepwise increased levels until...... is based on voltage applications in the neighbourhood of the quantile under investigation, the procedure is found to be insensitive to the underlying distributional assumptions...

  9. Measurement of extremely (2) H-enriched water samples by laser spectrometry: application to batch electrolytic concentration of environmental tritium samples.

    Science.gov (United States)

    Wassenaar, L I; Kumar, B; Douence, C; Belachew, D L; Aggarwal, P K

    2016-02-15

    Natural water samples artificially or experimentally enriched in deuterium ((2) H) at concentrations up to 10,000 ppm are required for various medical, environmental and hydrological tracer applications, but are difficult to measure using conventional stable isotope ratio mass spectrometry. Here we demonstrate that off-axis integrated cavity output (OA-ICOS) laser spectrometry, along with (2) H-enriched laboratory calibration standards and appropriate analysis templates, allows for low-cost, fast, and accurate determinations of water samples having δ(2) HVSMOW-SLAP values up to at least 57,000 ‰ (~9000 ppm) at a processing rate of 60 samples per day. As one practical application, extremely (2) H-enriched samples were measured by laser spectrometry and compared to the traditional (3) H Spike-Proxy method in order to determine tritium enrichment factors in the batch electrolysis of environmental waters. Highly (2) H-enriched samples were taken from different sets of electrolytically concentrated standards and low-level (tritium samples, and all cases returned accurate and precise initial low-level (3) H results. The ability to quickly and accurately measure extremely (2) H-enriched waters by laser spectrometry will facilitate the use of deuterium as a tracer in numerous environmental and other applications. For low-level tritium operations, this new analytical ability facilitated a 10-20 % increase in sample productivity through the elimination of spike standards and gravimetrics, and provides immediate feedback on electrolytic enrichment cell performance. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  10. A sub-sampled approach to extremely low-dose STEM

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, A. [OptimalSensing, Southlake, Texas 76092, USA; Duke University, ECE, Durham, North Carolina 27708, USA; Luzi, L. [Rice University, ECE, Houston, Texas 77005, USA; Yang, H. [Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; Kovarik, L. [Pacific NW National Laboratory, Richland, Washington 99354, USA; Mehdi, B. L. [Pacific NW National Laboratory, Richland, Washington 99354, USA; University of Liverpool, Materials Engineering, Liverpool L69 3GH, United Kingdom; Liyu, A. [Pacific NW National Laboratory, Richland, Washington 99354, USA; Gehm, M. E. [Duke University, ECE, Durham, North Carolina 27708, USA; Browning, N. D. [Pacific NW National Laboratory, Richland, Washington 99354, USA; University of Liverpool, Materials Engineering, Liverpool L69 3GH, United Kingdom

    2018-01-22

    The inpainting of randomly sub-sampled images acquired by scanning transmission electron microscopy (STEM) is an attractive method for imaging under low-dose conditions (≤ 1 e-2) without changing either the operation of the microscope or the physics of the imaging process. We show that 1) adaptive sub-sampling increases acquisition speed, resolution, and sensitivity; and 2) random (non-adaptive) sub-sampling is equivalent, but faster than, traditional low-dose techniques. Adaptive sub-sampling opens numerous possibilities for the analysis of beam sensitive materials and in-situ dynamic processes at the resolution limit of the aberration corrected microscope and is demonstrated here for the analysis of the node distribution in metal-organic frameworks (MOFs).

  11. A cross-sectional, randomized cluster sample survey of household vulnerability to extreme heat among slum dwellers in ahmedabad, india.

    Science.gov (United States)

    Tran, Kathy V; Azhar, Gulrez S; Nair, Rajesh; Knowlton, Kim; Jaiswal, Anjali; Sheffield, Perry; Mavalankar, Dileep; Hess, Jeremy

    2013-06-18

    Extreme heat is a significant public health concern in India; extreme heat hazards are projected to increase in frequency and severity with climate change. Few of the factors driving population heat vulnerability are documented, though poverty is a presumed risk factor. To facilitate public health preparedness, an assessment of factors affecting vulnerability among slum dwellers was conducted in summer 2011 in Ahmedabad, Gujarat, India. Indicators of heat exposure, susceptibility to heat illness, and adaptive capacity, all of which feed into heat vulnerability, was assessed through a cross-sectional household survey using randomized multistage cluster sampling. Associations between heat-related morbidity and vulnerability factors were identified using multivariate logistic regression with generalized estimating equations to account for clustering effects. Age, preexisting medical conditions, work location, and access to health information and resources were associated with self-reported heat illness. Several of these variables were unique to this study. As sociodemographics, occupational heat exposure, and access to resources were shown to increase vulnerability, future interventions (e.g., health education) might target specific populations among Ahmedabad urban slum dwellers to reduce vulnerability to extreme heat. Surveillance and evaluations of future interventions may also be worthwhile.

  12. Report of the advisory group meeting on elemental analysis of extremely small samples

    International Nuclear Information System (INIS)

    2002-01-01

    This publication contains summary of discussions held at the meeting with brief description and comparative characteristics of most common nuclear analytical techniques used for analysis of very small samples as well as the conclusions of the meeting. Some aspect of reference materials and quality control are also discussed. The publication also contains individual contributions made by the participants, each of these papers haven provided with an abstract and indexed separately

  13. Effects of sample size on estimation of rainfall extremes at high temperatures

    Science.gov (United States)

    Boessenkool, Berry; Bürger, Gerd; Heistermann, Maik

    2017-09-01

    High precipitation quantiles tend to rise with temperature, following the so-called Clausius-Clapeyron (CC) scaling. It is often reported that the CC-scaling relation breaks down and even reverts for very high temperatures. In our study, we investigate this reversal using observational climate data from 142 stations across Germany. One of the suggested meteorological explanations for the breakdown is limited moisture supply. Here we argue that, instead, it could simply originate from undersampling. As rainfall frequency generally decreases with higher temperatures, rainfall intensities as dictated by CC scaling are less likely to be recorded than for moderate temperatures. Empirical quantiles are conventionally estimated from order statistics via various forms of plotting position formulas. They have in common that their largest representable return period is given by the sample size. In small samples, high quantiles are underestimated accordingly. The small-sample effect is weaker, or disappears completely, when using parametric quantile estimates from a generalized Pareto distribution (GPD) fitted with L moments. For those, we obtain quantiles of rainfall intensities that continue to rise with temperature.

  14. Effects of sample size on estimation of rainfall extremes at high temperatures

    Directory of Open Access Journals (Sweden)

    B. Boessenkool

    2017-09-01

    Full Text Available High precipitation quantiles tend to rise with temperature, following the so-called Clausius–Clapeyron (CC scaling. It is often reported that the CC-scaling relation breaks down and even reverts for very high temperatures. In our study, we investigate this reversal using observational climate data from 142 stations across Germany. One of the suggested meteorological explanations for the breakdown is limited moisture supply. Here we argue that, instead, it could simply originate from undersampling. As rainfall frequency generally decreases with higher temperatures, rainfall intensities as dictated by CC scaling are less likely to be recorded than for moderate temperatures. Empirical quantiles are conventionally estimated from order statistics via various forms of plotting position formulas. They have in common that their largest representable return period is given by the sample size. In small samples, high quantiles are underestimated accordingly. The small-sample effect is weaker, or disappears completely, when using parametric quantile estimates from a generalized Pareto distribution (GPD fitted with L moments. For those, we obtain quantiles of rainfall intensities that continue to rise with temperature.

  15. Short communication prevalence of susceptibility to etravirine by genotype and phenotype in samples received for routine HIV type 1 resistance testing in the United States.

    Science.gov (United States)

    Picchio, Gaston; Vingerhoets, Johan; Tambuyzer, Lotke; Coakley, Eoin; Haddad, Mojgan; Witek, James

    2011-12-01

    Abstract The prevalence of susceptibility to etravirine was investigated among clinical samples submitted for routine clinical testing in the United States using two separate weighted genotypic scoring systems. The presence of etravirine mutations and susceptibility to etravirine by phenotype of clinical samples from HIV-1-infected patients, submitted to Monogram Biosciences for routine resistance testing between June 2008 and June 2009, were analyzed. Susceptibility by genotype was determined using the Monogram and Tibotec etravirine-weighted genotypic scoring systems, with scores of ≤3 and ≤2, respectively, indicating full susceptibility. Susceptibility by phenotype was determined using the PhenoSense HIV assay, with lower and higher clinical cut-offs of 2.9 and 10, respectively. The frequency of individual etravirine mutations and the impact of the K103N mutation on susceptibility to etravirine by genotype were also determined. Among the 5482 samples with ≥1 defined nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations associated with resistance, 67% were classed as susceptible to etravirine by genotype by both scoring systems. Susceptibility to etravirine by phenotype was higher (76%). The proportion of first-generation NNRTI-resistant samples with (n=3598) and without (n=1884) K103N with susceptibility to etravirine by genotype was 77% and 49%, respectively. Among samples susceptible to first-generation NNRTIs (n=9458), >99% of samples were susceptible to etravirine by phenotype (FC <2.9); the remaining samples had FC ≥2.9-10. In summary, among samples submitted for routine clinical testing in the United States, a high proportion of samples with first-generation NNRTI resistance was susceptible to etravirine by genotype and phenotype. A higher proportion of NNRTI-resistant samples with K103N than without was susceptible to etravirine.

  16. exTAS - next-generation TAS for small samples and extreme conditions

    International Nuclear Information System (INIS)

    Kulda, J.; Hiess, A.

    2011-01-01

    The currently used implementation of horizontally and vertically focusing optics in three-axis spectrometers (TAS) permits efficient studies of excitations in sub-cm 3 - sized single crystals]. With the present proposal we wish to stimulate a further paradigm shift into the domain of mm 3 -sized samples. exTAS combines highly focused mm-sized focal spots, boosting the sensitivity limits, with a spectrometer layout down-scaled to a table-top size to provide high flexibility in optimizing acceptance angles and to achieve sub-millimeter positioning accuracy. (authors)

  17. Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults.

    Directory of Open Access Journals (Sweden)

    Fang Chen

    Full Text Available Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419, we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010, and estimated an additive heritability of 44.7% (se: 3.7% for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1 whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2 whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the

  18. Preliminary Blood Pressure Screening in a Representative Sample of Extremely Obese Kuwaiti Adolescents

    Directory of Open Access Journals (Sweden)

    Rima Abdul Razzak

    2013-01-01

    Full Text Available A relationship between blood pressure (BP and obesity has been found in young adults, but no data are available for adolescents in Kuwait. 257 adolescent (11–19 years participants were categorized into two groups according to their BMI; 48 nonobese (21 males: 43.7% and 27 females: 56.3% with mean age of years and 209 obese (128 males: 61.25% and 81 females: 38.75% with mean age of years. The mean BMI was  kg/m2 for the nonobese group and  kg/m3 for the obese group. Most BP measures based on a single screening were significantly higher in the obese group. The prevalence of elevated BP was significantly higher in the obese subjects (nonobese: 13%; obese: 63%; . In the obese group, there was a significant positive correlation between total sample BMI and all BP measures except the pulse pressure. There was a similar rate of elevated blood pressure between males and females (64% versus 60%; . For both isolated systolic elevated BP and isolated diastolic elevated BP, the prevalences were comparable between the males (systolic: 42%; diastolic: 5% and females (systolic: 34%; diastolic: 14%. Only systolic BP was positively correlated with BMI in obese adolescent males (Spearman ; , with a significant correlation between BMI with diastolic (Spearman ; and mean BP (Spearman ; in females.

  19. Outcomes of empirical eating disorder phenotypes in a clinical female sample: results from a latent class analysis.

    Science.gov (United States)

    Dechartres, Agnes; Huas, Caroline; Godart, Nathalie; Pousset, Maud; Pham, Alexandra; Divac, Snezana M; Rouillon, Frederic; Falissard, Bruno

    2011-01-01

    To empirically classify phenotypes of eating disorders (ED) using latent class analysis (LCA), and to validate this classification based on clinical outcomes. LCA was applied to 968 inpatients. The resultant classes were validated by clinical outcomes including mortality. A 5-class solution showed the best fit. The symptoms of latent class 1 (LC1; 26% of the sample) resembled anorexia nervosa (AN), bingeing-purging (AN-B/P) subtype; those of LC2 (23%) resembled bulimia nervosa; those of LC3 (11%) were close to AN-B/P without weight and body concerns; those of LC4 resembled restrictive anorexia nervosa (RAN) without weight and body concerns, and those of LC5 RAN. A history of hospitalization for ED was significantly more frequent for LC3 and LC4. The lowest BMI at admission were presented in LC4. LC1 showed the highest level of psychological disturbances and LC4 the lowest. LC3 and LC4 differed from LC1 and LC5 by higher percentages of treatment dropout (64.9 vs. 57.2 and 55.7 vs. 47.5%, respectively; overall p = 0.001). Survival rates tended to be different between the LC (p = 0.09). Subgroups of AN patients with low weight and body concerns seem more severe at hospitalization and more difficult to manage, with a higher rate of treatment dropout than the 'typical' AN patients. Copyright © 2010 S. Karger AG, Basel.

  20. Extreme conditions magnetostriction study of the Shastry-Sutherland sample SCBO

    Science.gov (United States)

    Grockowiak, Audrey; Wehinger, BjöRn; Coniglio, William; Ruegg, Chistian; Tozer, Stanley; National High Magnetic Field Laboratory Team; Paul Scherrer Institute Collaboration

    The Shasty-Sutherland model, which consists of a set of spin 1/2 dimers on a 2D square lattice, is simple and soluble but captures a central theme of condensed matter physics by sitting precariously on the quantum edge between isolated, gapped excitations and collective, ordered ground states. This model is realized in SrCu2(BO3)2. Recent x-ray diffraction data revealed a direct correlation of the lattice with magnetic susceptibility measurements at low temperatures. The variation of the lattice parameters with temperature is thus directly linked to the spin response of the system. Indeed, scattering intensities from the spin waves, measured by inelastic neutron scattering experiments, decay accordingly. The magnetic correlations can thus be monitored by the lattice parameters and are thus sensitive to magnetostriction. Ambient pressure magnetostriction up to 100.7 T show clear signatures related to the magnetization plateaus at 30, 40 and 80T. Together with total energy calculations these studies revealed a strong magneto elastic coupling driven by the super exchange angle CuOCu. Applying hydrostatic external pressure results in continuous and discontinuous quantum phase transitions. Zero field high pressure neutron spectroscopy measurements have revealed so far three phases : spin dimer from 0 to 2GPa, antiferromagnetic from 4 to 6 GPa, and a 4-spin plaquette singlet state was recently identified in the 2 to 4GPa region. We report here on high pressure (up to 2GPa), high magnetic field (up to 65T) and 3He temperature magnetostriction experiments, using FBGs. Fiber Bragg Grating (FBG) Dilatometry permits to measure the magnetostriction of a sample in function of the response of an optical fiber to applied strain. This work was performed at the NHMFL, supported by the NSF Cooperative Agreement No. DMR-1157490 and the State of Florida, and the DOE NNSA DE-NA0001979 Grant.

  1. Extreme emission-line galaxies out to z ~ 1 in zCOSMOS. I. Sample and characterization of global properties

    Science.gov (United States)

    Amorín, R.; Pérez-Montero, E.; Contini, T.; Vílchez, J. M.; Bolzonella, M.; Tasca, L. A. M.; Lamareille, F.; Zamorani, G.; Maier, C.; Carollo, C. M.; Kneib, J.-P.; Le Fèvre, O.; Lilly, S.; Mainieri, V.; Renzini, A.; Scodeggio, M.; Bardelli, S.; Bongiorno, A.; Caputi, K.; Cucciati, O.; de la Torre, S.; de Ravel, L.; Franzetti, P.; Garilli, B.; Iovino, A.; Kampczyk, P.; Knobel, C.; Kovač, K.; Le Borgne, J.-F.; Le Brun, V.; Mignoli, M.; Pellò, R.; Peng, Y.; Presotto, V.; Ricciardelli, E.; Silverman, J. D.; Tanaka, M.; Tresse, L.; Vergani, D.; Zucca, E.

    2015-06-01

    Context. The study of large and representative samples of low-metallicity star-forming galaxies at different cosmic epochs is of great interest to the detailed understanding of the assembly history and evolution of low-mass galaxies. Aims: We present a thorough characterization of a large sample of 183 extreme emission-line galaxies (EELGs) at redshift 0.11 ≤ z ≤ 0.93 selected from the 20k zCOSMOS bright survey because of their unusually large emission line equivalent widths. Methods: We use multiwavelength COSMOS photometry, HST-ACS I-band imaging, and optical zCOSMOS spectroscopy to derive the main global properties of star-forming EELGs, such as sizes, stellar masses, star formation rates (SFR), and reliable oxygen abundances using both "direct" and "strong-line" methods. Results: The EELGs are extremely compact (r50 ~ 1.3 kpc), low-mass (M∗ ~ 107-1010 M⊙) galaxies forming stars at unusually high specific star formation rates (sSFR ≡ SFR/M⋆ up to 10-7 yr-1) compared to main sequence star-forming galaxies of the same stellar mass and redshift. At rest-frame UV wavelengths, the EELGs are luminous and show high surface brightness and include strong Lyα emitters, as revealed by GALEX spectroscopy. We show that zCOSMOS EELGs are high-ionization, low-metallicity systems, with median 12+log (O/H) = 8.16 ± 0.21 (0.2 Z⊙) including a handful of extremely metal-deficient (Universe, EELGs are most often found in relative isolation. While only very few EELGs belong to compact groups, almost one third of them are found in spectroscopically confirmed loose pairs or triplets. Conclusions: The zCOSMOS EELGs are galaxies caught in a transient and probably early period of their evolution, where they are efficiently building up a significant fraction of their present-day stellar mass in an ongoing, galaxy-wide starburst. Therefore, the EELGs constitute an ideal benchmark for comparison studies between low- and high-redshift low-mass star-forming galaxies. Full

  2. Determination of extremely low 236U/238U isotope ratios in environmental samples by sector-field inductively coupled plasma mass spectrometry using high-efficiency sample introduction

    International Nuclear Information System (INIS)

    Boulyga, Sergei F.; Heumann, Klaus G.

    2006-01-01

    A method by inductively coupled plasma mass spectrometry (Icp-Ms) was developed which allows the measurement of 236 U at concentration ranges down to 3 x 10 -14 g g -1 and extremely low 236 U/ 238 U isotope ratios in soil samples of 10 -7 . By using the high-efficiency solution introduction system APEX in connection with a sector-field ICP-MS a sensitivity of more than 5000 counts fg -1 uranium was achieved. The use of an aerosol desolvating unit reduced the formation rate of uranium hydride ions UH + /U + down to a level of 10 -6 . An abundance sensitivity of 3 x 10 -7 was observed for 236 U/ 238 U isotope ratio measurements at mass resolution 4000. The detection limit for 236 U and the lowest detectable 236 U/ 238 U isotope ratio were improved by more than two orders of magnitude compared with corresponding values by alpha spectrometry. Determination of uranium in soil samples collected in the vicinity of Chernobyl nuclear power plant (NPP) resulted in that the 236 U/ 238 U isotope ratio is a much more sensitive and accurate marker for environmental contamination by spent uranium in comparison to the 235 U/ 238 U isotope ratio. The ICP-MS technique allowed for the first time detection of irradiated uranium in soil samples even at distances more than 200 km to the north of Chernobyl NPP (Mogilev region). The concentration of 236 U in the upper 0-10 cm soil layers varied from 2 x 10 -9 g g -1 within radioactive spots close to the Chernobyl NPP to 3 x 10 -13 g g -1 on a sampling site located by >200 km from Chernobyl

  3. Determination of extremely low (236)U/(238)U isotope ratios in environmental samples by sector-field inductively coupled plasma mass spectrometry using high-efficiency sample introduction.

    Science.gov (United States)

    Boulyga, Sergei F; Heumann, Klaus G

    2006-01-01

    A method by inductively coupled plasma mass spectrometry (ICP-MS) was developed which allows the measurement of (236)U at concentration ranges down to 3 x 10(-14)g g(-1) and extremely low (236)U/(238)U isotope ratios in soil samples of 10(-7). By using the high-efficiency solution introduction system APEX in connection with a sector-field ICP-MS a sensitivity of more than 5,000 counts fg(-1) uranium was achieved. The use of an aerosol desolvating unit reduced the formation rate of uranium hydride ions UH(+)/U(+) down to a level of 10(-6). An abundance sensitivity of 3 x 10(-7) was observed for (236)U/(238)U isotope ratio measurements at mass resolution 4000. The detection limit for (236)U and the lowest detectable (236)U/(238)U isotope ratio were improved by more than two orders of magnitude compared with corresponding values by alpha spectrometry. Determination of uranium in soil samples collected in the vicinity of Chernobyl nuclear power plant (NPP) resulted in that the (236)U/(238)U isotope ratio is a much more sensitive and accurate marker for environmental contamination by spent uranium in comparison to the (235)U/(238)U isotope ratio. The ICP-MS technique allowed for the first time detection of irradiated uranium in soil samples even at distances more than 200 km to the north of Chernobyl NPP (Mogilev region). The concentration of (236)U in the upper 0-10 cm soil layers varied from 2 x 10(-9)g g(-1) within radioactive spots close to the Chernobyl NPP to 3 x 10(-13)g g(-1) on a sampling site located by >200 km from Chernobyl.

  4. Trends in darunavir resistance-associated mutations and phenotypic resistance in commercially tested United States clinical samples between 2006 and 2012.

    Science.gov (United States)

    Lathouwers, Erkki; Gupta, Soumi; Haddad, Mojgan; Paquet, Agnes; de Meyer, Sandra; Baugh, Bryan

    2015-06-01

    HIV-1 samples submitted by clinicians from the United States for routine drug susceptibility testing (PhenoSense GT) were evaluated for genotypic and phenotypic resistance to darunavir and other protease inhibitors (PIs). Among these samples (Monogram Biosciences database January 2006-June 2012; N=78,843), isolates harboring zero IAS-USA darunavir resistance-associated mutations (RAMs) increased from 77.7% in 2006 to 92.8% through the first half of 2012 (H1 2012; upward trend, p=0.0008); a downward trend seen for samples with three or more darunavir RAMs (7.5% in 2006 and 2.6% in H1 2012; p=0.002). Among samples with any PI resistance (N=15,932), samples harboring zero darunavir RAMs gradually increased (39.9% in 2006 vs. 55.0% in H1 2012; upward trend, p=0.005), but three or more darunavir RAMs did not change over time (21.7% in 2006 and 19.2% in H1 2012; p=0.27). During this period, the frequency of the 11 individual darunavir RAMs (IAS-USA 2011 list) decreased among all samples. The frequency of each darunavir RAM in PI-resistant samples decreased or remained relatively stable. The prevalence of samples with phenotypic resistance to darunavir (partial-to-full) decreased over time in all samples (8.2% in 2006 vs. 2.3% in H1 2012), as did resistance to other PIs (p<0.006 for all PIs). Phenotypic resistance to darunavir and other PIs also decreased in PI-resistant samples (darunavir: 23.9% in 2006 vs. 17.1% in H1 2012; p<0.013 for all PIs). Since approval of darunavir in 2006, there was a significant decrease in prevalence of samples with genotypic and phenotypic resistance to darunavir in commercially tested HIV-1 isolates. Furthermore, the prevalence of phenotypic resistance to darunavir was lower than all other PIs.

  5. Phenotypic Data Collection and Sample Preparation for Genomics of Wood Formation and Cellulosic Biomass Traits in Sunflower: Ames, IA location.

    Energy Technology Data Exchange (ETDEWEB)

    Marek, Laura F.

    2011-06-17

    Three fields were planted in Ames in 2010, two association mapping fields, N3 and A, and a recombinant inbred line field, N13. Phenotype data and images were transferred to UGA to support genetic and genomic analyses of woody biomass-related traits.

  6. Autism phenotype versus registered diagnosis in Swedish children: prevalence trends over 10 years in general population samples.

    Science.gov (United States)

    Lundström, Sebastian; Reichenberg, Abraham; Anckarsäter, Henrik; Lichtenstein, Paul; Gillberg, Christopher

    2015-04-28

    To compare the annual prevalence of the autism symptom phenotype and of registered diagnoses for autism spectrum disorder during a 10 year period in children. Population based study. Child and Adolescent Twin Study and national patient register, Sweden. 19, 993 twins (190 with autism spectrum disorder) and all children (n=1,078,975; 4620 with autism spectrum disorder) born in Sweden over a 10 year period from 1993 to 2002. Annual prevalence of the autism symptom phenotype (that is, symptoms on which the diagnostic criteria are based) assessed by a validated parental telephone interview (the Autism-Tics, ADHD and other Comorbidities inventory), and annual prevalence of reported diagnoses of autism spectrum disorder in the national patient register. The annual prevalence of the autism symptom phenotype was stable during the 10 year period (P=0.87 for linear time trend). In contrast, there was a monotonic significant increase in prevalence of registered diagnoses of autism spectrum disorder in the national patient register (Pautism symptom phenotype has remained stable in children in Sweden while the official prevalence for registered, clinically diagnosed, autism spectrum disorder has increased substantially. This suggests that administrative changes, affecting the registered prevalence, rather than secular factors affecting the pathogenesis, are important for the increase in reported prevalence of autism spectrum disorder. © Lundström et al 2015.

  7. Probability estimation of rare extreme events in the case of small samples: Technique and examples of analysis of earthquake catalogs

    Science.gov (United States)

    Pisarenko, V. F.; Rodkin, M. V.; Rukavishnikova, T. A.

    2017-11-01

    The most general approach to studying the recurrence law in the area of the rare largest events is associated with the use of limit law theorems of the theory of extreme values. In this paper, we use the Generalized Pareto Distribution (GPD). The unknown GPD parameters are typically determined by the method of maximal likelihood (ML). However, the ML estimation is only optimal for the case of fairly large samples (>200-300), whereas in many practical important cases, there are only dozens of large events. It is shown that in the case of a small number of events, the highest accuracy in the case of using the GPD is provided by the method of quantiles (MQs). In order to illustrate the obtained methodical results, we have formed the compiled data sets characterizing the tails of the distributions for typical subduction zones, regions of intracontinental seismicity, and for the zones of midoceanic (MO) ridges. This approach paves the way for designing a new method for seismic risk assessment. Here, instead of the unstable characteristics—the uppermost possible magnitude M max—it is recommended to use the quantiles of the distribution of random maxima for a future time interval. The results of calculating such quantiles are presented.

  8. Self-Reported Extremely Adverse Life Events and Longitudinal Changes in Five-Factor Model Personality Traits in an Urban Sample

    Science.gov (United States)

    Löckenhoff, Corinna E.; Terracciano, Antonio; Patriciu, Nicholas S.; Eaton, William W.; Costa, Paul T.

    2009-01-01

    This study examined longitudinal personality change in response to extremely adverse life events in a sample (N = 458) drawn from the East Baltimore Epidemiologic Catchment Area study. Five-factor model personality traits were assessed twice over an average interval of 8 years. Twenty-five percent of the participants reported an extremely horrifying or frightening event within 2 years before the second personality assessment. Relative to the rest of the sample, they showed increases in neuroticism, decreases in the compliance facet of agreeableness, and decreases in openness to values. Baseline personality was unrelated to future events, but among participants who reported extreme events, lower extraversion and/or conscientiousness at baseline as well as longitudinal increases in neuroticism predicted lower mental health at follow-up. PMID:19230009

  9. Thermal discomfort with cold extremities in relation to age, gender, and body mass index in a random sample of a Swiss urban population

    Directory of Open Access Journals (Sweden)

    Orgül Selim

    2010-06-01

    Full Text Available Abstract Background The aim of this epidemiological study was to investigate the relationship of thermal discomfort with cold extremities (TDCE to age, gender, and body mass index (BMI in a Swiss urban population. Methods In a random population sample of Basel city, 2,800 subjects aged 20-40 years were asked to complete a questionnaire evaluating the extent of cold extremities. Values of cold extremities were based on questionnaire-derived scores. The correlation of age, gender, and BMI to TDCE was analyzed using multiple regression analysis. Results A total of 1,001 women (72.3% response rate and 809 men (60% response rate returned a completed questionnaire. Statistical analyses revealed the following findings: Younger subjects suffered more intensely from cold extremities than the elderly, and women suffered more than men (particularly younger women. Slimmer subjects suffered significantly more often from cold extremities than subjects with higher BMIs. Conclusions Thermal discomfort with cold extremities (a relevant symptom of primary vascular dysregulation occurs at highest intensity in younger, slimmer women and at lowest intensity in elderly, stouter men.

  10. Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample.

    Directory of Open Access Journals (Sweden)

    Katsuhiko Nosho

    Full Text Available The CpG island methylator phenotype (CIMP is a distinct phenotype associated with microsatellite instability (MSI and BRAF mutation in colon cancer. Recent investigations have selected 5 promoters (CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1 as surrogate markers for CIMP-high. However, no study has comprehensively evaluated an expanded set of methylation markers (including these 5 markers using a large number of tumors, or deciphered the complex clinical and molecular associations with CIMP-high determined by the validated marker panel. METHOLODOLOGY/PRINCIPAL FINDINGS: DNA methylation at 16 CpG islands [the above 5 plus CDKN2A (p16, CHFR, CRABP1, HIC1, IGFBP3, MGMT, MINT1, MINT31, MLH1, p14 (CDKN2A/ARF and WRN] was quantified in 904 colorectal cancers by real-time PCR (MethyLight. In unsupervised hierarchical clustering analysis, the 5 markers (CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1, CDKN2A, CRABP1, MINT31, MLH1, p14 and WRN were generally clustered with each other and with MSI and BRAF mutation. KRAS mutation was not clustered with any methylation marker, suggesting its association with a random methylation pattern in CIMP-low tumors. Utilizing the validated CIMP marker panel (including the 5 markers, multivariate logistic regression demonstrated that CIMP-high was independently associated with older age, proximal location, poor differentiation, MSI-high, BRAF mutation, and inversely with LINE-1 hypomethylation and beta-catenin (CTNNB1 activation. Mucinous feature, signet ring cells, and p53-negativity were associated with CIMP-high in only univariate analysis. In stratified analyses, the relations of CIMP-high with poor differentiation, KRAS mutation and LINE-1 hypomethylation significantly differed according to MSI status.Our study provides valuable data for standardization of the use of CIMP-high-specific methylation markers. CIMP-high is independently associated with clinical and key molecular features in colorectal cancer. Our data also

  11. Phenotypic, molecular characterization, antimicrobial susceptibility and draft genome sequence of Corynebacterium argentoratense strains isolated from clinical samples

    Directory of Open Access Journals (Sweden)

    I. Fernández-Natal

    2016-03-01

    Full Text Available During a 12-year period we isolated five Corynebacterium argentoratense strains identified by phenotypic methods, including the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF and 16S rRNA gene sequencing. In addition, antimicrobial susceptibility was determined, and genome sequencing for the detection of antibiotic resistance genes was performed. The organisms were isolated from blood and throat cultures and could be identified by all methods used. All strains were resistant to cotrimoxazole, and resistance to β-lactams was partly present. Two strains were resistant to erythromycin and clindamycin. The draft genome sequences of theses isolates revealed the presence of the erm(X resistance gene that is embedded in the genetic structure of the transposable element Tn5423. Although rarely reported as a human pathogen, C. argentoratense can be involved in bacteraemia and probably in other infections. Our results also show that horizontal transfer of genes responsible for antibiotic resistance is occurring in this species.

  12. Reliability and validity of the Persian lower extremity functional scale (LEFS) in a heterogeneous sample of outpatients with lower limb musculoskeletal disorders.

    Science.gov (United States)

    Negahban, Hossein; Hessam, Masumeh; Tabatabaei, Saeid; Salehi, Reza; Sohani, Soheil Mansour; Mehravar, Mohammad

    2014-01-01

    The aim was to culturally translate and validate the Persian lower extremity functional scale (LEFS) in a heterogeneous sample of outpatients with lower extremity musculoskeletal disorders (n = 304). This is a prospective methodological study. After a standard forward-backward translation, psychometric properties were assessed in terms of test-retest reliability, internal consistency, construct validity, dimensionality, and ceiling or floor effects. The acceptable level of intraclass correlation coefficient >0.70 and Cronbach's alpha coefficient >0.70 was obtained for the Persian LEFS. Correlations between Persian LEFS and Short-Form 36 Health Survey (SF-36) subscales of Physical Health component (rs range = 0.38-0.78) were higher than correlations between Persian LEFS and SF-36 subscales of Mental Health component (rs range = 0.15-0.39). A corrected item--total correlation of >0.40 (Spearman's rho) was obtained for all items of the Persian LEFS. Horn's parallel analysis detected a total of two factors. No ceiling or floor effects were detected for the Persian LEFS. The Persian version of the LEFS is a reliable and valid instrument that can be used to measure functional status in Persian-speaking patients with different musculoskeletal disorders of the lower extremity. Implications for Rehabilitation The Persian lower extremity functional scale (LEFS) is a reliable, internally consistent and valid instrument, with no ceiling or floor effects, to determine functional status of heterogeneous patients with musculoskeletal disorders of the lower extremity. The Persian version of the LEFS can be used in clinical and research settings to measure function in Iranian patients with different musculoskeletal disorders of the lower extremity.

  13. Prevalence in the USA of rilpivirine resistance-associated mutations in clinical samples and effects on phenotypic susceptibility to rilpivirine and etravirine.

    Science.gov (United States)

    Picchio, Gaston R; Rimsky, Laurence T; Van Eygen, Veerle; Haddad, Mojgan; Napolitano, Laura A; Vingerhoets, Johan

    2014-01-01

    The prevalence of rilpivirine resistance-associated mutations (RAMs) in the USA, and their effect on phenotypic susceptibility to rilpivirine and etravirine, was evaluated in clinical samples from HIV-1-infected patients. In total, 15,991 samples submitted to Monogram Biosciences (South San Francisco, CA, USA) for routine resistance testing between January 2010 and June 2011 were assessed for the presence of known rilpivirine RAMs K101E/P, E138A/G/K/Q/R, V179L, Y181C/I/V, Y188L, H221Y, F227C and M230I/L; non-nucleoside reverse transcriptase inhibitor (NNRTI) RAMs K103N, L100I and L100I+K103N; and the nucleoside reverse transcriptase inhibitor (NRTI) RAMs M184I/V and their combinations with rilpivirine RAMs. Phenotypic susceptibility (PhenoSenseGT(®) assay; Monogram Biosciences) was evaluated, with reduced susceptibility defined as fold change (FC) in 50% inhibitory concentration (IC50)>2.0 for rilpivirine and FC>2.9 for etravirine. Of the 15,991 samples, 17% harboured ≥1 rilpivirine RAMs. The prevalence of most rilpivirine RAMs and combinations of NNRTI RAMs of interest was low (≤3%), except for Y181C (7%). Rilpivirine RAMs were often associated with reduced rilpivirine phenotypic susceptibility. Median FC values >2.0 were observed for clinical isolates with rilpivirine RAMs K101P, E138Q/R, Y181C/I/V, Y188L or M230L, and for the combination of E138K with M184I/V, and K101E with M184I. Most rilpivirine FC values >2.0 were associated with etravirine FC values >2.9 for individual rilpivirine RAMs and those combined with M184I/V. There was no relationship between the presence of K103N and rilpivirine FC. However, the L100I+K103N combination (without rilpivirine RAMs), at 2.0. Based on 15,991 US clinical samples from HIV-1-infected patients, the frequency of most known rilpivirine RAMs apart from Y181C was low.

  14. THE ROLE OF IRON IN Deinococcus radiodurans ENGINEERED FOR GROWTH ON TOLUENE AND THE ROLE OF MANGANESE IN THE EXTREME RADIATION RESISTANCE PHENOTYPE

    International Nuclear Information System (INIS)

    Hassan Brim; Elena K. Gaidamakova; Vera Y. Matrosova; Min Zhai; Amudhan Venkateswaran; Marina Omelchenko; Kira S. Makarova; Lawrence P. Wackett; James K. Fredrickson; Michael J. Daly

    2004-01-01

    Toluene and other fuel hydrocarbons are commonly found in association with radionuclides at numerous Department of Energy (DOE) sites, frequently occurring together with Cr(VI) and other heavy metals. In this study, the extremely radiation resistant bacterium Deinococcus radiodurans was engineered for complete toluene mineralization by cloned expression of tod and xyl genes of Pseudomonas putida. The recombinant Tod/Xyl strain showed significant incorporation of carbon from the toluene aromatic ring into cellular macromolecules and carbon dioxide, in the absence or presence of chronic radiation. We have shown that intracellular iron concentrations in wild-type D. radiodurans in minimal medium are exceptionally low and not sufficient to support growth on toluene using Fe-dependent oxygenases cloned from P. putida. Introducing the fur mutation into D. radiodurans increased intracellular Fe levels, and imparted on the engineered strain the ability to grow on meta-toluate as the sole carbon and energy source. The organism's native Cr(VI) reduction capabilities were facilitated by toluene when present as the sole carbon and energy source in natural sediment analogues of DOE contaminated environments. The engineered bacteria were able to oxidize toluene under both minimal and complex nutrient conditions, which is important since both conditions have environmental equivalents in the context of bioremediation processes. As such, the Tod/Xyl strain is providing a model for understanding the role of Fe and reduction of metals coupled to organic contaminant oxidation in aerobic radionuclide contaminated sediments. We have shown that D. radiodurans contains high intracellular manganese levels, and that Mn restriction sensitizes cells to irradiation. We propose that the unusually high Mn/Fe ratio of D. radiodurans facilitates survival by quenching oxidative stress during recovery.

  15. THE ROLE OF IRON IN Deinococcus radiodurans ENGINEERED FOR GROWTH ON TOLUENE AND THE ROLE OF MANGANESE IN THE EXTREME RADIATION RESISTANCE PHENOTYPE

    Energy Technology Data Exchange (ETDEWEB)

    Hassan Brim; Elena K. Gaidamakova; Vera Y. Matrosova; Min Zhai; Amudhan Venkateswaran; Marina Omelchenko; Kira S. Makarova; Lawrence P. Wackett; James K. Fredrickson; Michael J. Daly

    2004-03-17

    Toluene and other fuel hydrocarbons are commonly found in association with radionuclides at numerous Department of Energy (DOE) sites, frequently occurring together with Cr(VI) and other heavy metals. In this study, the extremely radiation resistant bacterium Deinococcus radiodurans was engineered for complete toluene mineralization by cloned expression of tod and xyl genes of Pseudomonas putida. The recombinant Tod/Xyl strain showed significant incorporation of carbon from the toluene aromatic ring into cellular macromolecules and carbon dioxide, in the absence or presence of chronic radiation. We have shown that intracellular iron concentrations in wild-type D. radiodurans in minimal medium are exceptionally low and not sufficient to support growth on toluene using Fe-dependent oxygenases cloned from P. putida. Introducing the fur mutation into D. radiodurans increased intracellular Fe levels, and imparted on the engineered strain the ability to grow on meta-toluate as the sole carbon and energy source. The organism's native Cr(VI) reduction capabilities were facilitated by toluene when present as the sole carbon and energy source in natural sediment analogues of DOE contaminated environments. The engineered bacteria were able to oxidize toluene under both minimal and complex nutrient conditions, which is important since both conditions have environmental equivalents in the context of bioremediation processes. As such, the Tod/Xyl strain is providing a model for understanding the role of Fe and reduction of metals coupled to organic contaminant oxidation in aerobic radionuclide contaminated sediments. We have shown that D. radiodurans contains high intracellular manganese levels, and that Mn restriction sensitizes cells to irradiation. We propose that the unusually high Mn/Fe ratio of D. radiodurans facilitates survival by quenching oxidative stress during recovery.

  16. Determination of Coreceptor Usage of Human Immunodeficiency Virus Type 1 from Patient Plasma Samples by Using a Recombinant Phenotypic Assay

    Science.gov (United States)

    Trouplin, Virginie; Salvatori, Francesca; Cappello, Fanny; Obry, Veronique; Brelot, Anne; Heveker, Nikolaus; Alizon, Marc; Scarlatti, Gabriella; Clavel, François; Mammano, Fabrizio

    2001-01-01

    We developed a recombinant virus technique to determine the coreceptor usage of human immunodeficiency virus type 1 (HIV-1) from plasma samples, the source expected to represent the most actively replicating virus population in infected subjects. This method is not subject to selective bias associated with virus isolation in culture, a step required for conventional tropism determination procedures. The addition of a simple subcloning step allowed semiquantitative evaluation of virus populations with a different coreceptor (CCR5 or CXCR4) usage specificity present in each plasma sample. This procedure detected mixtures of CCR5- and CXCR4-exclusive virus populations as well as dualtropic viral variants, in variable proportions. Sequence analysis of dualtropic clones indicated that changes in the V3 loop are necessary for the use of CXCR4 as a coreceptor, but the overall context of the V1-V3 region is important to preserve the capacity to use CCR5. This convenient technique can greatly assist the study of virus evolution and compartmentalization in infected individuals. PMID:11119595

  17. Prevalence and phenotypic characterization of Enterococcus species isolated from clinical samples of pediatric patients in Jimma University Specialized Hospital, south west Ethiopia.

    Science.gov (United States)

    Toru, Milkiyas; Beyene, Getnet; Kassa, Tesfaye; Gizachew, Zeleke; Howe, Rawleigh; Yeshitila, Biruk

    2018-05-08

    This study was done to determine the prevalence and phenotypic characterization of Enterococcus species isolated from clinical samples of pediatric patients in Jimma University Specialized Hospital, Southwest Ethiopia. The overall prevalence of Enterococci species was 5.5% (22/403). Five (22.7%) of Enterococci species were vancomycin resistant. Haemolysin, gelatinase and biofilm production was seen among 45.5, 68.2 and 77.3% of isolates respectively. The overall rate of antibiotic resistance was 95.5% (21/22). High resistance was observed against norfloxacin (87.5%), and tetracycline (77.3%). Whereas, low resistance (36.5%) was observed against ciprofloxacin and eighteen (80.8%) of the isolates were multi-drug resistant.

  18. Instrument developments for chemical and physical characterization, mapping and sampling of extreme environments (Antarctic sub ice environment)

    Science.gov (United States)

    Vogel, S. W.; Powell, R. D.; Griffith, I.; Lawson, T.; Schiraga, S.; Ludlam, G.; Oen, J.

    2009-12-01

    A number of instrumentation is currently under development designed to enable the study of subglacial environments in Antarctica through narrow kilometer long boreholes. Instrumentation includes: - slim line Sub-Ice ROV (SIR), - Geochemical Instrumentation Package for Sub Ice Environments (GIPSIE) to study geochemical fluxes in water and across the sediment water interface (CO2, CH4, dO, NH4, NO3, Si, PO4, pH, redox, T, H2, HS, O2, N2O, CTD, particle size, turbidity, color camera, current meter and automated water sampler) with real-time telemetry for targeted sampling, - long term energy-balance mooring system, - active source slide hammer sediment corer, and - integration of a current sensor into the ITP profiler. The instrumentation design is modular and suitable for remote operated as well as autonomous long-term deployment. Of interest to the broader science community is the development of the GIPSIE and efforts to document the effect of sample recovery from depth on the sample chemistry. The GIPSIE is a geochemical instrumentation package with life stream telemetry, allowing for user controlled targeted sampling of water column and the water sediment interphase for chemical and biological work based on actual measurements and not a preprogrammed automated system. The porewater profiler (pH, redox, T, H2, HS, O2, N2O) can penetrate the upper 50 cm of sediment and penetration is documented with real time video. Associated with GIPSIE is an on-site lab set-up, utilizing a set of identical sensors. Comparison between the insitu measurements and measurements taken onsite directly after samples are recovered from depth permits assessing the effect of sample recovery on water and sediment core chemistry. Sample recovery related changes are mainly caused by changes in the pressure temperature field and exposure of samples to atmospheric conditions. Exposure of anaerobic samples to oxygen is here a specific concern. Recovery from depth effects in generally p

  19. THE CHEMICAL ABUNDANCES OF STARS IN THE HALO (CASH) PROJECT. II. A SAMPLE OF 14 EXTREMELY METAL-POOR STARS ,

    International Nuclear Information System (INIS)

    Hollek, Julie K.; Sneden, Christopher; Shetrone, Matthew; Frebel, Anna; Roederer, Ian U.; Beers, Timothy C.; Kang, Sung-ju; Thom, Christopher

    2011-01-01

    We present a comprehensive abundance analysis of 20 elements for 16 new low-metallicity stars from the Chemical Abundances of Stars in the Halo (CASH) project. The abundances have been derived from both Hobby-Eberly Telescope High Resolution Spectrograph snapshot spectra (R ∼15, 000) and corresponding high-resolution (R ∼35, 000) Magellan Inamori Kyocera Echelle spectra. The stars span a metallicity range from [Fe/H] from –2.9 to –3.9, including four new stars with [Fe/H] < –3.7. We find four stars to be carbon-enhanced metal-poor (CEMP) stars, confirming the trend of increasing [C/Fe] abundance ratios with decreasing metallicity. Two of these objects can be classified as CEMP-no stars, adding to the growing number of these objects at [Fe/H]< – 3. We also find four neutron-capture-enhanced stars in the sample, one of which has [Eu/Fe] of 0.8 with clear r-process signatures. These pilot sample stars are the most metal-poor ([Fe/H] ∼< –3.0) of the brightest stars included in CASH and are used to calibrate a newly developed, automated stellar parameter and abundance determination pipeline. This code will be used for the entire ∼500 star CASH snapshot sample. We find that the pipeline results are statistically identical for snapshot spectra when compared to a traditional, manual analysis from a high-resolution spectrum.

  20. Moving into a new era of periodontal genetic studies: relevance of large case-control samples using severe phenotypes for genome-wide association studies.

    Science.gov (United States)

    Vaithilingam, R D; Safii, S H; Baharuddin, N A; Ng, C C; Cheong, S C; Bartold, P M; Schaefer, A S; Loos, B G

    2014-12-01

    Studies to elucidate the role of genetics as a risk factor for periodontal disease have gone through various phases. In the majority of cases, the initial 'hypothesis-dependent' candidate-gene polymorphism studies did not report valid genetic risk loci. Following a large-scale replication study, these initially positive results are believed to be caused by type 1 errors. However, susceptibility genes, such as CDKN2BAS (Cyclin Dependend KiNase 2B AntiSense RNA; alias ANRIL [ANtisense Rna In the Ink locus]), glycosyltransferase 6 domain containing 1 (GLT6D1) and cyclooxygenase 2 (COX2), have been reported as conclusive risk loci of periodontitis. The search for genetic risk factors accelerated with the advent of 'hypothesis-free' genome-wide association studies (GWAS). However, despite many different GWAS being performed for almost all human diseases, only three GWAS on periodontitis have been published - one reported genome-wide association of GLT6D1 with aggressive periodontitis (a severe phenotype of periodontitis), whereas the remaining two, which were performed on patients with chronic periodontitis, were not able to find significant associations. This review discusses the problems faced and the lessons learned from the search for genetic risk variants of periodontitis. Current and future strategies for identifying genetic variance in periodontitis, and the importance of planning a well-designed genetic study with large and sufficiently powered case-control samples of severe phenotypes, are also discussed. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  1. Phenotypic and Molecular Characterisation of Extended-Spectrum Beta-Lactamase Producing Escherichia coli Obtained from Animal Fecal Samples in Ado Ekiti, Nigeria

    Directory of Open Access Journals (Sweden)

    Olugbenga Adekunle Olowe

    2015-01-01

    Full Text Available Production of extended-spectrum β-lactamases (ESBLs producing E. coli in animals and different methods of identifications from Ado Ekiti, Ekiti State, Nigeria, were investigated. Three hundred and fifty fecal samples, collected from apparently healthy cattle and pigs, were cultured and identified following standard procedures. ESBL phenotypic detection was carried out using combination disc test, double disc synergism test, and ESBL brilliance agar screening. Molecular detection of TEM, SHV, and CTX-M genes was carried out using standard molecular method. One hundred and fourteen E. coli isolates were recovered from the 350 samples processed, out of which 72 (63.2% isolates were positive for ESBLs with multiple resistance to the antibiotics used. Eighty-one (71% isolates were positive for ESBL by combination disc test, 90 (78.9% were positive for double disc synergism test, and 93 (81.6% were positive for ESBL brilliance agar. TEM and CTX-M genes were detected in 48 (42.1% and 51 (44.7% isolates, respectively. SHV gene was not detected in any of the isolates while TEM and CTX-M were detected in 33 (28.9% isolates. This study showed high resistance of E. coli to antibiotics, particularly to the third generation cephalosporins. Regular monitoring and regulated use of antibiotics in livestock should be encouraged.

  2. Extreme robustness of scaling in sample space reducing processes explains Zipf’s law in diffusion on directed networks

    International Nuclear Information System (INIS)

    Corominas-Murtra, Bernat; Hanel, Rudolf; Thurner, Stefan

    2016-01-01

    It has been shown recently that a specific class of path-dependent stochastic processes, which reduce their sample space as they unfold, lead to exact scaling laws in frequency and rank distributions. Such sample space reducing processes offer an alternative new mechanism to understand the emergence of scaling in countless processes. The corresponding power law exponents were shown to be related to noise levels in the process. Here we show that the emergence of scaling is not limited to the simplest SSRPs, but holds for a huge domain of stochastic processes that are characterised by non-uniform prior distributions. We demonstrate mathematically that in the absence of noise the scaling exponents converge to −1 (Zipf’s law) for almost all prior distributions. As a consequence it becomes possible to fully understand targeted diffusion on weighted directed networks and its associated scaling laws in node visit distributions. The presence of cycles can be properly interpreted as playing the same role as noise in SSRPs and, accordingly, determine the scaling exponents. The result that Zipf’s law emerges as a generic feature of diffusion on networks, regardless of its details, and that the exponent of visiting times is related to the amount of cycles in a network could be relevant for a series of applications in traffic-, transport- and supply chain management. (paper)

  3. Characterization of multi-drug resistant ESBL producing nonfermenter bacteria isolated from patients blood samples using phenotypic methods in Shiraz (Iran

    Directory of Open Access Journals (Sweden)

    Maneli Amin Shahidi

    2015-10-01

    Full Text Available Background and Aim: The emergence of  nonfermenter bacteria that are resistant to multidrug resistant ESBL  are  nowadays a principal problem  for hospitalized patients. The present study aimed at surveying the emergence of nonfermenter bacteria resistant to multi-drug ESBL producing isolated from patients blood samples using BACTEC 9240 automatic system in Shiraz. Materials and Methods: In this cross-sectional study, 4825 blood specimens were collected from hospitalized patients in Shiraz (Iran, and positive samples were detected by means of  BACTEC 9240 automatic system. The isolates  containing nonfermenter bacteria were identified based on biochemical tests embedded in the API-20E system. Antibiotic sensitivity  test was performed  and identification of  ESBL producing strains were done  using phenotypic detection of extended spectrum beta-lactamase producing isolates(DDST according to CLSI(2013 guidelines.   Results: Out of 4825 blood samples, 1145 (24% specimen were gram-positive using BACTEC system. Among all isolated microorganisms, 206 isolates were non-fermenting gram- negative bacteria. The most common non-fermenter isolates were Pseudomonas spp. (48%, Acinetobacter spp. (41.7% ,and Stenotrophomonas spp. (8.2%. Seventy of them (81.4% were  Acinetobacter spp. which were ESBL positive. Among &beta-lactam antibiotics, Pseudomonas spp. showed  the best sensitivity to piperacillin-tazobactam (46.5%.  Conclusion: It was found that  &beta-lactam antibiotics are not effective against more than 40% of Pseudomonas spp. infections and 78% Acinetobacter infections. Emergence of multi-drug resistant strains that are resistant to most antibiotic classes is a major public health problem in Iran. To resolve this problem using of practical guidelines is critical.

  4. The Chemical Abundances of Stars in the Halo (CASH) Project. II. A Sample of 14 Extremely Metal-poor Stars

    Science.gov (United States)

    Hollek, Julie K.; Frebel, Anna; Roederer, Ian U.; Sneden, Christopher; Shetrone, Matthew; Beers, Timothy C.; Kang, Sung-ju; Thom, Christopher

    2011-11-01

    We present a comprehensive abundance analysis of 20 elements for 16 new low-metallicity stars from the Chemical Abundances of Stars in the Halo (CASH) project. The abundances have been derived from both Hobby-Eberly Telescope High Resolution Spectrograph snapshot spectra (R ~15, 000) and corresponding high-resolution (R ~35, 000) Magellan Inamori Kyocera Echelle spectra. The stars span a metallicity range from [Fe/H] from -2.9 to -3.9, including four new stars with [Fe/H] ratios with decreasing metallicity. Two of these objects can be classified as CEMP-no stars, adding to the growing number of these objects at [Fe/H]CASH and are used to calibrate a newly developed, automated stellar parameter and abundance determination pipeline. This code will be used for the entire ~500 star CASH snapshot sample. We find that the pipeline results are statistically identical for snapshot spectra when compared to a traditional, manual analysis from a high-resolution spectrum. Based on observations obtained with the Hobby-Eberly Telescope, which is a joint project of the University of Texas at Austin, the Pennsylvania State University, Stanford University, Ludwig-Maximilians-Universität München, and Georg-August-Universität Göttingen. Based on observations gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.

  5. Surgical Implications of Asymmetric Distribution of Dermal Collagen and Elastic Fibres in Two Orientations of Skin Samples from Extremities

    Directory of Open Access Journals (Sweden)

    Naveen Kumar

    2014-01-01

    Full Text Available Background. Clinically, scar related complications are observed to be dissimilar in different regions of the body. Unequal distribution of dermal collagen and elastic fibres in different orientations could be one of the multifocal causes of scar related complications, for which this evaluating study has been taken up. Materials and Method. 300 skin samples collected in horizontal and vertical orientations were studied histomorphometrically. This study involved image analysis of specially stained histological section using tissue-quant software. The outcome result was termed as quantitative fraction. From the result, various ratio values were also calculated for the ratio analysis. Results. The differences in the quantitative fraction of dermal elastic content between 2 directions were statistically significant at joint areas (shoulder joint, wrist, and ankle (P<0.001 but for collagen, significant difference was observed at shoulder joint and wrist only. Dermis of the forearm and thigh did not show any differences in their collagen content, but for elastic, thigh did show a significant difference while forearm had no change between 2 directions. Conclusion. Analysis of unequal content of dermal element in two directions under the perspective of wound healing consequences is subjective depending upon the anatomical position and functional status of the areas.

  6. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  7. Clinical and cytogenetic features of a Brazilian sample of patients with phenotype of oculo-auriculo-vertebral spectrum: a cross-sectional study

    Directory of Open Access Journals (Sweden)

    Alessandra Pawelec da Silva

    Full Text Available CONTEXT AND OBJECTIVE: Oculo-auriculo-vertebral spectrum (OAVS is considered to be a defect of embryogenesis involving structures originating from the first branchial arches. Our objective was to describe the clinical and cytogenetic findings from a sample of patients with the phenotype of OAVS.DESIGN AND SETTING: Cross-sectional study in a referral hospital in southern Brazil.METHODS: The sample consisted of 23 patients who presented clinical findings in at least two of these four areas: orocraniofacial, ocular, auricular and vertebral. The patients underwent a clinical protocol and cytogenetic evaluation through high-resolution karyotyping, fluorescence in situ hybridization for 5p and 22q11 microdeletions and investigation of chromosomal instability for Fanconi anemia.RESULTS: Cytogenetic abnormalities were observed in three cases (13% and consisted of: 47,XX,+mar; mos 47,XX,+mar/46,XX; and 46,XX,t(6;10(q13; q24. We observed cases of OAVS with histories of gestational exposition to fluoxetine, retinoic acid and crack. One of our patients was a discordant monozygotic twin who had shown asymmetrical growth restriction during pregnancy. Our patients with OAVS were characterized by a broad clinical spectrum and some presented atypical findings such as lower-limb reduction defect and a tumor in the right arm, suggestive of hemangioma/lymphangioma.CONCLUSIONS: We found a wide range of clinical characteristics among the patients with OAVS. Different chromosomal abnormalities and gestational expositions were also observed. Thus, our findings highlight the heterogeneity of the etiology of OAVS and the importance of these factors in the clinical and cytogenetic evaluation of these patients.

  8. The frequency of Listeria monocytogenes strains recovered from clinical and non-clinical samples using phenotypic methods and confirmed by PCR

    Directory of Open Access Journals (Sweden)

    abazar pournajaf

    2013-09-01

    Full Text Available Background: Listeria monocytogenes is a facultative intracellular pathogen that causes listeriosis which has extensive clinical manifestations. Infections with L. monocytogenes are a serious threat to immunocompromised persons. The aim of this study was to determine the frequency of L. monocytogenes strains recovered from clinical and non-clinical samples using phenotypic methods and confirmed by PCR. Materials and Methods: In this study, 617 specimens were analyzed. All specimens were cultured in the specific PALCAM agar. Colonies were initially identified by routine biochemical tests. Finally, PCR assays using primers specific for inlA gene were performed. Results: In all, 46 (8.2% L. monocytogenes isolates were recovered from 617 specimens. Fourteen (8.2% strains, including 4 (7.5%, 2 (5.7%, 5 (14.2% and 3 (8.5% isolates were obtained from placental tissue, urine, vaginal and rectal swabs, respectively. In addition, 9 (7.4% strains of L. monocytogenes which were isolated from 107 different dairy products originated from cheese 5 (7.1%, cream 2 (10% and kashk 2 (11.7%, respectively. Among 11 (5.2% strains isolated from 210 different meat products, 5 (5.5%, 4 (7.2% and 2 (3% strains belonged to sausage, meat and poultry extracts, respectively. Finally, 12 (9.2% Listeria strains were recovered from 130 animal specimens that included 6 (10%, 4 (8% and 2 (10% strains from goat, sheep and cattle, respectively. Furthermore, all Listeria isolates (100% were found to be carriers of  inlA gene in PCR assay. Conclusion: The present study showed that the clinical and non-clinical specimens were contaminated with L. monocytogenes. So, it seems necessary to use a simple and standard technique such as PCR for rapid detection of this organism from various sources.

  9. Phenotypic characterization and 16S rDNA identification of culturable non-obligate halophilic bacterial communities from a hypersaline lake, La Sal del Rey, in extreme South Texas (USA).

    Science.gov (United States)

    Phillips, Kristen; Zaidan, Frederic; Elizondo, Omar R; Lowe, Kristine L

    2012-02-02

    La Sal del Rey ("the King's Salt") is one of several naturally-occurring salt lakes in Hidalgo County, Texas and is part of the Lower Rio Grande Valley National Wildlife Refuge. The research objective was to isolate and characterize halophilic microorganisms from La Sal del Rey. Water samples were collected from the lake and a small creek that feeds into the lake. Soil samples were collected from land adjacent to the water sample locations. Sample salinity was determined using a refractometer. Samples were diluted and cultured on a synthetic saline medium to grow halophilic bacteria. The density of halophiles was estimated by viable plate counts. A collection of isolates was selected, gram-stained, tested for catalase, and characterized using API 20E® test strips. Isolates were putatively identified by sequencing the 16S rDNA. Carbon source utilization by the microbial community from each sample site was examined using EcoPlate™ assays and the carbon utilization total activity of the community was determined. Results showed that salinity ranged from 4 parts per thousand (ppt) at the lake water source to 420 ppt in water samples taken just along the lake shore. The density of halophilic bacteria in water samples ranged from 1.2 × 102 - 5.2 × 103 colony forming units per ml (cfu ml-1) whereas the density in soil samples ranged from 4.0 × 105 - 2.5 × 106 colony forming units per gram (cfu g-1). In general, as salinity increased the density of the bacterial community decreased. Microbial communities from water and soil samples were able to utilize 12 - 31 carbon substrates. The greatest number of substrates utilized was by water-borne communities compared to soil-based communities, especially at lower salinities. The majority of bacteria isolated were gram-negative, catalase-positive, rods. Biochemical profiles constructed from API 20E® test strips showed that bacterial isolates from low-salinity water samples (4 ppt) showed the greatest phenotypic diversity

  10. Impact of polymorphisms in WFS1 on prediabetic phenotypes in a population-based sample of middle-aged people with normal and abnormal glucose regulation

    DEFF Research Database (Denmark)

    Sparsø, T; Andersen, G; Albrechtsen, Anders

    2008-01-01

    AIM/HYPOTHESIS: Recently, variants in WFS1 have been shown to be associated with type 2 diabetes. We aimed to examine metabolic risk phenotypes of WFS1 variants in glucose-tolerant people and in individuals with abnormal glucose regulation. METHODS: The type 2 diabetes-associated WFS1 variant rs7...

  11. Determination of extremely low {sup 236}U/{sup 238}U isotope ratios in environmental samples by sector-field inductively coupled plasma mass spectrometry using high-efficiency sample introduction

    Energy Technology Data Exchange (ETDEWEB)

    Boulyga, Sergei F. [Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55099 Mainz (Germany)]. E-mail: sergei.boulyga@univie.ac.at; Heumann, Klaus G. [Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55099 Mainz (Germany)

    2006-07-01

    A method by inductively coupled plasma mass spectrometry (Icp-Ms) was developed which allows the measurement of {sup 236}U at concentration ranges down to 3 x 10{sup -14} g g{sup -1} and extremely low {sup 236}U/{sup 238}U isotope ratios in soil samples of 10{sup -7}. By using the high-efficiency solution introduction system APEX in connection with a sector-field ICP-MS a sensitivity of more than 5000 counts fg{sup -1} uranium was achieved. The use of an aerosol desolvating unit reduced the formation rate of uranium hydride ions UH{sup +}/U{sup +} down to a level of 10{sup -6}. An abundance sensitivity of 3 x 10{sup -7} was observed for {sup 236}U/{sup 238}U isotope ratio measurements at mass resolution 4000. The detection limit for {sup 236}U and the lowest detectable {sup 236}U/{sup 238}U isotope ratio were improved by more than two orders of magnitude compared with corresponding values by alpha spectrometry. Determination of uranium in soil samples collected in the vicinity of Chernobyl nuclear power plant (NPP) resulted in that the {sup 236}U/{sup 238}U isotope ratio is a much more sensitive and accurate marker for environmental contamination by spent uranium in comparison to the {sup 235}U/{sup 238}U isotope ratio. The ICP-MS technique allowed for the first time detection of irradiated uranium in soil samples even at distances more than 200 km to the north of Chernobyl NPP (Mogilev region). The concentration of {sup 236}U in the upper 0-10 cm soil layers varied from 2 x 10{sup -9} g g{sup -1} within radioactive spots close to the Chernobyl NPP to 3 x 10{sup -13} g g{sup -1} on a sampling site located by >200 km from Chernobyl.

  12. Mandelbrot's Extremism

    NARCIS (Netherlands)

    Beirlant, J.; Schoutens, W.; Segers, J.J.J.

    2004-01-01

    In the sixties Mandelbrot already showed that extreme price swings are more likely than some of us think or incorporate in our models.A modern toolbox for analyzing such rare events can be found in the field of extreme value theory.At the core of extreme value theory lies the modelling of maxima

  13. Evaluation of markers for CpG island methylator phenotype (CIMP) in colorectal cancer by a large population-based sample.

    Science.gov (United States)

    Ogino, Shuji; Kawasaki, Takako; Kirkner, Gregory J; Kraft, Peter; Loda, Massimo; Fuchs, Charles S

    2007-07-01

    The CpG island methylator phenotype (CIMP or CIMP-high) with extensive promoter methylation is a distinct phenotype in colorectal cancer. However, a choice of markers for CIMP has been controversial. A recent extensive investigation has selected five methylation markers (CACNA1G, IGF2, NEUROG1, RUNX3, and SOCS1) as surrogate markers for epigenomic aberrations in tumor. The use of these markers as a CIMP-specific panel needs to be validated by an independent, large dataset. Using MethyLight assays on 920 colorectal cancers from two large prospective cohort studies, we quantified DNA methylation in eight CIMP-specific markers [the above five plus CDKN2A (p16), CRABP1, and MLH1]. A CIMP-high cutoff was set at > or = 6/8 or > or = 5/8 methylated promoters, based on tumor distribution and BRAF/KRAS mutation frequencies. All but two very specific markers [MLH1 (98% specific) and SOCS1 (93% specific)] demonstrated > or = 85% sensitivity and > or = 80% specificity, indicating overall good concordance in methylation patterns and good performance of these markers. Based on sensitivity, specificity, and false positives and negatives, the eight markers were ranked in order as: RUNX3, CACNA1G, IGF2, MLH1, NEUROG1, CRABP1, SOCS1, and CDKN2A. In conclusion, a panel of markers including at least RUNX3, CACNA1G, IGF2, and MLH1 can serve as a sensitive and specific marker panel for CIMP-high.

  14. Extreme cosmos

    CERN Document Server

    Gaensler, Bryan

    2011-01-01

    The universe is all about extremes. Space has a temperature 270°C below freezing. Stars die in catastrophic supernova explosions a billion times brighter than the Sun. A black hole can generate 10 million trillion volts of electricity. And hypergiants are stars 2 billion kilometres across, larger than the orbit of Jupiter. Extreme Cosmos provides a stunning new view of the way the Universe works, seen through the lens of extremes: the fastest, hottest, heaviest, brightest, oldest, densest and even the loudest. This is an astronomy book that not only offers amazing facts and figures but also re

  15. Extreme-temperature lab on a chip for optogalvanic spectroscopy of ultra small samples - key components and a first integration attempt

    International Nuclear Information System (INIS)

    Berglund, Martin; Khaji, Zahra; Persson, Anders; Sturesson, Peter; Breivik, Johan Söderberg; Thornell, Greger; Klintberg, Lena

    2016-01-01

    This is a short summary of the authors’ recent R and D on valves, combustors, plasma sources, and pressure and temperature sensors, realized in high-temperature co-fired ceramics, and an account for the first attempt to monolithically integrate them to form a lab on a chip for sample administration, preparation and analysis, as a stage in optogalvanic spectroscopy. (paper)

  16. An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples

    Directory of Open Access Journals (Sweden)

    Laura Clusa

    2017-02-01

    Full Text Available Background Salmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar, brown trout Salmo trutta, brook trout Salvelinus fontinalis, and lake trout Salvelinus namaycush. In contrast, other salmonids are endangered in their native settings. Methods Here we have developed a method to identify salmonid species directly from water samples, focusing on the Iberian Peninsula as a case study. We have designed nested Salmonidae-specific primers within the 16S rDNA region. From these primers and a PCR-RFLP procedure the target species can be unequivocally identified from DNA extracted from water samples. Results The method was validated in aquarium experiments and in the field with water from watersheds with known salmonid populations. Finally, the method was applied to obtain a global view of the Salmonidae community in Nalón River (north coast of Spain. Discussion This new powerful, very sensitive (identifying the species down to 10 pg DNA/ml water and economical tool can be applied for monitoring the presence of salmonids in a variety of situations, from checking upstream colonization after removal of river barriers to monitoring potential escapes from fish farms.

  17. The effects of cognitive activity combined with active extremity exercise on balance, walking activity, memory level and quality of life of an older adult sample with dementia.

    Science.gov (United States)

    Yoon, Jung Eun; Lee, Suk Min; Lim, Hee Sung; Kim, Tae Hoon; Jeon, Ji Kyeng; Mun, Mee Hyang

    2013-12-01

    [Purpose] The purpose of this study was to compare the effectiveness of cognitive activity combined with active physical exercise for a sample of older adults with dementia. [Subjects] A convenience sample of 30 patients with dementia (Mini-Mental State Examination score between 16 and 23) was used. Participants were randomly allocated to one of two groups: cognitive activity combined with physical exercise CAE, n=11), and only cognitive activity CA, n=9). [Methods] Both groups participated in a therapeutic exercise program for 30 minutes, three days a week for 12 weeks. The CAE group performed an additional exercise for 30 minutes a day, three days a week for 12 weeks. A Wii Balance Board (WBB, Nintendo, Japan) was used to evaluate postural sway as an assessment of balance. The Berg Balance Scale (BBS) and Modified Falls Efficacy Scale (MFES) were used to assess dynamic balance abilities. The Timed Up-and-Go test (TUG) was used to assess gait, and the Digit Span Test (DST) and 7 Minute Screening Test (7MST) were used to measure memory performance. The Mini-Mental Status Exam-Korean version (MMSE-K), Kenny Self-Care Evaluation (KSCE), and Short Geriatric Depression Scale (GDS) were used to assess quality of life (QOL). [Results] There were significant beneficial effects of the therapeutic program on balance (velocity in EOWB, path length in ECNB, BBS, and MMFE), QOL (MMSE-KC, GDS, KSCE), and memory performance (DSB) in the CAE group compared to CA group, and between pre-test and post-test. [Conclusion] A 12-week CAE program resulted in improvements in balance, memory and QOL. Therefore, some older adults with dementia have the ability to acquire effective skills relevant to daily living.

  18. Versatile lipid profiling by liquid chromatography–high resolution mass spectrometry using all ion fragmentation and polarity switching. Preliminary application for serum samples phenotyping related to canine mammary cancer

    Energy Technology Data Exchange (ETDEWEB)

    Gallart-Ayala, H., E-mail: laberca@oniris-nantes.fr [LUNAM, Ecole Nationale Vétérinaire, Agroalimentaire et de l’Alimentation Nantes Atlantique (Oniris), USC 1329 INRA Laboratoire d’Etude des résidus et Contaminants dans les Aliments (LABERCA), Site de la Chantrerie – CS50707, 44307 Nantes cedex 3 (France); Courant, F.; Severe, S.; Antignac, J.-P. [LUNAM, Ecole Nationale Vétérinaire, Agroalimentaire et de l’Alimentation Nantes Atlantique (Oniris), USC 1329 INRA Laboratoire d’Etude des résidus et Contaminants dans les Aliments (LABERCA), Site de la Chantrerie – CS50707, 44307 Nantes cedex 3 (France); Morio, F.; Abadie, J. [LUNAM, Ecole Nationale Vétérinaire, Agroalimentaire et de l’Alimentation Nantes Atlantique (Oniris), Cancers Animaux, Modèles pour la Recherche en Oncologie Comparée (AMaROC), Site de la Chantrerie–CS50707, 44307 Nantes cedex 3 (France); Le Bizec, B. [LUNAM, Ecole Nationale Vétérinaire, Agroalimentaire et de l’Alimentation Nantes Atlantique (Oniris), USC 1329 INRA Laboratoire d’Etude des résidus et Contaminants dans les Aliments (LABERCA), Site de la Chantrerie – CS50707, 44307 Nantes cedex 3 (France)

    2013-09-24

    Graphical abstract: -- Highlights: •Lipidomics, high resolution mass spectrometry, polarity switching, serum, canine mammary cancer. -- Abstract: Lipids represent an extended class of substances characterized by such high variety and complexity that makes their unified analyses by liquid chromatography coupled to either high resolution or tandem mass spectrometry (LC–HRMS or LC–MS/MS) a real challenge. In the present study, a new versatile methodology associating ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC–HRMS/MS) have been developed for a comprehensive analysis of lipids. The use of polarity switching and “all ion fragmentation” (AIF) have been two action levels particularly exploited to finally permit the detection and identification of a multi-class and multi-analyte extended range of lipids in a single run. For identification purposes, both higher energy collision dissociation (HCD) and in-source CID (collision induced dissociation) fragmentation were evaluated in order to obtain information about the precursor and product ions in the same spectra. This approach provides both class-specific and lipid-specific fragments, enhancing lipid identification. Finally, the developed method was applied for differential phenotyping of serum samples collected from pet dogs developing spontaneous malignant mammary tumors and health controls. A biological signature associated with the presence of cancer was then successfully revealed from this lipidome analysis, which required to be further investigated and confirmed at larger scale.

  19. Versatile lipid profiling by liquid chromatography–high resolution mass spectrometry using all ion fragmentation and polarity switching. Preliminary application for serum samples phenotyping related to canine mammary cancer

    International Nuclear Information System (INIS)

    Gallart-Ayala, H.; Courant, F.; Severe, S.; Antignac, J.-P.; Morio, F.; Abadie, J.; Le Bizec, B.

    2013-01-01

    Graphical abstract: -- Highlights: •Lipidomics, high resolution mass spectrometry, polarity switching, serum, canine mammary cancer. -- Abstract: Lipids represent an extended class of substances characterized by such high variety and complexity that makes their unified analyses by liquid chromatography coupled to either high resolution or tandem mass spectrometry (LC–HRMS or LC–MS/MS) a real challenge. In the present study, a new versatile methodology associating ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC–HRMS/MS) have been developed for a comprehensive analysis of lipids. The use of polarity switching and “all ion fragmentation” (AIF) have been two action levels particularly exploited to finally permit the detection and identification of a multi-class and multi-analyte extended range of lipids in a single run. For identification purposes, both higher energy collision dissociation (HCD) and in-source CID (collision induced dissociation) fragmentation were evaluated in order to obtain information about the precursor and product ions in the same spectra. This approach provides both class-specific and lipid-specific fragments, enhancing lipid identification. Finally, the developed method was applied for differential phenotyping of serum samples collected from pet dogs developing spontaneous malignant mammary tumors and health controls. A biological signature associated with the presence of cancer was then successfully revealed from this lipidome analysis, which required to be further investigated and confirmed at larger scale

  20. Versatile lipid profiling by liquid chromatography-high resolution mass spectrometry using all ion fragmentation and polarity switching. Preliminary application for serum samples phenotyping related to canine mammary cancer.

    Science.gov (United States)

    Gallart-Ayala, H; Courant, F; Severe, S; Antignac, J-P; Morio, F; Abadie, J; Le Bizec, B

    2013-09-24

    Lipids represent an extended class of substances characterized by such high variety and complexity that makes their unified analyses by liquid chromatography coupled to either high resolution or tandem mass spectrometry (LC-HRMS or LC-MS/MS) a real challenge. In the present study, a new versatile methodology associating ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-HRMS/MS) have been developed for a comprehensive analysis of lipids. The use of polarity switching and "all ion fragmentation" (AIF) have been two action levels particularly exploited to finally permit the detection and identification of a multi-class and multi-analyte extended range of lipids in a single run. For identification purposes, both higher energy collision dissociation (HCD) and in-source CID (collision induced dissociation) fragmentation were evaluated in order to obtain information about the precursor and product ions in the same spectra. This approach provides both class-specific and lipid-specific fragments, enhancing lipid identification. Finally, the developed method was applied for differential phenotyping of serum samples collected from pet dogs developing spontaneous malignant mammary tumors and health controls. A biological signature associated with the presence of cancer was then successfully revealed from this lipidome analysis, which required to be further investigated and confirmed at larger scale. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Effects of low birth weight, maternal smoking in pregnancy and social class on the phenotypic manifestation of Attention Deficit Hyperactivity Disorder and associated antisocial behaviour: investigation in a clinical sample

    Directory of Open Access Journals (Sweden)

    van den Bree Marianne BM

    2007-06-01

    Full Text Available Abstract Background Attention Deficit Hyperactivity Disorder (ADHD is a genetically influenced condition although indicators of environmental risk including maternal smoking during pregnancy, low birth weight and low social class have also been found to be associated with the disorder. ADHD is a phenotypically heterogeneous disorder in terms of the predominant symptom types (inattention, hyperactive-impulsivity, their severity and comorbidity, notably Conduct Disorder. It is possible that these different clinical manifestations of the disorder may arise because of the differing effects of the environmental indicators of environmental risk. We set out to test this hypothesis. Methods In a sample of 356 children diagnosed with ADHD, we sought to investigate possible effects of three indicators of environmental risk – maternal smoking during pregnancy, birth weight and social class – on comorbid Conduct Disorder, conduct disorder symptoms and inattentive and hyperactive-impulsive symptom severity. Results Multiple regression analysis revealed that, after controlling for significant covariates, greater hyperactive-impulsive symptom severity was significantly associated with maternal smoking during pregnancy (r2 = 0.02, Beta = 0.11, t = 1.96, p = 0.05 and social class (r2 = 0.02, Beta = 0.12, t = 2.19, p = 0.03 whilst none of the environmental risk indicators significantly predicted number of inattentive symptoms. Conduct Disorder symptoms were positively predicted by maternal smoking in pregnancy (r2 = 0.04, Beta = 0.18, t = 3.34, p = 0.001 whilst both maternal smoking during pregnancy and social class significantly predicted a diagnosis of Conduct Disorder (OR = 3.14, 95% CI: 1.54, 6.41, Wald = 9.95, p = 0.002 and (OR = 1.95 95% CI: 1.18, 3.23 Wald = 6.78, p = 0.009 respectively. Conclusion These findings suggest that indicators of environmental risk, in this instance maternal smoking in pregnancy and environmental adversity indexed by lower

  2. From metabolome to phenotype

    DEFF Research Database (Denmark)

    Khakimov, Bekzod; Rasmussen, Morten Arendt; Kannangara, Rubini Maya

    2017-01-01

    for ideal vegetable protein production and for augmented β-glucan production. Seeds from three barley lines (Bomi, lys3.a and lys5.f) were sampled eight times during grain filling and analysed for metabolites using gas chromatography-mass spectrometry (GC-MS). The lys3.a mutation disrupts a regulator gene...... their successful application to link genetic and environmental factors with the seed phenotype of unique and agro-economically important barley models for optimal vegetable protein and dietary fibre production......., causing an increase in proteins rich in the essential amino acid lysine, while lys5.f carries a mutation in an ADP-glucose transporter gene leading to a significant increase in production of mixed-linkage β-glucan at the expense of α-glucan. Unique metabolic patterns associated with the tricarboxylic acid...

  3. Phenotypic plasticity and local adaptation in two extreme ...

    African Journals Online (AJOL)

    Principal coordinate analysis (PCoA) of allozymes revealed little genetic overlap among populations. Keywords: allozyme, genotype×environment interaction, genetic variation, local adaptation, reaction norms, starch gel electrophoresis, trade-off. African Journal of Range & Forage Science 2008, 25(3): 121–130 ...

  4. Extreme phenotypes in hypercholesterolemia : From genotype to therapy

    NARCIS (Netherlands)

    Sjouke, B.

    2017-01-01

    Familial hypercholesterolemia (FH) is an inherited disorder of cholesterol metabolism, resulting in increased LDL-cholesterol levels and, as a consequence, an increased risk for coronary heart disease. Recently, many causal FH mutations in different genes have been identified and advances in genetic

  5. Asthma phenotypes in childhood.

    Science.gov (United States)

    Reddy, Monica B; Covar, Ronina A

    2016-04-01

    This review describes the literature over the past 18 months that evaluated childhood asthma phenotypes, highlighting the key aspects of these studies, and comparing these studies to previous ones in this area. Recent studies on asthma phenotypes have identified new phenotypes on the basis of statistical analyses (using cluster analysis and latent class analysis methodology) and have evaluated the outcomes and associated risk factors of previously established early childhood asthma phenotypes that are based on asthma onset and patterns of wheezing illness. There have also been investigations focusing on immunologic, physiologic, and genetic correlates of various phenotypes, as well as identification of subphenotypes of severe childhood asthma. Childhood asthma remains a heterogeneous condition, and investigations into these various presentations, risk factors, and outcomes are important since they can offer therapeutic and prognostic relevance. Further investigation into the immunopathology and genetic basis underlying childhood phenotypes is important so therapy can be tailored accordingly.

  6. Extremely Preterm Birth

    Science.gov (United States)

    ... Events Advocacy For Patients About ACOG Extremely Preterm Birth Home For Patients Search FAQs Extremely Preterm Birth ... Spanish FAQ173, June 2016 PDF Format Extremely Preterm Birth Pregnancy When is a baby considered “preterm” or “ ...

  7. Federated Tensor Factorization for Computational Phenotyping

    Science.gov (United States)

    Kim, Yejin; Sun, Jimeng; Yu, Hwanjo; Jiang, Xiaoqian

    2017-01-01

    Tensor factorization models offer an effective approach to convert massive electronic health records into meaningful clinical concepts (phenotypes) for data analysis. These models need a large amount of diverse samples to avoid population bias. An open challenge is how to derive phenotypes jointly across multiple hospitals, in which direct patient-level data sharing is not possible (e.g., due to institutional policies). In this paper, we developed a novel solution to enable federated tensor factorization for computational phenotyping without sharing patient-level data. We developed secure data harmonization and federated computation procedures based on alternating direction method of multipliers (ADMM). Using this method, the multiple hospitals iteratively update tensors and transfer secure summarized information to a central server, and the server aggregates the information to generate phenotypes. We demonstrated with real medical datasets that our method resembles the centralized training model (based on combined datasets) in terms of accuracy and phenotypes discovery while respecting privacy. PMID:29071165

  8. Clinical phenotypes of asthma

    NARCIS (Netherlands)

    Bel, Elisabeth H.

    2004-01-01

    PURPOSE OF REVIEW: Asthma is a phenotypically heterogeneous disorder and, over the years, many different clinical subtypes of asthma have been described. A precise definition of asthma phenotypes is now becoming more and more important, not only for a better understanding of pathophysiologic

  9. Statistical Model of Extreme Shear

    DEFF Research Database (Denmark)

    Larsen, Gunner Chr.; Hansen, Kurt Schaldemose

    2004-01-01

    In order to continue cost-optimisation of modern large wind turbines, it is important to continously increase the knowledge on wind field parameters relevant to design loads. This paper presents a general statistical model that offers site-specific prediction of the probability density function...... by a model that, on a statistically consistent basis, describe the most likely spatial shape of an extreme wind shear event. Predictions from the model have been compared with results from an extreme value data analysis, based on a large number of high-sampled full-scale time series measurements...... are consistent, given the inevitabel uncertainties associated with model as well as with the extreme value data analysis. Keywords: Statistical model, extreme wind conditions, statistical analysis, turbulence, wind loading, statistical analysis, turbulence, wind loading, wind shear, wind turbines....

  10. The opposite end of the attention deficit hyperactivity disorder continuum: genetic and environmental aetiologies of extremely low ADHD traits.

    Science.gov (United States)

    Greven, Corina U; Merwood, Andrew; van der Meer, Jolanda M J; Haworth, Claire M A; Rommelse, Nanda; Buitelaar, Jan K

    2016-04-01

    Although attention deficit hyperactivity disorder (ADHD) is thought to reflect a continuously distributed quantitative trait, it is assessed through binary diagnosis or skewed measures biased towards its high, symptomatic extreme. A growing trend is to study the positive tail of normally distributed traits, a promising avenue, for example, to study high intelligence to increase power for gene-hunting for intelligence. However, the emergence of such a 'positive genetics' model has been tempered for ADHD due to poor phenotypic resolution at the low extreme. Overcoming this methodological limitation, we conduct the first study to assess the aetiologies of low extreme ADHD traits. In a population-representative sample of 2,143 twins, the Strength and Weaknesses of ADHD Symptoms and Normal behaviour (SWAN) questionnaire was used to assess ADHD traits on a continuum from low to high. Aetiological influences on extreme ADHD traits were estimated using DeFries-Fulker extremes analysis. ADHD traits were related to behavioural, cognitive and home environmental outcomes using regression. Low extreme ADHD traits were significantly influenced by shared environmental factors (23-35%) but were not significantly heritable. In contrast, high-extreme ADHD traits showed significant heritability (39-51%) but no shared environmental influences. Compared to individuals with high extreme or with average levels of ADHD traits, individuals with low extreme ADHD traits showed fewer internalizing and externalizing behaviour problems, better cognitive performance and more positive behaviours and positive home environmental outcomes. Shared environmental influences on low extreme ADHD traits may reflect passive gene-environment correlation, which arises because parents provide environments as well as passing on genes. Studying the low extreme opens new avenues to study mechanisms underlying previously neglected positive behaviours. This is different from the current deficit-based model of

  11. Extreme conditions (p, T, H)

    Energy Technology Data Exchange (ETDEWEB)

    Mesot, J [Lab. for Neutron Scattering ETH Zurich, Zurich (Switzerland) and Paul Scherrer Institute, Villigen (Switzerland)

    1996-11-01

    The aim of this paper is to summarize the sample environment which will be accessible at the SINQ. In order to illustrate the type of experiments which will be feasible under extreme conditions of temperature, magnetic field and pressure at the SINQ a few selected examples are also given. (author) 7 figs., 14 refs.

  12. Extreme Ionizing-Radiation-Resistant Bacterium

    Science.gov (United States)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

    2013-01-01

    There is a growing concern that desiccation and extreme radiation-resistant, non-spore-forming microorganisms associated with spacecraft surfaces can withstand space environmental conditions and subsequent proliferation on another solar body. Such forward contamination would jeopardize future life detection or sample return technologies. The prime focus of NASA s planetary protection efforts is the development of strategies for inactivating resistance-bearing micro-organisms. Eradi cation techniques can be designed to target resistance-conferring microbial populations by first identifying and understanding their physiologic and biochemical capabilities that confers its elevated tolerance (as is being studied in Deinococcus phoenicis, as a result of this description). Furthermore, hospitals, food, and government agencies frequently use biological indicators to ensure the efficacy of a wide range of radiation-based sterilization processes. Due to their resistance to a variety of perturbations, the nonspore forming D. phoenicis may be a more appropriate biological indicator than those currently in use. The high flux of cosmic rays during space travel and onto the unshielded surface of Mars poses a significant hazard to the survival of microbial life. Thus, radiation-resistant microorganisms are of particular concern that can survive extreme radiation, desiccation, and low temperatures experienced during space travel. Spore-forming bacteria, a common inhabitant of spacecraft assembly facilities, are known to tolerate these extreme conditions. Since the Viking era, spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. Members of the non-sporeforming bacterial community such as Deinococcus radiodurans can survive acute exposures to ionizing radiation (5 kGy), ultraviolet light (1 kJ/m2), and desiccation (years). These resistive phenotypes of Deinococcus enhance the

  13. Phenotypic covariance at species' borders.

    Science.gov (United States)

    Caley, M Julian; Cripps, Edward; Game, Edward T

    2013-05-28

    Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species' borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species' borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future.

  14. Wine Expertise Predicts Taste Phenotype.

    Science.gov (United States)

    Hayes, John E; Pickering, Gary J

    2012-03-01

    Taste phenotypes have long been studied in relation to alcohol intake, dependence, and family history, with contradictory findings. However, on balance - with appropriate caveats about populations tested, outcomes measured and psychophysical methods used - an association between variation in taste responsiveness and some alcohol behaviors is supported. Recent work suggests super-tasting (operationalized via propylthiouracil (PROP) bitterness) not only associates with heightened response but also with more acute discrimination between stimuli. Here, we explore relationships between food and beverage adventurousness and taste phenotype. A convenience sample of wine drinkers (n=330) were recruited in Ontario and phenotyped for PROP bitterness via filter paper disk. They also filled out a short questionnaire regarding willingness to try new foods, alcoholic beverages and wines as well as level of wine involvement, which was used to classify them as a wine expert (n=110) or wine consumer (n=220). In univariate logisitic models, food adventurousness predicted trying new wines and beverages but not expertise. Likewise, wine expertise predicted willingness to try new wines and beverages but not foods. In separate multivariate logistic models, willingness to try new wines and beverages was predicted by expertise and food adventurousness but not PROP. However, mean PROP bitterness was higher among wine experts than wine consumers, and the conditional distribution functions differed between experts and consumers. In contrast, PROP means and distributions did not differ with food adventurousness. These data suggest individuals may self-select for specific professions based on sensory ability (i.e., an active gene-environment correlation) but phenotype does not explain willingness to try new stimuli.

  15. Statistical Model of Extreme Shear

    DEFF Research Database (Denmark)

    Hansen, Kurt Schaldemose; Larsen, Gunner Chr.

    2005-01-01

    In order to continue cost-optimisation of modern large wind turbines, it is important to continuously increase the knowledge of wind field parameters relevant to design loads. This paper presents a general statistical model that offers site-specific prediction of the probability density function...... by a model that, on a statistically consistent basis, describes the most likely spatial shape of an extreme wind shear event. Predictions from the model have been compared with results from an extreme value data analysis, based on a large number of full-scale measurements recorded with a high sampling rate...

  16. Extreme environment electronics

    CERN Document Server

    Cressler, John D

    2012-01-01

    Unfriendly to conventional electronic devices, circuits, and systems, extreme environments represent a serious challenge to designers and mission architects. The first truly comprehensive guide to this specialized field, Extreme Environment Electronics explains the essential aspects of designing and using devices, circuits, and electronic systems intended to operate in extreme environments, including across wide temperature ranges and in radiation-intense scenarios such as space. The Definitive Guide to Extreme Environment Electronics Featuring contributions by some of the world's foremost exp

  17. Extreme value distributions

    CERN Document Server

    Ahsanullah, Mohammad

    2016-01-01

    The aim of the book is to give a through account of the basic theory of extreme value distributions. The book cover a wide range of materials available to date. The central ideas and results of extreme value distributions are presented. The book rwill be useful o applied statisticians as well statisticians interrested to work in the area of extreme value distributions.vmonograph presents the central ideas and results of extreme value distributions.The monograph gives self-contained of theory and applications of extreme value distributions.

  18. COPD: Definition and Phenotypes

    DEFF Research Database (Denmark)

    Vestbo, J.

    2014-01-01

    particles or gases. Exacerbations and comorbidities contribute to the overall severity in individual patients. The evolution of this definition and the diagnostic criteria currently in use are discussed. COPD is increasingly divided in subgroups or phenotypes based on specific features and association...

  19. Phenotypic Resistance to Antibiotics

    Directory of Open Access Journals (Sweden)

    Jose L. Martinez

    2013-04-01

    Full Text Available The development of antibiotic resistance is usually associated with genetic changes, either to the acquisition of resistance genes, or to mutations in elements relevant for the activity of the antibiotic. However, in some situations resistance can be achieved without any genetic alteration; this is called phenotypic resistance. Non-inherited resistance is associated to specific processes such as growth in biofilms, a stationary growth phase or persistence. These situations might occur during infection but they are not usually considered in classical susceptibility tests at the clinical microbiology laboratories. Recent work has also shown that the susceptibility to antibiotics is highly dependent on the bacterial metabolism and that global metabolic regulators can modulate this phenotype. This modulation includes situations in which bacteria can be more resistant or more susceptible to antibiotics. Understanding these processes will thus help in establishing novel therapeutic approaches based on the actual susceptibility shown by bacteria during infection, which might differ from that determined in the laboratory. In this review, we discuss different examples of phenotypic resistance and the mechanisms that regulate the crosstalk between bacterial metabolism and the susceptibility to antibiotics. Finally, information on strategies currently under development for diminishing the phenotypic resistance to antibiotics of bacterial pathogens is presented.

  20. phenotype correlation of methylene tetrahydrofolate reductase ...

    African Journals Online (AJOL)

    Rabah M. Shawky

    2014-06-21

    Jun 21, 2014 ... children with autism and to correlate them with different phenotypes. Subjects and ... of impairments in communication, reciprocal social interac- tions, and ... isolation was obtained from peripheral blood samples using the spin ... IQ, while ten of them (50%) had mild mental retardation and six patients (30%) ...

  1. How extreme is extreme hourly precipitation?

    Science.gov (United States)

    Papalexiou, Simon Michael; Dialynas, Yannis G.; Pappas, Christoforos

    2016-04-01

    The importance of accurate representation of precipitation at fine time scales (e.g., hourly), directly associated with flash flood events, is crucial in hydrological design and prediction. The upper part of a probability distribution, known as the distribution tail, determines the behavior of extreme events. In general, and loosely speaking, tails can be categorized in two families: the subexponential and the hyperexponential family, with the first generating more intense and more frequent extremes compared to the latter. In past studies, the focus has been mainly on daily precipitation, with the Gamma distribution being the most popular model. Here, we investigate the behaviour of tails of hourly precipitation by comparing the upper part of empirical distributions of thousands of records with three general types of tails corresponding to the Pareto, Lognormal, and Weibull distributions. Specifically, we use thousands of hourly rainfall records from all over the USA. The analysis indicates that heavier-tailed distributions describe better the observed hourly rainfall extremes in comparison to lighter tails. Traditional representations of the marginal distribution of hourly rainfall may significantly deviate from observed behaviours of extremes, with direct implications on hydroclimatic variables modelling and engineering design.

  2. Optimization with Extremal Dynamics

    International Nuclear Information System (INIS)

    Boettcher, Stefan; Percus, Allon G.

    2001-01-01

    We explore a new general-purpose heuristic for finding high-quality solutions to hard discrete optimization problems. The method, called extremal optimization, is inspired by self-organized criticality, a concept introduced to describe emergent complexity in physical systems. Extremal optimization successively updates extremely undesirable variables of a single suboptimal solution, assigning them new, random values. Large fluctuations ensue, efficiently exploring many local optima. We use extremal optimization to elucidate the phase transition in the 3-coloring problem, and we provide independent confirmation of previously reported extrapolations for the ground-state energy of ±J spin glasses in d=3 and 4

  3. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

    Science.gov (United States)

    Castoe, Todd A; de Koning, A P Jason; Hall, Kathryn T; Card, Daren C; Schield, Drew R; Fujita, Matthew K; Ruggiero, Robert P; Degner, Jack F; Daza, Juan M; Gu, Wanjun; Reyes-Velasco, Jacobo; Shaney, Kyle J; Castoe, Jill M; Fox, Samuel E; Poole, Alex W; Polanco, Daniel; Dobry, Jason; Vandewege, Michael W; Li, Qing; Schott, Ryan K; Kapusta, Aurélie; Minx, Patrick; Feschotte, Cédric; Uetz, Peter; Ray, David A; Hoffmann, Federico G; Bogden, Robert; Smith, Eric N; Chang, Belinda S W; Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Richardson, Michael K; Mackessy, Stephen P; Bronikowski, Anne M; Bronikowsi, Anne M; Yandell, Mark; Warren, Wesley C; Secor, Stephen M; Pollock, David D

    2013-12-17

    Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.

  4. Alteration of a human intestinal microbiota under extreme life environment in the Antarctica.

    Science.gov (United States)

    Jin, Jong-Sik; Touyama, Mutsumi; Yamada, Shin; Yamazaki, Takashi; Benno, Yoshimi

    2014-01-01

    The human intestinal microbiota (HIM) settles from birth and continues to change phenotype by some factors (e.g. host's diet) throughout life. However, the effect of extreme life environment on human HIM composition is not well known. To understand HIM fluctuation under extreme life environment in humans, fecal samples were collected from six Japanese men on a long Antarctic expedition. They explored Antarctica for 3 months and collected their fecal samples at once-monthly intervals. Using terminal restriction fragment length polymorphism (T-RFLP) and real time polymerase chain reaction (PCR) analysis, the composition of HIM in six subjects was investigated. Three subjects presented restoration of HIM after the expedition compared versus before and during the expedition. Two thirds samples collected during the expedition belonged to the same cluster in dendrogram. However, all through the expedition, T-RFLP patterns showed interindividual variability. Especially, Bifidobacterium spp. showed a tendency to decrease during and restore after the expedition. A reduction of Bifidobacterium spp. was observed in five subjects the first 1 month of the expedition. Bacteroides thetaiotaomicron, which is thought to proliferate during emotional stress, significantly decreased in one subject, indicating that other factors in addition to emotional stress may affect the composition of HIM in this study. These findings could be helpful to understand the effect of extreme life environment on HIM.

  5. Are BALQSOs extreme accretors?

    Science.gov (United States)

    Yuan, M. J.; Wills, B. J.

    2002-12-01

    Broad Absorption Line (BAL) QSOs are QSOs with massive absorbing outflows up to 0.2c. Two hypothesis have been suggested in the past about the nature of BALQSOs: Every QSO might have BAL outflow with some covering factor. BALQSOs are those which happen to have outflow along our line of sight. BALQSOs have intrinsically different physical properties than non-BALQSOs. Based on BALQSO's optical emission properties and a large set of correlations linking many general QSO emission line and continuum properties, it has been suggested that BALQSOs might accrete at near Eddington limit with abundant of fuel supplies. With new BALQSO Hβ region spectroscopic observation conducted at UKIRT and re-analysis of literature data for low and high redshift non-BALQSOs, We confirm that BALQSOs have extreme Fe II and [O III] emission line properties. Using results derived from the latest QSO Hβ region reverberation mapping, we calculated Eddington ratios (˙ {M}/˙ {M}Edd) for our BAL and non-BALQSOs. The Fe II and [O III] strengths are strongly correlated with Eddington ratios. Those correlations link Eddington ratio to a large set of general QSO properties through the Boroson & Green Eigenvector 1. We find that BALQSOs have Eddington ratios close to 1. However, all high redshift, high luminosity QSOs have rather high Eddington ratios. We argue that this is a side effect from selecting the brightest objects. In fact, our high redshift sample might constitute BALQSO's high Eddington ratio orientation parent population.

  6. Identification of 16q21 as a modifier of nonsyndromic orofacial cleft phenotypes

    DEFF Research Database (Denmark)

    Carlson, Jenna C; Standley, Jennifer; Petrin, Aline

    2017-01-01

    Orofacial clefts (OFCs) are common, complex birth defects with extremely heterogeneous phenotypic presentations. Two common subtypes-cleft lip alone (CL) and CL plus cleft palate (CLP)-are typically grouped into a single phenotype for genetic analysis (i.e., CL with or without cleft palate, CL/P)...

  7. ACE phenotyping in Gaucher disease.

    Science.gov (United States)

    Danilov, Sergei M; Tikhomirova, Victoria E; Metzger, Roman; Naperova, Irina A; Bukina, Tatiana M; Goker-Alpan, Ozlem; Tayebi, Nahid; Gayfullin, Nurshat M; Schwartz, David E; Samokhodskaya, Larisa M; Kost, Olga A; Sidransky, Ellen

    2018-04-01

    Gaucher disease is characterized by the activation of splenic and hepatic macrophages, accompanied by dramatically increased levels of angiotensin-converting enzyme (ACE). To evaluate the source of the elevated blood ACE, we performed complete ACE phenotyping using blood, spleen and liver samples from patients with Gaucher disease and controls. ACE phenotyping included 1) immunohistochemical staining for ACE; 2) measuring ACE activity with two substrates (HHL and ZPHL); 3) calculating the ratio of the rates of substrate hydrolysis (ZPHL/HHL ratio); 4) assessing the conformational fingerprint of ACE by evaluating the pattern of binding of monoclonal antibodies to 16 different ACE epitopes. We show that in patients with Gaucher disease, the dramatically increased levels of ACE originate from activated splenic and/or hepatic macrophages (Gaucher cells), and that both its conformational fingerprint and kinetic characteristics (ZPHL/HHL ratio) differ from controls and from patients with sarcoid granulomas. Furthermore, normal spleen was found to produce high levels of endogenous ACE inhibitors and a novel, tightly-bound 10-30 kDa ACE effector which is deficient in Gaucher spleen. The conformation of ACE is tissue-specific. In Gaucher disease, ACE produced by activated splenic macrophages differs from that in hepatic macrophages, as well as from macrophages and dendritic cells in sarcoid granulomas. The observed differences are likely due to altered ACE glycosylation or sialylation in these diseased organs. The conformational differences in ACE may serve as a specific biomarker for Gaucher disease. Copyright © 2018 Elsevier Inc. All rights reserved.

  8. Is there any relationship between haptoglobin phenotypes and ...

    African Journals Online (AJOL)

    This study was conducted to examine the possible association between Haptoglobin (Hp) phenotypes and diabetes retinopathy in some Ghanaians to determine whether a specific Hp phenotype predisposes diabetics to retinopathy. A total of 110 diabetics were enrolled into the study. Blood samples were taken from each ...

  9. ABO blood group phenotype frequency estimation using molecular phenotyping in rhesus and cynomolgus macaques.

    Science.gov (United States)

    Kanthaswamy, S; Ng, J; Oldt, R F; Valdivia, L; Houghton, P; Smith, D G

    2017-11-01

    A much larger sample (N = 2369) was used to evaluate a previously reported distribution of the A, AB and B blood group phenotypes in rhesus and cynomolgus macaques from six different regional populations. These samples, acquired from 15 different breeding and research facilities in the United States, were analyzed using a real-time quantitative polymerase chain reaction (qPCR) assay that targets single nucleotide polymorphisms (SNPs) responsible for the macaque A, B and AB phenotypes. The frequency distributions of blood group phenotypes of the two species differ significantly from each other and significant regional differentiation within the geographic ranges of each species was also observed. The B blood group phenotype was prevalent in rhesus macaques, especially those from India, while the frequencies of the A, B and AB phenotypes varied significantly among cynomolgus macaques from different geographic regions. The Mauritian cynomolgus macaques, despite having originated in Indonesia, showed significant (P ≪ .01) divergence from the Indonesian animals at the ABO blood group locus. Most Mauritian animals belonged to the B blood group while the Indonesian animals were mostly A. The close similarity in blood group frequency distributions between the Chinese rhesus and Indochinese cynomolgus macaques demonstrates that the introgression between these two species extends beyond the zone of intergradation in Indochina. This study underscores the importance of ABO blood group phenotyping of the domestic supply of macaques and their biospecimens. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  10. Invasion strategies in clonal aquatic plants: Are phenotypic differences caused by phenotypic plasticity or local adaptation?

    DEFF Research Database (Denmark)

    Riis, Tenna; Lambertini, Carla; Olesen, Birgit

    2010-01-01

    conditions and plant morphological characteristics. Conclusions: The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between......Background and Aims: The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important....... Methods: Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity...

  11. Classifying Returns as Extreme

    DEFF Research Database (Denmark)

    Christiansen, Charlotte

    2014-01-01

    I consider extreme returns for the stock and bond markets of 14 EU countries using two classification schemes: One, the univariate classification scheme from the previous literature that classifies extreme returns for each market separately, and two, a novel multivariate classification scheme tha...

  12. Age is associated with asthma phenotypes.

    Science.gov (United States)

    Ponte, Eduardo V; Lima, Aline; Almeida, Paula C A; de Jesus, Juliana P V; Lima, Valmar B; Scichilone, Nicola; Souza-Machado, Adelmir; Cruz, Álvaro A

    2017-11-01

    The relationship between age and asthma phenotypes is important as population is ageing, asthma is becoming common in older ages and recently developed treatments for asthma are guided by phenotypes. The aim of this study is to evaluate whether age is associated with specific asthma phenotypes. This is a cross-sectional study. We included subjects with asthma of varied degrees of severity. Subjects underwent spirometry, skin prick test to aeroallergens, answered the Asthma Control Questionnaire and had blood samples collected. We performed binary logistic regression analysis to evaluate whether age is associated with asthma phenotypes. We enrolled 868 subjects. In comparison with subjects ≤ 40 years, older subjects had high odds of irreversible airway obstruction (from 41 to 64 years, OR: 1.83 (95% CI: 1.32-2.54); ≥65 years, OR: 3.45 (2.12-5.60)) and severe asthma phenotypes (from 41 to 64 years, OR: 3.23 (2.26-4.62); ≥65 years, OR: 4.55 (2.39-8.67)). Older subjects had low odds of atopic (from 41 to 64 years, OR: 0.56 (0.39-0.79); ≥65 years, OR: 0.47 (0.27-0.84)) and eosinophilic phenotypes (from 41 to 64 years, OR: 0.63 (0.46-0.84); ≥65 years, OR: 0.39 (0.24-0.64)). Older subjects with asthma have low odds of atopic and eosinophilic phenotypes, whereas they present high odds of irreversible airway obstruction and severe asthma. © 2017 Asian Pacific Society of Respirology.

  13. Guidance for the utility of linear models in meta-analysis of genetic association studies of binary phenotypes.

    Science.gov (United States)

    Cook, James P; Mahajan, Anubha; Morris, Andrew P

    2017-02-01

    Linear mixed models are increasingly used for the analysis of genome-wide association studies (GWAS) of binary phenotypes because they can efficiently and robustly account for population stratification and relatedness through inclusion of random effects for a genetic relationship matrix. However, the utility of linear (mixed) models in the context of meta-analysis of GWAS of binary phenotypes has not been previously explored. In this investigation, we present simulations to compare the performance of linear and logistic regression models under alternative weighting schemes in a fixed-effects meta-analysis framework, considering designs that incorporate variable case-control imbalance, confounding factors and population stratification. Our results demonstrate that linear models can be used for meta-analysis of GWAS of binary phenotypes, without loss of power, even in the presence of extreme case-control imbalance, provided that one of the following schemes is used: (i) effective sample size weighting of Z-scores or (ii) inverse-variance weighting of allelic effect sizes after conversion onto the log-odds scale. Our conclusions thus provide essential recommendations for the development of robust protocols for meta-analysis of binary phenotypes with linear models.

  14. [Crossing borders. The motivation of extreme sportsmen].

    Science.gov (United States)

    Opaschowski, H W

    2005-08-01

    In his article "Crossing borders -- the motivation of extreme sportsmen" the author gets systematically to the bottom of the question of why extreme sportsmen voluntarily take risks and endanger themselves. Within the scope of a representative sampling 217 extreme sportsmen -- from the fields of mountain biking, trekking and free climbing, canoyning, river rafting and deep sea diving, paragliding, parachuting, bungee jumping and survival training -- give information about their personal motives. What fascinates them? The attraction of risk? The search for sensation? Or the drop out of everyday life? And what comes afterwards? Does in the end the whole life become an extreme sport? Fact is: they live extremely, because they want to move beyond well-trodden paths. To escape the boredom of everyday life they are searching for the kick, the thrill, the no-limit experience. It's about calculated risk between altitude flight and deep sea adventure.

  15. Extremal surface barriers

    International Nuclear Information System (INIS)

    Engelhardt, Netta; Wall, Aron C.

    2014-01-01

    We present a generic condition for Lorentzian manifolds to have a barrier that limits the reach of boundary-anchored extremal surfaces of arbitrary dimension. We show that any surface with nonpositive extrinsic curvature is a barrier, in the sense that extremal surfaces cannot be continuously deformed past it. Furthermore, the outermost barrier surface has nonnegative extrinsic curvature. Under certain conditions, we show that the existence of trapped surfaces implies a barrier, and conversely. In the context of AdS/CFT, these barriers imply that it is impossible to reconstruct the entire bulk using extremal surfaces. We comment on the implications for the firewall controversy

  16. Statistics of Extremes

    KAUST Repository

    Davison, Anthony C.; Huser, Raphaë l

    2015-01-01

    Statistics of extremes concerns inference for rare events. Often the events have never yet been observed, and their probabilities must therefore be estimated by extrapolation of tail models fitted to available data. Because data concerning the event

  17. Analysis of extreme events

    CSIR Research Space (South Africa)

    Khuluse, S

    2009-04-01

    Full Text Available ) determination of the distribution of the damage and (iii) preparation of products that enable prediction of future risk events. The methodology provided by extreme value theory can also be a powerful tool in risk analysis...

  18. Acute lower extremity ischaemia

    African Journals Online (AJOL)

    Acute lower extremity ischaemia. Acute lower limb ischaemia is a surgical emergency. ... is ~1.5 cases per 10 000 persons per year. Acute ischaemia ... Table 2. Clinical features discriminating embolic from thrombotic ALEXI. Clinical features.

  19. Extreme Programming: Maestro Style

    Science.gov (United States)

    Norris, Jeffrey; Fox, Jason; Rabe, Kenneth; Shu, I-Hsiang; Powell, Mark

    2009-01-01

    "Extreme Programming: Maestro Style" is the name of a computer programming methodology that has evolved as a custom version of a methodology, called extreme programming that has been practiced in the software industry since the late 1990s. The name of this version reflects its origin in the work of the Maestro team at NASA's Jet Propulsion Laboratory that develops software for Mars exploration missions. Extreme programming is oriented toward agile development of software resting on values of simplicity, communication, testing, and aggressiveness. Extreme programming involves use of methods of rapidly building and disseminating institutional knowledge among members of a computer-programming team to give all the members a shared view that matches the view of the customers for whom the software system is to be developed. Extreme programming includes frequent planning by programmers in collaboration with customers, continually examining and rewriting code in striving for the simplest workable software designs, a system metaphor (basically, an abstraction of the system that provides easy-to-remember software-naming conventions and insight into the architecture of the system), programmers working in pairs, adherence to a set of coding standards, collaboration of customers and programmers, frequent verbal communication, frequent releases of software in small increments of development, repeated testing of the developmental software by both programmers and customers, and continuous interaction between the team and the customers. The environment in which the Maestro team works requires the team to quickly adapt to changing needs of its customers. In addition, the team cannot afford to accept unnecessary development risk. Extreme programming enables the Maestro team to remain agile and provide high-quality software and service to its customers. However, several factors in the Maestro environment have made it necessary to modify some of the conventional extreme

  20. To What Extent Does DNA Methylation Affect Phenotypic Variation in Cattle?

    Directory of Open Access Journals (Sweden)

    Stephanie McKAY

    2015-07-01

    Full Text Available DNA methylation is an environmentally influenced epigenetic modification that regulates gene transcription and has the potential to influence variation in economically important phenotypes in agricultural species. We have utilized a novel approach to evaluate the relationship between genetic and epigenetic variation and downstream phenotypes. To begin with, we have integrated RNA-Seq and methyl binding domain sequencing (MBD-Seq data in order to determine the extent to which DNA methylation affects phenotypic variation in economically important traits of cattle. MBD-Seq is a technique that involves the sample enrichment of methylated genomic regions followed by their next-generation sequencing. This study utilized Illumina next generation sequencing technology to perform both RNA-Seq and MBD-Seq. NextGENe software (SoftGenetics, State College, PA was employed for quality trimming and aligning the sequence reads to the UMD3.1 bovine reference genome, generating counts of matched reads and methylated peak identification. Subsequently, we identified and quantified genome-wide methylated regions and characterized the extent of differential methylation and differential expression between two groups of animals with extreme phenotypes. The program edgeR from the R software package (version 3.0.1 was employed for identifying differentially methylated regions and regions of differential expression. Finally, Partial Correlation with Information Theory (PCIT was performed to identify transcripts and methylation events that exhibit differential hubbing. A differential hub is defined as a gene network hub that is more highly connected in one treatment group than the other. This analysis produced every possible pair-wise interaction that subsequently enabled us to look at network interactions of how methylation affects expression. (co-expression, co-methylation, methylation x expression. Genomic regions of interest derived from this analysis were then aligned

  1. Extreme meteorological conditions

    International Nuclear Information System (INIS)

    Altinger de Schwarzkopf, M.L.

    1983-01-01

    Different meteorological variables which may reach significant extreme values, such as the windspeed and, in particular, its occurrence through tornadoes and hurricanes that necesarily incide and wich must be taken into account at the time of nuclear power plants' installation, are analyzed. For this kind of study, it is necessary to determine the basic phenomenum of design. Two criteria are applied to define the basic values of design for extreme meteorological variables. The first one determines the expected extreme value: it is obtained from analyzing the recurence of the phenomenum in a convened period of time, wich may be generally of 50 years. The second one determines the extreme value of low probability, taking into account the nuclear power plant's operating life -f.ex. 25 years- and considering, during said lapse, the occurrence probabilities of extreme meteorological phenomena. The values may be determined either by the deterministic method, which is based on the acknowledgement of the fundamental physical characteristics of the phenomena or by the probabilistic method, that aims to the analysis of historical statistical data. Brief comments are made on the subject in relation to the Argentine Republic area. (R.J.S.) [es

  2. Deep Learning for Plant Phenotyping

    OpenAIRE

    Mori, Matteo

    2016-01-01

    Plant Phenotyping is an emerging science which provides us the knowledge to better understand plants. Indeed, the study of the link between genetic background and environment in which plants develop can help us to determine cures for plants’ sicknesses and new ways to improve yields using limited resources. In this regard, one of the main aspects of Plant Phenotyping that were studied in the past, was Root Phenotyping, which is based on the study of the root architectures. In particular, toda...

  3. Acclimatization to extreme heat

    Science.gov (United States)

    Warner, M. E.; Ganguly, A. R.; Bhatia, U.

    2017-12-01

    Heat extremes throughout the globe, as well as in the United States, are expected to increase. These heat extremes have been shown to impact human health, resulting in some of the highest levels of lives lost as compared with similar natural disasters. But in order to inform decision makers and best understand future mortality and morbidity, adaptation and mitigation must be considered. Defined as the ability for individuals or society to change behavior and/or adapt physiologically, acclimatization encompasses the gradual adaptation that occurs over time. Therefore, this research aims to account for acclimatization to extreme heat by using a hybrid methodology that incorporates future air conditioning use and installation patterns with future temperature-related time series data. While previous studies have not accounted for energy usage patterns and market saturation scenarios, we integrate such factors to compare the impact of air conditioning as a tool for acclimatization, with a particular emphasis on mortality within vulnerable communities.

  4. Extremely deformable structures

    CERN Document Server

    2015-01-01

    Recently, a new research stimulus has derived from the observation that soft structures, such as biological systems, but also rubber and gel, may work in a post critical regime, where elastic elements are subject to extreme deformations, though still exhibiting excellent mechanical performances. This is the realm of ‘extreme mechanics’, to which this book is addressed. The possibility of exploiting highly deformable structures opens new and unexpected technological possibilities. In particular, the challenge is the design of deformable and bi-stable mechanisms which can reach superior mechanical performances and can have a strong impact on several high-tech applications, including stretchable electronics, nanotube serpentines, deployable structures for aerospace engineering, cable deployment in the ocean, but also sensors and flexible actuators and vibration absorbers. Readers are introduced to a variety of interrelated topics involving the mechanics of extremely deformable structures, with emphasis on ...

  5. Statistics of Extremes

    KAUST Repository

    Davison, Anthony C.

    2015-04-10

    Statistics of extremes concerns inference for rare events. Often the events have never yet been observed, and their probabilities must therefore be estimated by extrapolation of tail models fitted to available data. Because data concerning the event of interest may be very limited, efficient methods of inference play an important role. This article reviews this domain, emphasizing current research topics. We first sketch the classical theory of extremes for maxima and threshold exceedances of stationary series. We then review multivariate theory, distinguishing asymptotic independence and dependence models, followed by a description of models for spatial and spatiotemporal extreme events. Finally, we discuss inference and describe two applications. Animations illustrate some of the main ideas. © 2015 by Annual Reviews. All rights reserved.

  6. Phenotypic and genetic heterogeneity in a genome-wide linkage study of asthma families

    Directory of Open Access Journals (Sweden)

    Schuster Antje

    2005-01-01

    Full Text Available Abstract Background Asthma is a complex genetic disease with more than 20 genome-wide scans conducted so far. Regions on almost every chromosome have been linked to asthma and several genes have been associated. However, most of these associations are weak and are still awaiting replication. Methods In this study, we conducted a second-stage genome-wide scan with 408 microsatellite markers on 201 asthma-affected sib pair families and defined clinical subgroups to identify phenotype-genotype relations. Results The lowest P value for asthma in the total sample was 0.003 on chromosome 11, while several of the clinical subsets reached lower significance levels than in the overall sample. Suggestive evidence for linkage (p = 0.0007 was found for total IgE on chromosomes 1, 7 and again on chromosome 11, as well as for HDM asthma on chromosome 12. Weaker linkage signals could be found on chromosomes 4 and 5 for early onset and HDM, and, newly described, on chromosome 2 for severe asthma and on chromosome 9 for hay fever. Conclusions This phenotypic dissection underlines the importance of detailed clinical characterisations and the extreme genetic heterogeneity of asthma.

  7. Adventure and Extreme Sports.

    Science.gov (United States)

    Gomez, Andrew Thomas; Rao, Ashwin

    2016-03-01

    Adventure and extreme sports often involve unpredictable and inhospitable environments, high velocities, and stunts. These activities vary widely and include sports like BASE jumping, snowboarding, kayaking, and surfing. Increasing interest and participation in adventure and extreme sports warrants understanding by clinicians to facilitate prevention, identification, and treatment of injuries unique to each sport. This article covers alpine skiing and snowboarding, skateboarding, surfing, bungee jumping, BASE jumping, and whitewater sports with emphasis on epidemiology, demographics, general injury mechanisms, specific injuries, chronic injuries, fatality data, and prevention. Overall, most injuries are related to overuse, trauma, and environmental or microbial exposure. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Extremal graph theory

    CERN Document Server

    Bollobas, Bela

    2004-01-01

    The ever-expanding field of extremal graph theory encompasses a diverse array of problem-solving methods, including applications to economics, computer science, and optimization theory. This volume, based on a series of lectures delivered to graduate students at the University of Cambridge, presents a concise yet comprehensive treatment of extremal graph theory.Unlike most graph theory treatises, this text features complete proofs for almost all of its results. Further insights into theory are provided by the numerous exercises of varying degrees of difficulty that accompany each chapter. A

  9. Magnetic resonance imaging phenotyping of Becker muscular dystrophy.

    Science.gov (United States)

    Faridian-Aragh, Neda; Wagner, Kathryn R; Leung, Doris G; Carrino, John A

    2014-12-01

    There is little information on magnetic resonance imaging (MRI) phenotypes of Becker muscular dystrophy (BMD). This study presents the MRI phenotyping of the upper and lower extremities of a large cohort of BMD patients. In this retrospective study, MRI images of 33 BMD subjects were evaluated for severity, distribution, and symmetry of involvement. Teres major, triceps long head, biceps brachii long head, gluteus maximus, gluteus medius, vasti, adductor longus, adductor magnus, semitendinosus, semimembranosus, and biceps femoris muscles showed the highest severity and frequency of involvement. All analyzed muscles had a high frequency of symmetric involvement. There was significant variability of involvement between muscles within some muscle groups, most notably the arm abductors, posterior arm muscles, medial thigh muscles, and lateral hip rotators. This study showed a distinctive pattern of involvement of extremity muscles in BMD subjects. © 2014 Wiley Periodicals, Inc.

  10. Extreme values, regular variation and point processes

    CERN Document Server

    Resnick, Sidney I

    1987-01-01

    Extremes Values, Regular Variation and Point Processes is a readable and efficient account of the fundamental mathematical and stochastic process techniques needed to study the behavior of extreme values of phenomena based on independent and identically distributed random variables and vectors It presents a coherent treatment of the distributional and sample path fundamental properties of extremes and records It emphasizes the core primacy of three topics necessary for understanding extremes the analytical theory of regularly varying functions; the probabilistic theory of point processes and random measures; and the link to asymptotic distribution approximations provided by the theory of weak convergence of probability measures in metric spaces The book is self-contained and requires an introductory measure-theoretic course in probability as a prerequisite Almost all sections have an extensive list of exercises which extend developments in the text, offer alternate approaches, test mastery and provide for enj...

  11. Stellar extreme ultraviolet astronomy

    International Nuclear Information System (INIS)

    Cash, W.C. Jr.

    1978-01-01

    The design, calibration, and launch of a rocket-borne imaging telescope for extreme ultraviolet astronomy are described. The telescope, which employed diamond-turned grazing incidence optics and a ranicon detector, was launched November 19, 1976, from the White Sands Missile Range. The telescope performed well and returned data on several potential stellar sources of extreme ultraviolet radiation. Upper limits ten to twenty times more sensitive than previously available were obtained for the extreme ultraviolet flux from the white dwarf Sirius B. These limits fall a factor of seven below the flux predicted for the star and demonstrate that the temperature of Sirius B is not 32,000 K as previously measured, but is below 30,000 K. The new upper limits also rule out the photosphere of the white dwarf as the source of the recently reported soft x-rays from Sirius. Two other white dwarf stars, Feige 24 and G191-B2B, were observed. Upper limits on the flux at 300 A were interpreted as lower limits on the interstellar hydrogen column densities to these stars. The lower limits indicate interstellar hydrogen densitites of greater than .02 cm -3 . Four nearby stars (Sirius, Procyon, Capella, and Mirzam) were observed in a search for intense low temperature coronae or extended chromospheres. No extreme ultraviolet radiation from these stars was detected, and upper limits to their coronal emisson measures are derived

  12. Extremity x-ray

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003461.htm Extremity x-ray To use the sharing features on this page, ... in the body Risks There is low-level radiation exposure. X-rays are monitored and regulated to provide the ...

  13. Extremity perfusion for sarcoma

    NARCIS (Netherlands)

    Hoekstra, Harald Joan

    2008-01-01

    For more than 50 years, the technique of extremity perfusion has been explored in the limb salvage treatment of local, recurrent, and multifocal sarcomas. The "discovery" of tumor necrosis factor-or. in combination with melphalan was a real breakthrough in the treatment of primarily irresectable

  14. Statistics of Local Extremes

    DEFF Research Database (Denmark)

    Larsen, Gunner Chr.; Bierbooms, W.; Hansen, Kurt Schaldemose

    2003-01-01

    . A theoretical expression for the probability density function associated with local extremes of a stochasticprocess is presented. The expression is basically based on the lower four statistical moments and a bandwidth parameter. The theoretical expression is subsequently verified by comparison with simulated...

  15. COMPUTER APPROACHES TO WHEAT HIGH-THROUGHPUT PHENOTYPING

    Directory of Open Access Journals (Sweden)

    Afonnikov D.

    2012-08-01

    Full Text Available The growing need for rapid and accurate approaches for large-scale assessment of phenotypic characters in plants becomes more and more obvious in the studies looking into relationships between genotype and phenotype. This need is due to the advent of high throughput methods for analysis of genomes. Nowadays, any genetic experiment involves data on thousands and dozens of thousands of plants. Traditional ways of assessing most phenotypic characteristics (those with reliance on the eye, the touch, the ruler are little effective on samples of such sizes. Modern approaches seek to take advantage of automated phenotyping, which warrants a much more rapid data acquisition, higher accuracy of the assessment of phenotypic features, measurement of new parameters of these features and exclusion of human subjectivity from the process. Additionally, automation allows measurement data to be rapidly loaded into computer databases, which reduces data processing time.In this work, we present the WheatPGE information system designed to solve the problem of integration of genotypic and phenotypic data and parameters of the environment, as well as to analyze the relationships between the genotype and phenotype in wheat. The system is used to consolidate miscellaneous data on a plant for storing and processing various morphological traits and genotypes of wheat plants as well as data on various environmental factors. The system is available at www.wheatdb.org. Its potential in genetic experiments has been demonstrated in high-throughput phenotyping of wheat leaf pubescence.

  16. Enabling phenotypic big data with PheNorm.

    Science.gov (United States)

    Yu, Sheng; Ma, Yumeng; Gronsbell, Jessica; Cai, Tianrun; Ananthakrishnan, Ashwin N; Gainer, Vivian S; Churchill, Susanne E; Szolovits, Peter; Murphy, Shawn N; Kohane, Isaac S; Liao, Katherine P; Cai, Tianxi

    2018-01-01

    Electronic health record (EHR)-based phenotyping infers whether a patient has a disease based on the information in his or her EHR. A human-annotated training set with gold-standard disease status labels is usually required to build an algorithm for phenotyping based on a set of predictive features. The time intensiveness of annotation and feature curation severely limits the ability to achieve high-throughput phenotyping. While previous studies have successfully automated feature curation, annotation remains a major bottleneck. In this paper, we present PheNorm, a phenotyping algorithm that does not require expert-labeled samples for training. The most predictive features, such as the number of International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes or mentions of the target phenotype, are normalized to resemble a normal mixture distribution with high area under the receiver operating curve (AUC) for prediction. The transformed features are then denoised and combined into a score for accurate disease classification. We validated the accuracy of PheNorm with 4 phenotypes: coronary artery disease, rheumatoid arthritis, Crohn's disease, and ulcerative colitis. The AUCs of the PheNorm score reached 0.90, 0.94, 0.95, and 0.94 for the 4 phenotypes, respectively, which were comparable to the accuracy of supervised algorithms trained with sample sizes of 100-300, with no statistically significant difference. The accuracy of the PheNorm algorithms is on par with algorithms trained with annotated samples. PheNorm fully automates the generation of accurate phenotyping algorithms and demonstrates the capacity for EHR-driven annotations to scale to the next level - phenotypic big data. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  17. Plant Phenotype Characterization System

    Energy Technology Data Exchange (ETDEWEB)

    Daniel W McDonald; Ronald B Michaels

    2005-09-09

    This report is the final scientific report for the DOE Inventions and Innovations Project: Plant Phenotype Characterization System, DE-FG36-04GO14334. The period of performance was September 30, 2004 through July 15, 2005. The project objective is to demonstrate the viability of a new scientific instrument concept for the study of plant root systems. The root systems of plants are thought to be important in plant yield and thus important to DOE goals in renewable energy sources. The scientific study and understanding of plant root systems is hampered by the difficulty in observing root activity and the inadequacy of existing root study instrumentation options. We have demonstrated a high throughput, non-invasive, high resolution technique for visualizing plant root systems in-situ. Our approach is based upon low-energy x-ray radiography and the use of containers and substrates (artificial soil) which are virtually transparent to x-rays. The system allows us to germinate and grow plant specimens in our containers and substrates and to generate x-ray images of the developing root system over time. The same plant can be imaged at different times in its development. The system can be used for root studies in plant physiology, plant morphology, plant breeding, plant functional genomics and plant genotype screening.

  18. Sex hormone binding globulin phenotypes

    DEFF Research Database (Denmark)

    Cornelisse, M M; Bennett, Patrick; Christiansen, M

    1994-01-01

    Human sex hormone binding globulin (SHBG) is encoded by a normal and a variant allele. The resulting SHBG phenotypes (the homozygous normal SHBG, the heterozygous SHBG and the homozygous variant SHBG phenotype) can be distinguished by their electrophoretic patterns. We developed a novel detection....... This method of detection was used to determine the distribution of SHBG phenotypes in healthy controls of both sexes and in five different pathological conditions characterized by changes in the SHBG level or endocrine disturbances (malignant and benign ovarian neoplasms, hirsutism, liver cirrhosis...... on the experimental values. Differences in SHBG phenotypes do not appear to have any clinical significance and no sex difference was found in the SHBG phenotype distribution....

  19. HIV coreceptor phenotyping in the clinical setting.

    Science.gov (United States)

    Low, Andrew J; Swenson, Luke C; Harrigan, P Richard

    2008-01-01

    The introduction of CCR5 antagonists increases the options available for constructing antiretroviral regimens. However, this option is coupled with the caveat that patients should be tested for HIV coreceptor tropism prior to initiating CCR5 antagonist-based therapy. Failure to screen for CXCR4 usage increases the risk of using an ineffective drug, thus reducing the likelihood of viral suppression and increasing their risk for developing antiretroviral resistance. This review discusses current and future methods of determining HIV tropism, with a focus on their utility in the clinical setting for screening purposes. Some of these methods include recombinant phenotypic tests, such as the Monogram Trofile assay, as well as genotype-based predictors, heteroduplex tracking assays, and flow cytometry based methods. Currently, the best evidence supports the use of phenotypic methods, although other methods of screening for HIV coreceptor usage prior to the administration of CCR5 antagonists may reduce costs and increase turnaround time over phenotypic methods. The presence of low levels of X4 virus is a challenge to all assay methods, resulting in reduced sensitivity in clinical, patient-derived samples when compared to clonally derived samples. Gaining a better understanding of the output of these assays and correlating them with clinical progression and therapy response will provide some indication on how both genotype-based, and phenotypic assays for determining HIV coreceptor usage can be improved. In addition, leveraging new technologies capable of detecting low-level minority species may provide the most significant advances in ensuring that individuals with low levels of dual/mixed tropic virus are not inadvertently prescribed CCR5 antagonists.

  20. Extremes in nature

    CERN Document Server

    Salvadori, Gianfausto; Kottegoda, Nathabandu T

    2007-01-01

    This book is about the theoretical and practical aspects of the statistics of Extreme Events in Nature. Most importantly, this is the first text in which Copulas are introduced and used in Geophysics. Several topics are fully original, and show how standard models and calculations can be improved by exploiting the opportunities offered by Copulas. In addition, new quantities useful for design and risk assessment are introduced.

  1. Phenotypic plasticity, costs of phenotypes, and costs of plasticity

    DEFF Research Database (Denmark)

    Callahan, Hilary S; Maughan, Heather; Steiner, Uli

    2008-01-01

    Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns...... of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both...... types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic...

  2. Rhabdomyosarcoma of the extremity

    International Nuclear Information System (INIS)

    Rao, Bhaskar N

    1997-01-01

    Rhabdomyosarcoma is the most common soft tissue sarcoma accounting for almost 55%. These tumors arise from unsegmented mesoderm or primitive mesenchyma, which have the capacity to differentiate into muscle. Less than 5% occur in the first year of life. Extremity rhabdomyosarcoma are mainly seen in the adolescent years. The most common histologic subtype is the alveolar variant. Other characteristics of extremity rhabdomyosarcoma include a predilection for lymph node metastasis, a high local failure, and a relatively low survival rate. They often present as slow painless masses; however, lesions in the hand and foot often present as painful masses and imaging studies may show invasion of the bone. Initial diagnostic approaches include needle biopsy or incisional biopsy for larger lesions. Excisional biopsy is indicated preferably for lesions less than 2.5 cm. following this in most instances therapy is initiated with multi agent chemotherapy depending upon response, the next modality may be either surgery with intent to cure or radiation therapy. Amputation of an extremity for local control is not considered in most instances. Prognostic factors that have been determined over the years to be of significance by multi variant analysis have included age, tumor size, invasiveness, presence of either nodal or distant metastasis, and complete excision whenever feasible, with supplemental radiation therapy for local control

  3. Stereology of extremes; bivariate models and computation

    Czech Academy of Sciences Publication Activity Database

    Beneš, Viktor; Bodlák, M.; Hlubinka, D.

    2003-01-01

    Roč. 5, č. 3 (2003), s. 289-308 ISSN 1387-5841 R&D Projects: GA AV ČR IAA1075201; GA ČR GA201/03/0946 Institutional research plan: CEZ:AV0Z1075907 Keywords : sample extremes * domain of attraction * normalizing constants Subject RIV: BA - General Mathematics

  4. Deep Phenotyping: Deep Learning For Temporal Phenotype/Genotype Classification

    OpenAIRE

    Najafi, Mohammad; Namin, Sarah; Esmaeilzadeh, Mohammad; Brown, Tim; Borevitz, Justin

    2017-01-01

    High resolution and high throughput, genotype to phenotype studies in plants are underway to accelerate breeding of climate ready crops. Complex developmental phenotypes are observed by imaging a variety of accessions in different environment conditions, however extracting the genetically heritable traits is challenging. In the recent years, deep learning techniques and in particular Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs) and Long-Short Term Memories (LSTMs), h...

  5. Altered fibre types in gastrocnemius muscle of high wheel-running selected mice with mini-muscle phenotypes.

    Science.gov (United States)

    Guderley, Helga; Joanisse, Denis R; Mokas, Sophie; Bilodeau, Geneviève M; Garland, Theodore

    2008-03-01

    Selective breeding of mice for high voluntary wheel running has favoured characteristics that facilitate sustained, aerobically supported activity, including a "mini-muscle" phenotype with markedly reduced hind limb muscle mass, increased mass-specific activities of oxidative enzymes, decreased % myosin heavy chain IIb, and, in the medial gastrocnemius, reduced twitch speed, reduced mass-specific isotonic power, and increased fatigue resistance. To evaluate whether selection has altered fibre type expression in mice with either "mini" or normal muscle phenotypes, we examined fibre types of red and white gastrocnemius. In both the medial and lateral gastrocnemius, the mini-phenotype increased activities of oxidative enzymes and decreased activities of glycolytic enzymes. In red muscle samples, the mini-phenotype markedly changed fibre types, with the % type I and type IIA fibres and the surface area of type IIA fibres increasing; in addition, mice from selected lines in general had an increased % type IIA fibres and larger type I fibres as compared with mice from control lines. White muscle samples from mini-mice showed dramatic structural alterations, with an atypical distribution of extremely small, unidentifiable fibres surrounded by larger, more oxidative fibres than normally present in white muscle. The increased proportion of oxidative fibres and these atypical small fibres together may explain the reduced mass and increased mitochondrial enzyme activities in mini-muscles. These and previous results demonstrate that extension of selective breeding beyond the time when the response of the selected trait (i.e. distance run) has levelled off can still modify the mechanistic underpinnings of this behaviour.

  6. Invasion strategies in clonal aquatic plants: are phenotypic differences caused by phenotypic plasticity or local adaptation?

    Science.gov (United States)

    Riis, Tenna; Lambertini, Carla; Olesen, Birgit; Clayton, John S.; Brix, Hans; Sorrell, Brian K.

    2010-01-01

    Background and Aims The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important. Here the primary adaptive strategy in three non-native, clonally reproducing macrophytes (Egeria densa, Elodea canadensis and Lagarosiphon major) in New Zealand freshwaters were examined and an attempt was made to link observed differences in plant morphology to local variation in habitat conditions. Methods Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity of these same populations was also quantified. Key Results For all three species, greater variation in plant characteristics was found before they were grown in standardized conditions. Moreover, field populations displayed remarkably little genetic variation and there was little interaction between habitat conditions and plant morphological characteristics. Conclusions The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between populations may facilitate ecotypic differentiation in the future cannot be excluded. These results thus indicate that invasive clonal aquatic plants adapt to new introduced areas by phenotypic plasticity. Inorganic carbon, nitrogen and phosphorous were important in controlling plant size of E. canadensis and L. major, but no other relationships between plant characteristics and habitat conditions were apparent. This implies that within-species differences in plant size can be explained

  7. Genotype-phenotype associations in obesity dependent on definition of the obesity phenotype.

    Science.gov (United States)

    Kring, Sofia Inez Iqbal; Larsen, Lesli Hingstrup; Holst, Claus; Toubro, Søren; Hansen, Torben; Astrup, Arne; Pedersen, Oluf; Sørensen, Thorkild I A

    2008-01-01

    In previous studies of associations of variants in the genes UCP2, UCP3, PPARG2, CART, GRL, MC4R, MKKS, SHP, GHRL, and MCHR1 with obesity, we have used a case-control approach with cases defined by a threshold for BMI. In the present study, we assess the association of seven abdominal, peripheral, and overall obesity phenotypes, which were analyzed quantitatively, and thirteen candidate gene polymorphisms in these ten genes in the same cohort. Obese Caucasian men (n = 234, BMI >or= 31.0 kg/m(2)) and a randomly sampled non-obese group (n = 323), originally identified at the draft board examinations, were re-examined at median ages of 47.0 or 49.0 years by anthropometry and DEXA scanning. Obesity phenotypes included BMI, fat body mass index, waist circumference, waist for given BMI, intra-abdominal adipose tissue, hip circumference and lower body fat mass (%). Using logistic regression models, we estimated the odds for defined genotypes (dominant or recessive genetic transmission) in relation to z-scores of the phenotypes. The minor (rare) allele for SHP 512G>C (rs6659176) was associated with increased hip circumference. The minor allele for UCP2 Ins45bp was associated with increased BMI, increased abdominal obesity, and increased hip circumference. The minor allele for UCP2 -866G>A (rs6593669) was associated with borderline increased fat body mass index. The minor allele for MCHR1 100213G>A (rs133072) was associated with reduced abdominal obesity. None of the other genotype-phenotype combinations showed appreciable associations. If replicated in independent studies with focus on the specific phenotypes, our explorative studies suggest significant associations between some candidate gene polymorphisms and distinct obesity phenotypes, predicting beneficial and detrimental effects, depending on compartments for body fat accumulation. Copyright 2008 S. Karger AG, Basel.

  8. PHENOTYPIC CORRELATIONS AND BODY WEIGHTS ...

    African Journals Online (AJOL)

    Dr Osondu

    Ethiopian Journal of Environmental Studies and Management Vol. 4 No.3 2011. PHENOTYPIC ... because of its high meat quality and acceptance by her populace. The meat is ... commands high price in the restaurants and markets than other ...

  9. Alterations in Skin Temperature and Sleep in the Fear of Harm Phenotype of Pediatric Bipolar Disorder

    Directory of Open Access Journals (Sweden)

    Patricia J. Murphy

    2014-08-01

    Full Text Available In children diagnosed with pediatric bipolar disorder (PBD, disturbances in the quality of sleep and wakefulness are prominent. A novel phenotype of PBD called Fear of Harm (FOH associated with separation anxiety and aggressive obsessions is associated with sleep onset insomnia, parasomnias (nightmares, night-terrors, enuresis, REM sleep-related problems, and morning sleep inertia. Children with FOH often experience thermal discomfort (e.g., feeling hot, excessive sweating in neutral ambient temperature conditions, as well as no discomfort during exposure to the extreme cold, and alternate noticeably between being excessively hot in the evening and cold in the morning. We hypothesized that these sleep- and temperature-related symptoms were overt symptoms of an impaired ability to dissipate heat, particularly in the evening hours near the time of sleep onset. We measured sleep/wake variables using actigraphy, and nocturnal skin temperature variables using thermal patches and a wireless device, and compared these data between children with PBD/FOH and a control sample of healthy children. The results are suggestive of a thermoregulatory dysfunction that is associated with sleep onset difficulties. Further, they are consistent with our hypothesis that alterations in neural circuitry common to thermoregulation and emotion regulation underlie affective and behavioral symptoms of the FOH phenotype.

  10. Shocking matter to extreme conditions

    International Nuclear Information System (INIS)

    Gupta, Y.M.; Sharma, S.M.

    1997-01-01

    A good understanding of the thermodynamic response of matter at high compression and high energy densities is important to several areas of physics. Shock-wave experiments are uniquely suited for obtaining data at extreme conditions, and a shock-compressed matter can be viewed as a condensed system with or without dissociation or as a strongly coupled plasma. This article reviews work by Da Silva et al. in which irradiances ranging from 5x10 superscript 12 to 2x10 superscript 14 W/cm 2 were used to generate 8- to 10-ns square pulses in liquid deuterium. The authors demonstrated negligible pre-heating of the sample, steady propagation of the shock wave, and direct determination of the shock wave velocity along with particle velocity and density in the shocked state. Da Silva et al. results are compared with models and other experimental information, and the usefulness of the data in other areas is assessed. 11 refs., 1 fig

  11. Caracterização fenotípica da resistência a antimicrobianos e detecção do gene mecA em Staphylococcus spp. coagulase-negativos isolados de amostras animais e humanas Phenotypic characterization of antimicrobial resistance and detection of the mecA gene in coagulase-negative Staphylococcus spp. isolates from animal and human samples

    Directory of Open Access Journals (Sweden)

    Lidiane de Castro Soares

    2008-08-01

    Full Text Available Os estafilococos coagulase-negativos (ECN fazem parte da microbiota normal da pele e, apesar de terem sido considerados saprófitas por muito tempo, o seu significado clínico como agente etiológico tem aumentado com o passar dos anos. Neste estudo, foram obtidos 72 isolados de ECN a partir de amostras do conduto auditivo de cães, de mastite bovina e de infecções humanas. Staphylococcus xylosus foi o microrganismo mais isolado, nas amostras animais, e S. cohnii subsp. cohnii em humanos. Os isolados foram avaliados de modo a traçar o perfil fenotípico de sua resistência aos antimicrobianos mais indicados no tratamento de infecções estafilocócicas. Foi detectado um elevado nível de resistência à penicilina e ampicilina. A gentamicina, a vancomicina e a associação ampicilina+sulbactam foram eficientes frente aos isolados testados. A resistência à oxacilina foi avaliada por meio dos testes de difusão em disco modificada, ágar screen, microdiluição em caldo e diluição em ágar para constatar, se à semelhança do que ocorre com os estafilococos coagulase-positivo, esta pode ser mediada pelo gene mecA e apresentada de forma heterogênea. A presença do gene mecA foi determinada pelo método da Reação em Cadeia de Polimerase (PCR, sendo 5,6% dos isolados mecA positivos.Coagulase-negative staphylococci (SCN make part of the normal microbiota skin and although they have been considered saprophytics for years, nowadays their clinical significance as an etiologic agent has increased. In this study, 72 SCN isolates obtained from external ear canals of dogs, bovine mastitis and human nosocomial infections were evaluated. Staphylococcus xylosus was the most prevalent microorganism in animal samples and S. cohnii subsp. cohnii in human samples. SCN isolates were evaluated in order to establish a phenotypical resistance pattern towards the most indicated antibiotics for staphyloccocal infections. A high level of resistance to penicillin

  12. Extreme Programming Pocket Guide

    CERN Document Server

    Chromatic

    2003-01-01

    Extreme Programming (XP) is a radical new approach to software development that has been accepted quickly because its core practices--the need for constant testing, programming in pairs, inviting customer input, and the communal ownership of code--resonate with developers everywhere. Although many developers feel that XP is rooted in commonsense, its vastly different approach can bring challenges, frustrations, and constant demands on your patience. Unless you've got unlimited time (and who does these days?), you can't always stop to thumb through hundreds of pages to find the piece of info

  13. Upper extremity golf injuries.

    Science.gov (United States)

    Cohn, Michael A; Lee, Steven K; Strauss, Eric J

    2013-01-01

    Golf is a global sport enjoyed by an estimated 60 million people around the world. Despite the common misconception that the risk of injury during the play of golf is minimal, golfers are subject to a myriad of potential pathologies. While the majority of injuries in golf are attributable to overuse, acute traumatic injuries can also occur. As the body's direct link to the golf club, the upper extremities are especially prone to injury. A thorough appreciation of the risk factors and patterns of injury will afford accurate diagnosis, treatment, and prevention of further injury.

  14. Phenotypic and genetic diversity in Sinorhizobium meliloti and S. medicae from drought and salt affected regions of Morocco

    Directory of Open Access Journals (Sweden)

    Udupa Sripada M

    2010-01-01

    Full Text Available Abstract Background Sinorhizobium meliloti and S. medicae are symbiotic nitrogen fixing bacteria in root nodules of forage legume alfalfa (Medicago sativa L.. In Morocco, alfalfa is usually grown in marginal soils of arid and semi-arid regions frequently affected by drought, extremes of temperature and soil pH, soil salinity and heavy metals, which affect biological nitrogen fixing ability of rhizobia and productivity of the host. This study examines phenotypic diversity for tolerance to the above stresses and genotypic diversity at Repetitive Extragenic Pallindromic DNA regions of Sinorhizobium nodulating alfalfa, sampled from marginal soils of arid and semi-arid regions of Morocco. Results RsaI digestion of PCR amplified 16S rDNA of the 157 sampled isolates, assigned 136 isolates as S. meliloti and the rest as S. medicae. Further phenotyping of these alfalfa rhizobia for tolerance to the environmental stresses revealed a large degree of variation: 55.41%, 82.16%, 57.96% and 3.18% of the total isolates were tolerant to NaCl (>513 mM, water stress (-1.5 MPa, high temperature (40°C and low pH (3.5, respectively. Sixty-seven isolates of S. meliloti and thirteen isolates of S. medicae that were tolerant to salinity were also tolerant to water stress. Most of the isolates of the two species showed tolerance to heavy metals (Cd, Mn and Zn and antibiotics (chloramphenicol, spectinomycin, streptomycin and tetracycline. The phenotypic clusters observed by the cluster analysis clearly showed adaptations of the S. meliloti and S. medicae strains to the multiple stresses. Genotyping with rep-PCR revealed higher genetic diversity within these phenotypic clusters and classified all the 157 isolates into 148 genotypes. No relationship between genotypic profiles and the phenotypes was observed. The Analysis of Molecular Variance revealed that largest proportion of significant (P Conclusion High degree of phenotypic and genotypic diversity is present in S

  15. Whole genome expression and biochemical correlates of extreme constitutional types defined in Ayurveda.

    Science.gov (United States)

    Prasher, Bhavana; Negi, Sapna; Aggarwal, Shilpi; Mandal, Amit K; Sethi, Tav P; Deshmukh, Shailaja R; Purohit, Sudha G; Sengupta, Shantanu; Khanna, Sangeeta; Mohammad, Farhan; Garg, Gaurav; Brahmachari, Samir K; Mukerji, Mitali

    2008-09-09

    Ayurveda is an ancient system of personalized medicine documented and practiced in India since 1500 B.C. According to this system an individual's basic constitution to a large extent determines predisposition and prognosis to diseases as well as therapy and life-style regime. Ayurveda describes seven broad constitution types (Prakritis) each with a varying degree of predisposition to different diseases. Amongst these, three most contrasting types, Vata, Pitta, Kapha, are the most vulnerable to diseases. In the realm of modern predictive medicine, efforts are being directed towards capturing disease phenotypes with greater precision for successful identification of markers for prospective disease conditions. In this study, we explore whether the different constitution types as described in Ayurveda has molecular correlates. Normal individuals of the three most contrasting constitutional types were identified following phenotyping criteria described in Ayurveda in Indian population of Indo-European origin. The peripheral blood samples of these individuals were analysed for genome wide expression levels, biochemical and hematological parameters. Gene Ontology (GO) and pathway based analysis was carried out on differentially expressed genes to explore if there were significant enrichments of functional categories among Prakriti types. Individuals from the three most contrasting constitutional types exhibit striking differences with respect to biochemical and hematological parameters and at genome wide expression levels. Biochemical profiles like liver function tests, lipid profiles, and hematological parameters like haemoglobin exhibited differences between Prakriti types. Functional categories of genes showing differential expression among Prakriti types were significantly enriched in core biological processes like transport, regulation of cyclin dependent protein kinase activity, immune response and regulation of blood coagulation. A significant enrichment of

  16. Testing the island effect on phenotypic diversification: insights from the Hemidactylus geckos of the Socotra Archipelago

    Science.gov (United States)

    Garcia-Porta, Joan; Šmíd, Jiří; Sol, Daniel; Fasola, Mauro; Carranza, Salvador

    2016-04-01

    Island colonization is often assumed to trigger extreme levels of phenotypic diversification. Yet, empirical evidence suggests that it does not always so. In this study we test this hypothesis using a completely sampled mainland-island system, the arid clade of Hemidactylus, a group of geckos mainly distributed across Africa, Arabia and the Socotra Archipelago. To such purpose, we generated a new molecular phylogeny of the group on which we mapped body size and head proportions. We then explored whether island and continental taxa shared the same morphospace and differed in their disparities and tempos of evolution. Insular species produced the most extreme sizes of the radiation, involving accelerated rates of evolution and higher disparities compared with most (but not all) of the continental groups. In contrast, head proportions exhibited constant evolutionary rates across the radiation and similar disparities in islands compared with the continent. These results, although generally consistent with the notion that islands promote high morphological disparity, reveal at the same time a complex scenario in which different traits may experience different evolutionary patterns in the same mainland-island system and continental groups do not always present low levels of morphological diversification compared to insular groups.

  17. Childhood asthma-predictive phenotype.

    Science.gov (United States)

    Guilbert, Theresa W; Mauger, David T; Lemanske, Robert F

    2014-01-01

    Wheezing is a fairly common symptom in early childhood, but only some of these toddlers will experience continued wheezing symptoms in later childhood. The definition of the asthma-predictive phenotype is in children with frequent, recurrent wheezing in early life who have risk factors associated with the continuation of asthma symptoms in later life. Several asthma-predictive phenotypes were developed retrospectively based on large, longitudinal cohort studies; however, it can be difficult to differentiate these phenotypes clinically as the expression of symptoms, and risk factors can change with time. Genetic, environmental, developmental, and host factors and their interactions may contribute to the development, severity, and persistence of the asthma phenotype over time. Key characteristics that distinguish the childhood asthma-predictive phenotype include the following: male sex; a history of wheezing, with lower respiratory tract infections; history of parental asthma; history of atopic dermatitis; eosinophilia; early sensitization to food or aeroallergens; or lower lung function in early life. Copyright © 2014 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  18. Clustering high-dimensional mixed data to uncover sub-phenotypes: joint analysis of phenotypic and genotypic data.

    Science.gov (United States)

    McParland, D; Phillips, C M; Brennan, L; Roche, H M; Gormley, I C

    2017-12-10

    The LIPGENE-SU.VI.MAX study, like many others, recorded high-dimensional continuous phenotypic data and categorical genotypic data. LIPGENE-SU.VI.MAX focuses on the need to account for both phenotypic and genetic factors when studying the metabolic syndrome (MetS), a complex disorder that can lead to higher risk of type 2 diabetes and cardiovascular disease. Interest lies in clustering the LIPGENE-SU.VI.MAX participants into homogeneous groups or sub-phenotypes, by jointly considering their phenotypic and genotypic data, and in determining which variables are discriminatory. A novel latent variable model that elegantly accommodates high dimensional, mixed data is developed to cluster LIPGENE-SU.VI.MAX participants using a Bayesian finite mixture model. A computationally efficient variable selection algorithm is incorporated, estimation is via a Gibbs sampling algorithm and an approximate BIC-MCMC criterion is developed to select the optimal model. Two clusters or sub-phenotypes ('healthy' and 'at risk') are uncovered. A small subset of variables is deemed discriminatory, which notably includes phenotypic and genotypic variables, highlighting the need to jointly consider both factors. Further, 7 years after the LIPGENE-SU.VI.MAX data were collected, participants underwent further analysis to diagnose presence or absence of the MetS. The two uncovered sub-phenotypes strongly correspond to the 7-year follow-up disease classification, highlighting the role of phenotypic and genotypic factors in the MetS and emphasising the potential utility of the clustering approach in early screening. Additionally, the ability of the proposed approach to define the uncertainty in sub-phenotype membership at the participant level is synonymous with the concepts of precision medicine and nutrition. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  19. Investigating NARCCAP Precipitation Extremes via Bivariate Extreme Value Theory (Invited)

    Science.gov (United States)

    Weller, G. B.; Cooley, D. S.; Sain, S. R.; Bukovsky, M. S.; Mearns, L. O.

    2013-12-01

    We introduce methodology from statistical extreme value theory to examine the ability of reanalysis-drive regional climate models to simulate past daily precipitation extremes. Going beyond a comparison of summary statistics such as 20-year return values, we study whether the most extreme precipitation events produced by climate model simulations exhibit correspondence to the most extreme events seen in observational records. The extent of this correspondence is formulated via the statistical concept of tail dependence. We examine several case studies of extreme precipitation events simulated by the six models of the North American Regional Climate Change Assessment Program (NARCCAP) driven by NCEP reanalysis. It is found that the NARCCAP models generally reproduce daily winter precipitation extremes along the Pacific coast quite well; in contrast, simulation of past daily summer precipitation extremes in a central US region is poor. Some differences in the strength of extremal correspondence are seen in the central region between models which employ spectral nudging and those which do not. We demonstrate how these techniques may be used to draw a link between extreme precipitation events and large-scale atmospheric drivers, as well as to downscale extreme precipitation simulated by a future run of a regional climate model. Specifically, we examine potential future changes in the nature of extreme precipitation along the Pacific coast produced by the pineapple express (PE) phenomenon. A link between extreme precipitation events and a "PE Index" derived from North Pacific sea-surface pressure fields is found. This link is used to study PE-influenced extreme precipitation produced by a future-scenario climate model run.

  20. Detection and attribution of extreme weather disasters

    Science.gov (United States)

    Huggel, Christian; Stone, Dáithí; Hansen, Gerrit

    2014-05-01

    Single disasters related to extreme weather events have caused loss and damage on the order of up to tens of billions US dollars over the past years. Recent disasters fueled the debate about whether and to what extent these events are related to climate change. In international climate negotiations disaster loss and damage is now high on the agenda, and related policy mechanisms have been discussed or are being implemented. In view of funding allocation and effective risk reduction strategies detection and attribution to climate change of extreme weather events and disasters is a key issue. Different avenues have so far been taken to address detection and attribution in this context. Physical climate sciences have developed approaches, among others, where variables that are reasonably sampled over climatically relevant time periods and related to the meteorological characteristics of the extreme event are examined. Trends in these variables (e.g. air or sea surface temperatures) are compared between observations and climate simulations with and without anthropogenic forcing. Generally, progress has been made in recent years in attribution of changes in the chance of some single extreme weather events to anthropogenic climate change but there remain important challenges. A different line of research is primarily concerned with losses related to the extreme weather events over time, using disaster databases. A growing consensus is that the increase in asset values and in exposure are main drivers of the strong increase of economic losses over the past several decades, and only a limited number of studies have found trends consistent with expectations from climate change. Here we propose a better integration of existing lines of research in detection and attribution of extreme weather events and disasters by applying a risk framework. Risk is thereby defined as a function of the probability of occurrence of an extreme weather event, and the associated consequences

  1. Phenotypic spectrum of GABRA1

    DEFF Research Database (Denmark)

    Johannesen, Katrine; Marini, Carla; Pfeffer, Siona

    2016-01-01

    OBJECTIVE: To delineate phenotypic heterogeneity, we describe the clinical features of a cohort of patients with GABRA1 gene mutations. METHODS: Patients with GABRA1 mutations were ascertained through an international collaboration. Clinical, EEG, and genetic data were collected. Functional analy...

  2. Leaf segmentation in plant phenotyping

    NARCIS (Netherlands)

    Scharr, Hanno; Minervini, Massimo; French, Andrew P.; Klukas, Christian; Kramer, David M.; Liu, Xiaoming; Luengo, Imanol; Pape, Jean Michel; Polder, Gerrit; Vukadinovic, Danijela; Yin, Xi; Tsaftaris, Sotirios A.

    2016-01-01

    Image-based plant phenotyping is a growing application area of computer vision in agriculture. A key task is the segmentation of all individual leaves in images. Here we focus on the most common rosette model plants, Arabidopsis and young tobacco. Although leaves do share appearance and shape

  3. Delineating SPTAN1 associated phenotypes

    DEFF Research Database (Denmark)

    Syrbe, Steffen; Harms, Frederike L; Parrini, Elena

    2017-01-01

    De novo in-frame deletions and duplications in the SPTAN1 gene, encoding the non-erythrocyte αII spectrin, have been associated with severe West syndrome with hypomyelination and pontocerebellar atrophy. We aimed at comprehensively delineating the phenotypic spectrum associated with SPTAN1 mutati...

  4. A note on extreme sets

    Directory of Open Access Journals (Sweden)

    Radosław Cymer

    2017-10-01

    Full Text Available In decomposition theory, extreme sets have been studied extensively due to its connection to perfect matchings in a graph. In this paper, we first define extreme sets with respect to degree-matchings and next investigate some of their properties. In particular, we prove the generalized Decomposition Theorem and give a characterization for the set of all extreme vertices in a graph.

  5. Analysis of Carotenoid Production by Halorubrum sp. TBZ126; an Extremely Halophilic Archeon from Urmia Lake

    Directory of Open Access Journals (Sweden)

    Davood Naziri

    2014-03-01

    Full Text Available Purpose: Carotenoids are of great interest in many scientific disciplines because of their wide distribution, diverse functions and interesting properties. The present report describes a new natural source for carotenoid production. Methods: Halorubrum sp., TBZ126, an extremely halophilic archaeon, was isolated from Urmia Lack following culture of water sample on marine agar medium and incubation at 30 °C. Then single colonies were cultivated in broth media. After that the cells were collected and carotenoids were extracted with acetone-methanol (7:3 v/v. The identification of carotenoids was performed by UV-VIS spectroscopy and confirmed by thin layer chromatography (TLC in the presence of antimony pentachloride (SbCl5. The production profile was analyzed using liquid-chromatography mass spectroscopy (LC-MS techniques. Phenotypic characteristics of the isolate were carried out and the 16S rRNA gene was amplified using polymerase chain reaction (PCR. Results: LC-MS analytical results revealed that produced carotenoids are bacterioruberin, lycopene and β-carotene. Bacterioruberin was found to be the predominant produced carotenoid. 16S rRNA analysis showed that TBZ126 has 100% similarity with Halorubrum chaoviator Halo-G*T (AM048786. Conclusion: Halorubrum sp. TBZ126, isolated from Urmia Lake has high capacity in the production of carotenoids. This extremely halophilic archaeon could be considered as a prokaryotic candidate for carotenoid production source for future studies.

  6. Likelihood estimators for multivariate extremes

    KAUST Repository

    Huser, Raphaë l; Davison, Anthony C.; Genton, Marc G.

    2015-01-01

    The main approach to inference for multivariate extremes consists in approximating the joint upper tail of the observations by a parametric family arising in the limit for extreme events. The latter may be expressed in terms of componentwise maxima, high threshold exceedances or point processes, yielding different but related asymptotic characterizations and estimators. The present paper clarifies the connections between the main likelihood estimators, and assesses their practical performance. We investigate their ability to estimate the extremal dependence structure and to predict future extremes, using exact calculations and simulation, in the case of the logistic model.

  7. Likelihood estimators for multivariate extremes

    KAUST Repository

    Huser, Raphaël

    2015-11-17

    The main approach to inference for multivariate extremes consists in approximating the joint upper tail of the observations by a parametric family arising in the limit for extreme events. The latter may be expressed in terms of componentwise maxima, high threshold exceedances or point processes, yielding different but related asymptotic characterizations and estimators. The present paper clarifies the connections between the main likelihood estimators, and assesses their practical performance. We investigate their ability to estimate the extremal dependence structure and to predict future extremes, using exact calculations and simulation, in the case of the logistic model.

  8. Interoperability between phenotype and anatomy ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Oellrich, Anika; Rebholz-Schuhmann, Dietrich

    2010-12-15

    Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning. We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge. http://bioonto.de/pmwiki.php/Main/PheneOntology.

  9. Multifractal Conceptualisation of Hydro-Meteorological Extremes

    Science.gov (United States)

    Tchiguirinskaia, I.; Schertzer, D.; Lovejoy, S.

    2009-04-01

    Hydrology and more generally sciences involved in water resources management, technological or operational developments face a fundamental difficulty: the extreme variability of hydro-meteorological fields. It clearly appears today that this variability is a function of the observation scale and yield hydro-meteorological hazards. Throughout the world, the development of multifractal theory offers new techniques for handling such non-classical variability over wide ranges of time and space scales. The resulting stochastic simulations with a very limited number of parameters well reproduce the long range dependencies and the clustering of rainfall extremes often yielding fat tailed (i.e., an algebraic type) probability distributions. The goal of this work was to investigate the ability of using very short or incomplete data records for reliable statistical predictions of the extremes. In particular we discuss how to evaluate the uncertainty in the empirical or semi-analytical multifractal outcomes. We consider three main aspects of the evaluation, such as the scaling adequacy, the multifractal parameter estimation error and the quantile estimation error. We first use the multiplicative cascade model to generate long series of multifractal data. The simulated samples had to cover the range of the universal multifractal parameters widely available in the scientific literature for the rainfall and river discharges. Using these long multifractal series and their sub-samples, we defined a metric for parameter estimation error. Then using the sets of estimated parameters, we obtained the quantile values for a range of excedance probabilities from 5% to 0.01%. Plotting the error bars on a quantile plot enable an approximation of confidence intervals that would be particularly important for the predictions of multifractal extremes. We finally illustrate the efficiency of such concept on its application to a large database (more than 16000 selected stations over USA and

  10. Prevalence and phenotypes of congenital myopathy due to α-actin 1 gene mutations

    DEFF Research Database (Denmark)

    Witting, Nanna; Werlauff, Ulla; Duno, Morten

    2016-01-01

    airway pressure. Limb flexor/extensor muscles and upper and lower extremities were affected equally. Pronounced neck flexor weakness was noted. CONCLUSIONS: Congenital myopathy caused by ACTA1 mutations is fatal in infancy in most cases. This study shows that the prevalence of α-actin myopathy in older...... patients with congenital myopathy is not negligible and that phenotypes can be quite mild....

  11. Further outlooks: extremely uncomfortable; Die weiteren Aussichten: extrem ungemuetlich

    Energy Technology Data Exchange (ETDEWEB)

    Resenhoeft, T.

    2006-07-01

    Climate is changing extremely in the last decades. Scientists dealing with extreme weather, should not only stare at computer simulations. They have also to turn towards psyche, seriously personal experiences, knowing statistics, relativise supposed sensational reports and last not least collecting more data. (GL)

  12. Heritability of eleven metabolic phenotypes in Danish and Chinese twins

    DEFF Research Database (Denmark)

    Li, Shuxia; Duan, Hongmei; Pang, Zengchang

    2013-01-01

    modeling was performed on full and nested models with the best fitting models selected. Results: Heritability estimates were compared between Danish and Chinese samples to identify differential genetic influences on each of the phenotypes. Except for hip circumference, all other body measures exhibited...

  13. Morphological analysis and DNA methylation in Conyza bonariensis L. cronquist (Asteraceae phenotypes

    Directory of Open Access Journals (Sweden)

    Juliana Maria de Paula

    2017-08-01

    Full Text Available ABSTRACT The species Conyza bonariensis (L. cause losses in agriculture due to their invasive capacity and resistance to herbicides like glyphosate. The species of this genus exhibit phenotypic plasticity, which complicates their identification and characterization. Thus, experiments were performed with 2 extreme C. bonariensis phenotypes (called broad leaf and narrow leaf in greenhouse conditions and in the laboratory, in order to verify if the morphological differences among these phenotypes are a genetic character or result from environmental effects. In addition to the comparative morphological analysis, assessment of DNA methylation profile was performed to detect the occurrence, or not, of differences in the epigenetic level. The morphological characteristics evaluated were length, width, shape, margin and leaves indument; plant height and stem indument; the number of capitula, flowers and seeds. The Methylation Sensitive Amplified Polymorphism technique was used to investigate the methylation levels. The morphological differences of phenotypes supposed to be C. bonariensis are probably genetic in origin and not the result of environmental effects, since, after 6 crop cycles in a greenhouse under the same environmental conditions, these phenotypes remained with the same morphological characteristics and seed production in relation to the original phenotypes found in the collection site. The different phenotypes did not show differences corresponding to DNA methylation patterns that could indicate an epigenetic effect as the cause of the differences between the 2 phenotypes. The results of morphological analysis and methylation probably indicate that maybe they are individuals of populations from different taxa not registered yet in the literature.

  14. Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation.

    Science.gov (United States)

    Lande, Russell

    2009-07-01

    Adaptation to a sudden extreme change in environment, beyond the usual range of background environmental fluctuations, is analysed using a quantitative genetic model of phenotypic plasticity. Generations are discrete, with time lag tau between a critical period for environmental influence on individual development and natural selection on adult phenotypes. The optimum phenotype, and genotypic norms of reaction, are linear functions of the environment. Reaction norm elevation and slope (plasticity) vary among genotypes. Initially, in the average background environment, the character is canalized with minimum genetic and phenotypic variance, and no correlation between reaction norm elevation and slope. The optimal plasticity is proportional to the predictability of environmental fluctuations over time lag tau. During the first generation in the new environment the mean fitness suddenly drops and the mean phenotype jumps towards the new optimum phenotype by plasticity. Subsequent adaptation occurs in two phases. Rapid evolution of increased plasticity allows the mean phenotype to closely approach the new optimum. The new phenotype then undergoes slow genetic assimilation, with reduction in plasticity compensated by genetic evolution of reaction norm elevation in the original environment.

  15. Assessing Climate Variability using Extreme Rainfall and ...

    African Journals Online (AJOL)

    user1

    extreme frequency); the average intensity of rainfall from extreme events ... frequency and extreme intensity indices, suggesting that extreme events are more frequent and intense during years with high rainfall. The proportion of total rainfall from ...

  16. Sampling and examination methods used for TMI-2 samples

    International Nuclear Information System (INIS)

    Marley, A.W.; Akers, D.W.; McIsaac, C.V.

    1988-01-01

    The purpose of this paper is to summarize the sampling and examination techniques that were used in the collection and analysis of TMI-2 samples. Samples ranging from auxiliary building air to core debris were collected and analyzed. Handling of the larger samples and many of the smaller samples had to be done remotely and many standard laboratory analytical techniques were modified to accommodate the extremely high radiation fields associated with these samples. The TMI-2 samples presented unique problems with sampling and the laboratory analysis of prior molten fuel debris. 14 refs., 8 figs

  17. Management of the mangled extremity

    NARCIS (Netherlands)

    Prasarn, Mark L.; Helfet, David L.; Kloen, Peter

    2012-01-01

    The management of a mangled extremity continues to be a matter of debate. With modern advances in trauma resuscitation, microvascular tissue transfer, and fracture fixation, severe traumatic extremity injuries that would historically have been amputated are often salvaged. Even if preserving a

  18. A decade of weather extremes

    NARCIS (Netherlands)

    Coumou, Dim; Rahmstorf, Stefan

    The ostensibly large number of recent extreme weather events has triggered intensive discussions, both in- and outside the scientific community, on whether they are related to global warming. Here, we review the evidence and argue that for some types of extreme - notably heatwaves, but also

  19. Attitude extremity, consensus and diagnosticity

    NARCIS (Netherlands)

    van der Pligt, J.; Ester, P.; van der Linden, J.

    1983-01-01

    Studied the effects of attitude extremity on perceived consensus and willingness to ascribe trait terms to others with either pro- or antinuclear attitudes. 611 Ss rated their attitudes toward nuclear energy on a 5-point scale. Results show that attitude extremity affected consensus estimates. Trait

  20. Metabolic Phenotyping of Diet and Dietary Intake.

    Science.gov (United States)

    Brignardello, J; Holmes, E; Garcia-Perez, I

    Nutrition provides the building blocks for growth, repair, and maintenance of the body and is key to maintaining health. Exposure to fast foods, mass production of dietary components, and wider importation of goods have challenged the balance between diet and health in recent decades, and both scientists and clinicians struggle to characterize the relationship between this changing dietary landscape and human metabolism with its consequent impact on health. Metabolic phenotyping of foods, using high-density data-generating technologies to profile the biochemical composition of foods, meals, and human samples (pre- and postfood intake), can be used to map the complex interaction between the diet and human metabolism and also to assess food quality and safety. Here, we outline some of the techniques currently used for metabolic phenotyping and describe key applications in the food sciences, ending with a broad outlook at some of the newer technologies in the field with a view to exploring their potential to address some of the critical challenges in nutritional science. © 2017 Elsevier Inc. All rights reserved.

  1. Automated phenotyping of permanent crops

    Science.gov (United States)

    McPeek, K. Thomas; Steddom, Karl; Zamudio, Joseph; Pant, Paras; Mullenbach, Tyler

    2017-05-01

    AGERpoint is defining a new technology space for the growers' industry by introducing novel applications for sensor technology and data analysis to growers of permanent crops. Serving data to a state-of-the-art analytics engine from a cutting edge sensor platform, a new paradigm in precision agriculture is being developed that allows growers to understand the unique needs of each tree, bush or vine in their operation. Autonomous aerial and terrestrial vehicles equipped with multiple varieties of remote sensing technologies give AGERpoint the ability to measure key morphological and spectral features of permanent crops. This work demonstrates how such phenotypic measurements combined with machine learning algorithms can be used to determine the variety of crops (e.g., almond and pecan trees). This phenotypic and varietal information represents the first step in enabling growers with the ability to tailor their management practices to individual plants and maximize their economic productivity.

  2. Phenotypic deconstruction of gene circuitry.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2013-06-01

    It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.

  3. Phenotypic deconstruction of gene circuitry

    Science.gov (United States)

    Lomnitz, Jason G.; Savageau, Michael A.

    2013-06-01

    It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.

  4. From plant genomes to phenotypes

    OpenAIRE

    Bolger, Marie; Gundlach, Heidrun; Scholz, Uwe; Mayer, Klaus; Usadel, Björn; Schwacke, Rainer; Schmutzer, Thomas; Chen, Jinbo; Arend, Daniel; Oppermann, Markus; Weise, Stephan; Lange, Matthias; Fiorani, Fabio; Spannagl, Manuel

    2017-01-01

    Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis.Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.

  5. Adaptive evolution of molecular phenotypes

    International Nuclear Information System (INIS)

    Held, Torsten; Nourmohammad, Armita; Lässig, Michael

    2014-01-01

    Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak. (paper)

  6. Machine learning approaches to decipher hormone and HER2 receptor status phenotypes in breast cancer.

    Science.gov (United States)

    Adabor, Emmanuel S; Acquaah-Mensah, George K

    2017-10-16

    Breast cancer prognosis and administration of therapies are aided by knowledge of hormonal and HER2 receptor status. Breast cancer lacking estrogen receptors, progesterone receptors and HER2 receptors are difficult to treat. Regarding large data repositories such as The Cancer Genome Atlas, available wet-lab methods for establishing the presence of these receptors do not always conclusively cover all available samples. To this end, we introduce median-supplement methods to identify hormonal and HER2 receptor status phenotypes of breast cancer patients using gene expression profiles. In these approaches, supplementary instances based on median patient gene expression are introduced to balance a training set from which we build simple models to identify the receptor expression status of patients. In addition, for the purpose of benchmarking, we examine major machine learning approaches that are also applicable to the problem of finding receptor status in breast cancer. We show that our methods are robust and have high sensitivity with extremely low false-positive rates compared with the well-established methods. A successful application of these methods will permit the simultaneous study of large collections of samples of breast cancer patients as well as save time and cost while standardizing interpretation of outcomes of such studies. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  7. Spatial dependence of extreme rainfall

    Science.gov (United States)

    Radi, Noor Fadhilah Ahmad; Zakaria, Roslinazairimah; Satari, Siti Zanariah; Azman, Muhammad Az-zuhri

    2017-05-01

    This study aims to model the spatial extreme daily rainfall process using the max-stable model. The max-stable model is used to capture the dependence structure of spatial properties of extreme rainfall. Three models from max-stable are considered namely Smith, Schlather and Brown-Resnick models. The methods are applied on 12 selected rainfall stations in Kelantan, Malaysia. Most of the extreme rainfall data occur during wet season from October to December of 1971 to 2012. This period is chosen to assure the available data is enough to satisfy the assumption of stationarity. The dependence parameters including the range and smoothness, are estimated using composite likelihood approach. Then, the bootstrap approach is applied to generate synthetic extreme rainfall data for all models using the estimated dependence parameters. The goodness of fit between the observed extreme rainfall and the synthetic data is assessed using the composite likelihood information criterion (CLIC). Results show that Schlather model is the best followed by Brown-Resnick and Smith models based on the smallest CLIC's value. Thus, the max-stable model is suitable to be used to model extreme rainfall in Kelantan. The study on spatial dependence in extreme rainfall modelling is important to reduce the uncertainties of the point estimates for the tail index. If the spatial dependency is estimated individually, the uncertainties will be large. Furthermore, in the case of joint return level is of interest, taking into accounts the spatial dependence properties will improve the estimation process.

  8. Evolution caused by extreme events.

    Science.gov (United States)

    Grant, Peter R; Grant, B Rosemary; Huey, Raymond B; Johnson, Marc T J; Knoll, Andrew H; Schmitt, Johanna

    2017-06-19

    Extreme events can be a major driver of evolutionary change over geological and contemporary timescales. Outstanding examples are evolutionary diversification following mass extinctions caused by extreme volcanism or asteroid impact. The evolution of organisms in contemporary time is typically viewed as a gradual and incremental process that results from genetic change, environmental perturbation or both. However, contemporary environments occasionally experience strong perturbations such as heat waves, floods, hurricanes, droughts and pest outbreaks. These extreme events set up strong selection pressures on organisms, and are small-scale analogues of the dramatic changes documented in the fossil record. Because extreme events are rare, almost by definition, they are difficult to study. So far most attention has been given to their ecological rather than to their evolutionary consequences. We review several case studies of contemporary evolution in response to two types of extreme environmental perturbations, episodic (pulse) or prolonged (press). Evolution is most likely to occur when extreme events alter community composition. We encourage investigators to be prepared for evolutionary change in response to rare events during long-term field studies.This article is part of the themed issue 'Behavioural, ecological and evolutionary responses to extreme climatic events'. © 2017 The Author(s).

  9. The probability distribution of extreme precipitation

    Science.gov (United States)

    Korolev, V. Yu.; Gorshenin, A. K.

    2017-12-01

    On the basis of the negative binomial distribution of the duration of wet periods calculated per day, an asymptotic model is proposed for distributing the maximum daily rainfall volume during the wet period, having the form of a mixture of Frechet distributions and coinciding with the distribution of the positive degree of a random variable having the Fisher-Snedecor distribution. The method of proving the corresponding result is based on limit theorems for extreme order statistics in samples of a random volume with a mixed Poisson distribution. The adequacy of the models proposed and methods of their statistical analysis is demonstrated by the example of estimating the extreme distribution parameters based on real data.

  10. Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

    Energy Technology Data Exchange (ETDEWEB)

    Makarova, Kira S.; Omelchenko, Marina V.; Gaidamakova, Elena K.; Matrosova, Vera Y.; Vasilenko, Alexander; Zhai, Min; Lapidus, Alla; Copeland, Alex; Kim, Edwin; Land, Miriam; Mavrommatis, Konstantinos; Pitluck, Samuel; Richardson, Paul M.; Detter, Chris; Brettin, Thomas; Saunders, Elizabeth; Lai, Barry; Ravel, Bruce; Kemner, Kenneth M.; Wolf, Yuri I.; Sorokin, Alexander; Gerasimova, Anna V.; Gelfand, Mikhail S.; Fredrickson, James K.; Koonin, Eugene V.; Daly, Michael J.

    2007-07-24

    Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at itsoptimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to

  11. High-throughput phenotyping and genomic selection: the frontiers of crop breeding converge.

    Science.gov (United States)

    Cabrera-Bosquet, Llorenç; Crossa, José; von Zitzewitz, Jarislav; Serret, María Dolors; Araus, José Luis

    2012-05-01

    Genomic selection (GS) and high-throughput phenotyping have recently been captivating the interest of the crop breeding community from both the public and private sectors world-wide. Both approaches promise to revolutionize the prediction of complex traits, including growth, yield and adaptation to stress. Whereas high-throughput phenotyping may help to improve understanding of crop physiology, most powerful techniques for high-throughput field phenotyping are empirical rather than analytical and comparable to genomic selection. Despite the fact that the two methodological approaches represent the extremes of what is understood as the breeding process (phenotype versus genome), they both consider the targeted traits (e.g. grain yield, growth, phenology, plant adaptation to stress) as a black box instead of dissecting them as a set of secondary traits (i.e. physiological) putatively related to the target trait. Both GS and high-throughput phenotyping have in common their empirical approach enabling breeders to use genome profile or phenotype without understanding the underlying biology. This short review discusses the main aspects of both approaches and focuses on the case of genomic selection of maize flowering traits and near-infrared spectroscopy (NIRS) and plant spectral reflectance as high-throughput field phenotyping methods for complex traits such as crop growth and yield. © 2012 Institute of Botany, Chinese Academy of Sciences.

  12. Hexafluorobenzene under Extreme Conditions.

    Science.gov (United States)

    Pravica, Michael; Sneed, Daniel; Wang, Yonggang; Smith, Quinlan; White, Melanie

    2016-03-17

    We report the results from three high pressure experiments on hexafluorobenzene (C6F6). In the first experiment, Raman spectra were recorded up to 34.4 GPa. A phase transition from I → II was observed near 2 GPa. Near 8.8 GPa, a phase transition to an unreported phase (III) commenced. Above 20.6 GPa, yet another phase was observed (IV). Pressure cycling was employed to determine that, below 25.6 GPa, all pressure-induced alterations were reversible. However, at pressures above 20 GPa, dramatic spectral changes and broadening were observed at 25.6 and 34.4 GPa. The sample irreversibly changed into a soft solid with waxlike consistency when pressure was reduced to ambient and was recoverable. In the second experiment, IR spectra were collected up to 14.6 GPa. The phase transition (II → III) near 8.8 GPa was confirmed. An angular dispersive X-ray diffraction experiment was conducted to 25.6 GPa. Phase transitions above 1.4 GPa (I → II), above 5.5 GPa (II → III), above 10 GPa (III → IV), and above 15.5 GPa (IV → V) were observed. Near 25.6 GPa, long-range crystalline order was lost as the X-ray diffraction spectrum presented evidence of an amorphous solid.

  13. Knowledge-based analysis of phenotypes

    KAUST Repository

    Hoendorf, Robert

    2016-01-27

    Phenotypes are the observable characteristics of an organism, and they are widely recorded in biology and medicine. To facilitate data integration, ontologies that formally describe phenotypes are being developed in several domains. I will describe a formal framework to describe phenotypes. A formalized theory of phenotypes is not only useful for domain analysis, but can also be applied to assist in the diagnosis of rare genetic diseases, and I will show how our results on the ontology of phenotypes is now applied in biomedical research.

  14. Racial Extremism in the Army

    National Research Council Canada - National Science Library

    Hudson, Walter M

    1998-01-01

    ... modem phenomenon of "skinheads." I then discuss the history of white supremacist extremism in the Army, culminating in the December, 1995 murders of two black civilians by soldiers assigned to the 82d Airborne Division at Fort Bragg, North Carolina...

  15. NIH Mouse Metabolic Phenotyping Centers: the power of centralized phenotyping.

    Science.gov (United States)

    Laughlin, Maren R; Lloyd, K C Kent; Cline, Gary W; Wasserman, David H

    2012-10-01

    The Mouse Metabolic Phenotyping Centers (MMPCs) were founded in 2001 by the National Institutes of Health (NIH) to advance biomedical research by providing the scientific community with standardized, high-quality phenotyping services for mouse models of diabetes, obesity, and their complications. The intent is to allow researchers to take optimum advantage of the many new mouse models produced in labs and in high-throughput public efforts. The six MMPCs are located at universities around the country and perform complex metabolic tests in intact mice and hormone and analyte assays in tissues on a fee-for-service basis. Testing is subsidized by the NIH in order to reduce the barriers for mouse researchers. Although data derived from these tests belong to the researcher submitting mice or tissues, these data are archived after publication in a public database run by the MMPC Coordinating and Bioinformatics Unit. It is hoped that data from experiments performed in many mouse models of metabolic diseases, using standard protocols, will be useful in understanding the nature of these complex disorders. The current areas of expertise include energy balance and body composition, insulin action and secretion, whole-body and tissue carbohydrate and lipid metabolism, cardiovascular and renal function, and metabolic pathway kinetics. In addition to providing services, the MMPC staff provides expertise and advice to researchers, and works to develop and refine test protocols to best meet the community's needs in light of current scientific developments. Test technology is disseminated by publications and through annual courses.

  16. World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonisation Project: I. Surgical phenotype data collection in endometriosis research

    DEFF Research Database (Denmark)

    Becker, Christian M.; Laufer, Marc R.; Stratton, Pamela

    2014-01-01

    ObjectiveTo standardize the recording of surgical phenotypic information on endometriosis and related sample collections obtained at laparoscopy, allowing large-scale collaborative research into the condition.......ObjectiveTo standardize the recording of surgical phenotypic information on endometriosis and related sample collections obtained at laparoscopy, allowing large-scale collaborative research into the condition....

  17. The Human Phenotype Ontology in 2017

    International Nuclear Information System (INIS)

    Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark; Foster, Erin; McMurry, Julie

    2016-01-01

    Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human PhenotypeOntology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

  18. Causal Analysis of the Unanticipated Extremity Exposure at HFEF

    Energy Technology Data Exchange (ETDEWEB)

    David E. James; Charles R. Posegate; Thomas P. Zahn; Alan G. Wagner

    2011-11-01

    This report covers the unintended extremity exposure to an operator while handling a metallurgical mount sample of irradiated fuel following an off-scale high beta radiation reading of the sample. The decision was made to continue working after the meter indicated high off-scale by the HPT Supervisor, which resulted in the operator at the next operation being exposed.

  19. Extremal dependencies and rank correlations in power law networks

    NARCIS (Netherlands)

    Volkovich, Y.; Litvak, Nelli; Zwart, B.; Jie, Z.

    2009-01-01

    We analyze dependencies in complex networks characterized by power laws (Web sample, Wikipedia sample and a preferential attachment graph) using statistical techniques from the extreme value theory and the theory of multivariate regular variation. To the best of our knowledge, this is the first

  20. Genotype-phenotype correlation of xeroderma pigmentosum in a Chinese Han population.

    Science.gov (United States)

    Sun, Z; Zhang, J; Guo, Y; Ni, C; Liang, J; Cheng, R; Li, M; Yao, Z

    2015-04-01

    Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by extreme sensitivity to sunlight, freckle-like pigmentation and a greatly increased incidence of skin cancers. Genetic mutation detection and genotype-phenotype analysis of XP are rarely reported in the Chinese Han population. To investigate the mutational spectrum of XP in a Chinese Han population, to discover any genotype-phenotype correlation and, consequently, to propose a simple and effective tool for the molecular diagnosis of XP. This study was carried out on 12 unrelated Chinese families that included 13 patients with clinically suspected XP. Genomic DNA was extracted from peripheral blood samples. Mutation screening was performed by direct sequencing of exons and flanking intron-exon boundaries for the entire coding region of eight XP genes. In 12 patients, direct sequencing of the whole coding region of eight XP genes revealed pathogenic mutations, including seven compound heterozygous mutations, three homozygous mutations and a Japanese founder mutation. Thirteen mutations have not been previously identified. This cohort was composed of four patients with XP-C (XPC), two with XP-G (ERCC5), three with XP-A (XPA) and three with XP-V (POLH). This study identified 13 novel mutations and extended the mutation spectrum of XP in the Chinese Han population. In this cohort, we found that patients with XP-G have no neurological symptoms, and patients with XP-A and XP-V have a high incidence of malignancy. Furthermore, lack of stringent protection against sunlight, late diagnosis and long duration of disease play an important role. © 2014 British Association of Dermatologists.

  1. Legacies from extreme drought increase ecosystem sensitivity to future extremes

    Science.gov (United States)

    Smith, M. D.; Knapp, A.; Hoover, D. L.; Avolio, M. L.; Felton, A. J.; Wilcox, K. R.

    2016-12-01

    Climate extremes, such as drought, are increasing in frequency and intensity, and the ecological consequences of these extreme events can be substantial and widespread. Although there is still much to be learned about how ecosystems will respond to an intensification of drought, even less is known about the factors that determine post-drought recovery of ecosystem function. Such knowledge is particularly important because post-drought recovery periods can be protracted depending on the extent to which key plant populations, community structure and biogeochemical processes are affected. These drought legacies may alter ecosystem function for many years post-drought and may impact future sensitivity to climate extremes. We experimentally imposed two extreme growing season droughts in a central US grassland to assess the impacts of repeated droughts on ecosystem resistance (response) and resilience (recovery). We found that this grassland was not resistant to the first extreme drought due to reduced productivity and differential sensitivity of the co-dominant C4 grass (Andropogon gerardii) and C3 forb (Solidago canadensis) species. This differential sensitivity led to a reordering of species abundances within the plant community. Yet, despite this large shift in plant community composition, which persisted post-drought, the grassland was highly resilient post-drought, due to increased abundance of the dominant C4 grass. Because of this shift to increased C4 grass dominance, we expected that previously-droughted grassland would be more resistant to a second extreme drought. However, contrary to these expectations, previously droughted grassland was more sensitive to drought than grassland that had not experienced drought. Thus, our result suggest that legacies of drought (shift in community composition) may increase ecosystem sensitivity to future extreme events.

  2. Global predictability of temperature extremes

    Science.gov (United States)

    Coughlan de Perez, Erin; van Aalst, Maarten; Bischiniotis, Konstantinos; Mason, Simon; Nissan, Hannah; Pappenberger, Florian; Stephens, Elisabeth; Zsoter, Ervin; van den Hurk, Bart

    2018-05-01

    Extreme temperatures are one of the leading causes of death and disease in both developed and developing countries, and heat extremes are projected to rise in many regions. To reduce risk, heatwave plans and cold weather plans have been effectively implemented around the world. However, much of the world’s population is not yet protected by such systems, including many data-scarce but also highly vulnerable regions. In this study, we assess at a global level where such systems have the potential to be effective at reducing risk from temperature extremes, characterizing (1) long-term average occurrence of heatwaves and coldwaves, (2) seasonality of these extremes, and (3) short-term predictability of these extreme events three to ten days in advance. Using both the NOAA and ECMWF weather forecast models, we develop global maps indicating a first approximation of the locations that are likely to benefit from the development of seasonal preparedness plans and/or short-term early warning systems for extreme temperature. The extratropics generally show both short-term skill as well as strong seasonality; in the tropics, most locations do also demonstrate one or both. In fact, almost 5 billion people live in regions that have seasonality and predictability of heatwaves and/or coldwaves. Climate adaptation investments in these regions can take advantage of seasonality and predictability to reduce risks to vulnerable populations.

  3. Phenotypic variability in Meesmann's dystrophy

    DEFF Research Database (Denmark)

    Ehlers, Niels; Hjortdal, Jesper; Nielsen, Kim

    2008-01-01

    symptoms often include blurred vision and ocular irritation. Typical cases may be entirely free of complaints. Intermittent pain episodes, such as occur in recurrent erosion syndrome, are not the rule. Genetic sequencing indicated a familial relationship with the originally described Meesmann family......'s dystrophy occurs worldwide. The largest family described is the original German one, now supplemented with a Danish branch. Despite the presence of an identical genetic defect, the clinical phenotype varies. This suggests that non-KRT12-related mechanisms are responsible for the variation....

  4. The thrifty phenotype hypothesis revisited

    DEFF Research Database (Denmark)

    Vaag, A A; Grunnet, L G; Arora, G P

    2012-01-01

    Twenty years ago, Hales and Barker along with their co-workers published some of their pioneering papers proposing the 'thrifty phenotype hypothesis' in Diabetologia (4;35:595-601 and 3;36:62-67). Their postulate that fetal programming could represent an important player in the origin of type 2...... of the underlying molecular mechanisms. Type 2 diabetes is a multiple-organ disease, and developmental programming, with its idea of organ plasticity, is a plausible hypothesis for a common basis for the widespread organ dysfunctions in type 2 diabetes and the metabolic syndrome. Only two among the 45 known type 2...

  5. Endometrial gene expression profile of pregnant sows with extreme phenotypes for reproductive efficiency.

    Science.gov (United States)

    Córdoba, S; Balcells, I; Castelló, A; Ovilo, C; Noguera, J L; Timoneda, O; Sánchez, A

    2015-10-05

    Prolificacy can directly impact porcine profitability, but large genetic variation and low heritability have been found regarding litter size among porcine breeds. To identify key differences in gene expression associated to swine reproductive efficiency, we performed a transcriptome analysis of sows' endometrium from an Iberian x Meishan F2 population at day 30-32 of gestation, classified according to their estimated breeding value (EBV) as high (H, EBV > 0) and low (L, EBV ratio = 3.50), PTHLH (p = 0.03; H/L ratio = 3.69), MMP8 (p = 0.01; H/L ratio =4.41) and SCNN1G (p = 0.04; H/L ratio = 3.42). Although selected miRNAs showed similar expression levels between H and L groups, significant correlation was found between the expression level of ssc-miR-133a (p < 0.01) and ssc-miR-92a (p < 0.01) and validated genes. These results provide a better understanding of the genetic architecture of prolificacy-related traits and embryo implantation failure in pigs.

  6. Boat sampling

    International Nuclear Information System (INIS)

    Citanovic, M.; Bezlaj, H.

    1994-01-01

    This presentation describes essential boat sampling activities: on site boat sampling process optimization and qualification; boat sampling of base material (beltline region); boat sampling of weld material (weld No. 4); problems accompanied with weld crown varieties, RPV shell inner radius tolerance, local corrosion pitting and water clarity. The equipment used for boat sampling is described too. 7 pictures

  7. Graph sampling

    OpenAIRE

    Zhang, L.-C.; Patone, M.

    2017-01-01

    We synthesise the existing theory of graph sampling. We propose a formal definition of sampling in finite graphs, and provide a classification of potential graph parameters. We develop a general approach of Horvitz–Thompson estimation to T-stage snowball sampling, and present various reformulations of some common network sampling methods in the literature in terms of the outlined graph sampling theory.

  8. Crenarchaeal biofilm formation under extreme conditions.

    Directory of Open Access Journals (Sweden)

    Andrea Koerdt

    Full Text Available BACKGROUND: Biofilm formation has been studied in much detail for a variety of bacterial species, as it plays a major role in the pathogenicity of bacteria. However, only limited information is available for the development of archaeal communities that are frequently found in many natural environments. METHODOLOGY: We have analyzed biofilm formation in three closely related hyperthermophilic crenarchaeotes: Sulfolobus acidocaldarius, S. solfataricus and S. tokodaii. We established a microtitre plate assay adapted to high temperatures to determine how pH and temperature influence biofilm formation in these organisms. Biofilm analysis by confocal laser scanning microscopy demonstrated that the three strains form very different communities ranging from simple carpet-like structures in S. solfataricus to high density tower-like structures in S. acidocaldarius in static systems. Lectin staining indicated that all three strains produced extracellular polysaccharides containing glucose, galactose, mannose and N-acetylglucosamine once biofilm formation was initiated. While flagella mutants had no phenotype in two days old static biofilms of S. solfataricus, a UV-induced pili deletion mutant showed decreased attachment of cells. CONCLUSION: The study gives first insights into formation and development of crenarchaeal biofilms in extreme environments.

  9. Computational discovery of extremal microstructure families

    Science.gov (United States)

    Chen, Desai; Skouras, Mélina; Zhu, Bo; Matusik, Wojciech

    2018-01-01

    Modern fabrication techniques, such as additive manufacturing, can be used to create materials with complex custom internal structures. These engineered materials exhibit a much broader range of bulk properties than their base materials and are typically referred to as metamaterials or microstructures. Although metamaterials with extraordinary properties have many applications, designing them is very difficult and is generally done by hand. We propose a computational approach to discover families of microstructures with extremal macroscale properties automatically. Using efficient simulation and sampling techniques, we compute the space of mechanical properties covered by physically realizable microstructures. Our system then clusters microstructures with common topologies into families. Parameterized templates are eventually extracted from families to generate new microstructure designs. We demonstrate these capabilities on the computational design of mechanical metamaterials and present five auxetic microstructure families with extremal elastic material properties. Our study opens the way for the completely automated discovery of extremal microstructures across multiple domains of physics, including applications reliant on thermal, electrical, and magnetic properties. PMID:29376124

  10. Sexuality in persons with lower extremity amputations.

    Science.gov (United States)

    Bodenheimer, C; Kerrigan, A J; Garber, S L; Monga, T N

    2000-06-15

    There is a paucity of information regarding sexual functioning in persons with lower extremity amputations. The purpose of this study was to describe sexual and psychological functioning and health status in persons with lower extremity amputation. Self-report surveys assessed sexual functioning (Derogatis Inventory), depression (Beck Depression Inventory, anxiety (State-Trait Anxiety Inventory), and health status (Health Status Questionnaire) in a convenience sample of 30 men with lower extremity amputations. Mean age of the participants was 57 years (range 32-79). Mean duration since amputation was 23 months (range 3-634 months). Twenty one subjects (70%) had trans-tibial and seven subjects (23%) had trans-femoral amputations. A majority of subjects were experiencing problems in several domains of sexual functioning. Fifty three percent (n = 16) of the subjects were engaged in sexual intercourse or oral sex at least once a month. Twenty seven percent (n = 8) were masturbating at least once a month. Nineteen subjects (63%) reported orgasmic problems and 67% were experiencing erectile difficulties. Despite these problems, interest in sex was high in over 90% of the subjects. There was no evidence of increased prevalence of depression or anxiety in these subjects when compared to other outpatient adult populations. Sexual problems were common in the subjects studied. Despite these problems, interest in sex remained high. Few investigations have been directed toward identifying the psychological and social factors that may contribute to these problems and more research with a larger population is needed in this area.

  11. Extreme value theory in emerging markets

    Directory of Open Access Journals (Sweden)

    Anđelić Goran

    2010-01-01

    Full Text Available This paper investigates the performance of extreme value theory (EVT with the daily stock index returns of four different emerging markets. The research covers the sample representing the Serbian (BELEXline, Croatian (CROBEX, Slovenian (SBI20, and Hungarian (BUX stock indexes using the data from January 2006 - September 2009. In the paper a performance test was carried out for the success of application of the extreme value theory in estimating and forecasting of the tails of daily return distribution of the analyzed stock indexes. Therefore the main goal is to determine whether EVT adequately estimates and forecasts the tails (2.5% and 5% at the tail of daily stock index return distribution in the emerging markets of Serbia, Croatia, Slovenia, and Hungary. The applied methodology during the research includes analysis, synthesis and statistical/mathematical methods. Research results according to estimated Generalized Pareto Distribution (GPD parameters indicate the necessity of applying market risk estimation methods, i.e. extreme value theory (EVT in the framework of a broader analysis of investment processes in emerging markets.

  12. Ideologies and Discourses: Extreme Narratives in Extreme Metal Music

    Directory of Open Access Journals (Sweden)

    Bojana Radovanović

    2016-10-01

    Full Text Available Historically speaking, metal music has always been about provoking a strong reaction. Depending on the characteristics of different sub-genres, one can focus on the sound, technique, visual appearance, and furthermore, the ideologies and ideas that are the foundation for each of the sub-genres. Although the majority of the metal community rejects accusations of being racially intolerant, some ideologies of extreme sub-genres (such as black metal are in fact formed around the ideas of self-conscious elitism expressed through interest in pagan mythology, racism, Nazism and fascism. There has been much interest in the Nazi era within the extreme metal scene thus influencing other sub-genres and artists. The aim of this paper is to examine various appearances of extreme narratives such as Nazism and racism in  different sub-genres of metal, bearing in mind variations dependent on geographical, political, and other factors.

  13. Independent test assessment using the extreme value distribution theory.

    Science.gov (United States)

    Almeida, Marcio; Blondell, Lucy; Peralta, Juan M; Kent, Jack W; Jun, Goo; Teslovich, Tanya M; Fuchsberger, Christian; Wood, Andrew R; Manning, Alisa K; Frayling, Timothy M; Cingolani, Pablo E; Sladek, Robert; Dyer, Thomas D; Abecasis, Goncalo; Duggirala, Ravindranath; Blangero, John

    2016-01-01

    The new generation of whole genome sequencing platforms offers great possibilities and challenges for dissecting the genetic basis of complex traits. With a very high number of sequence variants, a naïve multiple hypothesis threshold correction hinders the identification of reliable associations by the overreduction of statistical power. In this report, we examine 2 alternative approaches to improve the statistical power of a whole genome association study to detect reliable genetic associations. The approaches were tested using the Genetic Analysis Workshop 19 (GAW19) whole genome sequencing data. The first tested method estimates the real number of effective independent tests actually being performed in whole genome association project by the use of an extreme value distribution and a set of phenotype simulations. Given the familiar nature of the GAW19 data and the finite number of pedigree founders in the sample, the number of correlations between genotypes is greater than in a set of unrelated samples. Using our procedure, we estimate that the effective number represents only 15 % of the total number of independent tests performed. However, even using this corrected significance threshold, no genome-wide significant association could be detected for systolic and diastolic blood pressure traits. The second approach implements a biological relevance-driven hypothesis tested by exploiting prior computational predictions on the effect of nonsynonymous genetic variants detected in a whole genome sequencing association study. This guided testing approach was able to identify 2 promising single-nucleotide polymorphisms (SNPs), 1 for each trait, targeting biologically relevant genes that could help shed light on the genesis of the human hypertension. The first gene, PFH14 , associated with systolic blood pressure, interacts directly with genes involved in calcium-channel formation and the second gene, MAP4 , encodes a microtubule-associated protein and had already

  14. Playing by the rules? Phenotypic adaptation to temperate environments in an American marsupial

    Science.gov (United States)

    Harrigan, Ryan J.; Wayne, Robert K.

    2018-01-01

    Phenotypic variation along environmental gradients can provide evidence suggesting local adaptation has shaped observed morphological disparities. These differences, in traits such as body and extremity size, as well as skin and coat pigmentation, may affect the overall fitness of individuals in their environments. The Virginia opossum (Didelphis virginiana) is a marsupial that shows phenotypic variation across its range, one that has recently expanded into temperate environments. It is unknown, however, whether the variation observed in the species fits adaptive ecogeographic patterns, or if phenotypic change is associated with any environmental factors. Using phenotypic measurements of over 300 museum specimens of Virginia opossum, collected throughout its distribution range, we applied regression analysis to determine if phenotypes change along a latitudinal gradient. Then, using predictors from remote-sensing databases and a random forest algorithm, we tested environmental models to find the most important variables driving the phenotypic variation. We found that despite the recent expansion into temperate environments, the phenotypic variation in the Virginia opossum follows a latitudinal gradient fitting three adaptive ecogeographic patterns codified under Bergmann’s, Allen’s and Gloger’s rules. Temperature seasonality was an important predictor of body size variation, with larger opossums occurring at high latitudes with more seasonal environments. Annual mean temperature predicted important variation in extremity size, with smaller extremities found in northern populations. Finally, we found that precipitation and temperature seasonality as well as low temperatures were strong environmental predictors of skin and coat pigmentation variation; darker opossums are distributed at low latitudes in warmer environments with higher precipitation seasonality. These results indicate that the adaptive mechanisms underlying the variation in body size, extremity

  15. Playing by the rules? Phenotypic adaptation to temperate environments in an American marsupial

    Directory of Open Access Journals (Sweden)

    Sergio F. Nigenda-Morales

    2018-03-01

    Full Text Available Phenotypic variation along environmental gradients can provide evidence suggesting local adaptation has shaped observed morphological disparities. These differences, in traits such as body and extremity size, as well as skin and coat pigmentation, may affect the overall fitness of individuals in their environments. The Virginia opossum (Didelphis virginiana is a marsupial that shows phenotypic variation across its range, one that has recently expanded into temperate environments. It is unknown, however, whether the variation observed in the species fits adaptive ecogeographic patterns, or if phenotypic change is associated with any environmental factors. Using phenotypic measurements of over 300 museum specimens of Virginia opossum, collected throughout its distribution range, we applied regression analysis to determine if phenotypes change along a latitudinal gradient. Then, using predictors from remote-sensing databases and a random forest algorithm, we tested environmental models to find the most important variables driving the phenotypic variation. We found that despite the recent expansion into temperate environments, the phenotypic variation in the Virginia opossum follows a latitudinal gradient fitting three adaptive ecogeographic patterns codified under Bergmann’s, Allen’s and Gloger’s rules. Temperature seasonality was an important predictor of body size variation, with larger opossums occurring at high latitudes with more seasonal environments. Annual mean temperature predicted important variation in extremity size, with smaller extremities found in northern populations. Finally, we found that precipitation and temperature seasonality as well as low temperatures were strong environmental predictors of skin and coat pigmentation variation; darker opossums are distributed at low latitudes in warmer environments with higher precipitation seasonality. These results indicate that the adaptive mechanisms underlying the variation in

  16. The phenotypic equilibrium of cancer cells: From average-level stability to path-wise convergence.

    Science.gov (United States)

    Niu, Yuanling; Wang, Yue; Zhou, Da

    2015-12-07

    The phenotypic equilibrium, i.e. heterogeneous population of cancer cells tending to a fixed equilibrium of phenotypic proportions, has received much attention in cancer biology very recently. In the previous literature, some theoretical models were used to predict the experimental phenomena of the phenotypic equilibrium, which were often explained by different concepts of stabilities of the models. Here we present a stochastic multi-phenotype branching model by integrating conventional cellular hierarchy with phenotypic plasticity mechanisms of cancer cells. Based on our model, it is shown that: (i) our model can serve as a framework to unify the previous models for the phenotypic equilibrium, and then harmonizes the different kinds of average-level stabilities proposed in these models; and (ii) path-wise convergence of our model provides a deeper understanding to the phenotypic equilibrium from stochastic point of view. That is, the emergence of the phenotypic equilibrium is rooted in the stochastic nature of (almost) every sample path, the average-level stability just follows from it by averaging stochastic samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Aislamiento de Candida dubliniensis en distintos materiales clínicos: Análisis de métodos fenotípicos de diferenciación con Candida albicans Isolation of Candida dubliniensis in different clinical samples: Analysis of phenotypical methods to differenciate from Candida albicans

    Directory of Open Access Journals (Sweden)

    G. Pineda

    2008-12-01

    Full Text Available Con el objeto de estimar la frecuencia de aislamientos de Candida dubliniensis en materiales clínicos en el Hospital de Infecciosas F. J. Muñiz, se identificaron 388 levaduras entre setiembre de 2005 y agosto de 2007. Doscientos doce aislamientos presentaban color verde en CHROMagar® y producían tubos germinativos y clamidoconidias en agarleche. Para diferenciar cuales de ellos correspondían a Candida albicans o a C. dubliniensis, se utilizaron distintos métodos fenotípicos y se evaluó la utilidad de cada técnica a fin de proponer un algoritmo de identificación simple, económico y confiable. Se estudió el color en 2 medios con sustratos cromogénicos, la producción de clamidoconidias en medios de Staib, agar tomate-zanahoria y agar-tabaco; en este último medio también se evaluaron las características macromorfológicas de las colonias; se evaluó la presencia de actividad lipolítica (medio-opacidad, capacidad de desarrollo a 45 °C y asimilación de D-xilosa. El 6,1% (13/212 aislamientos correspondió a C. dubliniensis (3,3% del total de levaduras. No se pudo diferenciar entre ambas especies por el color en los medios cromogénicos usados. Las pruebas que resultaron más sensibles y específicas fueron crecimiento a 45 °C, asimilación de D-xilosa, color y desarrollo en agar-tabaco. C. albicans produjo clamidoconidias en los 3 medios diferenciales, entre 11,6% y 15,1% de los casos. La presencia de lipasas se evidenció en el 95,6% de C. albicans pero 2 de las 13 cepas de C. dubliniensis también presentaron halo de opacidad. Consideramos que se deben usar, al menos, 3 métodos diferentes para discriminar entre estas levaduras ya que ninguna prueba es absolutamente sensible o específica.In order to estimate the frequence of Candida dubliniensis in clinical samples in F. J. Muñiz Infectious Diseases Hospital, a total of 388 yeasts from September 2005 to August 2007. There were 212 isolates which presented a green color on

  18. Extreme climatic events in relation to global change and their impact on life histories

    Directory of Open Access Journals (Sweden)

    Juan MORENO, Anders Pape Møller

    2011-06-01

    Full Text Available Extreme weather conditions occur at an increasing rate as evidenced by higher frequency of hurricanes and more extreme precipitation and temperature anomalies. Such extreme environmental conditions will have important implications for all living organisms through greater frequency of reproductive failure and reduced adult survival. We review examples of reproductive failure and reduced survival related to extreme weather conditions. Phenotypic plasticity may not be sufficient to allow adaptation to extreme weather for many animals. Theory predicts reduced reproductive effort as a response to increased stochasticity. We predict that patterns of natural selection will change towards truncation selection as environmental conditions become more extreme. Such changes in patterns of selection may facilitate adaptation to extreme events. However, effects of selection on reproductive effort are difficult to detect. We present a number of predictions for the effects of extreme weather conditions in need of empirical tests. Finally, we suggest a number of empirical reviews that could improve our ability to judge the effects of extreme environmental conditions on life history [Current Zoology 57 (3: 375–389, 2011].

  19. Balanced sampling

    NARCIS (Netherlands)

    Brus, D.J.

    2015-01-01

    In balanced sampling a linear relation between the soil property of interest and one or more covariates with known means is exploited in selecting the sampling locations. Recent developments make this sampling design attractive for statistical soil surveys. This paper introduces balanced sampling

  20. Seasonal temperature extremes in Potsdam

    Science.gov (United States)

    Kundzewicz, Zbigniew; Huang, Shaochun

    2010-12-01

    The awareness of global warming is well established and results from the observations made on thousands of stations. This paper complements the large-scale results by examining a long time-series of high-quality temperature data from the Secular Meteorological Station in Potsdam, where observation records over the last 117 years, i.e., from January 1893 are available. Tendencies of change in seasonal temperature-related climate extremes are demonstrated. "Cold" extremes have become less frequent and less severe than in the past, while "warm" extremes have become more frequent and more severe. Moreover, the interval of the occurrence of frost has been decreasing, while the interval of the occurrence of hot days has been increasing. However, many changes are not statistically significant, since the variability of temperature indices at the Potsdam station has been very strong.

  1. Lymphoscintigraphy of the lower extremity

    International Nuclear Information System (INIS)

    Abbasi, N.Z.

    1990-01-01

    Fifty one lower extremities of 26 normal healthy volunteers and 26 extremities of 13 patients with oedema have been studied. Dynamic quantitative lymphoscintigraphy using 99Tc-m antimony sulphide colloid during passive exercise as well as before and after active exercise was performed. parameters of lymphatic function including percentage of radioactivity cleared from the injection site, the percentage uptake by the inguinal lymph nodes, the time of arrival of activity at the regional lymph nodes and the lymphatic reserve index have been evaluated. The percentage clearance of activity from the injection site was found technically difficult to standardize and proved to be an unreliable parameter of lymphatic function. However, the quantitation of nodal uptake, the lymphatic transit time and the lymphatic reserve capacity accurately depicted the lymphatic functional status of an individual. The physiologic parameters of lymphatic function of the contralateral lower extremities were compared and a physiologic difference in the lymphatic capacity of the two limbs was scintigraphically documented. (author)

  2. Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P; Lund, M S

    2009-01-01

    disequilibrium-based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals...... for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across...... the whole population based on LDC. The results showed that selecting individuals with similar haplotypes to the paternal haplotypes (minimum recombination criterion) using LAC compared to random phenotyping gave at least the same power to detect a QTL but decreased the accuracy of the QTL position. However...

  3. Ensemble Sampling

    OpenAIRE

    Lu, Xiuyuan; Van Roy, Benjamin

    2017-01-01

    Thompson sampling has emerged as an effective heuristic for a broad range of online decision problems. In its basic form, the algorithm requires computing and sampling from a posterior distribution over models, which is tractable only for simple special cases. This paper develops ensemble sampling, which aims to approximate Thompson sampling while maintaining tractability even in the face of complex models such as neural networks. Ensemble sampling dramatically expands on the range of applica...

  4. DNA-methylation profiling of fetal tissues reveals marked epigenetic differences between chorionic and amniotic samples.

    Directory of Open Access Journals (Sweden)

    Christel Eckmann-Scholz

    Full Text Available Epigenetic mechanisms including DNA methylation are supposed to play a key role in fetal development. Here we have investigated fetal DNA-methylation levels of 27,578 CpG loci in 47 chorionic villi (CVS and 16 amniotic cell (AC samples. Methylation levels differed significantly between karyotypically normal AC and CVS for 2,014 genes. AC showed more extreme DNA-methylation levels of these genes than CVS and the differentially methylated genes are significantly enriched for processes characteristic for the different cell types sampled. Furthermore, we identified 404 genes differentially methylated in CVS with trisomy 21. These genes were significantly enriched for high CG dinucleotid (CpG content and developmental processes associated with Down syndrome. Our study points to major tissue-specific differences of fetal DNA-methylation and gives rise to the hypothesis that part of the Down syndrome phenotype is epigenetically programmed in the first trimester of pregnancy.

  5. Refined Phenotyping of Modic Changes

    Science.gov (United States)

    Määttä, Juhani H.; Karppinen, Jaro; Paananen, Markus; Bow, Cora; Luk, Keith D.K.; Cheung, Kenneth M.C.; Samartzis, Dino

    2016-01-01

    Abstract Low back pain (LBP) is the world's most disabling condition. Modic changes (MC) are vertebral bone marrow changes adjacent to the endplates as noted on magnetic resonance imaging. The associations of specific MC types and patterns with prolonged, severe LBP and disability remain speculative. This study assessed the relationship of prolonged, severe LBP and back-related disability, with the presence and morphology of lumbar MC in a large cross-sectional population-based study of Southern Chinese. We addressed the topographical and morphological dimensions of MC along with other magnetic resonance imaging phenotypes (eg, disc degeneration and displacement) on the basis of axial T1 and sagittal T2-weighted imaging of L1-S1. Prolonged severe LBP was defined as LBP lasting ≥30 days during the past year, and a visual analog scale severest pain intensity of at least 6/10. An Oswestry Disability Index score of 15% was regarded as significant disability. We also assessed subject demographics, occupation, and lifestyle factors. In total, 1142 subjects (63% females, mean age 53 years) were assessed. Of these, 282 (24.7%) had MC (7.1% type I, 17.6% type II). MC subjects were older (P = 0.003), had more frequent disc displacements (P disability. The strength of the associations increased with the number of MC. This large-scale study is the first to definitively note MC types and specific morphologies to be independently associated with prolonged severe LBP and back-related disability. This proposed refined MC phenotype may have direct implications in clinical decision-making as to the development and management of LBP. Understanding of these imaging biomarkers can lead to new preventative and personalized therapeutics related to LBP. PMID:27258491

  6. Automation Rover for Extreme Environments

    Science.gov (United States)

    Sauder, Jonathan; Hilgemann, Evan; Johnson, Michael; Parness, Aaron; Hall, Jeffrey; Kawata, Jessie; Stack, Kathryn

    2017-01-01

    Almost 2,300 years ago the ancient Greeks built the Antikythera automaton. This purely mechanical computer accurately predicted past and future astronomical events long before electronics existed1. Automata have been credibly used for hundreds of years as computers, art pieces, and clocks. However, in the past several decades automata have become less popular as the capabilities of electronics increased, leaving them an unexplored solution for robotic spacecraft. The Automaton Rover for Extreme Environments (AREE) proposes an exciting paradigm shift from electronics to a fully mechanical system, enabling longitudinal exploration of the most extreme environments within the solar system.

  7. Hygienic diagnosis in extreme conditions

    International Nuclear Information System (INIS)

    Sofronov, G.A.

    1997-01-01

    Review for book by M.P. Zakharchenko, S.A. Lopatin, G.N. Novozhilov, V.I. Zakharov Hygienic diagnosis in extreme conditions is presented discussing the problem of people health preservation under extreme conditions. Hygienic diagnosis is considered illustrated by cases of hostilities (Afghan War), earthquake response in Armenia (1988) and Chernobyl accident response. Attention is paid to the estimation of radiation doses to people and characteristics of main types of dosimeters. The high scientific level of the book is marked

  8. Extreme Conditions Modeling Workshop Report

    Energy Technology Data Exchange (ETDEWEB)

    Coe, R. G.; Neary, V. S.; Lawson, M. J.; Yu, Y.; Weber, J.

    2014-07-01

    Sandia National Laboratories (SNL) and the National Renewable Energy Laboratory (NREL) hosted the Wave Energy Converter (WEC) Extreme Conditions Modeling (ECM) Workshop in Albuquerque, NM on May 13th-14th, 2014. The objective of the workshop was to review the current state of knowledge on how to model WECs in extreme conditions (e.g. hurricanes and other large storms) and to suggest how U.S. Department of Energy (DOE) and national laboratory resources could be used to improve ECM methods for the benefit of the wave energy industry.

  9. Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation.

    Science.gov (United States)

    Posey, Jennifer E; Harel, Tamar; Liu, Pengfei; Rosenfeld, Jill A; James, Regis A; Coban Akdemir, Zeynep H; Walkiewicz, Magdalena; Bi, Weimin; Xiao, Rui; Ding, Yan; Xia, Fan; Beaudet, Arthur L; Muzny, Donna M; Gibbs, Richard A; Boerwinkle, Eric; Eng, Christine M; Sutton, V Reid; Shaw, Chad A; Plon, Sharon E; Yang, Yaping; Lupski, James R

    2017-01-05

    Whole-exome sequencing can provide insight into the relationship between observed clinical phenotypes and underlying genotypes. We conducted a retrospective analysis of data from a series of 7374 consecutive unrelated patients who had been referred to a clinical diagnostic laboratory for whole-exome sequencing; our goal was to determine the frequency and clinical characteristics of patients for whom more than one molecular diagnosis was reported. The phenotypic similarity between molecularly diagnosed pairs of diseases was calculated with the use of terms from the Human Phenotype Ontology. A molecular diagnosis was rendered for 2076 of 7374 patients (28.2%); among these patients, 101 (4.9%) had diagnoses that involved two or more disease loci. We also analyzed parental samples, when available, and found that de novo variants accounted for 67.8% (61 of 90) of pathogenic variants in autosomal dominant disease genes and 51.7% (15 of 29) of pathogenic variants in X-linked disease genes; both variants were de novo in 44.7% (17 of 38) of patients with two monoallelic variants. Causal copy-number variants were found in 12 patients (11.9%) with multiple diagnoses. Phenotypic similarity scores were significantly lower among patients in whom the phenotype resulted from two distinct mendelian disorders that affected different organ systems (50 patients) than among patients with disorders that had overlapping phenotypic features (30 patients) (median score, 0.21 vs. 0.36; P=1.77×10 -7 ). In our study, we found multiple molecular diagnoses in 4.9% of cases in which whole-exome sequencing was informative. Our results show that structured clinical ontologies can be used to determine the degree of overlap between two mendelian diseases in the same patient; the diseases can be distinct or overlapping. Distinct disease phenotypes affect different organ systems, whereas overlapping disease phenotypes are more likely to be caused by two genes encoding proteins that interact within

  10. Moving in extreme environments: what's extreme and who decides?

    Science.gov (United States)

    Cotter, James David; Tipton, Michael J

    2014-01-01

    Humans work, rest and play in immensely varied extreme environments. The term 'extreme' typically refers to insufficiency or excess of one or more stressors, such as thermal energy or gravity. Individuals' behavioural and physiological capacity to endure and enjoy such environments varies immensely. Adverse effects of acute exposure to these environments are readily identifiable (e.g. heat stroke or bone fracture), whereas adverse effects of chronic exposure (e.g. stress fractures or osteoporosis) may be as important but much less discernable. Modern societies have increasingly sought to protect people from such stressors and, in that way, minimise their adverse effects. Regulations are thus established, and advice is provided on what is 'acceptable' exposure. Examples include work/rest cycles in the heat, hydration regimes, rates of ascent to and duration of stay at altitude and diving depth. While usually valuable and well intentioned, it is important to realise the breadth and importance of limitations associated with such guidelines. Regulations and advisories leave less room for self-determination, learning and perhaps adaptation. Regulations based on stress (e.g. work/rest cycles relative to WBGT) are more practical but less direct than those based on strain (e.g. core temperature), but even the latter can be substantively limited (e.g. by lack of criterion validation and allowance for behavioural regulation in the research on which they are based). Extreme Physiology & Medicine is publishing a series of reviews aimed at critically examining the issues involved with self- versus regulation-controlled human movement acutely and chronically in extreme environments. These papers, arising from a research symposium in 2013, are about the impact of people engaging in such environments and the effect of rules and guidelines on their safety, enjoyment, autonomy and productivity. The reviews will cover occupational heat stress, sporting heat stress, hydration, diving

  11. The phenotypic variance gradient - a novel concept.

    Science.gov (United States)

    Pertoldi, Cino; Bundgaard, Jørgen; Loeschcke, Volker; Barker, James Stuart Flinton

    2014-11-01

    Evolutionary ecologists commonly use reaction norms, which show the range of phenotypes produced by a set of genotypes exposed to different environments, to quantify the degree of phenotypic variance and the magnitude of plasticity of morphometric and life-history traits. Significant differences among the values of the slopes of the reaction norms are interpreted as significant differences in phenotypic plasticity, whereas significant differences among phenotypic variances (variance or coefficient of variation) are interpreted as differences in the degree of developmental instability or canalization. We highlight some potential problems with this approach to quantifying phenotypic variance and suggest a novel and more informative way to plot reaction norms: namely "a plot of log (variance) on the y-axis versus log (mean) on the x-axis, with a reference line added". This approach gives an immediate impression of how the degree of phenotypic variance varies across an environmental gradient, taking into account the consequences of the scaling effect of the variance with the mean. The evolutionary implications of the variation in the degree of phenotypic variance, which we call a "phenotypic variance gradient", are discussed together with its potential interactions with variation in the degree of phenotypic plasticity and canalization.

  12. Effects of Extreme Events on Arsenic Cycling in Salt Marshes

    Science.gov (United States)

    Northrup, Kristy; Capooci, Margaret; Seyfferth, Angelia L.

    2018-03-01

    Extreme events such as storm surges, intense precipitation, and supermoons cause anomalous and large fluctuations in water level in tidal salt marshes, which impacts the sediment biogeochemistry that dictates arsenic (As) cycling. In addition to changes in water level, which impacts soil redox potential, these extreme events may also change salinity due to freshwater inputs from precipitation or saltwater inputs due to surge. It is currently unknown how As mobility in tidal salt marshes will be impacted by extreme events, as fluctuations in salinity and redox potential may act synergistically to mobilize As. To investigate impacts of extreme events on As cycling in tidal salt marshes, we conducted a combined laboratory and field investigation. We monitored pore water and soil samples before, during, and after two extreme events: a supermoon lunar eclipse followed by a storm surge and precipitation induced by Hurricane Joaquin in fall 2015 at the St. Jones Reserve in Dover, Delaware, a representative tidal salt marsh in the Mid-Atlantic United States. We also conducted soil incubations of marsh sediments in batch and in flow-through experiments in which redox potential and/or salinity were manipulated. Field investigations showed that pore water As was inversely proportional to redox potential. During the extreme events, a distinct pulse of As was observed in the pore water with maximum salinity. Combined field and laboratory investigations revealed that this As pulse is likely due to rapid changes in salinity. These results have implications for As mobility in the face of extreme weather variability.

  13. A novel 3D imaging system for strawberry phenotyping

    Directory of Open Access Journals (Sweden)

    Joe Q. He

    2017-11-01

    Full Text Available Abstract Background Accurate and quantitative phenotypic data in plant breeding programmes is vital in breeding to assess the performance of genotypes and to make selections. Traditional strawberry phenotyping relies on the human eye to assess most external fruit quality attributes, which is time-consuming and subjective. 3D imaging is a promising high-throughput technique that allows multiple external fruit quality attributes to be measured simultaneously. Results A low cost multi-view stereo (MVS imaging system was developed, which captured data from 360° around a target strawberry fruit. A 3D point cloud of the sample was derived and analysed with custom-developed software to estimate berry height, length, width, volume, calyx size, colour and achene number. Analysis of these traits in 100 fruits showed good concordance with manual assessment methods. Conclusion This study demonstrates the feasibility of an MVS based 3D imaging system for the rapid and quantitative phenotyping of seven agronomically important external strawberry traits. With further improvement, this method could be applied in strawberry breeding programmes as a cost effective phenotyping technique.

  14. A novel 3D imaging system for strawberry phenotyping.

    Science.gov (United States)

    He, Joe Q; Harrison, Richard J; Li, Bo

    2017-01-01

    Accurate and quantitative phenotypic data in plant breeding programmes is vital in breeding to assess the performance of genotypes and to make selections. Traditional strawberry phenotyping relies on the human eye to assess most external fruit quality attributes, which is time-consuming and subjective. 3D imaging is a promising high-throughput technique that allows multiple external fruit quality attributes to be measured simultaneously. A low cost multi-view stereo (MVS) imaging system was developed, which captured data from 360° around a target strawberry fruit. A 3D point cloud of the sample was derived and analysed with custom-developed software to estimate berry height, length, width, volume, calyx size, colour and achene number. Analysis of these traits in 100 fruits showed good concordance with manual assessment methods. This study demonstrates the feasibility of an MVS based 3D imaging system for the rapid and quantitative phenotyping of seven agronomically important external strawberry traits. With further improvement, this method could be applied in strawberry breeding programmes as a cost effective phenotyping technique.

  15. A rare case of haemolytic disease of newborn with Bombay phenotype mother

    Directory of Open Access Journals (Sweden)

    Shamee Shastry

    2013-01-01

    Full Text Available We are reporting a rare case of severe hemolytic disease of newborn (HDN with Bombay phenotype mother. A retrospective study of a case with severe haemolytic disease of newborn with Bombay phenotype mother was done. Blood grouping, antibody screening, and lectin study was done on the blood sample of the baby and mother to confirm the diagnosis. Hematological and biochemical parameters were obtained from the hospital laboratory information system for the analysis. Blood group of the baby was A positive, direct antiglobulin test was negative. Blood group of the mother was confirmed to be Bombay phenotype, Hematological parameters showed all the signs of ongoing hemolysis and the bilirubin level was in the zone of exchange transfusion. Due to the unavailability of this rare phenotype blood unit, baby was managed conservatively. Anticipating the fetal anemia and HDN with mothers having Bombay phenotype and prior notification to the transfusion services will be of great help in optimizing the neonatal care and outcome.

  16. Correlation dimension and phase space contraction via extreme value theory

    Science.gov (United States)

    Faranda, Davide; Vaienti, Sandro

    2018-04-01

    We show how to obtain theoretical and numerical estimates of correlation dimension and phase space contraction by using the extreme value theory. The maxima of suitable observables sampled along the trajectory of a chaotic dynamical system converge asymptotically to classical extreme value laws where: (i) the inverse of the scale parameter gives the correlation dimension and (ii) the extremal index is associated with the rate of phase space contraction for backward iteration, which in dimension 1 and 2, is closely related to the positive Lyapunov exponent and in higher dimensions is related to the metric entropy. We call it the Dynamical Extremal Index. Numerical estimates are straightforward to obtain as they imply just a simple fit to a univariate distribution. Numerical tests range from low dimensional maps, to generalized Henon maps and climate data. The estimates of the indicators are particularly robust even with relatively short time series.

  17. Extreme-value dependence: An application to exchange rate markets

    Science.gov (United States)

    Fernandez, Viviana

    2007-04-01

    Extreme value theory (EVT) focuses on modeling the tail behavior of a loss distribution using only extreme values rather than the whole data set. For a sample of 10 countries with dirty/free float regimes, we investigate whether paired currencies exhibit a pattern of asymptotic dependence. That is, whether an extremely large appreciation or depreciation in the nominal exchange rate of one country might transmit to another. In general, after controlling for volatility clustering and inertia in returns, we do not find evidence of extreme-value dependence between paired exchange rates. However, for asymptotic-independent paired returns, we find that tail dependency of exchange rates is stronger under large appreciations than under large depreciations.

  18. Why do people buy dogs with potential welfare problems related to extreme conformation and inherited disease? A representative study of Danish owners of four small dog breeds

    OpenAIRE

    Sand?e, P.; Kondrup, S. V.; Bennett, P. C.; Forkman, B.; Meyer, I; Proschowsky, H. F.; Serpell, J. A.; Lund, T. B.

    2017-01-01

    number of dog breeds suffer from welfare problems due to extreme phenotypes and high levels of inherited diseases but the popularity of such breeds is not declining. Using a survey of owners of two popular breeds with extreme physical features (French Bulldog and Chihuahua), one with a high load of inherited diseases not directly related to conformation (Cavalier King Charles Spaniel), and one representing the same size range but without extreme conformation and with the same level of disease...

  19. Angiography of the upper extremity

    International Nuclear Information System (INIS)

    Janevski, B.K.

    1982-01-01

    This thesis provides a description of the technical and medical aspects of arteriography of the upper extremity and an extensive analysis of the angiographic anatomy and pathology of 750 selective studies performed in more than 500 patients. A short historical review is provided of angiography as a whole and of arteriography of the hand in particular. The method of percutaneous transfemoral catheterization of the arteries of the upper extremity and particularly the arteries of the hand is considered, discussing the problems the angiographer encounters frequently, describing the angiographic complications which may occur and emphasizing the measures to keep them to a minimum. The use of vasodilators in hand angiography is discussed. A short description of the embryological patterns persisting in the arteries of the arm is included in order to understand the congenital variations of the arteries of the upper extremity. The angiographic patterns and clinical aspects of the most common pathological processes involving the arteries of the upper extremities are presented. Special attention is paid to the correlation between angiography and pathology. (Auth.)

  20. Book review: Extreme ocean waves

    Science.gov (United States)

    Geist, Eric L.

    2011-01-01

    ‘‘Extreme Ocean Waves’’ is a collection of ten papers edited by Efim Pelinovsky and Christian Kharif that followed the April 2007 meeting of the General Assembly of the European Geosciences Union. A note on terminology: extreme waves in this volume broadly encompass different types of waves, includ- ing deep-water and shallow-water rogue waves (alternatively termed freak waves), storm surges from cyclones, and internal waves. Other types of waves such as tsunamis or rissaga (meteotsunamis) are not discussed in this volume. It is generally implied that ‘‘extreme’’ has a statistical connotation relative to the average or significant wave height specific to each type of wave. Throughout the book, in fact, the reader will find a combination of theoretical and statistical/ empirical treatment necessary for the complete examination of this subject. In the introduction, the editors underscore the importance of studying extreme waves, documenting several dramatic instances of damaging extreme waves that occurred in 2007. 

  1. Extreme Energy Events Monitoring report

    CERN Document Server

    Baimukhamedova, Nigina

    2015-01-01

    Following paper reflects the progress I made on Summer Student Program within Extreme Energy Events Monitor project I was working on. During 8 week period I managed to build a simple detector system that is capable of triggering events similar to explosions (sudden change in sound levels) and measuring approximate location of the event. Source codes are available upon request and settings described further.

  2. Astrobiology: Life in Extreme Environments

    Science.gov (United States)

    Kaur, Preeti

    2011-01-01

    Astrobiology is the study of the origin, evolution and distribution of life in the universe. It seeks to answer two important scientific questions: how did we get here and are we alone in the universe? Scientists begin by studying life on Earth and its limits. The discovery of extremophiles on Earth capable of surviving extremes encourages the…

  3. Cattle phenotypes can disguise their maternal ancestry.

    Science.gov (United States)

    Srirattana, Kanokwan; McCosker, Kieren; Schatz, Tim; St John, Justin C

    2017-06-26

    Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments. A phylogenetic tree of the full mtDNA sequences of different breeds of cattle, which were obtained from the NCBI database, showed that the mtDNA profiles of cattle do not always reflect their phenotype as some cattle with Bos taurus phenotypes had Bos indicus mtDNA, whilst some cattle with Bos indicus phenotypes had Bos taurus mtDNA. Using D-loop sequencing, we were able to contrast the phenotypes and mtDNA profiles from different species of cattle from the 2 distinct cattle breeding regions of Australia. We found that 67 of the 121 cattle with Bos indicus phenotypes from NT (55.4%) had Bos taurus mtDNA. In VIC, 92 of the 225 cattle with Bos taurus phenotypes (40.9%) possessed Bos indicus mtDNA. When focusing on oocytes from cattle with the Bos taurus phenotype in VIC, their respective oocytes with Bos indicus mtDNA had significantly lower levels of mtDNA copy number compared with oocytes possessing Bos taurus mtDNA (P cattle with a Bos taurus phenotype. The phenotype of cattle is not always related to their mtDNA profiles. MtDNA profiles should be considered for breeding programmes as they also influence phenotypic traits and reproductive capacity in terms of oocyte quality.

  4. Laser sampling

    International Nuclear Information System (INIS)

    Gorbatenko, A A; Revina, E I

    2015-01-01

    The review is devoted to the major advances in laser sampling. The advantages and drawbacks of the technique are considered. Specific features of combinations of laser sampling with various instrumental analytical methods, primarily inductively coupled plasma mass spectrometry, are discussed. Examples of practical implementation of hybrid methods involving laser sampling as well as corresponding analytical characteristics are presented. The bibliography includes 78 references

  5. Nutrition security under extreme events

    Science.gov (United States)

    Martinez, A.

    2017-12-01

    Nutrition security under extreme events. Zero hunger being one of the Sustainable Development Goal from the United Nations, food security has become a trending research topic. However extreme events impact on global food security is not yet 100% understood and there is a lack of comprehension of the underlying mechanisms of global food trade and nutrition security to improve countries resilience to extreme events. In a globalized world, food is still a highly regulated commodity and a strategic resource. A drought happening in a net food-exporter will have little to no effect on its own population but the repercussion on net food-importers can be extreme. In this project, we propose a methodology to describe and quantify the impact of a local drought to human health at a global scale. For this purpose, nutrition supply and global trade data from FAOSTAT have been used with domestic food production from national agencies and FAOSTAT, global precipitation from the Climate Research Unit and health data from the World Health Organization. A modified Herfindahl-Hirschman Index (HHI) has been developed to measure the level of resilience of one country to a drought happening in another country. This index describes how a country is dependent of importation and how diverse are its importation. Losses of production and exportation due to extreme events have been calculated using yield data and a simple food balance at country scale. Results show that countries the most affected by global droughts are the one with the highest dependency to one exporting country. Changes induced by droughts also disturbed their domestic proteins, fat and calories supply resulting most of the time in a higher intake of calories or fat over proteins.

  6. Unmanned Aerial Vehicle Remote Sensing for Field-Based Crop Phenotyping: Current Status and Perspectives

    Directory of Open Access Journals (Sweden)

    Guijun Yang

    2017-06-01

    Full Text Available Phenotyping plays an important role in crop science research; the accurate and rapid acquisition of phenotypic information of plants or cells in different environments is helpful for exploring the inheritance and expression patterns of the genome to determine the association of genomic and phenotypic information to increase the crop yield. Traditional methods for acquiring crop traits, such as plant height, leaf color, leaf area index (LAI, chlorophyll content, biomass and yield, rely on manual sampling, which is time-consuming and laborious. Unmanned aerial vehicle remote sensing platforms (UAV-RSPs equipped with different sensors have recently become an important approach for fast and non-destructive high throughput phenotyping and have the advantage of flexible and convenient operation, on-demand access to data and high spatial resolution. UAV-RSPs are a powerful tool for studying phenomics and genomics. As the methods and applications for field phenotyping using UAVs to users who willing to derive phenotypic parameters from large fields and tests with the minimum effort on field work and getting highly reliable results are necessary, the current status and perspectives on the topic of UAV-RSPs for field-based phenotyping were reviewed based on the literature survey of crop phenotyping using UAV-RSPs in the Web of Science™ Core Collection database and cases study by NERCITA. The reference for the selection of UAV platforms and remote sensing sensors, the commonly adopted methods and typical applications for analyzing phenotypic traits by UAV-RSPs, and the challenge for crop phenotyping by UAV-RSPs were considered. The review can provide theoretical and technical support to promote the applications of UAV-RSPs for crop phenotyping.

  7. Sex differences in genetic architecture of complex phenotypes?

    Directory of Open Access Journals (Sweden)

    Jacqueline M Vink

    Full Text Available We examined sex differences in familial resemblance for a broad range of behavioral, psychiatric and health related phenotypes (122 complex traits in children and adults. There is a renewed interest in the importance of genotype by sex interaction in, for example, genome-wide association (GWA studies of complex phenotypes. If different genes play a role across sex, GWA studies should consider the effect of genetic variants separately in men and women, which affects statistical power. Twin and family studies offer an opportunity to compare resemblance between opposite-sex family members to the resemblance between same-sex relatives, thereby presenting a test of quantitative and qualitative sex differences in the genetic architecture of complex traits. We analyzed data on lifestyle, personality, psychiatric disorder, health, growth, development and metabolic traits in dizygotic (DZ same-sex and opposite-sex twins, as these siblings are perfectly matched for age and prenatal exposures. Sample size varied from slightly over 300 subjects for measures of brain function such as EEG power to over 30,000 subjects for childhood psychopathology and birth weight. For most phenotypes, sample sizes were large, with an average sample size of 9027 individuals. By testing whether the resemblance in DZ opposite-sex pairs is the same as in DZ same-sex pairs, we obtain evidence for genetic qualitative sex-differences in the genetic architecture of complex traits for 4% of phenotypes. We conclude that for most traits that were examined, the current evidence is that same the genes are operating in men and women.

  8. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

    NARCIS (Netherlands)

    Kohler, S.; Doelken, S.C.; Mungall, C.J.; Bauer, S.; Firth, H.V.; Bailleul-Forestier, I.; Black, G.C.M.; Brown, D.L.; Brudno, M.; Campbell, J.; FitzPatrick, D.R.; Eppig, J.T.; Jackson, A.P.; Freson, K.; Girdea, M.; Helbig, I.; Hurst, J.A.; Jahn, J.; Jackson, L.G.; Kelly, A.M.; Ledbetter, D.H.; Mansour, S.; Martin, C.L.; Moss, C.; Mumford, A.; Ouwehand, W.H.; Park, S.M.; Riggs, E.R.; Scott, R.H.; Sisodiya, S.; Vooren, S. van der; Wapner, R.J.; Wilkie, A.O.; Wright, C.F.; Silfhout, A.T. van; Leeuw, N. de; Vries, B. de; Washingthon, N.L.; Smith, C.L.; Westerfield, M.; Schofield, P.; Ruef, B.J.; Gkoutos, G.V.; Haendel, M.; Smedley, D.; Lewis, S.E.; Robinson, P.N.

    2014-01-01

    The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have

  9. Daddy issues: paternal effects on phenotype.

    Science.gov (United States)

    Rando, Oliver J

    2012-11-09

    The once popular and then heretical idea that ancestral environment can affect the phenotype of future generations is coming back into vogue due to advances in the field of epigenetic inheritance. How paternal environmental conditions influence the phenotype of progeny is now a tractable question, and researchers are exploring potential mechanisms underlying such effects. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. Phenotypes of organ involvement in sarcoidosis

    NARCIS (Netherlands)

    Schupp, Jonas Christian; Freitag-Wolf, Sandra; Bargagli, Elena; Mihailović-Vučinić, Violeta; Rottoli, Paola; Grubanovic, Aleksandar; Müller, Annegret; Jochens, Arne; Tittmann, Lukas; Schnerch, Jasmin; Olivieri, Carmela; Fischer, Annegret; Jovanovic, Dragana; Filipovic, Snežana; Videnovic-Ivanovic, Jelica; Bresser, Paul; Jonkers, René; O'Reilly, Kate; Ho, Ling-Pei; Gaede, Karoline I.; Zabel, Peter; Dubaniewicz, Anna; Marshall, Ben; Kieszko, Robert; Milanowski, Janusz; Günther, Andreas; Weihrich, Anette; Petrek, Martin; Kolek, Vitezslav; Keane, Michael P.; O'Beirne, Sarah; Donnelly, Seamas; Haraldsdottir, Sigridur Olina; Jorundsdottir, Kristin B.; Costabel, Ulrich; Bonella, Francesco; Wallaert, Benoît; Grah, Christian; Peroš-Golubičić, Tatjana; Luisetti, Mauritio; Kadija, Zamir; Pabst, Stefan; Grohé, Christian; Strausz, János; Vašáková, Martina; Sterclova, Martina; Millar, Ann; Homolka, Jiří; Slováková, Alena; Kendrick, Yvonne; Crawshaw, Anjali; Wuyts, Wim; Spencer, Lisa; Pfeifer, Michael; Valeyre, Dominique; Poletti, Venerino; Wirtz, Hubertus; Prasse, Antje; Schreiber, Stefan; Krawczak, Michael; Müller-Quernheim, Joachim

    2018-01-01

    Sarcoidosis is a highly variable, systemic granulomatous disease of hitherto unknown aetiology. The GenPhenReSa (Genotype-Phenotype Relationship in Sarcoidosis) project represents a European multicentre study to investigate the influence of genotype on disease phenotypes in sarcoidosis. The baseline

  11. Emerging semantics to link phenotype and environment

    Directory of Open Access Journals (Sweden)

    Anne E. Thessen

    2015-12-01

    Full Text Available Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1 use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2 two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3 two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE and the Biological Collections Ontology (BCO; these provide a starting point for the development of a data model linking phenotypes and environments.

  12. Haptoglobin Phenotypes and Hypertension in Indigenous Zambians ...

    African Journals Online (AJOL)

    Haptoglobin Phenotypes and Hypertension in Indigenous Zambians at the University Teaching Hospital, Lusaka, Zambia. MM Phiri, T Kaile, FM Goma. Abstract. Objectives: The aim of the study was to investigate the association between presence of haptoglobin phenotypes and hypertension in indigenous Zambian patients ...

  13. Knowledge-based analysis of phenotypes

    KAUST Repository

    Hoendorf, Robert

    2016-01-01

    a formal framework to describe phenotypes. A formalized theory of phenotypes is not only useful for domain analysis, but can also be applied to assist in the diagnosis of rare genetic diseases, and I will show how our results on the ontology

  14. The Neuroanatomy of the Autistic Phenotype

    Science.gov (United States)

    Fahim, Cherine; Meguid, Nagwa A.; Nashaat, Neveen H.; Yoon, Uicheul; Mancini-Marie, Adham; Evans, Alan C.

    2012-01-01

    The autism phenotype is associated with an excess of brain volume due in part to decreased pruning during development. Here we aimed at assessing brain volume early in development to further elucidate previous findings in autism and determine whether this pattern is restricted to idiopathic autism or shared within the autistic phenotype (fragile X…

  15. Thermal Tolerance in Widespread and Tropical Drosophila Species: Does Phenotypic Plasticity Increase with Latitude?

    DEFF Research Database (Denmark)

    Overgaard, Johannes; Kristensen, Torsten Nygård; Mitchell, Katherin A

    2011-01-01

    The distribution of insects can often be related to variation in their response to thermal extremes, which in turn may reflect differences in plastic responses or innate variation in resistance. Species with widespread distributions are expected to have evolved higher levels of plasticity than....... The results do not support the hypothesis that widely distributed species have larger phenotypic plasticity for thermal tolerance limits, and Drosophila species distributions are therefore more closely linked to differences in innate thermal tolerance limits....

  16. Genetic Similarities between Compulsive Overeating and Addiction Phenotypes: A Case for "Food Addiction"?

    Science.gov (United States)

    Carlier, Nina; Marshe, Victoria S; Cmorejova, Jana; Davis, Caroline; Müller, Daniel J

    2015-12-01

    There exists a continuous spectrum of overeating, where at the extremes there are casual overindulgences and at the other a 'pathological' drive to consume palatable foods. It has been proposed that pathological eating behaviors may be the result of addictive appetitive behavior and loss of ability to regulate the consumption of highly processed foods containing refined carbohydrates, fats, salt, and caffeine. In this review, we highlight the genetic similarities underlying substance addiction phenotypes and overeating compulsions seen in individuals with binge eating disorder. We relate these similarities to findings from neuroimaging studies on reward processing and clinical diagnostic criteria based on addiction phenotypes. The abundance of similarities between compulsive overeating and substance addictions puts forth a case for a 'food addiction' phenotype as a valid, diagnosable disorder.

  17. Phenotypic plasticity of southern ocean diatoms: key to success in the sea ice habitat?

    Directory of Open Access Journals (Sweden)

    Olivia Sackett

    Full Text Available Diatoms are the primary source of nutrition and energy for the Southern Ocean ecosystem. Microalgae, including diatoms, synthesise biological macromolecules such as lipids, proteins and carbohydrates for growth, reproduction and acclimation to prevailing environmental conditions. Here we show that three key species of Southern Ocean diatom (Fragilariopsis cylindrus, Chaetoceros simplex and Pseudo-nitzschia subcurvata exhibited phenotypic plasticity in response to salinity and temperature regimes experienced during the seasonal formation and decay of sea ice. The degree of phenotypic plasticity, in terms of changes in macromolecular composition, was highly species-specific and consistent with each species' known distribution and abundance throughout sea ice, meltwater and pelagic habitats, suggesting that phenotypic plasticity may have been selected for by the extreme variability of the polar marine environment. We argue that changes in diatom macromolecular composition and shifts in species dominance in response to a changing climate have the potential to alter nutrient and energy fluxes throughout the Southern Ocean ecosystem.

  18. Are quantitative trait-dependent sampling designs cost-effective for analysis of rare and common variants?

    Science.gov (United States)

    Yilmaz, Yildiz E; Bull, Shelley B

    2011-11-29

    Use of trait-dependent sampling designs in whole-genome association studies of sequence data can reduce total sequencing costs with modest losses of statistical efficiency. In a quantitative trait (QT) analysis of data from the Genetic Analysis Workshop 17 mini-exome for unrelated individuals in the Asian subpopulation, we investigate alternative designs that sequence only 50% of the entire cohort. In addition to a simple random sampling design, we consider extreme-phenotype designs that are of increasing interest in genetic association analysis of QTs, especially in studies concerned with the detection of rare genetic variants. We also evaluate a novel sampling design in which all individuals have a nonzero probability of being selected into the sample but in which individuals with extreme phenotypes have a proportionately larger probability. We take differential sampling of individuals with informative trait values into account by inverse probability weighting using standard survey methods which thus generalizes to the source population. In replicate 1 data, we applied the designs in association analysis of Q1 with both rare and common variants in the FLT1 gene, based on knowledge of the generating model. Using all 200 replicate data sets, we similarly analyzed Q1 and Q4 (which is known to be free of association with FLT1) to evaluate relative efficiency, type I error, and power. Simulation study results suggest that the QT-dependent selection designs generally yield greater than 50% relative efficiency compared to using the entire cohort, implying cost-effectiveness of 50% sample selection and worthwhile reduction of sequencing costs.

  19. The effect of oxcarbazepine in peripheral neuropathic pain depends on pain phenotype: a randomised, double-blind, placebo-controlled phenotype-stratified study

    DEFF Research Database (Denmark)

    Demant, Dyveke T; Lund, Karen; Vollert, Jan

    2014-01-01

    In neuropathic pain it has been suggested that pain phenotype based on putative pain mechanisms may predict response to treatment. This was a randomised, double-blind, placebo-controlled, and phenotype-stratified study with 2 6-week treatment periods of oxcarbazepine (1800-2400mg) and placebo...... patients: 31 with the irritable and 52 with the nonirritable nociceptor phenotype. In the total sample, oxcarbazepine relieved pain of 0.7 points (on a numeric rating scale 0-10; 95% confidence interval [CI] 0.4-1.4) more than placebo (P=0.015) and there was a significant interaction between treatment....... The primary efficacy measure was change in median pain intensity between baseline and the last week of treatment measured on an 11-point numeric rating scale, and the primary objective was to compare the effect of oxcarbazepine in patients with and without the irritable nociceptor phenotype as defined...

  20. Evolving phenotypic networks in silico.

    Science.gov (United States)

    François, Paul

    2014-11-01

    Evolved gene networks are constrained by natural selection. Their structures and functions are consequently far from being random, as exemplified by the multiple instances of parallel/convergent evolution. One can thus ask if features of actual gene networks can be recovered from evolutionary first principles. I review a method for in silico evolution of small models of gene networks aiming at performing predefined biological functions. I summarize the current implementation of the algorithm, insisting on the construction of a proper "fitness" function. I illustrate the approach on three examples: biochemical adaptation, ligand discrimination and vertebrate segmentation (somitogenesis). While the structure of the evolved networks is variable, dynamics of our evolved networks are usually constrained and present many similar features to actual gene networks, including properties that were not explicitly selected for. In silico evolution can thus be used to predict biological behaviours without a detailed knowledge of the mapping between genotype and phenotype. Copyright © 2014 The Author. Published by Elsevier Ltd.. All rights reserved.

  1. Adjusting phenotypes by noise control.

    Directory of Open Access Journals (Sweden)

    Kyung H Kim

    2012-01-01

    Full Text Available Genetically identical cells can show phenotypic variability. This is often caused by stochastic events that originate from randomness in biochemical processes involving in gene expression and other extrinsic cellular processes. From an engineering perspective, there have been efforts focused on theory and experiments to control noise levels by perturbing and replacing gene network components. However, systematic methods for noise control are lacking mainly due to the intractable mathematical structure of noise propagation through reaction networks. Here, we provide a numerical analysis method by quantifying the parametric sensitivity of noise characteristics at the level of the linear noise approximation. Our analysis is readily applicable to various types of noise control and to different types of system; for example, we can orthogonally control the mean and noise levels and can control system dynamics such as noisy oscillations. As an illustration we applied our method to HIV and yeast gene expression systems and metabolic networks. The oscillatory signal control was applied to p53 oscillations from DNA damage. Furthermore, we showed that the efficiency of orthogonal control can be enhanced by applying extrinsic noise and feedback. Our noise control analysis can be applied to any stochastic model belonging to continuous time Markovian systems such as biological and chemical reaction systems, and even computer and social networks. We anticipate the proposed analysis to be a useful tool for designing and controlling synthetic gene networks.

  2. Nordic research infrastructures for plant phenotyping

    Directory of Open Access Journals (Sweden)

    Kristiina Himanen

    2018-03-01

    Full Text Available Plant phenomics refers to the systematic study of plant phenotypes. Together with closely monitored, controlled climates, it provides an essential component for the integrated analysis of genotype-phenotype-environment interactions. Currently, several plant growth and phenotyping facilities are under establishment globally, and numerous facilities are already in use. Alongside the development of the research infrastructures, several national and international networks have been established to support shared use of the new methodology. In this review, an overview is given of the Nordic plant phenotyping and climate control facilities. Since many areas of phenomics such as sensor-based phenotyping, image analysis and data standards are still developing, promotion of educational and networking activities is especially important. These facilities and networks will be instrumental in tackling plant breeding and plant protection challenges. They will also provide possibilities to study wild species and their ecological interactions under changing Nordic climate conditions.

  3. Extreme river flow dependence in Northern Scotland

    Science.gov (United States)

    Villoria, M. Franco; Scott, M.; Hoey, T.; Fischbacher-Smith, D.

    2012-04-01

    Various methods for the spatial analysis of hydrologic data have been developed recently. Here we present results using the conditional probability approach proposed by Keef et al. [Appl. Stat. (2009): 58,601-18] to investigate spatial interdependence in extreme river flows in Scotland. This approach does not require the specification of a correlation function, being mostly suitable for relatively small geographical areas. The work is motivated by the Flood Risk Management Act (Scotland (2009)) which requires maps of flood risk that take account of spatial dependence in extreme river flow. The method is based on two conditional measures of spatial flood risk: firstly the conditional probability PC(p) that a set of sites Y = (Y 1,...,Y d) within a region C of interest exceed a flow threshold Qp at time t (or any lag of t), given that in the specified conditioning site X > Qp; and, secondly the expected number of sites within C that will exceed a flow Qp on average (given that X > Qp). The conditional probabilities are estimated using the conditional distribution of Y |X = x (for large x), which can be modeled using a semi-parametric approach (Heffernan and Tawn [Roy. Statist. Soc. Ser. B (2004): 66,497-546]). Once the model is fitted, pseudo-samples can be generated to estimate functionals of the joint tails of the distribution of (Y,X). Conditional return level plots were directly compared to traditional return level plots thus improving our understanding of the dependence structure of extreme river flow events. Confidence intervals were calculated using block bootstrapping methods (100 replicates). We report results from applying this approach to a set of four rivers (Dulnain, Lossie, Ewe and Ness) in Northern Scotland. These sites were chosen based on data quality, spatial location and catchment characteristics. The river Ness, being the largest (catchment size 1839.1km2) was chosen as the conditioning river. Both the Ewe (441.1km2) and Ness catchments have

  4. The Nature of Stable Insomnia Phenotypes

    Science.gov (United States)

    Pillai, Vivek; Roth, Thomas; Drake, Christopher L.

    2015-01-01

    Study Objectives: We examined the 1-y stability of four insomnia symptom profiles: sleep onset insomnia; sleep maintenance insomnia; combined onset and maintenance insomnia; and neither criterion (i.e., insomnia cases that do not meet quantitative thresholds for onset or maintenance problems). Insomnia cases that exhibited the same symptom profile over a 1-y period were considered to be phenotypes, and were compared in terms of clinical and demographic characteristics. Design: Longitudinal. Setting: Urban, community-based. Participants: Nine hundred fifty-four adults with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition based current insomnia (46.6 ± 12.6 y; 69.4% female). Interventions: None. Measurements and results: At baseline, participants were divided into four symptom profile groups based on quantitative criteria. Follow-up assessment 1 y later revealed that approximately 60% of participants retained the same symptom profile, and were hence judged to be phenotypes. Stability varied significantly by phenotype, such that sleep onset insomnia (SOI) was the least stable (42%), whereas combined insomnia (CI) was the most stable (69%). Baseline symptom groups (cross-sectionally defined) differed significantly across various clinical indices, including daytime impairment, depression, and anxiety. Importantly, however, a comparison of stable phenotypes (longitudinally defined) did not reveal any differences in impairment or comorbid psychopathology. Another interesting finding was that whereas all other insomnia phenotypes showed evidence of an elevated wake drive both at night and during the day, the “neither criterion” phenotype did not; this latter phenotype exhibited significantly higher daytime sleepiness despite subthreshold onset and maintenance difficulties. Conclusions: By adopting a stringent, stability-based definition, this study offers timely and important data on the longitudinal trajectory of specific insomnia phenotypes. With

  5. Mutations in RIT1 cause Noonan syndrome - additional functional evidence and expanding the clinical phenotype.

    Science.gov (United States)

    Koenighofer, M; Hung, C Y; McCauley, J L; Dallman, J; Back, E J; Mihalek, I; Gripp, K W; Sol-Church, K; Rusconi, P; Zhang, Z; Shi, G-X; Andres, D A; Bodamer, O A

    2016-03-01

    RASopathies are a clinically heterogeneous group of conditions caused by mutations in 1 of 16 proteins in the RAS-mitogen activated protein kinase (RAS-MAPK) pathway. Recently, mutations in RIT1 were identified as a novel cause for Noonan syndrome. Here we provide additional functional evidence for a causal role of RIT1 mutations and expand the associated phenotypic spectrum. We identified two de novo missense variants p.Met90Ile and p.Ala57Gly. Both variants resulted in increased MEK-ERK signaling compared to wild-type, underscoring gain-of-function as the primary functional mechanism. Introduction of p.Met90Ile and p.Ala57Gly into zebrafish embryos reproduced not only aspects of the human phenotype but also revealed abnormalities of eye development, emphasizing the importance of RIT1 for spatial and temporal organization of the growing organism. In addition, we observed severe lymphedema of the lower extremity and genitalia in one patient. We provide additional evidence for a causal relationship between pathogenic mutations in RIT1, increased RAS-MAPK/MEK-ERK signaling and the clinical phenotype. The mutant RIT1 protein may possess reduced GTPase activity or a diminished ability to interact with cellular GTPase activating proteins; however the precise mechanism remains unknown. The phenotypic spectrum is likely to expand and includes lymphedema of the lower extremities in addition to nuchal hygroma. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  6. Sleep Duration and Breast Cancer Phenotype

    International Nuclear Information System (INIS)

    Khawaja, A.; Rao, S.

    2013-01-01

    Emerging evidence suggests that short sleep is associated with an increased risk of cancer; however, little has been done to study the role of sleep on tumor characteristics. In this study, we evaluated the relationship between sleep duration and tumor phenotype in 972 breast cancer patients. Sleep duration was inversely associated with tumor grade (univariate P= 0.032), particularly in postmenopausal women (univariate P= 0.018). This association did not reach statistical significance after adjustments for age, race, body mass index, hormone replacement therapy use, alcohol consumption, smoking, and physical activity in the entire study sample (P= 0.052), but it remained statistically significant (P= 0.049) among post-menopausal patients. We did not observe a statistically significant association between sleep duration and stage at diagnosis, ER, or HER2 receptor status. These results present a modest association between short duration of sleep and higher grade breast cancer in post-menopausal women. Further work needs to be done to validate these findings.

  7. Autism beyond diagnostic categories: characterization of autistic phenotypes in schizophrenia.

    Science.gov (United States)

    Kästner, Anne; Begemann, Martin; Michel, Tanja Maria; Everts, Sarah; Stepniak, Beata; Bach, Christiane; Poustka, Luise; Becker, Joachim; Banaschewski, Tobias; Dose, Matthias; Ehrenreich, Hannelore

    2015-05-13

    Behavioral phenotypical continua from health to disease suggest common underlying mechanisms with quantitative rather than qualitative differences. Until recently, autism spectrum disorders and schizophrenia were considered distinct nosologic entities. However, emerging evidence contributes to the blurring of symptomatic and genetic boundaries between these conditions. The present study aimed at quantifying behavioral phenotypes shared by autism spectrum disorders and schizophrenia to prepare the ground for biological pathway analyses. Specific items of the Positive and Negative Syndrome Scale were employed and summed up to form a dimensional autism severity score (PAUSS). The score was created in a schizophrenia sample (N = 1156) and validated in adult high-functioning autism spectrum disorder (ASD) patients (N = 165). To this end, the Autism Diagnostic Observation Schedule (ADOS), the Autism (AQ) and Empathy Quotient (EQ) self-rating questionnaires were applied back to back with the newly developed PAUSS. PAUSS differentiated between ASD, schizophrenia and a disease-control sample and substantially correlated with the Autism Diagnostic Observation Schedule. Patients with ADOS scores ≥12 obtained highest, those with scores genetic constellations modulating autistic phenotypes.

  8. 1H NMR spectroscopy-based interventional metabolic phenotyping

    DEFF Research Database (Denmark)

    Lauridsen, Michael B; Bliddal, Henning; Christensen, Robin

    2010-01-01

    1H NMR spectroscopy-based metabolic phenotyping was used to identify biomarkers in the plasma of patients with rheumatoid arthritis (RA). Forty-seven patients with RA (23 with active disease at baseline and 24 in remission) and 51 healthy subjects were evaluated during a one-year follow-up with a......1H NMR spectroscopy-based metabolic phenotyping was used to identify biomarkers in the plasma of patients with rheumatoid arthritis (RA). Forty-seven patients with RA (23 with active disease at baseline and 24 in remission) and 51 healthy subjects were evaluated during a one-year follow......-up with assessments of disease activity (DAS-28) and 1H NMR spectroscopy of plasma samples. Discriminant analysis provided evidence that the metabolic profiles predicted disease severity. Cholesterol, lactate, acetylated glycoprotein, and lipid signatures were found to be candidate biomarkers for disease severity.......0007). However, after 31 days of optimized therapy, the two patient groups were not significantly different (P=0.91). The metabolic profiles of both groups of RA patients were different from the healthy subjects. 1H NMR-based metabolic phenotyping of plasma samples in patients with RA is well suited...

  9. Pediatric lower extremity mower injuries.

    Science.gov (United States)

    Hill, Sean M; Elwood, Eric T

    2011-09-01

    Lawn mower injuries in children represent an unfortunate common problem to the plastic reconstructive surgeon. There are approximately 68,000 per year reported in the United States. Compounding this problem is the fact that a standard treatment algorithm does not exist. This study follows a series of 7 pediatric patients treated for lower extremity mower injuries by a single plastic surgeon. The extent of soft tissue injury varied. All patients were treated with negative pressure wound therapy as a bridge to definitive closure. Of the 7 patients, 4 required skin grafts, 1 required primary closure, 1 underwent a lower extremity amputation secondary to wounds, and 1 was repaired using a cross-leg flap. Function limitations were minimal for all of our patients after reconstruction. Our basic treatment algorithm is presented with initial debridement followed by the simplest method possible for wound closure using negative pressure wound therapy, if necessary.

  10. Extreme Conditions Modeling Workshop Report

    Energy Technology Data Exchange (ETDEWEB)

    Coe, Ryan Geoffrey [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Neary, Vincent Sinclair [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Lawon, Michael J. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Yu, Yi-Hsiang [National Renewable Energy Lab. (NREL), Golden, CO (United States); Weber, Jochem [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2014-07-01

    Sandia National Laboratories (SNL) and the National Renewable Energy Laboratory (NREL) hosted the Wave Energy Converter (WEC) Extreme Conditions Modeling (ECM) Workshop in Albuquerque, New Mexico on May 13–14, 2014. The objective of the workshop was to review the current state of knowledge on how to numerically and experimentally model WECs in extreme conditions (e.g. large ocean storms) and to suggest how national laboratory resources could be used to improve ECM methods for the benefit of the wave energy industry. More than 30 U.S. and European WEC experts from industry, academia, and national research institutes attended the workshop, which consisted of presentations from W EC developers, invited keynote presentations from subject matter experts, breakout sessions, and a final plenary session .

  11. Extreme project. Progress report 2006

    International Nuclear Information System (INIS)

    Eyrolle, F.; Masson, O.; Charmasson, S.

    2007-01-01

    The E.X.T.R.E.M.E. project introduced in 2005 to the S.E.S.U.R.E. / L.E.R.C.M. has for objectives to acquire data on the consequences of the extreme climatic meteorological episodes on the distribution of the artificial radioisotopes within the various compartments of the geosphere. This report presents the synthesis of the actions developed in 2006 in positioning and in co financing of the project by means of regional or national research programs (C.A.R.M.A., E.X.T.R.E.M.A., E.C.C.O.R.E.V.I.), of data acquisition, valuation and scientific collaboration. (N.C.)

  12. On causality of extreme events

    Directory of Open Access Journals (Sweden)

    Massimiliano Zanin

    2016-06-01

    Full Text Available Multiple metrics have been developed to detect causality relations between data describing the elements constituting complex systems, all of them considering their evolution through time. Here we propose a metric able to detect causality within static data sets, by analysing how extreme events in one element correspond to the appearance of extreme events in a second one. The metric is able to detect non-linear causalities; to analyse both cross-sectional and longitudinal data sets; and to discriminate between real causalities and correlations caused by confounding factors. We validate the metric through synthetic data, dynamical and chaotic systems, and data representing the human brain activity in a cognitive task. We further show how the proposed metric is able to outperform classical causality metrics, provided non-linear relationships are present and large enough data sets are available.

  13. Extreme Nonlinear Optics An Introduction

    CERN Document Server

    Wegener, Martin

    2005-01-01

    Following the birth of the laser in 1960, the field of "nonlinear optics" rapidly emerged. Today, laser intensities and pulse durations are readily available, for which the concepts and approximations of traditional nonlinear optics no longer apply. In this regime of "extreme nonlinear optics," a large variety of novel and unusual effects arise, for example frequency doubling in inversion symmetric materials or high-harmonic generation in gases, which can lead to attosecond electromagnetic pulses or pulse trains. Other examples of "extreme nonlinear optics" cover diverse areas such as solid-state physics, atomic physics, relativistic free electrons in a vacuum and even the vacuum itself. This book starts with an introduction to the field based primarily on extensions of two famous textbook examples, namely the Lorentz oscillator model and the Drude model. Here the level of sophistication should be accessible to any undergraduate physics student. Many graphical illustrations and examples are given. The followi...

  14. Soil sampling

    International Nuclear Information System (INIS)

    Fortunati, G.U.; Banfi, C.; Pasturenzi, M.

    1994-01-01

    This study attempts to survey the problems associated with techniques and strategies of soil sampling. Keeping in mind the well defined objectives of a sampling campaign, the aim was to highlight the most important aspect of representativeness of samples as a function of the available resources. Particular emphasis was given to the techniques and particularly to a description of the many types of samplers which are in use. The procedures and techniques employed during the investigations following the Seveso accident are described. (orig.)

  15. Promoting Exit from Violent Extremism

    DEFF Research Database (Denmark)

    Dalgaard-Nielsen, Anja

    2013-01-01

    A number of Western countries are currently adding exit programs targeting militant Islamists to their counterterrorism efforts. Drawing on research into voluntary exit from violent extremism, this article identifies themes and issues that seem to cause doubt, leading to exit. It then provides a ...... the influence attempt as subtle as possible, use narratives and self-affirmatory strategies to reduce resistance to persuasion, and consider the possibility to promote attitudinal change via behavioral change as an alternative to seek to influence beliefs directly....

  16. Racial Extremism in the Army

    Science.gov (United States)

    1998-04-01

    of Deference ...................................................................................................... 46 1. The Separation of Powers Doctrine...to the military. This deference has a two-fold basis. First, the separation of powers in the U.S. Constitution gives authority to the executive (and...Why should there be judicial deference to the Army’s policy on extremism? There are two principal reasons. First, the Constitution’s separation of powers doctrine

  17. Large Extremity Peripheral Nerve Repair

    Science.gov (United States)

    2016-12-01

    LM, de Crombrugghe B. Some recent advances in the chemistry and biology of trans- forming growth factor-beta. J Cell Biol 1987;105:1039e45. 12. Hao Y...SUPPLEMENTARY NOTES 14. ABSTRACT In current war trauma, 20-30% of all extremity injuries and >80% of penetrating injuries being associated with peripheral nerve...through both axonal advance and in revascularization of the graft following placement. We are confident that this technology may allow us to

  18. Language sampling

    DEFF Research Database (Denmark)

    Rijkhoff, Jan; Bakker, Dik

    1998-01-01

    This article has two aims: [1] to present a revised version of the sampling method that was originally proposed in 1993 by Rijkhoff, Bakker, Hengeveld and Kahrel, and [2] to discuss a number of other approaches to language sampling in the light of our own method. We will also demonstrate how our...... sampling method is used with different genetic classifications (Voegelin & Voegelin 1977, Ruhlen 1987, Grimes ed. 1997) and argue that —on the whole— our sampling technique compares favourably with other methods, especially in the case of exploratory research....

  19. Technology improves upper extremity rehabilitation.

    Science.gov (United States)

    Kowalczewski, Jan; Prochazka, Arthur

    2011-01-01

    Stroke survivors with hemiparesis and spinal cord injury (SCI) survivors with tetraplegia find it difficult or impossible to perform many activities of daily life. There is growing evidence that intensive exercise therapy, especially when supplemented with functional electrical stimulation (FES), can improve upper extremity function, but delivering the treatment can be costly, particularly after recipients leave rehabilitation facilities. Recently, there has been a growing level of interest among researchers and healthcare policymakers to deliver upper extremity treatments to people in their homes using in-home teletherapy (IHT). The few studies that have been carried out so far have encountered a variety of logistical and technical problems, not least the difficulty of conducting properly controlled and blinded protocols that satisfy the requirements of high-level evidence-based research. In most cases, the equipment and communications technology were not designed for individuals with upper extremity disability. It is clear that exercise therapy combined with interventions such as FES, supervised over the Internet, will soon be adopted worldwide in one form or another. Therefore it is timely that researchers, clinicians, and healthcare planners interested in assessing IHT be aware of the pros and cons of the new technology and the factors involved in designing appropriate studies of it. It is crucial to understand the technical barriers, the role of telesupervisors, the motor improvements that participants can reasonably expect and the process of optimizing IHT-exercise therapy protocols to maximize the benefits of the emerging technology. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. Typologies of extreme longevity myths.

    Science.gov (United States)

    Young, Robert D; Desjardins, Bertrand; McLaughlin, Kirsten; Poulain, Michel; Perls, Thomas T

    2010-01-01

    Purpose. Political, national, religious, and other motivations have led the media and even scientists to errantly accept extreme longevity claims prima facie. We describe various causes of false claims of extraordinary longevity. Design and Methods. American Social Security Death Index files for the period 1980-2009 were queried for individuals with birth and death dates yielding ages 110+ years of age. Frequency was compared to a list of age-validated supercentenarians maintained by the Gerontology Research Group who died during the same time period. Age claims of 110+ years and the age validation experiences of the authors facilitated a list of typologies of false age claims. Results. Invalid age claim rates increase with age from 65% at age 110-111 to 98% by age 115 to 100% for 120+ years. Eleven typologies of false claims were: Religious Authority Myth, Village Elder Myth, Fountain of Youth Myth (substance), Shangri-La Myth (geographic), Nationalist Pride, Spiritual Practice, Familial Longevity, Individual and/or Family Notoriety, Military Service, Administrative Entry Error, and Pension-Social Entitlement Fraud. Conclusions. Understanding various causes of false extreme age claims is important for placing current, past, and future extreme longevity claims in context and for providing a necessary level of skepticism.

  1. Moderate and extreme maternal obesity.

    LENUS (Irish Health Repository)

    Abdelmaboud, M O

    2012-05-01

    The aim of this study was to investigate the prevalence of moderate and extreme obesity among an Irish obstetric population over a 10-year period, and to evaluate the obstetric features of such pregnancies. Of 31,869 women delivered during the years 2000-2009, there were 306 women in the study group, including 173 in the moderate or Class 2 obese category (BMI 35-39.9) and 133 in the extreme or Class 3 obese category (BMI > or = 40).The prevalence of obese women with BMI > or = 35 was 9.6 per 1000 (0.96%), with an upward trend observed from 2.1 per 1000 in the year 2000, to 11.8 per 1000 in the year 2009 (P = 0.001). There was an increase in emergency caesarean section (EMCS) risk for primigravida versus multigravid women, within both obese categories (P < 0.001). However, there was no significant difference in EMCS rates observed between Class 2 and Class 3 obese women, when matched for parity. The prevalence of moderate and extreme obesity reported in this population is high, and appears to be increasing. The increased rates of abdominal delivery, and the levels of associated morbidity observed, have serious implications for such women embarking on pregnancy.

  2. Attribution of climate extreme events

    Science.gov (United States)

    Trenberth, Kevin E.; Fasullo, John T.; Shepherd, Theodore G.

    2015-08-01

    There is a tremendous desire to attribute causes to weather and climate events that is often challenging from a physical standpoint. Headlines attributing an event solely to either human-induced climate change or natural variability can be misleading when both are invariably in play. The conventional attribution framework struggles with dynamically driven extremes because of the small signal-to-noise ratios and often uncertain nature of the forced changes. Here, we suggest that a different framing is desirable, which asks why such extremes unfold the way they do. Specifically, we suggest that it is more useful to regard the extreme circulation regime or weather event as being largely unaffected by climate change, and question whether known changes in the climate system's thermodynamic state affected the impact of the particular event. Some examples briefly illustrated include 'snowmaggedon' in February 2010, superstorm Sandy in October 2012 and supertyphoon Haiyan in November 2013, and, in more detail, the Boulder floods of September 2013, all of which were influenced by high sea surface temperatures that had a discernible human component.

  3. Typologies of Extreme Longevity Myths

    Directory of Open Access Journals (Sweden)

    Robert D. Young

    2010-01-01

    Full Text Available Purpose. Political, national, religious, and other motivations have led the media and even scientists to errantly accept extreme longevity claims prima facie. We describe various causes of false claims of extraordinary longevity. Design and Methods. American Social Security Death Index files for the period 1980–2009 were queried for individuals with birth and death dates yielding ages 110+ years of age. Frequency was compared to a list of age-validated supercentenarians maintained by the Gerontology Research Group who died during the same time period. Age claims of 110+ years and the age validation experiences of the authors facilitated a list of typologies of false age claims. Results. Invalid age claim rates increase with age from 65% at age 110-111 to 98% by age 115 to 100% for 120+ years. Eleven typologies of false claims were: Religious Authority Myth, Village Elder Myth, Fountain of Youth Myth (substance, Shangri-La Myth (geographic, Nationalist Pride, Spiritual Practice, Familial Longevity, Individual and/or Family Notoriety, Military Service, Administrative Entry Error, and Pension-Social Entitlement Fraud. Conclusions. Understanding various causes of false extreme age claims is important for placing current, past, and future extreme longevity claims in context and for providing a necessary level of skepticism.

  4. Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes

    KAUST Repository

    AlShahrani, Mona; Hoehndorf, Robert

    2018-01-01

    In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease's (or patient's) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse. Results: We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprising of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.

  5. Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes

    KAUST Repository

    Alshahrani, Mona

    2018-04-30

    In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease\\'s (or patient\\'s) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse. Results: We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprising of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.

  6. Phenotypic variance explained by local ancestry in admixed African Americans.

    Science.gov (United States)

    Shriner, Daniel; Bentley, Amy R; Doumatey, Ayo P; Chen, Guanjie; Zhou, Jie; Adeyemo, Adebowale; Rotimi, Charles N

    2015-01-01

    We surveyed 26 quantitative traits and disease outcomes to understand the proportion of phenotypic variance explained by local ancestry in admixed African Americans. After inferring local ancestry as the number of African-ancestry chromosomes at hundreds of thousands of genotyped loci across all autosomes, we used a linear mixed effects model to estimate the variance explained by local ancestry in two large independent samples of unrelated African Americans. We found that local ancestry at major and polygenic effect genes can explain up to 20 and 8% of phenotypic variance, respectively. These findings provide evidence that most but not all additive genetic variance is explained by genetic markers undifferentiated by ancestry. These results also inform the proportion of health disparities due to genetic risk factors and the magnitude of error in association studies not controlling for local ancestry.

  7. MicroRNAs in Muscle: Characterizing the Powerlifter Phenotype

    Science.gov (United States)

    D'Souza, Randall F.; Bjørnsen, Thomas; Zeng, Nina; Aasen, Kirsten M. M.; Raastad, Truls; Cameron-Smith, David; Mitchell, Cameron J.

    2017-01-01

    Powerlifters are the epitome of muscular adaptation and are able to generate extreme forces. The molecular mechanisms underpinning the significant capacity for force generation and hypertrophy are not fully elucidated. MicroRNAs (miRs) are short non-coding RNA sequences that control gene expression via promotion of transcript breakdown and/or translational inhibition. Differences in basal miR expression may partially account for phenotypic differences in muscle mass and function between powerlifters and untrained age-matched controls. Muscle biopsies were obtained from m. vastus lateralis of 15 national level powerlifters (25.1 ± 5.8 years) and 13 untrained controls (24.1 ± 2.0 years). The powerlifters were stronger than the controls (isokinetic knee extension at 60°/s: 307.8 ± 51.6 Nm vs. 211.9 ± 41.9 Nm, respectively P powerlifters and five having lower expression. Established transcriptionally regulated miR downstream gene targets involved in muscle mass regulation, including myostatin and MyoD, were also differentially expressed between groups. Correlation analysis demonstrates the abundance of eight miRs was correlated to phenotype including peak strength, fiber size, satellite cell abundance, and fiber type regardless of grouping. The unique miR expression profiles between groups allow for categorization of individuals as either powerlifter or healthy controls based on a five miR signature (miR-126, -23b, -16, -23a, -15a) with considerable accuracy (100%). Thus, this unique miR expression may be important to the characterization of the powerlifter phenotype. PMID:28638346

  8. Diarrheagenic Escherichia coli Markers and Phenotypes among Fecal E. coli Isolates Collected from Nicaraguan Infants ▿

    OpenAIRE

    Reyes, Daniel; Vilchez, Samuel; Paniagua, Margarita; Colque-Navarro, Patricia; Weintraub, Andrej; Möllby, Roland; Kühn, Inger

    2010-01-01

    We analyzed the prevalence of diarrheagenic Escherichia coli (DEC) markers and common phenotypes in 2,164 E. coli isolates from 282 DEC-positive samples. Enteropathogenic E. coli (EPEC) and enteroaggregative E. coli (EAEC) were very diverse and were not correlated with diarrhea. Enterotoxigenic E. coli (ETEC) estA and enterohemorrhagic E. coli (EHEC) belonged to a few phenotypes and were significantly correlated with diarrhea.

  9. Targeting phenotypically tolerant Mycobacterium tuberculosis

    Science.gov (United States)

    Gold, Ben; Nathan, Carl

    2016-01-01

    While the immune system is credited with averting tuberculosis in billions of individuals exposed to Mycobacterium tuberculosis, the immune system is also culpable for tempering the ability of antibiotics to deliver swift and durable cure of disease. In individuals afflicted with tuberculosis, host immunity produces diverse microenvironmental niches that support suboptimal growth, or complete growth arrest, of M. tuberculosis. The physiological state of nonreplication in bacteria is associated with phenotypic drug tolerance. Many of these host microenvironments, when modeled in vitro by carbon starvation, complete nutrient starvation, stationary phase, acidic pH, reactive nitrogen intermediates, hypoxia, biofilms, and withholding streptomycin from the streptomycin-addicted strain SS18b, render M. tuberculosis profoundly tolerant to many of the antibiotics that are given to tuberculosis patients in a clinical setting. Targeting nonreplicating persisters is anticipated to reduce the duration of antibiotic treatment and rate of post-treatment relapse. Some promising drugs to treat tuberculosis, such as rifampicin and bedaquiline, only kill nonreplicating M. tuberculosis in vitro at concentrations far greater than their minimal inhibitory concentrations against replicating bacilli. There is an urgent demand to identify which of the currently used antibiotics, and which of the molecules in academic and corporate screening collections, have potent bactericidal action on nonreplicating M. tuberculosis. With this goal, we review methods of high throughput screening to target nonreplicating M. tuberculosis and methods to progress candidate molecules. A classification based on structures and putative targets of molecules that have been reported to kill nonreplicating M. tuberculosis revealed a rich diversity in pharmacophores. However, few of these compounds were tested under conditions that would exclude the impact of adsorbed compound acting during the recovery phase of

  10. Prospect for extreme field science

    Energy Technology Data Exchange (ETDEWEB)

    Tajima, T. [Ludwig Maximilian Univ. and Max Planck Institute for Quantum Optics, Garching (Germany); Japan Atomic Energy Agency, Kyoto and KEK, Tsukuba (Japan)

    2009-11-15

    The kind of laser extreme light infrastructure (ELI) provides will usher in a class of experiments we have only dreamed of for years. The characteristics that ELI brings in include: the highest intensity ever, large fluence, and relatively high repetition rate. A personal view of the author on the prospect of harnessing this unprecedented opportunity for advancing science of extreme fields is presented. The first characteristic of ELI, its intensity, will allow us to access, as many have stressed already, extreme fields that hover around the Schwinger field or at the very least the neighboring fields in which vacuum begins to behave as a nonlinear medium. In this sense, we are seriously probing the 'material' property of vacuum and thus the property that theory of relativity itself described and will entail. We will probe both special theory and general theory of relativity in regimes that have been never tested so far. We may see a glimpse into the reach of relativity or even its breakdown in some extreme regimes. We will learn Einstein and may even go beyond Einstein, if our journey is led. Laser-driven acceleration both by the laser field itself and by the wakefield that is triggered in a plasma is huge. Energies, if not luminosity, we can access, may be unprecedented going far beyond TeV. The nice thing about ELI is that it has relatively high repetition rate and average fluence as compared with other extreme lasers. This high fluence can be a key element that leads to applications to high energy physics, such as gamma-gamma collider driver experiment, and some gamma ray experiments that may be relevant in the frontier of photo-nuclear physics, and atomic energy applications. Needless to say, high fluence is one of most important features that industrial and medical applications may need. If we are lucky, we may see a door opens at the frontier of novel physics that may not be available by any other means. (authors)

  11. Integrating phenotype ontologies with PhenomeNET

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel

    2017-12-19

    Background Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomical details being captured in clinical and model organism databases presents complex problems when attempting to match classes across species and across phenotypes as diverse as behaviour and neoplasia. We have previously developed PhenomeNET, a system for disease gene prioritization that includes as one of its components an ontology designed to integrate phenotype ontologies. While not applicable to matching arbitrary ontologies, PhenomeNET can be used to identify related phenotypes in different species, including human, mouse, zebrafish, nematode worm, fruit fly, and yeast. Results Here, we apply the PhenomeNET to identify related classes from two phenotype and two disease ontologies using automated reasoning. We demonstrate that we can identify a large number of mappings, some of which require automated reasoning and cannot easily be identified through lexical approaches alone. Combining automated reasoning with lexical matching further improves results in aligning ontologies. Conclusions PhenomeNET can be used to align and integrate phenotype ontologies. The results can be utilized for biomedical analyses in which phenomena observed in model organisms are used to identify causative genes and mutations underlying human disease.

  12. Redefining Aging in HIV Infection Using Phenotypes.

    Science.gov (United States)

    Stoff, David M; Goodkin, Karl; Jeste, Dilip; Marquine, Maria

    2017-10-01

    This article critically reviews the utility of "phenotypes" as behavioral descriptors in aging/HIV research that inform biological underpinnings and treatment development. We adopt a phenotypic redefinition of aging conceptualized within a broader context of HIV infection and of aging. Phenotypes are defined as dimensions of behavior, closely related to fundamental mechanisms, and, thus, may be more informative than chronological age. Primary emphasis in this review is given to comorbid aging and cognitive aging, though other phenotypes (i.e., disability, frailty, accelerated aging, successful aging) are also discussed in relation to comorbid aging and cognitive aging. The main findings that emerged from this review are as follows: (1) the phenotypes, comorbid aging and cognitive aging, are distinct from each other, yet overlapping; (2) associative relationships are the rule in HIV for comorbid and cognitive aging phenotypes; and (3) HIV behavioral interventions for both comorbid aging and cognitive aging have been limited. Three paths for research progress are identified for phenotype-defined aging/HIV research (i.e., clinical and behavioral specification, biological mechanisms, intervention targets), and some important research questions are suggested within each of these research paths.

  13. Evolution of molecular phenotypes under stabilizing selection

    International Nuclear Information System (INIS)

    Nourmohammad, Armita; Schiffels, Stephan; Lässig, Michael

    2013-01-01

    Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype’s genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes. (paper)

  14. Sample preparation

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    Sample preparation prior to HPLC analysis is certainly one of the most important steps to consider in trace or ultratrace analysis. For many years scientists have tried to simplify the sample preparation process. It is rarely possible to inject a neat liquid sample or a sample where preparation may not be any more complex than dissolution of the sample in a given solvent. The last process alone can remove insoluble materials, which is especially helpful with the samples in complex matrices if other interactions do not affect extraction. Here, it is very likely a large number of components will not dissolve and are, therefore, eliminated by a simple filtration process. In most cases, the process of sample preparation is not as simple as dissolution of the component interest. At times, enrichment is necessary, that is, the component of interest is present in very large volume or mass of material. It needs to be concentrated in some manner so a small volume of the concentrated or enriched sample can be injected into HPLC. 88 refs

  15. Sampling Development

    Science.gov (United States)

    Adolph, Karen E.; Robinson, Scott R.

    2011-01-01

    Research in developmental psychology requires sampling at different time points. Accurate depictions of developmental change provide a foundation for further empirical studies and theories about developmental mechanisms. However, overreliance on widely spaced sampling intervals in cross-sectional and longitudinal designs threatens the validity of…

  16. Phenotypic and gene expression responses of E. coli to antibiotics during spaceflight

    Science.gov (United States)

    Zea, Luis

    Bacterial susceptibility to antibiotics has been shown in vitro to be reduced during spaceflight; however, the underlying mechanisms responsible for this outcome are not fully understood. In particular, it is not yet clear whether this observed response is due to increased drug resistance (a microbial defense response) or decreased drug efficacy (a microgravity biophysical mass transport effect). To gain insight into the differentiation between these two potential causes, an investigation was undertaken onboard the International Space Station (ISS) in 2014 termed Antibiotic Effectiveness in Space-1 (AES-1). For this purpose, E. coli was challenged with two antibiotics, Gentamicin Sulfate and Colistin Sulfate, at concentrations higher than those needed to inhibit growth on Earth. Phenotypic parameters (cell size, cell envelope thickness, population density and lag phase duration) and gene expression were compared between the spaceflight samples and ground controls cultured in varying levels of drug concentration. It was observed that flight samples proliferated in antibiotic concentrations that were inhibitory on Earth, growing on average to a 13-fold greater concentration than matched 1g controls. Furthermore, at the highest drug concentrations in space, E. coli cells were observed to aggregate into visible clusters. In spaceflight, cell size was significantly reduced, translating to a decrease in cell surface area to about one half of the ground controls. Smaller cell surface area can in turn proportionally reduce the rate of antibiotic molecules reaching the cell. Additionally, it was observed that genes --- in some cases more than 2000 --- were overexpressed in space with respect to ground controls. Up-regulated genes include poxB, which helps catabolize glucose into organic acids that alter acidity around and inside the cell, and the gadABC family genes, which confer resistance to extreme acid conditions. The next step is to characterize the mechanisms behind

  17. Wet gas sampling

    Energy Technology Data Exchange (ETDEWEB)

    Welker, T.F.

    1997-07-01

    The quality of gas has changed drastically in the past few years. Most gas is wet with hydrocarbons, water, and heavier contaminants that tend to condense if not handled properly. If a gas stream is contaminated with condensables, the sampling of that stream must be done in a manner that will ensure all of the components in the stream are introduced into the sample container as the composite. The sampling and handling of wet gas is extremely difficult under ideal conditions. There are no ideal conditions in the real world. The problems related to offshore operations and other wet gas systems, as well as the transportation of the sample, are additional problems that must be overcome if the analysis is to mean anything to the producer and gatherer. The sampling of wet gas systems is decidedly more difficult than sampling conventional dry gas systems. Wet gas systems were generally going to result in the measurement of one heating value at the inlet of the pipe and a drastic reduction in the heating value of the gas at the outlet end of the system. This is caused by the fallout or accumulation of the heavier products that, at the inlet, may be in the vapor state in the pipeline; hence, the high gravity and high BTU. But, in fact, because of pressure and temperature variances, these liquids condense and form a liquid that is actually running down the pipe as a stream or is accumulated in drips to be blown from the system. (author)

  18. Environmental sampling

    International Nuclear Information System (INIS)

    Puckett, J.M.

    1998-01-01

    Environmental Sampling (ES) is a technology option that can have application in transparency in nuclear nonproliferation. The basic process is to take a sample from the environment, e.g., soil, water, vegetation, or dust and debris from a surface, and through very careful sample preparation and analysis, determine the types, elemental concentration, and isotopic composition of actinides in the sample. The sample is prepared and the analysis performed in a clean chemistry laboratory (CCL). This ES capability is part of the IAEA Strengthened Safeguards System. Such a Laboratory is planned to be built by JAERI at Tokai and will give Japan an intrinsic ES capability. This paper presents options for the use of ES as a transparency measure for nuclear nonproliferation

  19. Kinematic and neuromuscular relationships between lower extremity clinical movement assessments.

    Science.gov (United States)

    Mauntel, Timothy C; Cram, Tyler R; Frank, Barnett S; Begalle, Rebecca L; Norcross, Marc F; Blackburn, J Troy; Padua, Darin A

    2018-06-01

    Lower extremity injuries have immediate and long-term consequences. Lower extremity movement assessments can assist with identifying individuals at greater injury risk and guide injury prevention interventions. Movement assessments identify similar movement characteristics and evidence suggests large magnitude kinematic relationships exist between movement patterns observed across assessments; however, the magnitude of the relationships for electromyographic (EMG) measures across movement assessments remains largely unknown. This study examined relationships between lower extremity kinematic and EMG measures during jump landings and single leg squats. Lower extremity three-dimensional kinematic and EMG data were sampled from healthy adults (males = 20, females = 20) during the movement assessments. Pearson correlations examined the relationships of the kinematic and EMG measures and paired samples t-tests compared mean kinematic and EMG measures between the assessments. Overall, significant moderate correlations were observed for lower extremity kinematic (r avg  = 0.41, r range  = 0.10-0.61) and EMG (r avg  = 0.47, r range  = 0.32-0.80) measures across assessments. Kinematic and EMG measures were greater during the jump landings. Jump landings and single leg squats place different demands on the body and necessitate different kinematic and EMG patterns, such that these measures are not highly correlated between assessments. Clinicians should, therefore, use multiple assessments to identify aberrant movement and neuromuscular control patterns so that comprehensive interventions can be implemented.

  20. Transcriptome and network changes in climbers at extreme altitudes.

    Directory of Open Access Journals (Sweden)

    Fang Chen

    Full Text Available Extreme altitude can induce a range of cellular and systemic responses. Although it is known that hypoxia underlies the major changes and that the physiological responses include hemodynamic changes and erythropoiesis, the molecular mechanisms and signaling pathways mediating such changes are largely unknown. To obtain a more complete picture of the transcriptional regulatory landscape and networks involved in extreme altitude response, we followed four climbers on an expedition up Mount Xixiabangma (8,012 m, and collected blood samples at four stages during the climb for mRNA and miRNA expression assays. By analyzing dynamic changes of gene networks in response to extreme altitudes, we uncovered a highly modular network with 7 modules of various functions that changed in response to extreme altitudes. The erythrocyte differentiation module is the most prominently up-regulated, reflecting increased erythrocyte differentiation from hematopoietic stem cells, probably at the expense of differentiation into other cell lineages. These changes are accompanied by coordinated down-regulation of general translation. Network topology and flow analyses also uncovered regulators known to modulate hypoxia responses and erythrocyte development, as well as unknown regulators, such as the OCT4 gene, an important regulator in stem cells and assumed to only function in stem cells. We predicted computationally and validated experimentally that increased OCT4 expression at extreme altitude can directly elevate the expression of hemoglobin genes. Our approach established a new framework for analyzing the transcriptional regulatory network from a very limited number of samples.

  1. The nature of stable insomnia phenotypes.

    Science.gov (United States)

    Pillai, Vivek; Roth, Thomas; Drake, Christopher L

    2015-01-01

    We examined the 1-y stability of four insomnia symptom profiles: sleep onset insomnia; sleep maintenance insomnia; combined onset and maintenance insomnia; and neither criterion (i.e., insomnia cases that do not meet quantitative thresholds for onset or maintenance problems). Insomnia cases that exhibited the same symptom profile over a 1-y period were considered to be phenotypes, and were compared in terms of clinical and demographic characteristics. Longitudinal. Urban, community-based. Nine hundred fifty-four adults with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition based current insomnia (46.6 ± 12.6 y; 69.4% female). None. At baseline, participants were divided into four symptom profile groups based on quantitative criteria. Follow-up assessment 1 y later revealed that approximately 60% of participants retained the same symptom profile, and were hence judged to be phenotypes. Stability varied significantly by phenotype, such that sleep onset insomnia (SOI) was the least stable (42%), whereas combined insomnia (CI) was the most stable (69%). Baseline symptom groups (cross-sectionally defined) differed significantly across various clinical indices, including daytime impairment, depression, and anxiety. Importantly, however, a comparison of stable phenotypes (longitudinally defined) did not reveal any differences in impairment or comorbid psychopathology. Another interesting finding was that whereas all other insomnia phenotypes showed evidence of an elevated wake drive both at night and during the day, the 'neither criterion' phenotype did not; this latter phenotype exhibited significantly higher daytime sleepiness despite subthreshold onset and maintenance difficulties. By adopting a stringent, stability-based definition, this study offers timely and important data on the longitudinal trajectory of specific insomnia phenotypes. With the exception of daytime sleepiness, few clinical differences are apparent across stable phenotypes.

  2. Microbial Fuel Cells under Extreme Salinity

    Science.gov (United States)

    Monzon del Olmo, Oihane

    I developed a Microbial Fuel Cell (MFC) that unprecedentedly works (i.e., produces electricity) under extreme salinity (≈ 100 g/L NaCl). Many industries, such as oil and gas extraction, generate hypersaline wastewaters with high organic strength, accounting for about 5% of worldwide generated effluents, which represent a major challenge for pollution control and resource recovery. This study assesses the potential for microbial fuel cells (MFCs) to treat such wastewaters and generate electricity under extreme saline conditions. Specifically, the focus is on the feasibility to treat hypersaline wastewater generated by the emerging unconventional oil and gas industry (hydraulic fracturing) and so, with mean salinity of 100 g/L NaCl (3-fold higher than sea water). The success of this novel technology strongly depends on finding a competent and resilient microbial community that can degrade the waste under extreme saline conditions and be able to use the anode as their terminal electron acceptor (exoelectrogenic capability). I demonstrated that MFCs can produce electricity at extremely high salinity (up to 250 g/l NaCl) with a power production of 71mW/m2. Pyrosequencing analysis of the anode population showed the predominance of Halanaerobium spp. (85%), which has been found in shale formations and oil reservoirs. Promoting Quorum sensing (QS, cell to cell communication between bacteria to control gene expression) was used as strategy to increase the attachment of bacteria to the anode and thus improve the MFC performance. Results show that the power output can be bolstered by adding 100nM of quinolone signal with an increase in power density of 30%, for the first time showing QS in Halanaerobium extremophiles. To make this technology closer to market applications, experiments with real wastewaters were also carried out. A sample of produced wastewater from Barnet Shale, Texas (86 g/L NaCl) produced electricity when fed in an MFC, leading to my discovery of another

  3. Phenotypic and genetic characterization of a novel phenotype in pigs characterized by juvenile hairlessness and age dependent emphysema

    DEFF Research Database (Denmark)

    Bruun, Camilla S.; Jørgensen, Claus B.; Bay, Lene

    2008-01-01

    Background: A pig phenotype characterized by juvenile hairlessness, thin skin and age dependent lung emphysema has been discovered in a Danish pig herd. The trait shows autosomal co-dominant inheritance with all three genotypes distinguishable. Since the phenotype shows resemblance to the integrin...... of musculi arrectores pili, and at puberty or later localized areas of emphysema are seen in the lungs. Comparative mapping predicted that the porcine ITGB6 and ITGAV orthologs map to SSC15. In an experimentall family (n=113), showing segregation of the trait, the candidate region was confirmed by linkage...... splicing of the ITGB6 pre-mRNA was detected. For both ITGB6 and ITGAV quantitative PCR revealed no significant difference in the expression levels in normal and affected animals. In a western blot, ITGB6 was detected in lung protein samples of all three genotypes. This result was supported by flow...

  4. Phenotyping animal models of diabetic neuropathy

    DEFF Research Database (Denmark)

    Biessels, G J; Bril, V; Calcutt, N A

    2014-01-01

    NIDDK, JDRF, and the Diabetic Neuropathy Study Group of EASD sponsored a meeting to explore the current status of animal models of diabetic peripheral neuropathy. The goal of the workshop was to develop a set of consensus criteria for the phenotyping of rodent models of diabetic neuropathy...... with a discussion on the merits and limitations of a unified approach to phenotyping rodent models of diabetic neuropathy and a consensus formed on the definition of the minimum criteria required for establishing the presence of the disease. A neuropathy phenotype in rodents was defined as the presence...

  5. Characterization of in vitro phenotypes of Burkholderia pseudomallei and Burkholderia mallei strains potentially associated with persistent infection in mice.

    Science.gov (United States)

    Bernhards, R C; Cote, C K; Amemiya, K; Waag, D M; Klimko, C P; Worsham, P L; Welkos, S L

    2017-03-01

    Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm), the agents of melioidosis and glanders, respectively, are Tier 1 biothreats. They infect humans and animals, causing disease ranging from acute and fatal to protracted and chronic. Chronic infections are especially challenging to treat, and the identification of in vitro phenotypic markers which signal progression from acute to persistent infection would be extremely valuable. First, a phenotyping strategy was developed employing colony morphotyping, chemical sensitivity testing, macrophage infection, and lipopolysaccharide fingerprint analyses to distinguish Burkholderia strains. Then mouse spleen isolates collected 3-180 days after infection were characterized phenotypically. Isolates from long-term infections often exhibited increased colony morphology differences and altered patterns of antimicrobial sensitivity and macrophage infection. Some of the Bp and Bm persistent infection isolates clearly displayed enhanced virulence in mice. Future studies will evaluate the potential role and significance of these phenotypic markers in signaling the establishment of a chronic infection.

  6. Spherical sampling

    CERN Document Server

    Freeden, Willi; Schreiner, Michael

    2018-01-01

    This book presents, in a consistent and unified overview, results and developments in the field of today´s spherical sampling, particularly arising in mathematical geosciences. Although the book often refers to original contributions, the authors made them accessible to (graduate) students and scientists not only from mathematics but also from geosciences and geoengineering. Building a library of topics in spherical sampling theory it shows how advances in this theory lead to new discoveries in mathematical, geodetic, geophysical as well as other scientific branches like neuro-medicine. A must-to-read for everybody working in the area of spherical sampling.

  7. The ARID1B phenotype: what we have learned so far.

    Science.gov (United States)

    Santen, Gijs W E; Clayton-Smith, Jill

    2014-09-01

    Evidence is now accumulating from a number of sequencing studies that ARID1B not only appears to be one of the most frequently mutated intellectual disability (ID) genes, but that the range of phenotypes caused by ARID1B mutations seems to be extremely wide. Thus, it is one of the most interesting ID genes identified so far in the exome sequencing era. In this article, we review the literature surrounding ARID1B and attempt to delineate the ARID1B phenotype. The vast majority of published ARID1B patients have been ascertained through studies of Coffin-Siris syndrome (CSS), which leads to bias when documenting the frequencies of phenotypic features. Additional observations of those individuals ascertained through exome sequencing studies helps in delineation of the broader clinical phenotype. We are currently establishing an ARID1B consortium, aimed at collecting ARID1B patients identified through genome-wide sequencing strategies. We hope that this endeavor will eventually lead to a more comprehensive view of the ARID1B phenotype. © 2014 Wiley Periodicals, Inc.

  8. Investigating the Association between Autistic-Like and Internalizing Traits in a Community-Based Twin Sample

    Science.gov (United States)

    Hallett, Victoria; Ronald, Angelica; Happe, Francesca

    2009-01-01

    The phenotypic and etiologic relation between internalizing and autistic-like traits is studied using a community-based twin sample. Internalizing and autistic-like traits showed moderate phenotypic overlap but have specific genetic influences.

  9. Outcomes for Extremely Premature Infants

    Science.gov (United States)

    Glass, Hannah C.; Costarino, Andrew T.; Stayer, Stephen A.; Brett, Claire; Cladis, Franklyn; Davis, Peter J.

    2015-01-01

    Premature birth is a significant cause of infant and child morbidity and mortality. In the United States, the premature birth rate, which had steadily increased during the 1990s and early 2000s, has decreased annually for four years and is now approximately 11.5%. Human viability, defined as gestational age at which the chance of survival is 50%, is currently approximately 23–24 weeks in developed countries. Infant girls, on average, have better outcomes than infant boys. A relatively uncomplicated course in the intensive care nursery for an extremely premature infant results in a discharge date close to the prenatal EDC. Despite technological advances and efforts of child health experts during the last generation, the extremely premature infant (less than 28 weeks gestation) and extremely low birth weight infant (ELBW) (CPAP, mechanical ventilation, and exogenous surfactant increased survival and spurred the development of neonatal intensive care in the 1970s through the early 1990s. Routine administration of antenatal steroids during premature labor improved neonatal mortality and morbidity in the late 1990s. The recognition that chronic postnatal administration of steroids to infants should be avoided may have improved outcomes in the early 2000s. Evidence from recent trials attempting to define the appropriate target for oxygen saturation in preterm infants suggests arterial oxygen saturation between 91–95% (compared to 85–89%) avoids excess mortality. However, final analyses of data from these trials have not been published, so definitive recommendations are still pending The development of neonatal neurocognitive care visits may improve neurocognitive outcomes in this high-risk group. Long-term follow up to detect and address developmental, learning, behavioral, and social problems is critical for children born at these early gestational ages. The striking similarities in response to extreme prematurity in the lung and brain imply that agents and

  10. Gravity and Extreme Magnetism SMEX

    Science.gov (United States)

    2012-01-01

    The Gravity and Extreme Magnetism SMEX mission will be the first mission to catalogue the X-ray polarisation of many astrophysical objects including black-holes and pulsars. This first of its kind mission is enabled by the novel use of a time projection chamber as an X-ray polarimeter. The detector has been developed over the last 5 years, with the current effort charged toward a demonstration of it's technical readiness to be at level 6 prior to the preliminary design review. This talk will describe the design GEMS polarimeter and the results to date from the engineering test unit.

  11. Fluidic sampling

    International Nuclear Information System (INIS)

    Houck, E.D.

    1992-01-01

    This paper covers the development of the fluidic sampler and its testing in a fluidic transfer system. The major findings of this paper are as follows. Fluidic jet samples can dependably produce unbiased samples of acceptable volume. The fluidic transfer system with a fluidic sampler in-line will transfer water to a net lift of 37.2--39.9 feet at an average ratio of 0.02--0.05 gpm (77--192 cc/min). The fluidic sample system circulation rate compares very favorably with the normal 0.016--0.026 gpm (60--100 cc/min) circulation rate that is commonly produced for this lift and solution with the jet-assisted airlift sample system that is normally used at ICPP. The volume of the sample taken with a fluidic sampler is dependant on the motive pressure to the fluidic sampler, the sample bottle size and on the fluidic sampler jet characteristics. The fluidic sampler should be supplied with fluid having the motive pressure of the 140--150 percent of the peak vacuum producing motive pressure for the jet in the sampler. Fluidic transfer systems should be operated by emptying a full pumping chamber to nearly empty or empty during the pumping cycle, this maximizes the solution transfer rate

  12. Classifying Returns as Extreme: European Stock and Bond Markets

    DEFF Research Database (Denmark)

    Christiansen, Charlotte

    whereby a shorter sample period is needed. For the bond markets the simultaneous extreme return variable (used for analyzing integration and contagion of financial markets) is not statistically different for the two schemes. For the stock markets there are differences, but they are disappearing......I consider the stock and bond markets of 14 EU countries. I use two classification schemes for defining extreme returns: One, the existing univariate classification scheme which considers each market separately. Two, the new multivariate classification scheme that considers all the markets jointly...

  13. Phenotypic profiles of Armenian grape cultivars

    Directory of Open Access Journals (Sweden)

    Aroutiounian Rouben

    2015-01-01

    Full Text Available The conservation and sustainable use of grapevine biodiversity in Armenia is particularly important due to the large number of traditional local varieties. Being partially different from European grapevine gene pool, the material of Armenian local cultivars significantly contributes to the understanding of the genetic variation and is valuable source for target selection. During last years many Armenian grapevine cultivars have been already described and their genotypes determined, but some local varieties and wild accessions remain unidentified and their phenotypic characteristics overlooked. The comprehensive analysis of phenotypes is essential for research, including genetic association studies, cultivar evaluation and selection. The goal of our research was the phenotyping on the base of reproductive, carpological and analytical characteristics of 80 Armenian aboriginal and new grape cultivars. Description of phenotypic profiles is important step towards identification and conservation of genetic resources of Armenian grapes. In future, these data can be applied for breeding of improved grape varieties targeted to fresh consumption and wine production.

  14. Phenotypic diversity and phylogenetic relationship between the ...

    African Journals Online (AJOL)

    Phenotypic diversity and phylogenetic relationship between the Bakosi/Baweri and other pig breeds ( Sus scrofa Domesticus ) in the humid forest with monomodal rainfall agro-ecological zone of Cameroon.

  15. Mining skeletal phenotype descriptions from scientific literature.

    Directory of Open Access Journals (Sweden)

    Tudor Groza

    Full Text Available Phenotype descriptions are important for our understanding of genetics, as they enable the computation and analysis of a varied range of issues related to the genetic and developmental bases of correlated characters. The literature contains a wealth of such phenotype descriptions, usually reported as free-text entries, similar to typical clinical summaries. In this paper, we focus on creating and making available an annotated corpus of skeletal phenotype descriptions. In addition, we present and evaluate a hybrid Machine Learning approach for mining phenotype descriptions from free text. Our hybrid approach uses an ensemble of four classifiers and experiments with several aggregation techniques. The best scoring technique achieves an F-1 score of 71.52%, which is close to the state-of-the-art in other domains, where training data exists in abundance. Finally, we discuss the influence of the features chosen for the model on the overall performance of the method.

  16. Integrating phenotype ontologies with PhenomeNET

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel; Gkoutos, Georgios V.; Schofield, Paul N.; Hoehndorf, Robert

    2017-01-01

    in clinical and model organism databases presents complex problems when attempting to match classes across species and across phenotypes as diverse as behaviour and neoplasia. We have previously developed PhenomeNET, a system for disease gene prioritization

  17. Wiedemann-Rautenstrauch syndrome: A phenotype analysis

    NARCIS (Netherlands)

    Paolacci, Stefano; Bertola, Debora; Franco, José; Mohammed, Shehla; Tartaglia, Marco; Wollnik, Bernd; Hennekam, Raoul C.

    2017-01-01

    Wiedemann-Rautenstrauch syndrome (WRS) is a neonatal progeroid disorder characterized by growth retardation, lipodystrophy, a distinctive face, and dental anomalies. Patients reported to date demonstrate a remarkable variability in phenotype, which hampers diagnostics. We performed a literature

  18. REVIEW ARTICLE One gene, many phenotypes

    African Journals Online (AJOL)

    salah

    Phenotype descriptions are valuable information right at the interface of medi- cine and biology. ... the interaction of alleles at different loci. Modifier genes. 5. ... the amount of normal protein is called ..... Institute, using computer simulations,.

  19. The spatial patterns of directional phenotypic selection

    KAUST Repository

    Siepielski, Adam M.; Gotanda, Kiyoko M.; Morrissey, Michael B.; Diamond, Sarah E.; DiBattista, Joseph; Carlson, Stephanie Marie

    2013-01-01

    the spatial patterns of selection, namely the extent of variation among populations in the strength and direction of selection. Here, we analyse a data set of spatially replicated studies of directional phenotypic selection from natural populations. The data

  20. Phenotypic variability among strains of Pasteurella multocida ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-05-02

    May 2, 2008 ... Available online at http://www.academicjournals.org/AJB. ISSN 1684–5315 ... extended phenotypic characterization methods supported by DNA ... septicaemia African (Obudu) strain (E:2) which are currently employed as ...

  1. Climate change & extreme weather vulnerability assessment framework.

    Science.gov (United States)

    2012-12-01

    The Federal Highway Administrations (FHWAs) Climate Change and Extreme Weather Vulnerability : Assessment Framework is a guide for transportation agencies interested in assessing their vulnerability : to climate change and extreme weather event...

  2. Frequently Asked Questions (FAQ) about Extreme Heat

    Science.gov (United States)

    ... Extreme Heat Older Adults (Aged 65+) Infants and Children Chronic Medical Conditions Low Income Athletes Outdoor Workers Pets Hot Weather Tips Warning Signs and Symptoms FAQs Social Media How to Stay Cool Missouri Cooling Centers Extreme ...

  3. Atypical disease phenotypes in pediatric ulcerative colitis

    DEFF Research Database (Denmark)

    Levine, Arie; de Bie, Charlotte I; Turner, Dan

    2013-01-01

    Definitive diagnosis of pediatric ulcerative colitis (UC) may be particularly challenging since isolated colitis with overlapping features is common in pediatric Crohn's disease (CD), while atypical phenotypes of UC are not uncommon. The Paris classification allows more accurate phenotyping...... of atypical inflammatory bowel disease (IBD) patients. Our aim was to identify the prevalence of atypical disease patterns in new-onset pediatric UC using the Paris classification....

  4. A Regulatory RNA Inducing Transgenerationally Inherited Phenotypes

    DEFF Research Database (Denmark)

    Jensen, Lea Møller

    . The variation in Arabidopsis enables different regulatory networks and mechanisms to shape the phenotypic characteristics. The thesis describes the identification of regulatory RNA encoded by an enzyme encoding gene. The RNA regulates by inducing transgenerationally inherited phenotypes. The function of the RNA...... is dependent on the genetic background illustrating that polymorphisms are found in either interactors or target genes of the RNA. Furthermore, the RNA provides a mechanistic link between accumulation of glucosinolate and onset of flowering....

  5. Sampling methodology and PCB analysis

    International Nuclear Information System (INIS)

    Dominelli, N.

    1995-01-01

    As a class of compounds PCBs are extremely stable and resist chemical and biological decomposition. Diluted solutions exposed to a range of environmental conditions will undergo some preferential degradation and the resulting mixture may differ considerably from the original PCB used as insulating fluid in electrical equipment. The structure of mixtures of PCBs (synthetic compounds prepared by direct chlorination of biphenyl with chlorine gas) is extremely complex and presents a formidable analytical problem, further complicated by the presence of PCBs as contaminants in oils to soils to water. This paper provides some guidance into sampling and analytical procedures; it also points out various potential problems encountered during these processes. The guidelines provided deal with sample collection, storage and handling, sample stability, laboratory analysis (usually gas chromatography), determination of PCB concentration, calculation of total PCB content, and quality assurance. 1 fig

  6. Partial phenotyping in voluntary blood donors of Gujarat State

    Directory of Open Access Journals (Sweden)

    Maitrey Gajjar

    2016-01-01

    Full Text Available Introduction: Partial phenotyping of voluntary blood donors has vital role in transfusion practice, population genetic study and in resolving legal issues.The Rh blood group is one of the most complex and highly immunogenic blood group known in humans. The Kell system, discovered in 1946, is the third most potent system at triggering hemolytic transfusion reactions and consists of 25 highly immunogenic antigens. Knowledge of Rh & Kell phenotypes in given population is relevant for better planning and management of blood bank; the main goal is to find compatible blood for patients needing multiple blood transfusions. The aim of this study was to evaluate the frequency of Rh & Kell phenotype of voluntary donors in Gujarat state. Materials and Methods: The present study was conducted by taking 5670 samples from random voluntary blood donors coming in blood donation camp. Written consent was taken for donor phenotyping. The antigen typing of donors was performed by Qwalys-3(manufacturer: Diagast by using electromagnetic technology on Duolys plates. Results: Out of 5670 donors, the most common Rh antigen observed in the study population was e (99.07% followed by D (95.40%, C (88.77%, c (55.89% and E (17.88%. The frequency of the Kell antigen (K was 1.78 %. Discussion: The antigen frequencies among blood donors from Gujarat were compared with those published for other Indian populations. The frequency of D antigen in our study (95.4% and north Indian donors (93.6 was significantly higher than in the Caucasians (85% and lower than in the Chinese (99%. The frequencies of C, c and E antigens were dissimilar to other ethnic groups while the ′e′ antigen was present in high frequency in our study as also in the other ethnic groups. Kell antigen (K was found in only 101 (1.78 % donors out of 5670. Frequency of Kell antigen in Caucasian and Black populations is 9% & 2% respectively. The most common Kell phenotype was K-k+, not just in Indians (96.5% but

  7. Phenex: ontological annotation of phenotypic diversity.

    Directory of Open Access Journals (Sweden)

    James P Balhoff

    2010-05-01

    Full Text Available Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

  8. Phenex: ontological annotation of phenotypic diversity.

    Science.gov (United States)

    Balhoff, James P; Dahdul, Wasila M; Kothari, Cartik R; Lapp, Hilmar; Lundberg, John G; Mabee, Paula; Midford, Peter E; Westerfield, Monte; Vision, Todd J

    2010-05-05

    Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

  9. Extreme Maximum Land Surface Temperatures.

    Science.gov (United States)

    Garratt, J. R.

    1992-09-01

    There are numerous reports in the literature of observations of land surface temperatures. Some of these, almost all made in situ, reveal maximum values in the 50°-70°C range, with a few, made in desert regions, near 80°C. Consideration of a simplified form of the surface energy balance equation, utilizing likely upper values of absorbed shortwave flux (1000 W m2) and screen air temperature (55°C), that surface temperatures in the vicinity of 90°-100°C may occur for dry, darkish soils of low thermal conductivity (0.1-0.2 W m1 K1). Numerical simulations confirm this and suggest that temperature gradients in the first few centimeters of soil may reach 0.5°-1°C mm1 under these extreme conditions. The study bears upon the intrinsic interest of identifying extreme maximum temperatures and yields interesting information regarding the comfort zone of animals (including man).

  10. Lactase persistence versus lactose intolerance: Is there an intermediate phenotype?

    Science.gov (United States)

    Dzialanski, Zbigniew; Barany, Michael; Engfeldt, Peter; Magnuson, Anders; Olsson, Lovisa A; Nilsson, Torbjörn K

    2016-02-01

    According to the prevailing theory about the genetic background to lactose intolerance, there are three genotypes but only two adult physiological phenotypes: lactase persistence in individuals with the CT and TT genotypes and lactase non-persistence in individuals with the CC genotype. However, analysis of lactase activity from intestinal biopsies has revealed three distinct levels of activity, suggesting that an intermediate physiological phenotype may exist. To assess possible disparities between different genotypes with regard to biomarkers of lactase activity and physical symptoms during an oral lactose load test. A retrospective study using an oral lactose load test (n=487). Concentrations of hydrogen in exhaled air and blood glucose were measured. Afterwards, subjects were asked to provide oral mucosa samples for genotyping and answer a questionnaire (participation rate 56%, n=274). Mean hydrogen levels in exhaled air at 120min were significantly higher in the CT genotype than in the TT genotype. There was no significant difference in blood glucose levels between the two groups. Reported symptoms, with the possible exception of abdominal pain, were equally prevalent in both groups. Subjects with the CT and TT genotypes, hitherto classified as lactase-persistent, differ in their physiological response to lactose intake, indicating differences in phenotype which could have clinical significance. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  11. Genotype–phenotype correlations in individuals with pathogenic RERE variants

    Science.gov (United States)

    Jordan, Valerie K.; Fregeau, Brieana; Ge, Xiaoyan; Giordano, Jessica; Wapner, Ronald J.; Balci, Tugce B.; Carter, Melissa T.; Bernat, John A.; Moccia, Amanda N.; Srivastava, Anshika; Martin, Donna M.; Bielas, Stephanie L.; Pappas, John; Svoboda, Melissa D.; Rio, Marlène; Boddaert, Nathalie; Cantagrel, Vincent; Lewis, Andrea M.; Scaglia, Fernando; Kohler, Jennefer N.; Bernstein, Jonathan A.; Dries, Annika M.; Rosenfeld, Jill A.; DeFilippo, Colette; Thorson, Willa; Yang, Yaping; Sherr, Elliott H.; Bi, Weimin; Scott, Daryl A.

    2018-01-01

    Heterozygous variants in the arginine-glutamic acid dipeptide repeats gene (RERE) have been shown to cause neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH). Here, we report nine individuals with NEDBEH who carry partial deletions or deleterious sequence variants in RERE. These variants were found to be de novo in all cases in which parental samples were available. An analysis of data from individuals with NEDBEH suggests that point mutations affecting the Atrophin-1 domain of RERE are associated with an increased risk of structural eye defects, congenital heart defects, renal anomalies, and sensorineural hearing loss when compared with loss-of-function variants that are likely to lead to haploinsufficiency. A high percentage of RERE pathogenic variants affect a histidine-rich region in the Atrophin-1 domain. We have also identified a recurrent two-amino-acid duplication in this region that is associated with the development of a CHARGE syndrome-like phenotype. We conclude that mutations affecting RERE result in a spectrum of clinical phenotypes. Genotype–phenotype correlations exist and can be used to guide medical decision making. Consideration should also be given to screening for RERE variants in individuals who fulfill diagnostic criteria for CHARGE syndrome but do not carry pathogenic variants in CHD7. PMID:29330883

  12. The greenhouse effect and extreme weather

    International Nuclear Information System (INIS)

    Groenaas, Sigbjoern; Kvamstoe, Nils Gunnar

    2002-01-01

    The article asserts that an anthropogenic global warming is occurring. This greenhouse effect is expected to cause more occurrences of extreme weather. It is extremely difficult, however, to relate specific weather catastrophes to global warming with certainty, since such extreme weather conditions are rare historically. The subject is controversial. The article also discusses the public debate and the risk of floods

  13. Autoimmune gastritis: histology phenotype and OLGA staging.

    Science.gov (United States)

    Rugge, M; Fassan, M; Pizzi, M; Zorzetto, V; Maddalo, G; Realdon, S; De Bernard, M; Betterle, C; Cappellesso, R; Pennelli, G; de Boni, M; Farinati, F

    2012-06-01

    Among Western populations, the declining incidence of Helicobacter pylori infection coincides with a growing clinical impact of autoimmune gastritis. To describe the histological phenotype of autoimmune gastritis, also to test the prognostic impact of OLGA staging in the autoimmune setting. A single-institutional series (spanning the years 2003-2011) of 562 consecutive patients (M:F ratio: 1:3.7; mean age = 57.6 ± 14.4 years) with serologically confirmed autoimmune gastritis underwent histology review and OLGA staging. Helicobacter pylori infection was ascertained histologically in 44/562 cases (7.8%). Forty six biopsy sets (8.2%) featured OLGA stages III-IV; they included all four cases of incidental epithelial neoplasia (three intraepithelial and one invasive; three of these four cases had concomitant H. pylori infection). There were 230 (40.9%) and 139 (24.7%) cases, respectively, of linear and micro-nodular enterochromaffin-like cell hyperplasia; 19 (3.4%) type I carcinoids were detected. The series included 116 patients who underwent repeated endoscopy/biopsy sampling (mean time elapsing between the two procedures = 54 months; range 24-108). Paired histology showed a significant (P = 0.009) trend towards a stage progression [the stage increased in 25/116 cases (22%); it remained unchanged in 87/116 cases (75%)]. In autoimmune gastritis, the cancer risk is restricted to high-risk gastritis stages (III-IV), and is associated mainly with concomitant H. pylori infection. OLGA staging consistently depicts the time-dependent organic progression of the autoimmune disease and provides key information for secondary gastric cancer prevention strategies. © 2012 Blackwell Publishing Ltd.

  14. Population FBA predicts metabolic phenotypes in yeast.

    Directory of Open Access Journals (Sweden)

    Piyush Labhsetwar

    2017-09-01

    Full Text Available Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism, Population flux balance analysis (Population FBA successfully described metabolic heterogeneity in a population of independent Escherichia coli cells growing in a defined medium. We extend the methodology to account for correlations in protein expression arising from the co-regulation of genes and apply it to study the growth of independent Saccharomyces cerevisiae cells in two different growth media. We find the partitioning of flux between fermentation and respiration predicted by our model agrees with recent 13C fluxomics experiments, and that our model largely recovers the Crabtree effect (the experimentally known bias among certain yeast species toward fermentation with the production of ethanol even in the presence of oxygen, while FBA without proteomics constraints predicts respirative metabolism almost exclusively. The comparisons to the 13C study showed improvement upon inclusion of the correlations and motivated a technique to systematically identify inconsistent kinetic parameters in the literature. The minor secretion fluxes for glycerol and acetate are underestimated by our method, which indicate a need for further refinements to the metabolic model. For yeast cells grown in synthetic defined (SD medium, the calculated broad distribution of growth rates matches experimental observations from single cell studies, and we characterize several metabolic phenotypes within our modeled populations that make use of diverse pathways. Fast growing yeast cells are predicted to perform significant amount of respiration, use serine-glycine cycle and produce ethanol in mitochondria as opposed to slow growing cells. We use a genetic algorithm to determine the proteomics constraints necessary to reproduce the growth rate distributions seen experimentally. We find that a core set of 51 constraints are essential but

  15. High Pressure Atmospheric Sampling Inlet System for Venus or the Gas Giants, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Thorleaf Research, Inc. proposes to develop a miniaturized high pressure atmospheric sampling inlet system for sample acquisition in extreme planetary environments,...

  16. Modelling of extreme gusts for design calculations (NewGust)

    Energy Technology Data Exchange (ETDEWEB)

    Bierbooms, W; Cheng, Po-Wen [Delft Univ. of Technology, Inst. for Wind Energy, Delft (Netherlands); Larsen, G [Risoe National Lab., Roskilde (Denmark); Juul Pedersen, B [Vestas Wind Systems A/S, Lem (Denmark); Hansen, K [Tecnical Univ. of Denmark (Denmark)

    1999-03-01

    The main objective of the NewGust project is to come to a realistic and verified description of extreme gusts based on the stochastic properties of wind. In this paper the first results of the project are presented. Theoretical considerations indicate that the shape of extreme gusts is very sharp. Based on simulated wind time series, mean gust shapes (for several amplitudes and mean wind speeds) are determined and compared with the theoretical curves. The resemblance turned out to be very good. Furthermore, the influence of the sampling rate and the dynamics of a cup anemometer on the empirical mean gust shape are examined. The promising results are confirmed by a (preliminary) verification based on measured wind time series, available from the database on wind characteristics. The mean shape of gusts, of certain amplitude, together with their probability of occurrence can be used to obtain the distribution of the extreme response of wind turbines to gust loading. (au)

  17. Deconstruction of Vulnerability to Complex Diseases: Enhanced Effect Sizes and Power of Intermediate Phenotypes

    Directory of Open Access Journals (Sweden)

    David Goldman

    2007-01-01

    Full Text Available The deconstruction of vulnerability to complex disease with the help of intermediate phenotypes, including the heritable and disease-associated endophenotypes, is a legacy of Henri Begleiter. Systematic searches for genes influencing complex disorders, including bipolar disorder, have recently been completed using whole genome association (WGA, identifying a series of validated loci. Using this information, it is possible to compare effect sizes of disease loci discovered in very large samples to the effect sizes of replicated functional loci determining intermediate phenotypes that are of essential interest in psychiatric disorders. It is shown that the genes influencing intermediate phenotypes tend to have a larger effect size. Furthermore, the WGA results reveal that the number of loci of large effect size for complex diseases is limited, and yet multiple functional loci have already been identified for intermediate phenotypes relevant to psychiatric diseases, and without the benefit of WGA.

  18. Detailed Analysis of Solar Data Related to Historical Extreme Geomagnetic Storms: 1868 – 2010

    DEFF Research Database (Denmark)

    Lefèvre, Laure; Vennerstrøm, Susanne; Dumbović, Mateja

    2016-01-01

    An analysis of historical Sun–Earth connection events in the context of the most extreme space weather events of the last ∼ 150 years is presented. To identify the key factors leading to these extreme events, a sample of the most important geomagnetic storms was selected based mainly on the well-...

  19. Extremity doses to interventional radiologists

    International Nuclear Information System (INIS)

    Wihtby, M.; Martin, C. J.

    2002-01-01

    Radiologists performing interventional procedures are often required to stand close to the patient's side when carrying out manipulations under fluoroscopic control. This can result in their extremities receiving a high radiation dose, due to scattered radiation. These doses are sometimes high enough to warrant that the radiologist in question be designated a classified radiation worker. Classification in the UK is a result of any worker receiving or likely to receive in the course of their duties in excess of 3/10ths of any annual dose limit (500mSv to extremities, skin). The doses to the legs of radiologists have received less attention than those to the hands, however the doses may be high, due to the proximity of the legs and feet to scattered radiation. The legs can be exposed to a relatively high level of scattered radiation as the radiation in produced from scatter of the un attenuated beam from the bottom of the patient couch. The routine monitoring of extremity doses in interventional radiology is difficult due to several factors. Firstly a wide range of interventional procedures in undertaken in every radiology department, and these procedures require many different techniques, equipment and skills. This means that the position the radiologist adopts in relation to scattering medium and therefore their exposure, depends heavily on the type of procedure. As the hands which manipulate the catheters within the patient are often located close to the patients side and to the area under irradiation, the distribution of dose across the hands can be variable, with very high localised doses, making routine monitoring difficult. The purpose of this study was to determine the magnitude and distribution of dose to the hands and legs of interventional radiologists carrying out a wide range of both diagnostic and therapeutic interventional procedures. To ascertain the most effective method of monitoring the highest dose in accordance with the Basic safety standards

  20. Trajectories of the healthy ageing phenotype among middle-aged and older Britons, 2004-2013.

    Science.gov (United States)

    Tampubolon, Gindo

    2016-06-01

    Since the ageing population demands a response to ensure older people remain healthy and active, we studied the dynamics of a recently proposed healthy ageing phenotype. We drew the phenotype's trajectories and tested whether their levels and rates of change are influenced by health behaviours, comorbidities and socioeconomic positions earlier in the life course. The English Longitudinal Ageing Study, a prospective, nationally representative sample of people aged ≥50 years, measured a set of eight biomarkers which make up the outcome of the healthy ageing phenotype three times over nearly a decade (N2004=5009, N2008=5301, N2013=4455). A cluster of health behaviours, comorbidities and socioeconomic positions were also measured repeatedly. We assessed the phenotype's distribution non-parametrically, then fitted linear mixed models to phenotypic change and further examined time interactions with gender and socioeconomic position. We ran additional analyses to test robustness. Women had a wider distribution of the healthy ageing phenotype than men had. The phenotype declined annually by -0.242 (95% confidence interval [CI]: -0.352, -0.131). However, there was considerable heterogeneity in the levels and rates of phenotypic change. Women started at higher levels, then declined more steeply by -0.293 (CI: -0.403, -0.183) annually, leading to crossover in the trajectories. Smoking and physical activity assessed on the Allied Dunbar scale were strongly associated with the trajectories. Though marked by secular decline, the trajectories of the healthy ageing phenotype showed distinct socioeconomic gradients. The trajectories were also susceptible to variations in health behaviours, strengthening the case for serial interventions to attain healthy and active ageing. Copyright © 2016 The Author. Published by Elsevier Ireland Ltd.. All rights reserved.

  1. Semiparametric Allelic Tests for Mapping Multiple Phenotypes: Binomial Regression and Mahalanobis Distance.

    Science.gov (United States)

    Majumdar, Arunabha; Witte, John S; Ghosh, Saurabh

    2015-12-01

    Binary phenotypes commonly arise due to multiple underlying quantitative precursors and genetic variants may impact multiple traits in a pleiotropic manner. Hence, simultaneously analyzing such correlated traits may be more powerful than analyzing individual traits. Various genotype-level methods, e.g., MultiPhen (O'Reilly et al. []), have been developed to identify genetic factors underlying a multivariate phenotype. For univariate phenotypes, the usefulness and applicability of allele-level tests have been investigated. The test of allele frequency difference among cases and controls is commonly used for mapping case-control association. However, allelic methods for multivariate association mapping have not been studied much. In this article, we explore two allelic tests of multivariate association: one using a Binomial regression model based on inverted regression of genotype on phenotype (Binomial regression-based Association of Multivariate Phenotypes [BAMP]), and the other employing the Mahalanobis distance between two sample means of the multivariate phenotype vector for two alleles at a single-nucleotide polymorphism (Distance-based Association of Multivariate Phenotypes [DAMP]). These methods can incorporate both discrete and continuous phenotypes. Some theoretical properties for BAMP are studied. Using simulations, the power of the methods for detecting multivariate association is compared with the genotype-level test MultiPhen's. The allelic tests yield marginally higher power than MultiPhen for multivariate phenotypes. For one/two binary traits under recessive mode of inheritance, allelic tests are found to be substantially more powerful. All three tests are applied to two different real data and the results offer some support for the simulation study. We propose a hybrid approach for testing multivariate association that implements MultiPhen when Hardy-Weinberg Equilibrium (HWE) is violated and BAMP otherwise, because the allelic approaches assume HWE

  2. Sampling methods

    International Nuclear Information System (INIS)

    Loughran, R.J.; Wallbrink, P.J.; Walling, D.E.; Appleby, P.G.

    2002-01-01

    Methods for the collection of soil samples to determine levels of 137 Cs and other fallout radionuclides, such as excess 210 Pb and 7 Be, will depend on the purposes (aims) of the project, site and soil characteristics, analytical capacity, the total number of samples that can be analysed and the sample mass required. The latter two will depend partly on detector type and capabilities. A variety of field methods have been developed for different field conditions and circumstances over the past twenty years, many of them inherited or adapted from soil science and sedimentology. The use of them inherited or adapted from soil science and sedimentology. The use of 137 Cs in erosion studies has been widely developed, while the application of fallout 210 Pb and 7 Be is still developing. Although it is possible to measure these nuclides simultaneously, it is common for experiments to designed around the use of 137 Cs along. Caesium studies typically involve comparison of the inventories found at eroded or sedimentation sites with that of a 'reference' site. An accurate characterization of the depth distribution of these fallout nuclides is often required in order to apply and/or calibrate the conversion models. However, depending on the tracer involved, the depth distribution, and thus the sampling resolution required to define it, differs. For example, a depth resolution of 1 cm is often adequate when using 137 Cs. However, fallout 210 Pb and 7 Be commonly has very strong surface maxima that decrease exponentially with depth, and fine depth increments are required at or close to the soil surface. Consequently, different depth incremental sampling methods are required when using different fallout radionuclides. Geomorphic investigations also frequently require determination of the depth-distribution of fallout nuclides on slopes and depositional sites as well as their total inventories

  3. Weather extremes could affect agriculture

    Science.gov (United States)

    Balcerak, Ernie

    2012-05-01

    As Earth's climate warms, agricultural producers will need to adapt. Changes, especially increases in extreme events, are already having an impact on food production, according to speakers at a 1 May session on agriculture and food security at the AGU Science Policy Conference. Christopher Field, director of the Department of Global Ecology at the Carnegie Institution for Science of Washington, D. C., pointed out the complex factors that come into play in understanding food security, including spatially varying controls and stresses, incomplete models, and the potential for threshold responses. Factors that are likely to cause problems include increasing population; increasing preference for meat, which needs more land and energy inputs to produce; climate change; and increasing use of agricultural lands for biomass energy.

  4. Generic Hurricane Extreme Seas State

    DEFF Research Database (Denmark)

    Wehmeyer, Christof; Skourup, Jesper; Frigaard, Peter

    2012-01-01

    Extreme sea states, which the IEC 61400-3 (2008) standard requires for the ultimate limit state (ULS) analysis of offshore wind turbines are derived to establish the design basis for the conceptual layout of deep water floating offshore wind turbine foundations in hurricane affected areas....... Especially in the initial phase of floating foundation concept development, site specific metocean data are usually not available. As the areas of interest are furthermore not covered by any design standard, in terms of design sea states, generic and in engineering terms applicable environmental background...... data is required for a type specific conceptual design. ULS conditions for different return periods are developed, which can subsequently be applied in siteindependent analysis and conceptual design. Recordings provided by National Oceanic and Atmospheric Administration (NOAA), of hurricanes along...

  5. Pneumatic tourniquets in extremity surgery.

    LENUS (Irish Health Repository)

    Wakai, A

    2012-02-03

    Pneumatic tourniquets maintain a relatively bloodless field during extremity surgery, minimize blood loss, aid identification of vital structures, and expedite the procedure. However, they may induce an ischemia-reperfusion injury with potentially harmful local and systemic consequences. Modern pneumatic tourniquets are designed with mechanisms to regulate and maintain pressure. Routine maintenance helps ensure that these systems are working properly. The complications of tourniquet use include postoperative swelling, delay of recovery of muscle power, compression neurapraxia, wound hematoma with the potential for infection, vascular injury, tissue necrosis, and compartment syndrome. Systemic complications can also occur. The incidence of complications can be minimized by use of wider tourniquets, careful preoperative patient evaluation, and adherence to accepted principles of tourniquet use.

  6. Genomics of an extreme psychrophile, Psychromonas ingrahamii

    Directory of Open Access Journals (Sweden)

    Hauser Loren J

    2008-05-01

    Full Text Available Abstract Background The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. Results Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1 there are 6 classes of proteins, at least one more than other bacteria, (2 integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3 there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4 one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1 P. ingrahamii has a large number (61 of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2 P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3 P. ingrahamii has a large number (11 of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4 Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5 Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. Conclusion The results of this genomic analysis

  7. GeneYenta: a phenotype-based rare disease case matching tool based on online dating algorithms for the acceleration of exome interpretation.

    Science.gov (United States)

    Gottlieb, Michael M; Arenillas, David J; Maithripala, Savanie; Maurer, Zachary D; Tarailo Graovac, Maja; Armstrong, Linlea; Patel, Millan; van Karnebeek, Clara; Wasserman, Wyeth W

    2015-04-01

    Advances in next-generation sequencing (NGS) technologies have helped reveal causal variants for genetic diseases. In order to establish causality, it is often necessary to compare genomes of unrelated individuals with similar disease phenotypes to identify common disrupted genes. When working with cases of rare genetic disorders, finding similar individuals can be extremely difficult. We introduce a web tool, GeneYenta, which facilitates the matchmaking process, allowing clinicians to coordinate detailed comparisons for phenotypically similar cases. Importantly, the system is focused on phenotype annotation, with explicit limitations on highly confidential data that create barriers to participation. The procedure for matching of patient phenotypes, inspired by online dating services, uses an ontology-based semantic case matching algorithm with attribute weighting. We evaluate the capacity of the system using a curated reference data set and 19 clinician entered cases comparing four matching algorithms. We find that the inclusion of clinician weights can augment phenotype matching. © 2015 WILEY PERIODICALS, INC.

  8. Can Concentration - Discharge Relationships Diagnose Material Source During Extreme Events?

    Science.gov (United States)

    Karwan, D. L.; Godsey, S.; Rose, L.

    2017-12-01

    Floods can carry >90% of the basin material exported in a given year as well as alter flow pathways and material sources. In turn, sediment and solute fluxes can increase flood damages and negatively impact water quality and integrate physical and chemical weathering of landscapes and channels. Concentration-discharge (C-Q) relationships are used to both describe export patterns as well as compute them. Metrics for describing C-Q patterns and inferring their controls are vulnerable to infrequent sampling that affects how C-Q relationships are interpolated and interpreted. C-Q relationships are typically evaluated from multiple samples, but because hydrological extremes are rare, data are often unavailable for extreme events. Because solute and sediment C-Q relationships likely respond to changes in hydrologic extremes in different ways, there is a pressing need to define their behavior under extreme conditions, including how to properly sample to capture these patterns. In the absence of such knowledge, improving load estimates in extreme floods will likely remain difficult. Here we explore the use of C-Q relationships to determine when an event alters a watershed system such that it enters a new material source/transport regime. We focus on watersheds with sediment and discharge time series include low-frequency and/or extreme events. For example, we compare solute and sediment patterns in White Clay Creek in southeastern Pennsylvania across a range of flows inclusive of multiple hurricanes for which we have ample ancillary hydrochemical data. TSS is consistently mobilized during high flow events, even during extreme floods associated with hurricanes, and sediment fingerprinting indicates different sediment sources, including in-channel remobilization and landscape erosion, are active at different times. In other words, TSS mobilization in C-Q space is not sensitive to the source of material being mobilized. Unlike sediments, weathering solutes in this watershed

  9. Overeating phenotypes in overweight and obese children.

    Science.gov (United States)

    Boutelle, Kerri N; Peterson, Carol B; Crosby, Ross D; Rydell, Sarah A; Zucker, Nancy; Harnack, Lisa

    2014-05-01

    The purpose of this study was to identify overeating phenotypes and their correlates in overweight and obese children. One hundred and seventeen treatment-seeking overweight and obese 8-12year-old children and their parents completed the study. Children completed an eating in the absence of hunger (EAH) paradigm, the Eating Disorder Examination interview, and measurements of height and weight. Parents and children completed questionnaires that evaluated satiety responsiveness, food responsiveness, negative affect eating, external eating and eating in the absence of hunger. Latent profile analysis was used to identify heterogeneity in overeating phenotypes in the child participants. Latent classes were then compared on measures of demographics, obesity status and nutritional intake. Three latent classes of overweight and obese children were identified: High Satiety Responsive, High Food Responsive, and Moderate Satiety and Food Responsive. Results indicated that the High Food Responsive group had higher BMI and BMI-Z scores compared to the High Satiety Responsive group. No differences were found among classes in demographics or nutritional intake. This study identified three overeating phenotypes, supporting the heterogeneity of eating patterns associated with overweight and obesity in treatment-seeking children. These finding suggest that these phenotypes can potentially be used to identify high risk groups, inform prevention and intervention targets, and develop specific treatments for these behavioral phenotypes. Copyright © 2014. Published by Elsevier Ltd.

  10. [New population curves in spanish extremely preterm neonates].

    Science.gov (United States)

    García-Muñoz Rodrigo, F; García-Alix Pérez, A; Figueras Aloy, J; Saavedra Santana, P

    2014-08-01

    Most anthropometric reference data for extremely preterm infants used in Spain are outdated and based on non-Spanish populations, or are derived from small hospital-based samples that failed to include neonates of borderline viability. To develop gender-specific, population-based curves for birth weight, length, and head circumference in extremely preterm Caucasian infants, using a large contemporary sample size of Spanish singletons. Anthropometric data from neonates ≤ 28 weeks of gestational age were collected between January 2002 and December 2010 using the Spanish database SEN1500. Gestational age was estimated according to obstetric data (early pregnancy ultrasound). The data were analyzed with the SPSS.20 package, and centile tables were created for males and females using the Cole and Green LMS method. This study presents the first population-based growth curves for extremely preterm infants, including those of borderline viability, in Spain. A sexual dimorphism is evident for all of the studied parameters, starting at early gestation. These new gender-specific and population-based data could be useful for the improvement of growth assessments of extremely preterm infants in our country, for the development of epidemiological studies, for the evaluation of temporal trends, and for clinical or public health interventions seeking to optimize fetal growth. Copyright © 2013 Asociación Española de Pediatría. Published by Elsevier Espana. All rights reserved.

  11. Microbial community analysis of field-grown soybeans with different nodulation phenotypes.

    Science.gov (United States)

    Ikeda, Seishi; Rallos, Lynn Esther E; Okubo, Takashi; Eda, Shima; Inaba, Shoko; Mitsui, Hisayuki; Minamisawa, Kiwamu

    2008-09-01

    Microorganisms associated with the stems and roots of nonnodulated (Nod(-)), wild-type nodulated (Nod(+)), and hypernodulated (Nod(++)) soybeans [Glycine max (L.) Merril] were analyzed by ribosomal intergenic transcribed spacer analysis (RISA) and automated RISA (ARISA). RISA of stem samples detected no bands specific to the nodulation phenotype, whereas RISA of root samples revealed differential bands for the nodulation phenotypes. Pseudomonas fluorescens was exclusively associated with Nod(+) soybean roots. Fusarium solani was stably associated with nodulated (Nod(+) and Nod(++)) roots and less abundant in Nod(-) soybeans, whereas the abundance of basidiomycetes was just the opposite. The phylogenetic analyses suggested that these basidiomycetous fungi might represent a root-associated group in the Auriculariales. Principal-component analysis of the ARISA results showed that there was no clear relationship between nodulation phenotype and bacterial community structure in the stem. In contrast, both the bacterial and fungal community structures in the roots were related to nodulation phenotype. The principal-component analysis further suggested that bacterial community structure in roots could be classified into three groups according to the nodulation phenotype (Nod(-), Nod(+), or Nod(++)). The analysis of root samples indicated that the microbial community in Nod(-) soybeans was more similar to that in Nod(++) soybeans than to that in Nod(+) soybeans.

  12. Indications of an extreme event deposits along the west coast of India: evidences from GPR investigations

    Digital Repository Service at National Institute of Oceanography (India)

    Loveson, V.J.; Gujar, A.R.; Iyer, S.D.; Srivastava, P.; Tirodkar, G.; Luis, R.A.A.

    to an extreme event. Sand samples were collected from two trial pits along the GPR profiles to understand the sedimentology and mineralogy in the backshore area. These data together with beach profiles and geomorphological maps suggest that the sands were...

  13. Magnetic-Field-Assisted Assembly of Ordered Multifunctional Ceramic Nanocomposites for Extreme Environments

    Science.gov (United States)

    2016-04-01

    SUBJECT TERMS carbon nanotubes, composite, electromagnetic shielding , extreme environments, magnetism, fibers, woven composite, boron nitride...The samples were sealed in glass vial and exposed to the magnetic field immediately after deposition prior to crystallization of PEG that allowed

  14. Constraints on the evolution of phenotypic plasticity

    DEFF Research Database (Denmark)

    Murren, Courtney J; Auld, Josh R.; Callahan, Hilary S

    2015-01-01

    Phenotypic plasticity is ubiquitous and generally regarded as a key mechanism for enabling organisms to survive in the face of environmental change. Because no organism is infinitely or ideally plastic, theory suggests that there must be limits (for example, the lack of ability to produce...... an optimal trait) to the evolution of phenotypic plasticity, or that plasticity may have inherent significant costs. Yet numerous experimental studies have not detected widespread costs. Explicitly differentiating plasticity costs from phenotype costs, we re-evaluate fundamental questions of the limits...... to the evolution of plasticity and of generalists vs specialists. We advocate for the view that relaxed selection and variable selection intensities are likely more important constraints to the evolution of plasticity than the costs of plasticity. Some forms of plasticity, such as learning, may be inherently...

  15. Phenotype Development in Adolescents With Tourette Syndrome

    DEFF Research Database (Denmark)

    Groth, Camilla; Debes, Nanette Mol; Skov, Liselotte

    2017-01-01

    Tourette syndrome (TS) is a neurodevelopmental disorder characterized by frequent comorbidities and a wide spectrum of phenotype presentations. This study aimed to describe the development of phenotypes in TS and tic-related impairment in a large longitudinal study of 226 children and adolescents...... followed up after 6 years. The participants were clinically examined to assess tic severity and impairment, obsessive compulsive disorder (OCD), and attention-deficit/hyperactivity disorder (ADHD). The development in phenotypes changed toward less comorbidity with 40% TS-only (no OCD or ADHD) (TS without...... OCD or ADHD) at baseline and 55% at follow-up.Tic-related impairment was expected to improve with an age-related tic decline, but surprisingly the impairment score did not reflect the tic decline. Sex, vocal and motor tics, and OCD and ADHD severity were highly significantly correlated...

  16. Delineating the GRIN1 phenotypic spectrum

    DEFF Research Database (Denmark)

    Lemke, Johannes R; Geider, Kirsten; Helbig, Katherine L

    2016-01-01

    consequences of GRIN1 mutations were investigated in Xenopus laevis oocytes. RESULTS: We identified heterozygous de novo GRIN1 mutations in 14 individuals and reviewed the phenotypes of all 9 previously reported patients. These 23 individuals presented with a distinct phenotype of profound developmental delay......, severe intellectual disability with absent speech, muscular hypotonia, hyperkinetic movement disorder, oculogyric crises, cortical blindness, generalized cerebral atrophy, and epilepsy. Mutations cluster within transmembrane segments and result in loss of channel function of varying severity...... impairment as well as oculomotor and movement disorders being discriminating phenotypic features. Loss of NMDA receptor function appears to be the underlying disease mechanism. The identification of both heterozygous and homozygous mutations blurs the borders of dominant and recessive inheritance of GRIN1...

  17. Semi-supervised Learning for Phenotyping Tasks.

    Science.gov (United States)

    Dligach, Dmitriy; Miller, Timothy; Savova, Guergana K

    2015-01-01

    Supervised learning is the dominant approach to automatic electronic health records-based phenotyping, but it is expensive due to the cost of manual chart review. Semi-supervised learning takes advantage of both scarce labeled and plentiful unlabeled data. In this work, we study a family of semi-supervised learning algorithms based on Expectation Maximization (EM) in the context of several phenotyping tasks. We first experiment with the basic EM algorithm. When the modeling assumptions are violated, basic EM leads to inaccurate parameter estimation. Augmented EM attenuates this shortcoming by introducing a weighting factor that downweights the unlabeled data. Cross-validation does not always lead to the best setting of the weighting factor and other heuristic methods may be preferred. We show that accurate phenotyping models can be trained with only a few hundred labeled (and a large number of unlabeled) examples, potentially providing substantial savings in the amount of the required manual chart review.

  18. Extreme Rainfall In A City

    Science.gov (United States)

    Nkemdirim, Lawrence

    Cities contain many structures and activities that are vulnerable to severe weather. Heavy precipitation cause floods which can damage structures, compromise transportation and water supply systems, and slow down economic and social activities. Rain induced flood patterns in cities must be well understood to enable effective placement of flood control and other regulatory measures. The planning goal is not to eliminate all floods but to reduce their frequency and resulting damage. Possible approaches to such planning include probability based extreme event analysis. Precipitation is normally the most variable hydrologic element over a given area. This variability results from the distribution of clouds and in cloud processes in the atmosphere, the storm path, and the distribution of topographical features on the ground along path. Some studies suggest that point rainfall patterns are also affected by urban industrial effects hence some agreement that cities are wetter than the country surrounding them. However, there are still questions regarding the intra- urban distribution of precipitation. The sealed surfaces, urban structures, and the urban heat anomaly increase convection in cities which may enhance the generation of clouds. Increased dust and gaseous aerosols loads are effective condensation and sublimation nuclei which may also enhance the generation of precipitation. Based on these associations, the greatest amount of convection type rainfall should occur at city center. A study of summer rainfall in Calgary showed that frequencies of trace amounts of rainfall and events under 0.2mm are highest downtown than elsewhere. For amounts greater than than 0.2 mm, downtown sites were not favored. The most compelling evidence for urban-industrial precipitation enhancement came from the Metromex project around St. Loius, Missouri where maximum increases of between 5 to 30 per cent in summer rainfall downwind of the city was linked to urbanization and

  19. Study of Extreme Weather Hazards Using GRACE

    Science.gov (United States)

    Zhang, Y.; Shum, C. K.; Shang, K.; Guo, J.; Schwartz, F. W.; Akyılmaz, O.; Feng, W.; Forootan, E.; LIU, G.; Zhong, M.

    2017-12-01

    Extreme weather events significantly affect humans and economics in the region. Synoptic and timely observations of these abrupt meteoro-hydrological hazards would benefit disaster management and improve storm forecasting. Contemporary processing of the Gravity Recovery and Climate Experiment (GRACE) twin-satellite data at monthly sampling would miss or under-sample abrupt events such as large ice storms with durations much shorter than a month. Here, we employ the energy balance approach processing GRACE Level 1 data, which is flexible to allow sub-monthly solutions at daily sampling covering the genesis and evolution of large winter storms. We studied the 2008 Southeast China snow and ice storm, which lasted from mid-January to mid-February, and affected 21 out of China's 34 provinces with heavy snows, ice and freezing rains, caused extensive damage and transportation disruption, displaced nearly 1.7 million people, and claimed 129 lives. We also investigated the devastating North America blizzard which occurred during late January through mid-February 2010. The massive accumulations of snow and ice in both storms slightly changed the gravity field of the Earth, and were sensitive to the GRACE satellite measurements, manifested as transient terrestrial water storage (TWS) change. We compared our solutions with other available high temporal frequency GRACE solutions. The GRACE observed total storage change for both storms are in good agreement with in situ precipitation measurements, and with GRACE observations clearly show the complex genesis, decline, strengthening and melting phases depicting the detailed evolution of these example large snow storms.

  20. Relationship between endophenotype and phenotype in ADHD

    Directory of Open Access Journals (Sweden)

    Buitelaar Jan K

    2008-01-01

    Full Text Available Abstract Background It has been hypothesized that genetic and environmental factors relate to psychiatric disorders through the effect of intermediating, vulnerability traits called endophenotypes. The study had a threefold aim: to examine the predictive validity of an endophenotypic construct for the ADHD diagnosis, to test whether the magnitude of group differences at the endophenotypic and phenotypic level is comparable, and to investigate whether four factors (gender, age, IQ, rater bias have an effect (moderation or mediation on the relation between endophenotype and phenotype. Methods Ten neurocognitive tasks were administered to 143 children with ADHD, 68 non-affected siblings, and 120 control children (first-borns and 132 children with ADHD, 78 non-affected siblings, and 113 controls (second-borns (5 – 19 years. The task measures have been investigated previously for their endophenotypic viability and were combined to one component which was labeled 'the endophenotypic construct': one measure representative of endophenotypic functioning across several domains of functioning. Results The endophenotypic construct classified children with moderate accuracy (about 50% for each of the three groups. Non-affected children differed as much from controls at the endophenotypic as at the phenotypic level, but affected children displayed a more severe phenotype than endophenotype. Although a potentially moderating effect (age and several mediating effects (gender, age, IQ were found affecting the relation between endophenotypic construct and phenotype, none of the effects studied could account for the finding that affected children had a more severe phenotype than endophenotype. Conclusion Endophenotypic functioning is moderately predictive of the ADHD diagnosis, though findings suggest substantial overlap exists between endophenotypic functioning in the groups of affected children, non-affected siblings, and controls. Results suggest other

  1. Phenotypic Approaches to Drought in Cassava: Review

    Directory of Open Access Journals (Sweden)

    Emmanuel eOkogbenin

    2013-05-01

    Full Text Available Cassava is an important crop in Africa, Asia, Latin America and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12 - 18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance

  2. Public perceptions of climate change and extreme weather events

    Science.gov (United States)

    Bruine de Bruin, W.; Dessai, S.; Morgan, G.; Taylor, A.; Wong-Parodi, G.

    2013-12-01

    Climate experts face a serious communication challenge. Public debate about climate change continues, even though at the same time people seem to complain about extreme weather events becoming increasingly common. As compared to the abstract concept of ';climate change,' (changes in) extreme weather events are indeed easier to perceive, more vivid, and personally relevant. Public perception research in different countries has suggested that people commonly expect that climate change will lead to increases in temperature, and that unseasonably warm weather is likely to be interpreted as evidence of climate change. However, relatively little is known about whether public concerns about climate change may also be driven by changes in other types of extreme weather events, such as exceptional amounts of precipitation or flooding. We therefore examined how perceptions of and personal experiences with changes in these specific weather events are related to public concerns about climate change. In this presentation, we will discuss findings from two large public perception surveys conducted in flood-prone Pittsburgh, Pennsylvania (US) and with a national sample in the UK, where extreme flooding has recently occurred across the country. Participants completed questions about their perceptions of and experiences with specific extreme weather events, and their beliefs about climate change. We then conducted linear regressions to predict individual differences in climate-change beliefs, using perceptions of and experiences with specific extreme weather events as predictors, while controlling for demographic characteristics. The US study found that people (a) perceive flood chances to be increasing over the decades, (b) believe climate change to play a role in increases in future flood chances, and (c) would interpret future increases in flooding as evidence for climate change. The UK study found that (a) UK residents are more likely to perceive increases in ';wet' events such

  3. Satisfaction with upper extremity surgery in individuals with tetraplegia

    DEFF Research Database (Denmark)

    Gregersen, Hanne; Lybæk, Mille; Lauge Johannesen, Inger

    2015-01-01

    OBJECTIVE: To supplement the scant information available regarding the satisfaction of patients with tetraplegia following upper extremity reconstructive surgery for such individuals with spinal cord injury (SCI). STUDY DESIGN: Retrospective study with questionnaire follow-up. SETTING: The Danish...... to strongly disagree regarding satisfaction. Forty patients completed the questionnaire. RESULTS: Median time from first surgery was 13 years (2-36). Sixty-five percent of the sample had a C5-C6 SCI, with 64% experiencing complete injury. Initially, 76% of the sample expressed general satisfaction with life...... Spinal Cord Injury Centers. MATERIAL AND METHODS: In the initial review period, 119 upper extremity surgeries were performed on patients with tetraplegia (n = 49). Seven died and the remaining 42 were invited to complete a follow-up questionnaire with a five-level scale ranging from strongly agree...

  4. A New Family of Consistent and Asymptotically-Normal Estimators for the Extremal Index

    Directory of Open Access Journals (Sweden)

    Jose Olmo

    2015-08-01

    Full Text Available The extremal index (θ is the key parameter for extending extreme value theory results from i.i.d. to stationary sequences. One important property of this parameter is that its inverse determines the degree of clustering in the extremes. This article introduces a novel interpretation of the extremal index as a limiting probability characterized by two Poisson processes and a simple family of estimators derived from this new characterization. Unlike most estimators for θ in the literature, this estimator is consistent, asymptotically normal and very stable across partitions of the sample. Further, we show in an extensive simulation study that this estimator outperforms in finite samples the logs, blocks and runs estimation methods. Finally, we apply this new estimator to test for clustering of extremes in monthly time series of unemployment growth and inflation rates and conclude that runs of large unemployment rates are more prolonged than periods of high inflation.

  5. Extreme heat and runoff extremes in the Swiss Alps

    Directory of Open Access Journals (Sweden)

    M. Zappa

    2007-06-01

    Full Text Available The hydrological response of Swiss river basins to the 2003 European summer heatwave was evaluated by a combined analysis of historical discharge records and specific applications of distributed hydrological modeling. In the summer of 2003, the discharge from headwater streams of the Swiss Central Plateau was only 40%–60% of the long-term average. For alpine basins runoff was about 60%–80% of the average. Glacierized basins showed the opposite behavior. According to the degree of glacierization, the average summer runoff was close or even above average. The hydrological model PREVAH was applied for the period 1982–2005. Even if the model was not calibrated for such extreme meteorological conditions, it was well able to simulate the hydrological responses of three basins. The aridity index φ describes feedbacks between hydrological and meteorological anomalies, and was adopted as an indicator of hydrological drought. The anomalies of φ and temperature in the summer of 2003 exceeded the 1982–2005 mean by more than 2 standard deviations. Catchments without glaciers showed negative correlations between φ and discharge R. In basins with about 15% glacierization, φ and R were not correlated. River basins with higher glacier percentages showed a positive correlation between φ and R. Icemelt was positively correlated with φ and reduced the variability of discharge with larger amounts of meltwater. Runoff generation from the non-glaciated sub-areas was limited by high evapotranspiration and reduced precipitation. The 2003 summer heatwave could be a precursor to similar events in the near future. Hydrological models and further data analysis will allow the identification of the most sensitive regions where heatwaves may become a recurrent natural hazard with large environmental, social and economical impacts.

  6. BELM: Bayesian extreme learning machine.

    Science.gov (United States)

    Soria-Olivas, Emilio; Gómez-Sanchis, Juan; Martín, José D; Vila-Francés, Joan; Martínez, Marcelino; Magdalena, José R; Serrano, Antonio J

    2011-03-01

    The theory of extreme learning machine (ELM) has become very popular on the last few years. ELM is a new approach for learning the parameters of the hidden layers of a multilayer neural network (as the multilayer perceptron or the radial basis function neural network). Its main advantage is the lower computational cost, which is especially relevant when dealing with many patterns defined in a high-dimensional space. This brief proposes a bayesian approach to ELM, which presents some advantages over other approaches: it allows the introduction of a priori knowledge; obtains the confidence intervals (CIs) without the need of applying methods that are computationally intensive, e.g., bootstrap; and presents high generalization capabilities. Bayesian ELM is benchmarked against classical ELM in several artificial and real datasets that are widely used for the evaluation of machine learning algorithms. Achieved results show that the proposed approach produces a competitive accuracy with some additional advantages, namely, automatic production of CIs, reduction of probability of model overfitting, and use of a priori knowledge.

  7. Driving Extreme Efficiency to Market

    Science.gov (United States)

    Garbesi, Karina

    2014-03-01

    The rapid development of extremely energy efficient appliances and equipment is essential to curtail catastrophic climate disruption. This will require the on-going development of products that apply all best-practices and that take advantage of the synergies of hybridization and building integration. Beyond that, it requires the development of new disruptive technologies and concepts. To facilitate these goals, in 2011 the Lawrence Berkeley National Laboratory and the U.S. Department of Energy launched the Max Tech and Beyond Design Competition for Ultra-Low-Energy-Use Appliances and Equipment. Now in its third year, the competition supports faculty-lead student design teams at U.S. universities to develop and test new technology prototypes. This talk describes what the competition and the Max Tech Program are doing to drive such rapid technology progress and to facilitate the entry to the market of successful Max Tech prototypes. The talk also initiates a discussion of physicists' unique role in driving that technology progress faster and farther. Emerging Technologies, Building Technologies Office, U.S. Department of Energy.

  8. Masks for extreme ultraviolet lithography

    International Nuclear Information System (INIS)

    Cardinale, G; Goldsmith, J; Kearney, P A; Larson, C; Moore, C E; Prisbrey, S; Tong, W; Vernon, S P; Weber, F; Yan, P-Y.

    1998-01-01

    In extreme ultraviolet lithography (EUVL), the technology specific requirements on the mask are a direct consequence of the utilization of radiation in the spectral region between 10 and 15 nm. At these wavelengths, all condensed materials are highly absorbing and efficient radiation transport mandates the use of all-reflective optical systems. Reflectivity is achieved with resonant, wavelength-matched multilayer (ML) coatings on all of the optical surfaces - including the mask. The EUV mask has a unique architecture - it consists of a substrate with a highly reflective ML coating (the mask blank) that is subsequently over-coated with a patterned absorber layer (the mask). Particulate contamination on the EUVL mask surface, errors in absorber definition and defects in the ML coating all have the potential to print in the lithographic process. While highly developed technologies exist for repair of the absorber layer, no viable strategy for the repair of ML coating defects has been identified. In this paper the state-of-the-art in ML deposition technology, optical inspection of EUVL mask blank defects and candidate absorber patterning approaches are reviewed

  9. Gene adaptation to extreme environments

    International Nuclear Information System (INIS)

    Marlaire, P.; Rodriguez, V.; Kerner, N.

    2005-01-01

    Full text: This work is oriented to the study of gene adaptation to extreme conditions, such as the hydrothermal system located in Copahue, Neuquen, Argentina. The organisms living there develop under two pressure selection conditions: the high temperature of thermal water and the strong impact of ultraviolet (UV) radiation. Several microorganisms found in this region were isolated and different colonies resistant to UV radiation were selected, a Geobacillus thermoleovorans strain identified through 16S RNA sequence, being the most remarkable. A gene library was prepared out of this strain with UV sensitive bacteria BH200 (uvrA::Tn10). A number of clones were isolated by means of UV selection, the most outstanding being a gene carrier able to codify for the guanosine monophosphate synthetase enzyme (GMPs). The suitability of said enzyme was proved by means of additional assays performed on ght 1 bacteria (guaA26::Tn 10) which lacked the enzyme. A transcript of 1100 pb was detected through Northern Blot. The result was consistent with that obtained for the mapping of the starting transcription site. The cloned GMPs produces an increase in growth speed and a greater biomass in BH200 bacteria. (author)

  10. Infection in the ischemic lower extremity.

    Science.gov (United States)

    Fry, D E; Marek, J M; Langsfeld, M

    1998-06-01

    Infections in the lower extremity of the patient with ischemia can cover a broad spectrum of different diseases. An understanding of the particular pathophysiologic circumstances in the ischemic extremity can be of great value in understanding the natural history of the disease and the potential complications that may occur. Optimizing blood flow to the extremity by using revascularization techniques is important for any patient with an ischemic lower extremity complicated by infection or ulceration. Infections in the ischemic lower extremity require local débridement and systemic antibiotics. For severe infections, such as necrotizing fasciitis or the fetid foot, more extensive local débridement and even amputation may be required. Fundamentals of managing prosthetic graft infection require removing the infected prosthesis, local wound débridement, and systemic antibiotics while attempting to preserve viability of the lower extremity using autogenous graft reconstruction.

  11. Sample-taking apparatus

    Energy Technology Data Exchange (ETDEWEB)

    Tanov, Y I; Ismailov, R A; Orazov, A

    1980-10-07

    The invention refers to the equipment for testing water-bearing levels in loose rocks. Its purpose is to simultaneously remove with the rock sample a separate fluid sample from the assigned interval. The sample-taking apparatus contains a core lifter which can be submerged into the casting string with housing and front endpiece in the form of a rod with a piston which covers the cavity of the core lifter, as well as mechanism for fixing and moving the endpiece within the core lifter cavity. The device differs from the known similar devices because the upper part of the housing of the core lifter is equipped with a filter and mobile casting which covers the filter. In this case the casing is connected to the endpiece rod and the endpiece is installed with the possibility of movement which is limited with fixing in the upper position and in the extreme upper position it divides the core lifter cavity into two parts, filter settling tank and core-receiving cavity.

  12. Climate change in the oceans: evolutionary versus phenotypically plastic responses of marine animals and plants.

    Science.gov (United States)

    Reusch, Thorsten B H

    2014-01-01

    I summarize marine studies on plastic versus adaptive responses to global change. Due to the lack of time series, this review focuses largely on the potential for adaptive evolution in marine animals and plants. The approaches were mainly synchronic comparisons of phenotypically divergent populations, substituting spatial contrasts in temperature or CO2 environments for temporal changes, or in assessments of adaptive genetic diversity within populations for traits important under global change. The available literature is biased towards gastropods, crustaceans, cnidarians and macroalgae. Focal traits were mostly environmental tolerances, which correspond to phenotypic buffering, a plasticity type that maintains a functional phenotype despite external disturbance. Almost all studies address coastal species that are already today exposed to fluctuations in temperature, pH and oxygen levels. Recommendations for future research include (i) initiation and analyses of observational and experimental temporal studies encompassing diverse phenotypic traits (including diapausing cues, dispersal traits, reproductive timing, morphology) (ii) quantification of nongenetic trans-generational effects along with components of additive genetic variance (iii) adaptive changes in microbe-host associations under the holobiont model in response to global change (iv) evolution of plasticity patterns under increasingly fluctuating environments and extreme conditions and (v) joint consideration of demography and evolutionary adaptation in evolutionary rescue approaches.

  13. Presbycusis phenotypes form a heterogeneous continuum when ordered by degree and configuration of hearing loss.

    Science.gov (United States)

    Allen, Paul D; Eddins, David A

    2010-06-01

    Many reports have documented age-by-frequency increases in average auditory thresholds in various human populations. Despite this, the prevalence of different patterns of hearing loss in presbycusis remains uncertain. We examined 'presbycusis phenotypes' in a database of 960 subjects (552 female, 408 male, 18-92 years) that each had 30 measures of peripheral hearing sensitivity: pure tone audiograms for left and right ears from 0.25 to 8 kHz and DPOAE for each ear with F(mean)=1-6.4 kHz. Surprisingly, the hearing phenotypes did not naturally separate into discrete classes of presbycusis. Principal component (PC) analysis revealed that two principal components account for 74% of the variance among the 30 measures of hearing. The two components represent the overall degree (PC1) and configuration of loss (Flat vs. Sloping; PC2) and the phenotypes form a continuum when plotted against them. A heuristic partitioning of this continuum produced classes of presbycusis that vary in their degree of Sloping or Flat hearing loss, suggesting that the previously reported sub-types of presbycusis arise from the categorical segregation of a continuous and heterogeneous distribution. Further, most phenotypes lie intermediate to the extremes of either Flat or Sloping loss, indicating that if audiometric configuration does predict presbycusis etiology, then a mixed origin is the most prevalent. Copyright 2010 Elsevier B.V. All rights reserved.

  14. Phenotypic and genotypic variability of disc flower corolla length and nectar content in sunflower

    Directory of Open Access Journals (Sweden)

    Joksimović Jovan

    2003-01-01

    Full Text Available The nectar content and disc flower corolla length are the two most important parameters of attractiveness to pollinators in sunflower. The phenotypic and genotypic variability of these two traits was studied in four commercially important hybrids and their parental components in a trial with three fertilizer doses over two years. The results showed that, looking at individual genotypes, the variability of disc flower corolla length was affected the most by year (85.38-97.46%. As the study years were extremely different, the phenotypic variance of the hybrids and parental components was calculated for each year separately. In such conditions, looking at all of the crossing combinations, the largest contribution to phenotypic variance of the corolla length was that of genotype: 57.27-61.11% (NS-H-45 64.51-84.84% (Velja; 96.74-97.20% (NS-H-702 and 13.92-73.17% (NS-H-111. A similar situation was observed for the phenotypic variability of nectar content, where genotype also had the largest influence, namely 39.77-48.25% in NS-H-45; 39.06-42.51% in Velja; 31.97-72.36% in NS-H-702; and 62.13-94.96% in NS-H-111.

  15. Developmental phenotypic plasticity helps bridge stochastic weather events associated with climate change.

    Science.gov (United States)

    Burggren, Warren

    2018-05-10

    The slow, inexorable rise in annual average global temperatures and acidification of the oceans are often advanced as consequences of global change. However, many environmental changes, especially those involving weather (as opposed to climate), are often stochastic, variable and extreme, particularly in temperate terrestrial or freshwater habitats. Moreover, few studies of animal and plant phenotypic plasticity employ realistic (i.e. short-term, stochastic) environmental change in their protocols. Here, I posit that the frequently abrupt environmental changes (days, weeks, months) accompanying much longer-term general climate change (e.g. global warming over decades or centuries) require consideration of the true nature of environmental change (as opposed to statistical means) coupled with an expansion of focus to consider developmental phenotypic plasticity. Such plasticity can be in multiple forms - obligatory/facultative, beneficial/deleterious - depending upon the degree and rate of environmental variability at specific points in organismal development. Essentially, adult phenotypic plasticity, as important as it is, will be irrelevant if developing offspring lack sufficient plasticity to create modified phenotypes necessary for survival. © 2018. Published by The Company of Biologists Ltd.

  16. Utilizing intraspecific variation in phenotypic plasticity to bolster agricultural and forest productivity under climate change.

    Science.gov (United States)

    Aspinwall, Michael J; Loik, Michael E; Resco de Dios, Victor; Tjoelker, Mark G; Payton, Paxton R; Tissue, David T

    2015-09-01

    Climate change threatens the ability of agriculture and forestry to meet growing global demands for food, fibre and wood products. Information gathered from genotype-by-environment interactions (G × E), which demonstrate intraspecific variation in phenotypic plasticity (the ability of a genotype to alter its phenotype in response to environmental change), may prove important for bolstering agricultural and forest productivity under climate change. Nonetheless, very few studies have explicitly quantified genotype plasticity-productivity relationships in agriculture or forestry. Here, we conceptualize the importance of intraspecific variation in agricultural and forest species plasticity, and discuss the physiological and genetic factors contributing to intraspecific variation in phenotypic plasticity. Our discussion highlights the need for an integrated understanding of the mechanisms of G × E, more extensive assessments of genotypic responses to climate change under field conditions, and explicit testing of genotype plasticity-productivity relationships. Ultimately, further investigation of intraspecific variation in phenotypic plasticity in agriculture and forestry may prove important for identifying genotypes capable of increasing or sustaining productivity under more extreme climatic conditions. © 2014 John Wiley & Sons Ltd.

  17. On the Extreme Wave Height Analysis

    DEFF Research Database (Denmark)

    Burcharth, H. F.; Liu, Zhou

    1994-01-01

    The determination of the design wave height is usually based on the statistical analysis of long-term extreme wave height measurements. After an introduction to the procedure of the extreme wave height analysis, the paper presents new development concerning various aspects of the extreme wave...... height analysis. Finally, the paper gives a practical example based on a data set of the hindcasted wave heights for a deep water location in the Mediterranean Sea....

  18. MicroRNAs in Muscle: Characterizing the Powerlifter Phenotype

    Directory of Open Access Journals (Sweden)

    Randall F. D'Souza

    2017-06-01

    Full Text Available Powerlifters are the epitome of muscular adaptation and are able to generate extreme forces. The molecular mechanisms underpinning the significant capacity for force generation and hypertrophy are not fully elucidated. MicroRNAs (miRs are short non-coding RNA sequences that control gene expression via promotion of transcript breakdown and/or translational inhibition. Differences in basal miR expression may partially account for phenotypic differences in muscle mass and function between powerlifters and untrained age-matched controls. Muscle biopsies were obtained from m. vastus lateralis of 15 national level powerlifters (25.1 ± 5.8 years and 13 untrained controls (24.1 ± 2.0 years. The powerlifters were stronger than the controls (isokinetic knee extension at 60°/s: 307.8 ± 51.6 Nm vs. 211.9 ± 41.9 Nm, respectively P < 0.001, and also had larger muscle fibers (type I CSA 9,122 ± 1,238 vs. 4,511 ± 798 μm2p < 0.001 and type II CSA 11,100 ± 1,656 vs. 5,468 ± 1,477 μm2p < 0.001. Of the 17 miRs species analyzed, 12 were differently expressed (p < 0.05 between groups with 7 being more abundant in powerlifters and five having lower expression. Established transcriptionally regulated miR downstream gene targets involved in muscle mass regulation, including myostatin and MyoD, were also differentially expressed between groups. Correlation analysis demonstrates the abundance of eight miRs was correlated to phenotype including peak strength, fiber size, satellite cell abundance, and fiber type regardless of grouping. The unique miR expression profiles between groups allow for categorization of individuals as either powerlifter or healthy controls based on a five miR signature (miR-126, -23b, -16, -23a, -15a with considerable accuracy (100%. Thus, this unique miR expression may be important to the characterization of the powerlifter phenotype.

  19. Extreme Events in Nature and Society

    CERN Document Server

    Albeverio, Sergio; Kantz, Holger

    2006-01-01

    Significant, and usually unwelcome, surprises, such as floods, financial crisis, epileptic seizures, or material rupture, are the topics of Extreme Events in Nature and Society. The book, authored by foremost experts in these fields, reveals unifying and distinguishing features of extreme events, including problems of understanding and modelling their origin, spatial and temporal extension, and potential impact. The chapters converge towards the difficult problem of anticipation: forecasting the event and proposing measures to moderate or prevent it. Extreme Events in Nature and Society will interest not only specialists, but also the general reader eager to learn how the multifaceted field of extreme events can be viewed as a coherent whole.

  20. Controlling extreme events on complex networks

    Science.gov (United States)

    Chen, Yu-Zhong; Huang, Zi-Gang; Lai, Ying-Cheng

    2014-08-01

    Extreme events, a type of collective behavior in complex networked dynamical systems, often can have catastrophic consequences. To develop effective strategies to control extreme events is of fundamental importance and practical interest. Utilizing transportation dynamics on complex networks as a prototypical setting, we find that making the network ``mobile'' can effectively suppress extreme events. A striking, resonance-like phenomenon is uncovered, where an optimal degree of mobility exists for which the probability of extreme events is minimized. We derive an analytic theory to understand the mechanism of control at a detailed and quantitative level, and validate the theory numerically. Implications of our finding to current areas such as cybersecurity are discussed.

  1. Phenotypic plasticity and longevity in plants and animals: cause and effect?

    Science.gov (United States)

    Borges, Renee M

    2009-10-01

    Immobile plants and immobile modular animals outlive unitary animals. This paper discusses competing but not necessarily mutually exclusive theories to explain this extreme longevity, especially from the perspective of phenotypic plasticity. Stem cell immortality, vascular autonomy, and epicormic branching are some important features of the phenotypic plasticity of plants that contribute to their longevity. Monocarpy versus polycarpy can also influence the kind of senescent processes experienced by plants. How density-dependent phenomena affecting the establishment of juveniles in these immobile organisms can influence the evolution of senescence, and consequently longevity, is reviewed and discussed. Whether climate change scenarios will favour long-lived or short-lived organisms, with their attendant levels of plasticity, is also presented.

  2. A Metastatistical Approach to Satellite Estimates of Extreme Rainfall Events

    Science.gov (United States)

    Zorzetto, E.; Marani, M.

    2017-12-01

    The estimation of the average recurrence interval of intense rainfall events is a central issue for both hydrologic modeling and engineering design. These estimates require the inference of the properties of the right tail of the statistical distribution of precipitation, a task often performed using the Generalized Extreme Value (GEV) distribution, estimated either from a samples of annual maxima (AM) or with a peaks over threshold (POT) approach. However, these approaches require long and homogeneous rainfall records, which often are not available, especially in the case of remote-sensed rainfall datasets. We use here, and tailor it to remotely-sensed rainfall estimates, an alternative approach, based on the metastatistical extreme value distribution (MEVD), which produces estimates of rainfall extreme values based on the probability distribution function (pdf) of all measured `ordinary' rainfall event. This methodology also accounts for the interannual variations observed in the pdf of daily rainfall by integrating over the sample space of its random parameters. We illustrate the application of this framework to the TRMM Multi-satellite Precipitation Analysis rainfall dataset, where MEVD optimally exploits the relatively short datasets of satellite-sensed rainfall, while taking full advantage of its high spatial resolution and quasi-global coverage. Accuracy of TRMM precipitation estimates and scale issues are here investigated for a case study located in the Little Washita watershed, Oklahoma, using a dense network of rain gauges for independent ground validation. The methodology contributes to our understanding of the risk of extreme rainfall events, as it allows i) an optimal use of the TRMM datasets in estimating the tail of the probability distribution of daily rainfall, and ii) a global mapping of daily rainfall extremes and distributional tail properties, bridging the existing gaps in rain gauges networks.

  3. Extracellular vesicle-mediated phenotype switching in malignant and non-malignant colon cells

    International Nuclear Information System (INIS)

    Mulvey, Hillary E.; Chang, Audrey; Adler, Jason; Del Tatto, Michael; Perez, Kimberly; Quesenberry, Peter J.; Chatterjee, Devasis

    2015-01-01

    Extracellular vesicles (EVs) are secreted from many cells, carrying cargoes including proteins and nucleic acids. Research has shown that EVs play a role in a variety of biological processes including immunity, bone formation and recently they have been implicated in promotion of a metastatic phenotype. EVs were isolated from HCT116 colon cancer cells, 1459 non-malignant colon fibroblast cells, and tumor and normal colon tissue from a patient sample. Co-cultures were performed with 1459 cells and malignant vesicles, as well as HCT116 cells and non-malignant vesicles. Malignant phenotype was measured using soft agar colony formation assay. Co-cultures were also analyzed for protein levels using mass spectrometry. The importance of 14-3-3 zeta/delta in transfer of malignant phenotype was explored using siRNA. Additionally, luciferase reporter assay was used to measure the transcriptional activity of NF-κB. This study demonstrates the ability of EVs derived from malignant colon cancer cell line and malignant patient tissue to induce the malignant phenotype in non-malignant colon cells. Similarly, EVs derived from non-malignant colon cell lines and normal patient tissue reversed the malignant phenotype of HCT116 cells. Cells expressing an EV-induced malignant phenotype showed increased transcriptional activity of NF-κB which was inhibited by the NF--κB inhibitor, BAY117082. We also demonstrate that knock down of 14-3-3 zeta/delta reduced anchorage-independent growth of HCT116 cells and 1459 cells co-cultured with HCT derived EVs. Evidence of EV-mediated induction of malignant phenotype, and reversal of malignant phenotype, provides rational basis for further study of the role of EVs in tumorigenesis. Identification of 14-3-3 zeta/delta as up-regulated in malignancy suggests its potential as a putative drug target for the treatment of colorectal cancer

  4. Phenotypic characterisation and molecular polymorphism of ...

    African Journals Online (AJOL)

    The study of the phenotypic characterisation and molecular polymorphism of local chicken populations was carried out in Benin on 326 chickens of the Forest ecological area and 316 of the Savannah ecological area, all were 7 months old at least. The collection of blood for the molecular typing was achieved on 121 ...

  5. Evidence for a Broad Autism Phenotype

    NARCIS (Netherlands)

    K. de Groot (Kristel); J.W. van Strien (Jan)

    2017-01-01

    textabstractThe broad autism phenotype implies the existence of a continuum ranging from individuals displaying almost no autistic traits to severely impaired diagnosed individuals. Recent studies have linked this variation in autistic traits to several domains of functioning. However, studies

  6. Phenotype Presentation of Hypophosphatemic Rickets in Adults

    DEFF Research Database (Denmark)

    Beck-Nielsen, Signe S; Brusgaard, Klaus; Rasmussen, Lars M

    2010-01-01

    Hypophosphatemic rickets (HR) is a group of rare disorders caused by excessive renal phosphate wasting. The purpose of this cross-sectional study of 38 HR patients was to characterize the phenotype of adult HR patients. Moreover, skeletal and endodontic severity scores were defined to assess poss...

  7. Phenotypic and molecular characterization of Salmonella serotypes ...

    African Journals Online (AJOL)

    The presence of Salmonella and human pathogens in unpasteurized milk remains a public health hazard. The study reported the phenotypic and molecular characterization of Salmonella serotypes in cow raw milk, cheese and traditional yoghurt marketed for man's consumption in Nigeria. Isolation of Salmonella was done ...

  8. (RR) soybean cultivars estimated by phenotypic characteristics

    African Journals Online (AJOL)

    SAM

    2014-06-25

    Jun 25, 2014 ... phenotypic characteristics and microsatellite molecular markers (SSR). ... discriminatory analysis, principal components, coordinate and cluster analysis .... were employed with 10.000 simulations to attribute significance values to ...... association analysis of protein and oil content in food-grade soybeans ...

  9. Colorectal Cancer "Methylator Phenotype": Fact or Artifact?

    Directory of Open Access Journals (Sweden)

    Charles Anacleto

    2005-04-01

    Full Text Available It has been proposed that human colorectal tumors can be classified into two groups: one in which methylation is rare, and another with methylation of several loci associated with a "CpG island methylated phenotype (CIMP," characterized by preferential proximal location in the colon, but otherwise poorly defined. There is considerable overlap between this putative methylator phenotype and the well-known mutator phenotype associated with microsatellite instability (MSI. We have examined hypermethylation of the promoter region of five genes (DAPK, MGMT, hMLH1, p16INK4a, and p14ARF in 106 primary colorectal cancers. A graph depicting the frequency of methylated loci in the series of tumors showed a continuous, monotonically decreasing distribution quite different from the previously claimed discontinuity. We observed a significant association between the presence of three or more methylated loci and the proximal location of the tumors. However, if we remove from analysis the tumors with hMLH1 methylation or those with MSI, the significance vanishes, suggesting that the association between multiple methylations and proximal location was indirect due to the correlation with MSI. Thus, our data do not support the independent existence of the so-called methylator phenotype and suggest that it rather may represent a statistical artifact caused by confounding of associations.

  10. Magnetotactic Bacteria from Extreme Environments

    Directory of Open Access Journals (Sweden)

    Christopher T. Lefèvre

    2013-03-01

    Full Text Available Magnetotactic bacteria (MTB represent a diverse collection of motile prokaryotes that biomineralize intracellular, membrane-bounded, tens-of-nanometer-sized crystals of a magnetic mineral called magnetosomes. Magnetosome minerals consist of either magnetite (Fe3O4 or greigite (Fe3S4 and cause cells to align along the Earth’s geomagnetic field lines as they swim, a trait called magnetotaxis. MTB are known to mainly inhabit the oxic–anoxic interface (OAI in water columns or sediments of aquatic habitats and it is currently thought that magnetosomes function as a means of making chemotaxis more efficient in locating and maintaining an optimal position for growth and survival at the OAI. Known cultured and uncultured MTB are phylogenetically associated with the Alpha-, Gamma- and Deltaproteobacteria classes of the phylum Proteobacteria, the Nitrospirae phylum and the candidate division OP3, part of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC bacterial superphylum. MTB are generally thought to be ubiquitous in aquatic environments as they are cosmopolitan in distribution and have been found in every continent although for years MTB were thought to be restricted to habitats with pH values near neutral and at ambient temperature. Recently, however, moderate thermophilic and alkaliphilic MTB have been described including: an uncultured, moderately thermophilic magnetotactic bacterium present in hot springs in northern Nevada with a probable upper growth limit of about 63 °C; and several strains of obligately alkaliphilic MTB isolated in pure culture from different aquatic habitats in California, including the hypersaline, extremely alkaline Mono Lake, with an optimal growth pH of >9.0.

  11. Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community

    Directory of Open Access Journals (Sweden)

    Yook Karen

    2011-01-01

    Full Text Available Abstract Background Caenorhabditis elegans gene-based phenotype information dates back to the 1970's, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in order to understand nervous system function. Since then C. elegans has become an important genetic model system for the study of basic biological and biomedical principles, largely through the use of phenotype analysis. Because of the growth of C. elegans as a genetically tractable model organism and the development of large-scale analyses, there has been a significant increase of phenotype data that needs to be managed and made accessible to the research community. To do so, a standardized vocabulary is necessary to integrate phenotype data from diverse sources, permit integration with other data types and render the data in a computable form. Results We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO. The WPO is currently comprised of 1,880 phenotype terms, 74% of which have been used in the annotation of phenotypes associated with greater than 18,000 C. elegans genes. The scope of the WPO is not exclusively limited to C. elegans biology, rather it is devised to also incorporate phenotypes observed in related nematode species. We have enriched the value of the WPO by integrating it with other ontologies, thereby increasing the accessibility of worm phenotypes to non-nematode biologists. We are actively developing the WPO to continue to fulfill the evolving needs of the scientific community and hope to engage researchers in this crucial endeavor. Conclusions We provide a phenotype ontology (WPO that will help to facilitate data retrieval, and cross-species comparisons within the nematode community. In the larger scientific community, the WPO will permit data integration, and

  12. Hand dominance in upper extremity musculoskeletal disorders.

    Science.gov (United States)

    Shiri, Rahman; Varonen, Helena; Heliövaara, Markku; Viikari-Juntura, Eira

    2007-05-01

    To investigate the role of hand dominance in common upper extremity musculoskeletal disorders (UEMSD) in a population study. The target population consisted of a representative sample of people aged 30 years or older residing in Finland during 2000-2001. Of the 7977 eligible subjects, 6254 (78.4%) were included in the study. The prevalence of UEMSD was as follows: rotator cuff tendinitis 3.8%, bicipital tendinitis 0.5%, lateral epicondylitis 1.1%, medial epicondylitis 0.3%, carpal tunnel syndrome (CTS) 3.8%, and surgery due to CTS 1.3%. CTS was 2.5 times as prevalent in women as men, whereas the other UEMSD were as common in both sexes. Rotator cuff and bicipital tendinitis and medial epicondylitis were more prevalent in the dominant arm only in women, whereas lateral epicondylitis was more prevalent in the dominant elbow in both sexes. The higher prevalence of rotator cuff and bicipital tendinitis in the dominant side persisted beyond working age. The prevalence of CTS did not differ by hand dominance. Dominant hand had been operated more frequently for CTS in women. Our findings show that UEMSD are more prevalent in the dominant than nondominant arm mainly in women. For shoulder tendinitis, the difference persists throughout adult age. Physical load factors may have long-lasting effects on the shoulder and they may play a greater role in women than men.

  13. Assessment of metabolic phenotypic variability in children’s urine using 1H NMR spectroscopy

    Science.gov (United States)

    Maitre, Léa; Lau, Chung-Ho E.; Vizcaino, Esther; Robinson, Oliver; Casas, Maribel; Siskos, Alexandros P.; Want, Elizabeth J.; Athersuch, Toby; Slama, Remy; Vrijheid, Martine; Keun, Hector C.; Coen, Muireann

    2017-04-01

    The application of metabolic phenotyping in clinical and epidemiological studies is limited by a poor understanding of inter-individual, intra-individual and temporal variability in metabolic phenotypes. Using 1H NMR spectroscopy we characterised short-term variability in urinary metabolites measured from 20 children aged 8-9 years old. Daily spot morning, night-time and pooled (50:50 morning and night-time) urine samples across six days (18 samples per child) were analysed, and 44 metabolites quantified. Intraclass correlation coefficients (ICC) and mixed effect models were applied to assess the reproducibility and biological variance of metabolic phenotypes. Excellent analytical reproducibility and precision was demonstrated for the 1H NMR spectroscopic platform (median CV 7.2%). Pooled samples captured the best inter-individual variability with an ICC of 0.40 (median). Trimethylamine, N-acetyl neuraminic acid, 3-hydroxyisobutyrate, 3-hydroxybutyrate/3-aminoisobutyrate, tyrosine, valine and 3-hydroxyisovalerate exhibited the highest stability with over 50% of variance specific to the child. The pooled sample was shown to capture the most inter-individual variance in the metabolic phenotype, which is of importance for molecular epidemiology study design. A substantial proportion of the variation in the urinary metabolome of children is specific to the individual, underlining the potential of such data to inform clinical and exposome studies conducted early in life.

  14. LP (a) levels and apo (a) phenotypes in urban black South African ...

    African Journals Online (AJOL)

    300 U/I), intermediate (300 - 700 UII) and high (> 700 UII) plasma Lp (a) ... Tygerberg Hospital, Tygerberg, W Cape ... up to 200-fold difference in Lp (a) concentrations.' In addition, ethnic .... An interesting observation was the large number of phenotypes, Le. ... sample of black Americans with a high-resolution SOS- agarose ...

  15. The Broader Autism Phenotype and Friendships in Non-Clinical Dyads

    Science.gov (United States)

    Wainer, Allison L.; Block, Nicole; Donnellan, M. Brent; Ingersoll, Brooke

    2013-01-01

    The broader autism phenotype (BAP) is a set of subclinical traits qualitatively similar to those observed in autism spectrum disorders. The current study sought to elucidate the association between self- and informant-reports of the BAP and friendships, in a non-clinical sample of college student dyads. Self-informant agreement of the BAP and…

  16. Extreme Growth Failure is a Common Presentation of Ligase IV Deficiency

    Science.gov (United States)

    Murray, Jennie E; Bicknell, Louise S; Yigit, Gökhan; Duker, Angela L; van Kogelenberg, Margriet; Haghayegh, Sara; Wieczorek, Dagmar; Kayserili, Hülya; Albert, Michael H; Wise, Carol A; Brandon, January; Kleefstra, Tjitske; Warris, Adilia; van der Flier, Michiel; Bamforth, J Steven; Doonanco, Kurston; Adès, Lesley; Ma, Alan; Field, Michael; Johnson, Diana; Shackley, Fiona; Firth, Helen; Woods, C Geoffrey; Nürnberg, Peter; Gatti, Richard A; Hurles, Matthew; Bober, Michael B; Wollnik, Bernd; Jackson, Andrew P

    2014-01-01

    Ligase IV syndrome is a rare differential diagnosis for Nijmegen breakage syndrome owing to a shared predisposition to lympho-reticular malignancies, significant microcephaly, and radiation hypersensitivity. Only 16 cases with mutations in LIG4 have been described to date with phenotypes varying from malignancy in developmentally normal individuals, to severe combined immunodeficiency and early mortality. Here, we report the identification of biallelic truncating LIG4 mutations in 11 patients with microcephalic primordial dwarfism presenting with restricted prenatal growth and extreme postnatal global growth failure (average OFC −10.1 s.d., height −5.1 s.d.). Subsequently, most patients developed thrombocytopenia and leucopenia later in childhood and many were found to have previously unrecognized immunodeficiency following molecular diagnosis. None have yet developed malignancy, though all patients tested had cellular radiosensitivity. A genotype–phenotype correlation was also noted with position of truncating mutations corresponding to disease severity. This work extends the phenotypic spectrum associated with LIG4 mutations, establishing that extreme growth retardation with microcephaly is a common presentation of bilallelic truncating mutations. Such growth failure is therefore sufficient to consider a diagnosis of LIG4 deficiency and early recognition of such cases is important as bone marrow failure, immunodeficiency, and sometimes malignancy are long term sequelae of this disorder. PMID:24123394

  17. Genetic and phenotypic diversity of Rhizobium isolates from Southern Ecuador

    Directory of Open Access Journals (Sweden)

    Roldán Torres-Gutiérrez

    Full Text Available ABSTRACT Rhizobium-legume symbioses play relevant roles in agriculture but have not been well studied in Ecuador. The aim of this study was to characterize the genetic and phenotypic diversity of Rhizobium isolates associated with Phaseolus vulgaris from southern Ecuador. Morpho-cultural characterization, biochemical tests and physiological analyses were conducted to authenticate and determine the diversity of bacteria Rhizobium-like isolates. The genetic diversity of the isolates was determined by molecular techniques, which consisted of bacteria DNA extraction and amplification and sequencing of the 16S rRNA gene. The nodulation parameters and nitrogen fixation for P. vulgaris under greenhouse conditions were also assessed to determine the phenotypic diversity among isolates. Furthermore, bacteria indole-acetic-acid production was evaluated by the colorimetric method. Morpho-cultural and biochemical characteristic assessments demonstrated that Rhizobium-like bacteria was associated with the P. vulgaris nodules. The diversity among the isolates, as determined by physiological analyses, revealed the potential of several isolates to grow at different pH values, salinity conditions and temperatures. Partial sequencing of the 16S rRNA gene identified the Rhizobium genus in every sampling site. From a total of 20 aligned sequences, nine species of Rhizobium were identified. Nodule formation and biomass, as well as nitrogen fixation, showed an increase in plant phenotypic parameters, which could be influenced by IAA production, especially for the strains R. mesoamericanum NAM1 and R. leguminosarum bv. viciae COL6. These results demonstrated the efficiency of native symbiotic diazotrophic strains inoculants for legume production. This work can serve as the basis for additional studies of native Rhizobium strains and to help spread the use of biofertilizers in Ecuadorian fields.

  18. Local connectome phenotypes predict social, health, and cognitive factors

    Directory of Open Access Journals (Sweden)

    Michael A. Powell

    2018-03-01

    Full Text Available The unique architecture of the human connectome is defined initially by genetics and subsequently sculpted over time with experience. Thus, similarities in predisposition and experience that lead to similarities in social, biological, and cognitive attributes should also be reflected in the local architecture of white matter fascicles. Here we employ a method known as local connectome fingerprinting that uses diffusion MRI to measure the fiber-wise characteristics of macroscopic white matter pathways throughout the brain. This fingerprinting approach was applied to a large sample (N = 841 of subjects from the Human Connectome Project, revealing a reliable degree of between-subject correlation in the local connectome fingerprints, with a relatively complex, low-dimensional substructure. Using a cross-validated, high-dimensional regression analysis approach, we derived local connectome phenotype (LCP maps that could reliably predict a subset of subject attributes measured, including demographic, health, and cognitive measures. These LCP maps were highly specific to the attribute being predicted but also sensitive to correlations between attributes. Collectively, these results indicate that the local architecture of white matter fascicles reflects a meaningful portion of the variability shared between subjects along several dimensions. The local connectome is the pattern of fiber systems (i.e., number of fibers, orientation, and size within a voxel, and it reflects the proximal characteristics of white matter fascicles distributed throughout the brain. Here we show how variability in the local connectome is correlated in a principled way across individuals. This intersubject correlation is reliable enough that unique phenotype maps can be learned to predict between-subject variability in a range of social, health, and cognitive attributes. This work shows, for the first time, how the local connectome has both the sensitivity and the specificity to

  19. Phenotyping of lumbosacral stenosis in Labrador retrievers using computed tomography.

    Science.gov (United States)

    Mukherjee, Meenakshi; Jones, Jeryl C; Holásková, Ida; Raylman, Raymond; Meade, Jean

    2017-09-01

    Deep phenotyping tools for characterizing preclinical morphological conditions are important for supporting genetic research studies. Objectives of this retrospective, cross-sectional, methods comparison study were to describe and compare qualitative and quantitative deep phenotypic characteristics of lumbosacral stenosis in Labrador retrievers using computed tomography (CT). Lumbosacral CT scans and medical records were retrieved from data archives at three veterinary hospitals. Using previously published qualitative CT diagnostic criteria, a board-certified veterinary radiologist assigned dogs as either lumbosacral stenosis positive or lumbosacral stenosis negative at six vertebral locations. A second observer independently measured vertebral canal area, vertebral fat area, and vertebral body area; and calculated ratios of vertebral canal area/vertebral body area and vertebral fat area/vertebral body area (fat area ratio) at all six locations. Twenty-five dogs were sampled (lumbosacral stenosis negative, 11 dogs; lumbosacral stenosis positive, 14 dogs). Of the six locations, cranial L6 was the most affected by lumbosacral stenosis (33%). Five of six dogs (83%) with clinical signs of lumbosacral pain were lumbosacral stenosis positive at two or more levels. All four quantitative variables were significantly smaller at the cranial aspects of the L6 and L7 vertebral foramina than at the caudal aspects (P stenosis positive status at all six locations with cranial L6 having the greatest predictive value (R 2 = 0.43) and range of predictive probability (25-90%). Findings from the current study supported the use of CT as a deep phenotyping tool for future research studies of lumbosacral stenosis in Labrador retrievers. © 2017 American College of Veterinary Radiology.

  20. Thermodynamics of extremal rotating thin shells in an extremal BTZ spacetime and the extremal black hole entropy

    Science.gov (United States)

    Lemos, José P. S.; Minamitsuji, Masato; Zaslavskii, Oleg B.

    2017-02-01

    In a (2 +1 )-dimensional spacetime with a negative cosmological constant, the thermodynamics and the entropy of an extremal rotating thin shell, i.e., an extremal rotating ring, are investigated. The outer and inner regions with respect to the shell are taken to be the Bañados-Teitelbom-Zanelli (BTZ) spacetime and the vacuum ground state anti-de Sitter spacetime, respectively. By applying the first law of thermodynamics to the extremal thin shell, one shows that the entropy of the shell is an arbitrary well-behaved function of the gravitational area A+ alone, S =S (A+). When the thin shell approaches its own gravitational radius r+ and turns into an extremal rotating BTZ black hole, it is found that the entropy of the spacetime remains such a function of A+, both when the local temperature of the shell at the gravitational radius is zero and nonzero. It is thus vindicated by this analysis that extremal black holes, here extremal BTZ black holes, have different properties from the corresponding nonextremal black holes, which have a definite entropy, the Bekenstein-Hawking entropy S (A+)=A/+4G , where G is the gravitational constant. It is argued that for extremal black holes, in particular for extremal BTZ black holes, one should set 0 ≤S (A+)≤A/+4G;i.e., the extremal black hole entropy has values in between zero and the maximum Bekenstein-Hawking entropy A/+4 G . Thus, rather than having just two entropies for extremal black holes, as previous results have debated, namely, 0 and A/+4 G , it is shown here that extremal black holes, in particular extremal BTZ black holes, may have a continuous range of entropies, limited by precisely those two entropies. Surely, the entropy that a particular extremal black hole picks must depend on past processes, notably on how it was formed. A remarkable relation between the third law of thermodynamics and the impossibility for a massive body to reach the velocity of light is also found. In addition, in the procedure, it

  1. Area spectra of near extremal black holes

    International Nuclear Information System (INIS)

    Chen, Deyou; Yang, Haitang; Zu, Xiaotao

    2010-01-01

    Motivated by Maggiore's new interpretation of quasinormal modes, we investigate area spectra of a near extremal Schwarzschild-de Sitter black hole and a higher-dimensional near extremal Reissner-Nordstrom-de Sitter black hole. The result shows that the area spectra are equally spaced and irrelevant to the parameters of the black holes. (orig.)

  2. Meaning and Forms of Political Extremism

    Directory of Open Access Journals (Sweden)

    Uwe Backes

    2007-12-01

    Full Text Available The article seeks to contribute to the conceptualisation of political extremism and to lay a foundation for further theoretical studies which are explanatory in nature. A sketch of the history of the concepts follows a discussion of structural characteristics and then a typological examination of forms of extremism, particularly those of the 20th and 21st century.

  3. Extremely strict ideals in Banach spaces

    Indian Academy of Sciences (India)

    Abstract. Motivated by the notion of an ideal introduced by Godefroy et al. (Stu- dia Math. 104 (1993) 13–59), in this article, we introduce and study the notion of an extremely strict ideal. For a Poulsen simplex K, we show that the space of affine contin- uous functions on K is an extremely strict ideal in the space of continuous ...

  4. SIZE AND SHAPE FACTOR EXTREMES OF SPHEROIDS

    Directory of Open Access Journals (Sweden)

    Daniel Hlubinka

    2011-05-01

    Full Text Available In the paper we consider random prolate (oblate spheroids and their random profiles. The limiting distribution of the extremal characteristics of the spheroids is related to the limiting distribution of the corresponding extremal characteristics of the profiles. The difference between the analysis of the prolate and oblate spheroids is discussed. We propose the possible application of the theoretical results.

  5. Complex Plasma Research Under Extreme Conditions

    International Nuclear Information System (INIS)

    Ishihara, Osamu

    2008-01-01

    Complex plasma research under extreme conditions is described. The extreme conditions include low-dimensionality for self-organized structures of dust particles, dust magnetization in high magnetic field, criticality in phase transition, and cryogenic environment for Coulomb crystals and dust dynamics.

  6. A Fourier analysis of extremal events

    DEFF Research Database (Denmark)

    Zhao, Yuwei

    is the extremal periodogram. The extremal periodogram shares numerous asymptotic properties with the periodogram of a linear process in classical time series analysis: the asymptotic distribution of the periodogram ordinates at the Fourier frequencies have a similar form and smoothed versions of the periodogram...

  7. Roentgenological findings in muscular alterations of extremities

    International Nuclear Information System (INIS)

    Palvoelgyi, R.

    1978-01-01

    A survey of roentgenological findings in muscular alterations of extremities based on the author's experiences and on the literature is presented. Following a description of the normal roentgen anatomy, the alterations in different diseases of interstitial lipomatosis are demonstrated. By roentgenological examinations differt muscular lesions of the extremities can be differentiated and the clinical follow-up verified. (orig.) [de

  8. Extremal vectors and rectifiability | Enflo | Quaestiones Mathematicae

    African Journals Online (AJOL)

    Extremal vectors and rectifiability. ... The concept of extremal vectors of a linear operator with a dense range but not onto on a Hilbert space was introduced by P. Enflo in 1996 as a new approach to study invariant subspaces ... We show that in general curves that map numbers to backward minimal vectors are not rectifiable.

  9. Phenotypic equilibrium as probabilistic convergence in multi-phenotype cell population dynamics.

    Directory of Open Access Journals (Sweden)

    Da-Quan Jiang

    Full Text Available We consider the cell population dynamics with n different phenotypes. Both the Markovian branching process model (stochastic model and the ordinary differential equation (ODE system model (deterministic model are presented, and exploited to investigate the dynamics of the phenotypic proportions. We will prove that in both models, these proportions will tend to constants regardless of initial population states ("phenotypic equilibrium" under weak conditions, which explains the experimental phenomenon in Gupta et al.'s paper. We also prove that Gupta et al.'s explanation is the ODE model under a special assumption. As an application, we will give sufficient and necessary conditions under which the proportion of one phenotype tends to 0 (die out or 1 (dominate. We also extend our results to non-Markovian cases.

  10. Heavy fermions and extreme conditions

    International Nuclear Information System (INIS)

    Cheikine, Ilia

    2000-01-01

    Three heavy electron systems, CeCu 2 Si 2 , CePd 2 Si 2 and UGe 2 , were investigated by transport, quantum oscillations (CePd 2 Si 2 ) and neutron diffraction (UGe 2 ) measurements. The experiments were performed under extreme conditions of very low temperature, high magnetic field and hydrostatic pressure. In the case of CeCu 2 Si 2 , we followed the evolution of the magnetic A-phase that is found to collapse rapidly under pressure. We found evidence for a relation between the A-phase and the presence of a maximum in the temperature dependence of H c2 . Our analysis showed that at low pressure, the sign of the exchange integral should be negative, thus superconductivity is enhanced by an increase in the paramagnetic susceptibility as in the Jaccarino-Peter effect. The anisotropy of the initial slope of H c2 and therefore that of the effective mass was found to change under pressure. For CePd 2 Si 2 , both the de Haas-van Alphen effect at ambient pressure and the electrical resistivity under pressure were studied. The latter reveals a non-Fermi liquid behavior in the vicinity of the antiferromagnetic quantum critical point, P c ∼ kbar. The analysis of H c2 at P c shows that the superconducting state is well described by a weak coupling, clean limit model with a slightly anisotropic orbital limit and a strongly anisotropic paramagnetic one. UGe 2 is shown to demonstrate the coexistence of ferromagnetism and superconductivity that develops just below the ferromagnetic quantum critical point, P c ∼16 kbar. The measurements of the resistivity under pressure point to a possible existence of another phase boundary and thus another quantum critical point, P x ∼ 12 kbar, within the ferromagnetic state. The P-T phase diagram containing both P c and P x was sketched, and a possible relation between P x and the development of superconductivity was discussed. The temperature dependence of H c2 demonstrates a variety of novel behaviors, which cannot be understood within

  11. Decomposing phenotype descriptions for the human skeletal phenome.

    Science.gov (United States)

    Groza, Tudor; Hunter, Jane; Zankl, Andreas

    2013-01-01

    Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. The intrinsic value and knowledge captured within such descriptions can only be expressed by taking advantage of their inner structure that implicitly combines qualities and anatomical entities. We present a meta-model (the Phenotype Fragment Ontology) and a processing pipeline that enable together the automatic decomposition and conceptualization of phenotype descriptions for the human skeletal phenome. We use this approach to showcase the usefulness of the generic concept of phenotype decomposition by performing an experimental study on all skeletal phenotype concepts defined in the Human Phenotype Ontology.

  12. Kabuki syndrome: expanding the phenotype to include microphthalmia and anophthalmia.

    Science.gov (United States)

    McVeigh, Terri P; Banka, Siddharth; Reardon, William

    2015-10-01

    Kabuki syndrome is a rare genetic malformation syndrome that is characterized by distinct facies, structural defects and intellectual disability. Kabuki syndrome may be caused by mutations in one of two histone methyltransferase genes: KMT2D and KDM6A. We describe a male child of nonconsanguineous Irish parents presenting with multiple malformations, including bilateral extreme microphthalmia; cleft palate; congenital diaphragmatic hernia; duplex kidney; as well as facial features of Kabuki syndrome, including interrupted eyebrows and lower lid ectropion. A de-novo germline mutation in KMT2D was identified. Whole-exome sequencing failed to reveal mutations in any of the known microphthalmia/anopthalmia genes. We also identified four other patients with Kabuki syndrome and microphthalmia. We postulate that Kabuki syndrome may produce this type of ocular phenotype as a result of extensive interaction between KMT2D, WAR complex proteins and PAXIP1. Children presenting with microphthalmia/anophthalmia should be examined closely for other signs of Kabuki syndrome, especially at an age where the facial gestalt might be less readily appreciable.

  13. Phenotypic transformation affects associative learning in the desert locust.

    Science.gov (United States)

    Simões, Patrício M V; Niven, Jeremy E; Ott, Swidbert R

    2013-12-02

    In desert locusts, increased population densities drive phenotypic transformation from the solitarious to the gregarious phase within a generation [1-4]. Here we show that when presented with odor-food associations, the two extreme phases differ in aversive but not appetitive associative learning, with solitarious locusts showing a conditioned aversion more quickly than gregarious locusts. The acquisition of new learned aversions was blocked entirely in acutely crowded solitarious (transiens) locusts, whereas appetitive learning and prior learned associations were unaffected. These differences in aversive learning support phase-specific feeding strategies. Associative training with hyoscyamine, a plant alkaloid found in the locusts' habitat [5, 6], elicits a phase-dependent odor preference: solitarious locusts avoid an odor associated with hyoscyamine, whereas gregarious locusts do not. Remarkably, when solitarious locusts are crowded and then reconditioned with the odor-hyoscyamine pairing as transiens, the specific blockade of aversive acquisition enables them to override their prior aversive memory with an appetitive one. Under fierce food competition, as occurs during crowding in the field, this provides a neuroecological mechanism enabling locusts to reassign an appetitive value to an odor that they learned previously to avoid. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Phenotypic diagnosis of dwarfism in six Friesian horses.

    Science.gov (United States)

    Back, W; van der Lugt, J J; Nikkels, P G J; van den Belt, A J M; van der Kolk, J H; Stout, T A E

    2008-05-01

    An extreme form of abnormal development, dwarfism, is common in man and some animals, but has not been officially reported in horses. Within the Friesian horse breed, congenital dwarfism has been recognised for many years, but no detailed report exists on its phenotype. The most salient feature of the dwarf syndrome is the physeal growth retardation in both limbs and ribs. Affected animals have approximately 25% shorter fore- and hindlimbs and approximately 50% reduced bodyweight. Postnatal growth is still possible in these animals, albeit at a slower rate: the head and back grow faster than the limbs and ribs leading to the characteristic disproportional growth disturbance. Thus, adult dwarfs exhibit a normal, but a relatively larger head conformation, a broader chest with narrowing at the costochondral junction, a disproportionally long back, abnormally short limbs, hyperextension of the fetlocks and narrow long-toed hooves. Furthermore, a dysplastic metaphysis of the distal metacarpus and metatarsus is radiographically evident. Microscopic analysis of the growth plates at the costochondral junction shows an irregular transition from cartilage to bone, and thickening and disturbed formation of chondrocyte columns, which is similar to findings in osteochondrodysplasia.

  15. The personal dispositions of violent extremism

    Directory of Open Access Journals (Sweden)

    Davydov D.G.

    2017-04-01

    Full Text Available The paper presents the differences in the nature of extremism and radicalism, and the necessity of introducing the concept of "violent extremism." It is shown that the ideology is the explanation of extremist behavior, rather than its cause. The ideology of extremism often eclectic, contradictory and can easily be transformed by changing the object of hostility, depending on the situation. For the description of the psychological causes of extremism it is proposed to use the concept of personal disposition. Disposition is the preferred way to subjective interpretation of reality and reflects both the specific needs of a person as well the typical social situations where it realized and personal experience. Considered the following dispositions of violent extremism: the Cult of force and aggression, Intolerance, Out-group hostility Conventional coercion, Social pessimism and destructiveness, Mystical, Fighting and overcoming, Nihilism to law, Anti-subjectivism. It is proposed to use these dispositions as diagnostic criteria and for preventing and correcting.

  16. Sensitivity of European wheat to extreme weather

    DEFF Research Database (Denmark)

    Mäkinen, H; Kaseva, J; Trnka, M

    2018-01-01

    The frequency and intensity of extreme weather is increasing concomitant with changes in the global climate change. Although wheat is the most important food crop in Europe, there is currently no comprehensive empirical information available regarding the sensitivity of European wheat to extreme...... weather. In this study, we assessed the sensitivity of European wheat yields to extreme weather related to phenology (sowing, heading) in cultivar trials across Europe (latitudes 37.21° to 61.34° and longitudes −6.02° to 26.24°) during the period 1991–2014. All the observed agro-climatic extremes (≥31 °C...... wheat cultivars that responded positively (+10%) to drought after sowing, or frost during winter (−15 °C and −20 °C). Positive responses to extremes were often shown by cultivars associated with specific regions, such as good performance under high temperatures by southern-origin cultivars. Consequently...

  17. Mortality impact of extreme winter temperatures

    Science.gov (United States)

    Díaz, Julio; García, Ricardo; López, César; Linares, Cristina; Tobías, Aurelio; Prieto, Luis

    2005-01-01

    During the last few years great attention has been paid to the evaluation of the impact of extreme temperatures on human health. This paper examines the effect of extreme winter temperature on mortality in Madrid for people older than 65, using ARIMA and GAM models. Data correspond to 1,815 winter days over the period 1986 1997, during which time a total of 133,000 deaths occurred. The daily maximum temperature (Tmax) was shown to be the best thermal indicator of the impact of climate on mortality. When total mortality was considered, the maximum impact occured 7 8 days after a temperature extreme; for circulatory diseases the lag was between 7 and 14 days. When respiratory causes were considered, two mortality peaks were evident at 4 5 and 11 days. When the impact of winter extreme temperatures was compared with that associated with summer extremes, it was found to occur over a longer term, and appeared to be more indirect.

  18. Extreme Weather and Climate: Workshop Report

    Science.gov (United States)

    Sobel, Adam; Camargo, Suzana; Debucquoy, Wim; Deodatis, George; Gerrard, Michael; Hall, Timothy; Hallman, Robert; Keenan, Jesse; Lall, Upmanu; Levy, Marc; hide

    2016-01-01

    Extreme events are the aspects of climate to which human society is most sensitive. Due to both their severity and their rarity, extreme events can challenge the capacity of physical, social, economic and political infrastructures, turning natural events into human disasters. Yet, because they are low frequency events, the science of extreme events is very challenging. Among the challenges is the difficulty of connecting extreme events to longer-term, large-scale variability and trends in the climate system, including anthropogenic climate change. How can we best quantify the risks posed by extreme weather events, both in the current climate and in the warmer and different climates to come? How can we better predict them? What can we do to reduce the harm done by such events? In response to these questions, the Initiative on Extreme Weather and Climate has been created at Columbia University in New York City (extreme weather.columbia.edu). This Initiative is a University-wide activity focused on understanding the risks to human life, property, infrastructure, communities, institutions, ecosystems, and landscapes from extreme weather events, both in the present and future climates, and on developing solutions to mitigate those risks. In May 2015,the Initiative held its first science workshop, entitled Extreme Weather and Climate: Hazards, Impacts, Actions. The purpose of the workshop was to define the scope of the Initiative and tremendously broad intellectual footprint of the topic indicated by the titles of the presentations (see Table 1). The intent of the workshop was to stimulate thought across disciplinary lines by juxtaposing talks whose subjects differed dramatically. Each session concluded with question and answer panel sessions. Approximately, 150 people were in attendance throughout the day. Below is a brief synopsis of each presentation. The synopses collectively reflect the variety and richness of the emerging extreme event research agenda.

  19. Advanced phenotyping and phenotype data analysis for the plant growth and development study

    Directory of Open Access Journals (Sweden)

    Md. Matiur eRahaman

    2015-08-01

    Full Text Available Due to increase in the consumption of food, feed, fuel and to ensure global food security for rapidly growing human population, there is need to breed high yielding crops that can adapt to future climate. To solve these global issues, novel approaches are required to provide quantitative phenotypes to elucidate the genetic basis of agriculturally import traits and to screen germplasm with super performance in function under resource-limited environment. At present, plant phenomics has offered and integrated suite technologies for understanding the complete set of phenotypes of plants, towards the progression of the full characteristics of plants with whole sequenced genomes. In this aspect, high-throughput phenotyping platforms have been developed that enables to capture extensive and intensive phenotype data from non-destructive imaging over time. These developments advance our view on plant growth and performance with responses to the changing climate and environment. In this paper, we present a brief review on currently developed high-throughput plant phenotyping infrastructures based on imaging techniques and corresponding principles for phenotype data analysis.

  20. Elucidating the genotype–phenotype map by automatic enumeration and analysis of the phenotypic repertoire

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2015-01-01

    Background: The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process. Methods: The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters. Results: Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed. Conclusions: Starting with a system’s relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy. PMID:26998346

  1. Elucidating the genotype-phenotype map by automatic enumeration and analysis of the phenotypic repertoire.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process. The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters. Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed. Starting with a system's relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy.

  2. The origin of human complex diversity: Stochastic epistatic modules and the intrinsic compatibility between distributional robustness and phenotypic changeability.

    Science.gov (United States)

    Ijichi, Shinji; Ijichi, Naomi; Ijichi, Yukina; Imamura, Chikako; Sameshima, Hisami; Kawaike, Yoichi; Morioka, Hirofumi

    2018-01-01

    The continuing prevalence of a highly heritable and hypo-reproductive extreme tail of a human neurobehavioral quantitative diversity suggests the possibility that the reproductive majority retains the genetic mechanism for the extremes. From the perspective of stochastic epistasis, the effect of an epistatic modifier variant can randomly vary in both phenotypic value and effect direction among the careers depending on the genetic individuality, and the modifier careers are ubiquitous in the population distribution. The neutrality of the mean genetic effect in the careers warrants the survival of the variant under selection pressures. Functionally or metabolically related modifier variants make an epistatic network module and dozens of modules may be involved in the phenotype. To assess the significance of stochastic epistasis, a simplified module-based model was employed. The individual repertoire of the modifier variants in a module also participates in the genetic individuality which determines the genetic contribution of each modifier in the career. Because the entire contribution of a module to the phenotypic outcome is consequently unpredictable in the model, the module effect represents the total contribution of the related modifiers as a stochastic unit in the simulations. As a result, the intrinsic compatibility between distributional robustness and quantitative changeability could mathematically be simulated using the model. The artificial normal distribution shape in large-sized simulations was preserved in each generation even if the lowest fitness tail was un-reproductive. The robustness of normality beyond generations is analogous to the real situations of human complex diversity including neurodevelopmental conditions. The repeated regeneration of the un-reproductive extreme tail may be inevitable for the reproductive majority's competence to survive and change, suggesting implications of the extremes for others. Further model-simulations to

  3. Why do people buy dogs with potential welfare problems related to extreme conformation and inherited disease? A representative study of Danish owners of four small dog breeds.

    Science.gov (United States)

    Sandøe, P; Kondrup, S V; Bennett, P C; Forkman, B; Meyer, I; Proschowsky, H F; Serpell, J A; Lund, T B

    2017-01-01

    A number of dog breeds suffer from welfare problems due to extreme phenotypes and high levels of inherited diseases but the popularity of such breeds is not declining. Using a survey of owners of two popular breeds with extreme physical features (French Bulldog and Chihuahua), one with a high load of inherited diseases not directly related to conformation (Cavalier King Charles Spaniel), and one representing the same size range but without extreme conformation and with the same level of disease as the overall dog population (Cairn Terrier), we investigated this seeming paradox. We examined planning and motivational factors behind acquisition of the dogs, and whether levels of experienced health and behavior problems were associated with the quality of the owner-dog relationship and the intention to re-procure a dog of the same breed. Owners of each of the four breeds (750/breed) were randomly drawn from a nationwide Danish dog registry and invited to participate. Of these, 911 responded, giving a final sample of 846. There were clear differences between owners of the four breeds with respect to degree of planning prior to purchase, with owners of Chihuahuas exhibiting less. Motivations behind choice of dog were also different. Health and other breed attributes were more important to owners of Cairn Terriers, whereas the dog's personality was reported to be more important for owners of French Bulldogs and Cavalier King Charles Spaniels but less important for Chihuahua owners. Higher levels of health and behavior problems were positively associated with a closer owner-dog relationship for owners of Cavalier King Charles Spaniels and Chihuahuas but, for owners of French Bulldogs, high levels of problems were negatively associated with an intention to procure the same breed again. In light of these findings, it appears less paradoxical that people continue to buy dogs with welfare problems.

  4. The phenotypic manifestations of rare CNVs in schizophrenia.

    Science.gov (United States)

    Merikangas, Alison K; Segurado, Ricardo; Cormican, Paul; Heron, Elizabeth A; Anney, Richard J L; Moore, Susan; Kelleher, Eric; Hargreaves, April; Anderson-Schmidt, Heike; Gill, Michael; Gallagher, Louise; Corvin, Aiden

    2014-09-01

    There is compelling evidence for the role of copy number variants (CNVs) in schizophrenia susceptibility, and it has been estimated that up to 2-3% of schizophrenia cases may carry rare CNVs. Despite evidence that these events are associated with an increased risk across categorical neurodevelopmental disorders, there is limited understanding of the impact of CNVs on the core features of disorders like schizophrenia. Our objective was to evaluate associations between rare CNVs in differentially brain expressed (BE) genes and the core features and clinical correlates of schizophrenia. The sample included 386 cases of Irish ancestry with a diagnosis of schizophrenia, at least one rare CNV impacting any gene, and a core set of phenotypic measures. Statistically significant associations between deletions in differentially BE genes were found for family history of mental illness (decreased prevalence of all CNVs and deletions, unadjusted and adjusted) and for paternal age (increase in deletions only, unadjusted, among those with later ages at birth of patient). The strong effect of a lack of a family history on BE genes suggests that CNVs may comprise one pathway to schizophrenia, whereas a positive family history could index other genetic mechanisms that increase schizophrenia vulnerability. To our knowledge, this is the first investigation of the association between genome-wide CNVs and risk factors and sub-phenotypic features of schizophrenia beyond cognitive function. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Migration Phenotype of Brain-Cancer Cells Predicts Patient Outcomes

    Directory of Open Access Journals (Sweden)

    Chris L. Smith

    2016-06-01

    Full Text Available Glioblastoma multiforme is a heterogeneous and infiltrative cancer with dismal prognosis. Studying the migratory behavior of tumor-derived cell populations can be informative, but it places a high premium on the precision of in vitro methods and the relevance of in vivo conditions. In particular, the analysis of 2D cell migration may not reflect invasion into 3D extracellular matrices in vivo. Here, we describe a method that allows time-resolved studies of primary cell migration with single-cell resolution on a fibrillar surface that closely mimics in vivo 3D migration. We used this platform to screen 14 patient-derived glioblastoma samples. We observed that the migratory phenotype of a subset of cells in response to platelet-derived growth factor was highly predictive of tumor location and recurrence in the clinic. Therefore, migratory phenotypic classifiers analyzed at the single-cell level in a patient-specific way can provide high diagnostic and prognostic value for invasive cancers.

  6. Progeny Clustering: A Method to Identify Biological Phenotypes

    Science.gov (United States)

    Hu, Chenyue W.; Kornblau, Steven M.; Slater, John H.; Qutub, Amina A.

    2015-01-01

    Estimating the optimal number of clusters is a major challenge in applying cluster analysis to any type of dataset, especially to biomedical datasets, which are high-dimensional and complex. Here, we introduce an improved method, Progeny Clustering, which is stability-based and exceptionally efficient in computing, to find the ideal number of clusters. The algorithm employs a novel Progeny Sampling method to reconstruct cluster identity, a co-occurrence probability matrix to assess the clustering stability, and a set of reference datasets to overcome inherent biases in the algorithm and data space. Our method was shown successful and robust when applied to two synthetic datasets (datasets of two-dimensions and ten-dimensions containing eight dimensions of pure noise), two standard biological datasets (the Iris dataset and Rat CNS dataset) and two biological datasets (a cell phenotype dataset and an acute myeloid leukemia (AML) reverse phase protein array (RPPA) dataset). Progeny Clustering outperformed some popular clustering evaluation methods in the ten-dimensional synthetic dataset as well as in the cell phenotype dataset, and it was the only method that successfully discovered clinically meaningful patient groupings in the AML RPPA dataset. PMID:26267476

  7. Sex differences in correlates of intermediate phenotypes and prevalent cardiovascular disease in the general population

    Directory of Open Access Journals (Sweden)

    Renate B. Schnabel

    2015-04-01

    Full Text Available Background-There are marked sex differences in cardiovascular disease [CVD] manifestation. It is largely unknown how the distribution of CVD risk factors or intermediate phenotypes explain sex-specific differences.Methods and Results-In 5000 individuals of the population-based Gutenberg Health Study, mean age 55±11 years, 51% males, we examined sex-specific associations of classical CVD risk factors with intima-media thickness, ankle-brachial index, flow-mediated dilation, peripheral arterial tonometry, echocardiographic and electrocardiographic variables. Intermediate cardiovascular phenotypes were related to prevalent CVD (coronary artery disease, heart failure, stroke, myocardial infarction, lower extremity artery disease [LEAD] N=561.We observed differential distributions of CVD risk factors with a higher risk factor burden in men. Manifest coronary artery disease, stroke, myocardial infarction and LEAD were more frequent in men; the proportion of heart failure was higher in women. Intermediate phenotypes showed clear sex differences with more beneficial values in women. Fairly linear changes towards less beneficial values with age were observed in both sexes. In multivariable-adjusted regression analyses age, systolic blood pressure and body mass index were consistently associated with intermediate phenotypes in both sexes with different ranking according to random forests, maximum model R² 0.43. Risk factor-adjusted associations with prevalent CVD showed some differences by sex. No interactions by menopausal status were observed. Conclusions-In a population-based cohort we observed sex differences in risk factors and a broad range of intermediate phenotypes of noninvasive cardiovascular structure and function. Their relation to prevalent CVD differed markedly. Our results indicate the need of future investigations to understand sex differences in CVD manifestation.

  8. Topological structure of the space of phenotypes: the case of RNA neutral networks.

    Directory of Open Access Journals (Sweden)

    Jacobo Aguirre

    Full Text Available The evolution and adaptation of molecular populations is constrained by the diversity accessible through mutational processes. RNA is a paradigmatic example of biopolymer where genotype (sequence and phenotype (approximated by the secondary structure fold are identified in a single molecule. The extreme redundancy of the genotype-phenotype map leads to large ensembles of RNA sequences that fold into the same secondary structure and can be connected through single-point mutations. These ensembles define neutral networks of phenotypes in sequence space. Here we analyze the topological properties of neutral networks formed by 12-nucleotides RNA sequences, obtained through the exhaustive folding of sequence space. A total of 4(12 sequences fragments into 645 subnetworks that correspond to 57 different secondary structures. The topological analysis reveals that each subnetwork is far from being random: it has a degree distribution with a well-defined average and a small dispersion, a high clustering coefficient, and an average shortest path between nodes close to its minimum possible value, i.e. the Hamming distance between sequences. RNA neutral networks are assortative due to the correlation in the composition of neighboring sequences, a feature that together with the symmetries inherent to the folding process explains the existence of communities. Several topological relationships can be analytically derived attending to structural restrictions and generic properties of the folding process. The average degree of these phenotypic networks grows logarithmically with their size, such that abundant phenotypes have the additional advantage of being more robust to mutations. This property prevents fragmentation of neutral networks and thus enhances the navigability of sequence space. In summary, RNA neutral networks show unique topological properties, unknown to other networks previously described.

  9. New genes as drivers of phenotypic evolution

    Science.gov (United States)

    Chen, Sidi; Krinsky, Benjamin H.; Long, Manyuan

    2014-01-01

    During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution. PMID:23949544

  10. Animal biometrics: quantifying and detecting phenotypic appearance.

    Science.gov (United States)

    Kühl, Hjalmar S; Burghardt, Tilo

    2013-07-01

    Animal biometrics is an emerging field that develops quantified approaches for representing and detecting the phenotypic appearance of species, individuals, behaviors, and morphological traits. It operates at the intersection between pattern recognition, ecology, and information sciences, producing computerized systems for phenotypic measurement and interpretation. Animal biometrics can benefit a wide range of disciplines, including biogeography, population ecology, and behavioral research. Currently, real-world applications are gaining momentum, augmenting the quantity and quality of ecological data collection and processing. However, to advance animal biometrics will require integration of methodologies among the scientific disciplines involved. Such efforts will be worthwhile because the great potential of this approach rests with the formal abstraction of phenomics, to create tractable interfaces between different organizational levels of life. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Smooth muscle cell phenotypic switching in stroke.

    Science.gov (United States)

    Poittevin, Marine; Lozeron, Pierre; Hilal, Rose; Levy, Bernard I; Merkulova-Rainon, Tatiana; Kubis, Nathalie

    2014-06-01

    Disruption of cerebral blood flow after stroke induces cerebral tissue injury through multiple mechanisms that are not yet fully understood. Smooth muscle cells (SMCs) in blood vessel walls play a key role in cerebral blood flow control. Cerebral ischemia triggers these cells to switch to a phenotype that will be either detrimental or beneficial to brain repair. Moreover, SMC can be primarily affected genetically or by toxic metabolic molecules. After stroke, this pathological phenotype has an impact on the incidence, pattern, severity, and outcome of the cerebral ischemic disease. Although little research has been conducted on the pathological role and molecular mechanisms of SMC in cerebrovascular ischemic diseases, some therapeutic targets have already been identified and could be considered for further pharmacological development. We examine these different aspects in this review.

  12. Phenotype development in TgHD minipigs

    Czech Academy of Sciences Publication Activity Database

    Ellederová, Zdeňka; Vidinská, Daniela; Mačáková, Monika; Kučerová, S.; Bohuslavová, Božena; Sedláčková, M.; Lišková, Irena; Valeková, Ivona; Baxa, Monika; Ardan, Taras; Juhás, Štefan; Motlík, Jan

    2015-01-01

    Roč. 78, Suppl 2 (2015), s. 11-11 ISSN 1210-7859. [Conference on Animal Models for neurodegenerative Diseases /3./. 08.11.2015-10.11.2015, Liblice] R&D Projects: GA MŠk ED2.1.00/03.0124; GA MŠk(CZ) 7F14308 Institutional support: RVO:67985904 Keywords : phenotype * minipig model of Huntington ´s disease * reproductive failure Subject RIV: EB - Genetics ; Molecular Biology

  13. Molecular and phenotypic characterization of anamorphic fungi

    OpenAIRE

    Madrid Lorca, Hugo

    2011-01-01

    Anamorphic fungi (those reproducing asexually) are a big part of kingdom Fungi. Most of them occur as saprobes in nature, but numerous species are pathogenic to plants and animals including man. With the aim of contributing to the knowledge of the diversity and distribution of anamorphic fungi, we performed a phenotypic and molecular characterization of environmental and clinical isolates of these fungi. Based on a polyphasic taxonomy approach which included morphology, physiology and DNA seq...

  14. Connectomic intermediate phenotypes for psychiatric disorders

    Directory of Open Access Journals (Sweden)

    Alex eFornito

    2012-04-01

    Full Text Available Psychiatric disorders are phenotypically heterogeneous entities with a complex genetic basis. To mitigate this complexity, many investigators study so-called intermediate phenotypes that putatively provide a more direct index of the physiological effects of candidate genetic risk variants than overt psychiatric syndromes. Magnetic resonance imaging (MRI is a particularly popular technique for measuring such phenotypes because it allows interrogation of diverse aspects of brain structure and function in vivo. Much of this work however, has focused on relatively simple measures that quantify variations in the physiology or tissue integrity of specific brain regions in isolation, contradicting an emerging consensus that most major psychiatric disorders do not arise from isolated dysfunction in one or a few brain regions, but rather from disturbed interactions within and between distributed neural circuits; i.e., they are disorders of brain connectivity. The recent proliferation of new MRI techniques for comprehensively mapping the entire connectivity architecture of the brain, termed the human connectome, has provided a rich repertoire of tools for understanding how genetic variants implicated in mental disorder impact distinct neural circuits. In this article, we review research using these connectomic techniques to understand how genetic variation influences the connectivity and topology of human brain networks. We highlight recent evidence from twin and imaging genetics studies suggesting that the penetrance of candidate risk variants for mental illness, such as those in SLC6A4, MAOA, ZNF804A and APOE, may be higher for intermediate phenotypes characterised at the level of distributed neural systems than at the level of spatially localised brain regions. The findings indicate that imaging connectomics provides a powerful framework for understanding how genetic risk for psychiatric disease is expressed through altered structure and function of

  15. NF1 Neuronal Genotype Phenotype Relationships

    Science.gov (United States)

    2017-06-01

    interesting results from the Drosophila functional assays, at present we have decided to focus our attention on selected NF1 patient missense mutations...complexity of NF1 disease phenotypes in different tissues, age and sex dependency of symptoms, impact of environmental factors and genetic heterogeneity...suggesting the role of modifier genes [12]. This work aims to shed light on this issue by studying the functional consequences of selected NF1

  16. Extreme weather events and infectious disease outbreaks.

    Science.gov (United States)

    McMichael, Anthony J

    2015-01-01

    Human-driven climatic changes will fundamentally influence patterns of human health, including infectious disease clusters and epidemics following extreme weather events. Extreme weather events are projected to increase further with the advance of human-driven climate change. Both recent and historical experiences indicate that infectious disease outbreaks very often follow extreme weather events, as microbes, vectors and reservoir animal hosts exploit the disrupted social and environmental conditions of extreme weather events. This review article examines infectious disease risks associated with extreme weather events; it draws on recent experiences including Hurricane Katrina in 2005 and the 2010 Pakistan mega-floods, and historical examples from previous centuries of epidemics and 'pestilence' associated with extreme weather disasters and climatic changes. A fuller understanding of climatic change, the precursors and triggers of extreme weather events and health consequences is needed in order to anticipate and respond to the infectious disease risks associated with human-driven climate change. Post-event risks to human health can be constrained, nonetheless, by reducing background rates of persistent infection, preparatory action such as coordinated disease surveillance and vaccination coverage, and strengthened disaster response. In the face of changing climate and weather conditions, it is critically important to think in ecological terms about the determinants of health, disease and death in human populations.

  17. Extremely low temperature properties of epoxy GFRP

    International Nuclear Information System (INIS)

    Kadotani, Kenzo; Nagai, Matao; Aki, Fumitake.

    1983-01-01

    The examination of fiber-reinforced plastics, that is, plastics such as epoxy, polyester and polyimide reinforced with high strength fibers such as glass, carbon, boron and steel, for extremely low temperature use began from the fuel tanks of rockets. Therafter, the trial manufacture of superconducting generators and extremely low temperature transformers and the manufacture of superconducting magnets for nuclear fusion experimental setups became active, and high performance FRPs have been adopted, of which the extremely low temperature properties have been sufficiently grasped. Recently, the cryostats made of FRPs have been developed, fully utilizing such features of FRPs as high strength, high rigidity, non-magnetic material, insulation, low heat conductivity, light weight and the freedom of molding. In this paper, the mechanical properties at extremely low temperature of the plastic composite materials used as insulators and structural materials for extremely low temperature superconducting equipment is outlined, and in particular, glass fiber-reinforced epoxy laminates are described somewhat in detail. The fracture strain of GFRP at extremely low temperature is about 1.3 times as large as that at room temperature, but at extremely low temperature, clear cracking occurred at 40% of the fracture strain. The linear thermal contraction of GFRP showed remarkable anisotropy. (Kako, I.)

  18. Performance testing of extremity dosimeters, Study 2

    International Nuclear Information System (INIS)

    Harty, R.; Reece, W.D.; Hooker, C.D.

    1990-04-01

    The Health Physics Society Standards Committee (HPSSC) Working Group on Performance Testing of Extremity Dosimeters has issued a draft of a proposed standard for extremity dosimeters. The draft standard proposes methods to be used for testing dosimetry systems that determine occupational radiation dose to the extremities and the performance criterion used to determine compliance with the standard. Pacific Northwest Laboratory (PNL) has conducted two separate evaluations of the performance of extremity dosimeter processors to determine the appropriateness of the draft standard, as well as to obtain information regarding the performance of extremity dosimeters. Based on the information obtained during the facility visits and the results obtained from the performance testing, it was recommended that changes be made to ensure that the draft standard is appropriate for extremity dosimeters. The changes include: subdividing the mixture category and the beta particle category; eliminating the neutron category until appropriate flux-to-dose equivalent conversion factors are derived; and changing the tolerance level for the performance criterion to provide consistency with the performance criterion for whole body dosimeters, and to avoid making the draft standard overly difficult for processors of extremity dosimeters to pass. 20 refs., 10 figs., 6 tabs

  19. Probabilistic analysis of extreme wind events

    Energy Technology Data Exchange (ETDEWEB)

    Chaviaropoulos, P.K. [Center for Renewable Energy Sources (CRES), Pikermi Attikis (Greece)

    1997-12-31

    A vital task in wind engineering and meterology is to understand, measure, analyse and forecast extreme wind conditions, due to their significant effects on human activities and installations like buildings, bridges or wind turbines. The latest version of the IEC standard (1996) pays particular attention to the extreme wind events that have to be taken into account when designing or certifying a wind generator. Actually, the extreme wind events within a 50 year period are those which determine the ``static`` design of most of the wind turbine components. The extremes which are important for the safety of wind generators are those associated with the so-called ``survival wind speed``, the extreme operating gusts and the extreme wind direction changes. A probabilistic approach for the analysis of these events is proposed in this paper. Emphasis is put on establishing the relation between extreme values and physically meaningful ``site calibration`` parameters, like probability distribution of the annual wind speed, turbulence intensity and power spectra properties. (Author)

  20. One gene, many phenotypes | Shawky | Egyptian Journal of Medical ...

    African Journals Online (AJOL)

    ... mechanisms underlying genotype-phenotype discrepancies is important, as it will move clinical genetics towards predictive medicine, allowing better selection of therapeutic strategies and individualized counseling of persons affected with genetic disorders. Keywords: Gene, phenotype, mosaicism, epigenetics, pleiotropy ...

  1. Phenotypic Variability in the Coccolithophore Emiliania huxleyi.

    Science.gov (United States)

    Blanco-Ameijeiras, Sonia; Lebrato, Mario; Stoll, Heather M; Iglesias-Rodriguez, Debora; Müller, Marius N; Méndez-Vicente, Ana; Oschlies, Andreas

    2016-01-01

    Coccolithophores are a vital part of oceanic phytoplankton assemblages that produce organic matter and calcium carbonate (CaCO3) containing traces of other elements (i.e. Sr and Mg). Their associated carbon export from the euphotic zone to the oceans' interior plays a crucial role in CO2 feedback mechanisms and biogeochemical cycles. The coccolithophore Emiliania huxleyi has been widely studied as a model organism to understand physiological, biogeochemical, and ecological processes in marine sciences. Here, we show the inter-strain variability in physiological and biogeochemical traits in 13 strains of E. huxleyi from various biogeographical provinces obtained from culture collections commonly used in the literature. Our results demonstrate that inter-strain genetic variability has greater potential to induce larger phenotypic differences than the phenotypic plasticity of single strains cultured under a broad range of variable environmental conditions. The range of variation found in physiological parameters and calcite Sr:Ca highlights the need to reconsider phenotypic variability in paleoproxy calibrations and model parameterizations to adequately translate findings from single strain laboratory experiments to the real ocean.

  2. Phenotypic Variability in the Coccolithophore Emiliania huxleyi.

    Directory of Open Access Journals (Sweden)

    Sonia Blanco-Ameijeiras

    Full Text Available Coccolithophores are a vital part of oceanic phytoplankton assemblages that produce organic matter and calcium carbonate (CaCO3 containing traces of other elements (i.e. Sr and Mg. Their associated carbon export from the euphotic zone to the oceans' interior plays a crucial role in CO2 feedback mechanisms and biogeochemical cycles. The coccolithophore Emiliania huxleyi has been widely studied as a model organism to understand physiological, biogeochemical, and ecological processes in marine sciences. Here, we show the inter-strain variability in physiological and biogeochemical traits in 13 strains of E. huxleyi from various biogeographical provinces obtained from culture collections commonly used in the literature. Our results demonstrate that inter-strain genetic variability has greater potential to induce larger phenotypic differences than the phenotypic plasticity of single strains cultured under a broad range of variable environmental conditions. The range of variation found in physiological parameters and calcite Sr:Ca highlights the need to reconsider phenotypic variability in paleoproxy calibrations and model parameterizations to adequately translate findings from single strain laboratory experiments to the real ocean.

  3. A simple phenotypic classification for celiac disease

    Directory of Open Access Journals (Sweden)

    Ajit Sood

    2018-04-01

    Full Text Available Background/Aims : Celiac disease is a global health problem. The presentation of celiac disease has unfolded over years and it is now known that it can manifest at different ages, has varied presentations, and is prone to develop complications, if not managed properly. Although the Oslo definitions provide consensus on the various terminologies used in literature, there is no phenotypic classification providing a composite diagnosis for the disease. Methods : Various variables identified for phenotypic classification included age at diagnosis, age at onset of symptoms, clinical presentation, family history and complications. These were applied to the existing registry of 1,664 patients at Dayanand Medical College and Hospital, Ludhiana, India. In addition, age was evaluated as below 15 and below 18 years. Cross tabulations were used for the verification of the classification using the existing data. Expert opinion was sought from both international and national experts of varying fields. Results : After empirical verification, age at diagnosis was considered appropriate in between A1 (<18 and A2 (≧18. The disease presentation has been classified into 3 types–P1 (classical, P2 (non-classical and P3 (asymptomatic. Complications were considered as absent (C0 or present (C1. A single phenotypic classification based on these 3 characteristics, namely age at the diagnosis, clinical presentation, and intestinal complications (APC classification was derived. Conclusions : APC classification (age at diagnosis, presentation, complications is a simple disease explanatory classification for patients with celiac disease aimed at providing a composite diagnosis.

  4. Dissecting phenotypic variation among AIS patients

    International Nuclear Information System (INIS)

    Wang Minghua; Wang Jiucun; Zhang Zhen; Zhao Zhimin; Zhang Rongmei; Hu Xiaohua; Tan Tao; Luo Shijing; Luo Zewei

    2005-01-01

    We have created genital skin fibroblast cell lines directly from three patients in a Chinese family affected by androgen insensitivity syndrome (AIS). All patients in the family share an identical AR Arg 840 Cys mutant but show different disease phenotypes. By using the cell lines, we find that the mutation has not influenced a normal androgen-binding capacity at 37 deg C but has reduced the affinity for androgens and may cause thermolability of the androgen-receptor complex. The impaired nuclear trafficking of the androgen receptor in the cell lines is highly correlated with the severity of donors' disease phenotype. The transactivity of the mutant is substantially weakened and the extent of the reduced transactivity reflects severity of the donors' disease symptom. Our data reveal that although etiology of AIS is monogenic and the mutant may alter the major biological functions of its wild allele, the function of the mutant AR can also be influenced by the different genetic backgrounds and thus explains the divergent disease phenotypes

  5. The phenotypic spectrum of congenital Zika syndrome.

    Science.gov (United States)

    Del Campo, Miguel; Feitosa, Ian M L; Ribeiro, Erlane M; Horovitz, Dafne D G; Pessoa, André L S; França, Giovanny V A; García-Alix, Alfredo; Doriqui, Maria J R; Wanderley, Hector Y C; Sanseverino, Maria V T; Neri, João I C F; Pina-Neto, João M; Santos, Emerson S; Verçosa, Islane; Cernach, Mirlene C S P; Medeiros, Paula F V; Kerbage, Saile C; Silva, André A; van der Linden, Vanessa; Martelli, Celina M T; Cordeiro, Marli T; Dhalia, Rafael; Vianna, Fernanda S L; Victora, Cesar G; Cavalcanti, Denise P; Schuler-Faccini, Lavinia

    2017-04-01

    In October 2015, Zika virus (ZIKV) outbreak the Brazilian Ministry of Health (MoH). In response, the Brazilian Society of Medical Genetics established a task force (SBGM-ZETF) to study the phenotype of infants born with microcephaly due to ZIKV congenital infection and delineate the phenotypic spectrum of this newly recognized teratogen. This study was based on the clinical evaluation and neuroimaging of 83 infants born during the period from July, 2015 to March, 2016 and registered by the SBGM-ZETF. All 83 infants had significant findings on neuroimaging consistent with ZIKV congenital infection and 12 had confirmed ZIKV IgM in CSF. A recognizable phenotype of microcephaly, anomalies of the shape of skull and redundancy of the scalp consistent with the Fetal Brain Disruption Sequence (FBDS) was present in 70% of infants, but was most often subtle. In addition, features consistent with fetal immobility, ranging from dimples (30.1%), distal hand/finger contractures (20.5%), and feet malpositions (15.7%), to generalized arthrogryposis (9.6%), were present in these infants. Some cases had milder microcephaly or even a normal head circumference (HC), and other less distinctive findings. The detailed observation of the dysmorphic and neurologic features in these infants provides insight into the mechanisms and timings of the brain disruption and the sequence of developmental anomalies that may occur after prenatal infection by the ZIKV. © 2017 Wiley Periodicals, Inc.

  6. Associations between phenotypes of preeclampsia and thrombophilia.

    Science.gov (United States)

    Berks, Durk; Duvekot, Johannes J; Basalan, Hillal; De Maat, Moniek P M; Steegers, Eric A P; Visser, Willy

    2015-11-01

    Preeclampsia complicates 2-8% of all pregnancies. Studies on the association of preeclampsia with thrombophilia are conflicting. Clinical heterogeneity of the disease may be one of the explanations. The present study addresses the question whether different phenotypes of preeclampsia are associated with thrombophilia factors. Study design We planned a retrospective cohort study. From 1985 until 2010 women with preeclampsia were offered postpartum screening for the following thrombophilia factors: anti-phospholipid antibodies, APC-resistance, protein C deficiency and protein S deficiency, hyperhomocysteineamia, factor V Leiden and Prothrombin gene mutation. Hospital records were used to obtain information on phenotypes of the preeclampsia and placental histology. We identified 844 women with singleton pregnancies who were screened for thrombophilia factors. HELLP complicated 49% of pregnancies; Fetal growth restriction complicated 61% of pregnancies. Early delivery (preeclampsia was associated with protein S deficiency (p=0.01). Fetal growth restriction was associated with anti-phospholipid antibodies (ppreeclampsia was associated with anti-phospholipid antibodies (p=0.01). Extensive placental infarction (>10%) was associated with anti-phospholipid antibodies (ppreeclampsia, especially if complicated by fetal growth restriction, are associated with anti-phospholipid antibodies. Other phenotypes of preeclampsia, especially HELLP syndrome, were not associated with thrombophilia. We advise only to test for anti-phospholipid antibodies after early onset preeclampsia, especially if complicated by fetal growth restriction. We suggest enough evidence is presented to justify no further studies are needed. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  7. Genetic variants influencing phenotypic variance heterogeneity.

    Science.gov (United States)

    Ek, Weronica E; Rask-Andersen, Mathias; Karlsson, Torgny; Enroth, Stefan; Gyllensten, Ulf; Johansson, Åsa

    2018-03-01

    Most genetic studies identify genetic variants associated with disease risk or with the mean value of a quantitative trait. More rarely, genetic variants associated with variance heterogeneity are considered. In this study, we have identified such variance single-nucleotide polymorphisms (vSNPs) and examined if these represent biological gene × gene or gene × environment interactions or statistical artifacts caused by multiple linked genetic variants influencing the same phenotype. We have performed a genome-wide study, to identify vSNPs associated with variance heterogeneity in DNA methylation levels. Genotype data from over 10 million single-nucleotide polymorphisms (SNPs), and DNA methylation levels at over 430 000 CpG sites, were analyzed in 729 individuals. We identified vSNPs for 7195 CpG sites (P mean DNA methylation levels. We further showed that variance heterogeneity between genotypes mainly represents additional, often rare, SNPs in linkage disequilibrium (LD) with the respective vSNP and for some vSNPs, multiple low frequency variants co-segregating with one of the vSNP alleles. Therefore, our results suggest that variance heterogeneity of DNA methylation mainly represents phenotypic effects by multiple SNPs, rather than biological interactions. Such effects may also be important for interpreting variance heterogeneity of more complex clinical phenotypes.

  8. Aberrant phenotypes in peripheral T cell lymphomas.

    Science.gov (United States)

    Hastrup, N; Ralfkiaer, E; Pallesen, G

    1989-01-01

    Seventy six peripheral T cell lymphomas were examined immunohistologically to test their reactivity with a panel of monoclonal antibodies against 11 T cell associated antigens (CD1-8, CD27, UCHL1, and the T cell antigen receptor). Sixty two (82%) lymphomas showed aberrant phenotypes, and four main categories were distinguished as follows: (i) lack of one or several pan-T cell antigens (49, 64% of the cases); (ii) loss of both the CD4 and CD8 antigens (11, 15% of the cases); (iii) coexpression of the CD4 and CD8 antigens (13, 17% of the cases); and (iv) expression of the CD1 antigen (eight, 11% of the cases). No correlation was seen between the occurrence of aberrant phenotypes and the histological subtype. It is concluded that the demonstration of an aberrant phenotype is a valuable supplement to histological assessment in the diagnosis of peripheral T cell lymphomas. It is recommended that the panel of monoclonal antibodies against T cell differentiation antigens should be fairly large, as apparently any antigen may be lost in the process of malignant transformation. Images Figure PMID:2469701

  9. Cluster analysis in phenotyping a Portuguese population.

    Science.gov (United States)

    Loureiro, C C; Sa-Couto, P; Todo-Bom, A; Bousquet, J

    2015-09-03

    Unbiased cluster analysis using clinical parameters has identified asthma phenotypes. Adding inflammatory biomarkers to this analysis provided a better insight into the disease mechanisms. This approach has not yet been applied to asthmatic Portuguese patients. To identify phenotypes of asthma using cluster analysis in a Portuguese asthmatic population treated in secondary medical care. Consecutive patients with asthma were recruited from the outpatient clinic. Patients were optimally treated according to GINA guidelines and enrolled in the study. Procedures were performed according to a standard evaluation of asthma. Phenotypes were identified by cluster analysis using Ward's clustering method. Of the 72 patients enrolled, 57 had full data and were included for cluster analysis. Distribution was set in 5 clusters described as follows: cluster (C) 1, early onset mild allergic asthma; C2, moderate allergic asthma, with long evolution, female prevalence and mixed inflammation; C3, allergic brittle asthma in young females with early disease onset and no evidence of inflammation; C4, severe asthma in obese females with late disease onset, highly symptomatic despite low Th2 inflammation; C5, severe asthma with chronic airflow obstruction, late disease onset and eosinophilic inflammation. In our study population, the identified clusters were mainly coincident with other larger-scale cluster analysis. Variables such as age at disease onset, obesity, lung function, FeNO (Th2 biomarker) and disease severity were important for cluster distinction. Copyright © 2015. Published by Elsevier España, S.L.U.

  10. A radial velocity survey of extremely hydrogen-deficient stars

    International Nuclear Information System (INIS)

    Jeffery, C.S.; Kiel Univ.; Drilling, J.S.; Heber, U.

    1987-01-01

    A radial velocity survey of hot extremely hydrogen-deficient stars has been carried out in order to search for possible binaries. The survey found three stars to have large velocity variations. Of these, two are known hydrogen-deficient binaries and one, HDE 320156 (= LSS 4300), is a suspected binary. HDE 320156 (= LSS 4300) is therefore confirmed to be a single-lined spectroscopic hydrogen-deficient binary. The hydrogen-deficient binary stars all show weak C-lines. The remaining stars in the sample are C-strong extreme-helium (EHe) stars and did not show large-amplitude velocity variations. Small-amplitude radial velocity variations known to be present amongst the EHe stars are largely undetected. Evidence for variability is, however, present in the known variable V2076 Oph (HD 160641) and in LS IV - 1 0 2 with amplitudes between 10 and 20 km s -1 . (author)

  11. The genotype-phenotype map of an evolving digital organism

    OpenAIRE

    Fortuna, Miguel A.; Zaman, Luis; Ofria, Charles; Wagner, Andreas

    2017-01-01

    To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms fr...

  12. EMPReSS: European mouse phenotyping resource for standardized screens.

    Science.gov (United States)

    Green, Eain C J; Gkoutos, Georgios V; Lad, Heena V; Blake, Andrew; Weekes, Joseph; Hancock, John M

    2005-06-15

    Standardized phenotyping protocols are essential for the characterization of phenotypes so that results are comparable between different laboratories and phenotypic data can be related to ontological descriptions in an automated manner. We describe a web-based resource for the visualization, searching and downloading of standard operating procedures and other documents, the European Mouse Phenotyping Resource for Standardized Screens-EMPReSS. Direct access: http://www.empress.har.mrc.ac.uk e.green@har.mrc.ac.uk.

  13. [Injury mechanisms in extreme violence settings].

    Science.gov (United States)

    Arcaute-Velazquez, Fernando Federico; García-Núñez, Luis Manuel; Noyola-Vilallobos, Héctor Faustino; Espinoza-Mercado, Fernando; Rodríguez-Vega, Carlos Eynar

    2016-01-01

    Extreme violence events are consequence of current world-wide economic, political and social conditions. Injury patterns found among victims of extreme violence events are very complex, obeying several high-energy injury mechanisms. In this article, we present the basic concepts of trauma kinematics that regulate the clinical approach to victims of extreme violence events, in the hope that clinicians increase their theoretical armamentarium, and reflecting on obtaining better outcomes. Copyright © 2016. Published by Masson Doyma México S.A.

  14. Long term oscillations in Danish rainfall extremes

    DEFF Research Database (Denmark)

    Gregersen, Ida Bülow; Madsen, Henrik; Rosbjerg, Dan

    The frequent flooding of European cities within the last decade has motivated a vast number of studies, among others addressing the non-stationary behaviour of hydrological extremes driven by anthropogenic climate change. However, when considering future extremes it also becomes relevant to search...... for and understand natural variations on which the anthropogenic changes are imposed. This study identifies multi-decadal variations in six 137-years-long diurnal rainfall series from Denmark and southern Sweden, focusing on extremes with a reoccurrence level relevant for Danish drainage design. By means of a Peak...

  15. Spectral density regression for bivariate extremes

    KAUST Repository

    Castro Camilo, Daniela

    2016-05-11

    We introduce a density regression model for the spectral density of a bivariate extreme value distribution, that allows us to assess how extremal dependence can change over a covariate. Inference is performed through a double kernel estimator, which can be seen as an extension of the Nadaraya–Watson estimator where the usual scalar responses are replaced by mean constrained densities on the unit interval. Numerical experiments with the methods illustrate their resilience in a variety of contexts of practical interest. An extreme temperature dataset is used to illustrate our methods. © 2016 Springer-Verlag Berlin Heidelberg

  16. Online transfer learning with extreme learning machine

    Science.gov (United States)

    Yin, Haibo; Yang, Yun-an

    2017-05-01

    In this paper, we propose a new transfer learning algorithm for online training. The proposed algorithm, which is called Online Transfer Extreme Learning Machine (OTELM), is based on Online Sequential Extreme Learning Machine (OSELM) while it introduces Semi-Supervised Extreme Learning Machine (SSELM) to transfer knowledge from the source to the target domain. With the manifold regularization, SSELM picks out instances from the source domain that are less relevant to those in the target domain to initialize the online training, so as to improve the classification performance. Experimental results demonstrate that the proposed OTELM can effectively use instances in the source domain to enhance the learning performance.

  17. Hydrologic extremes - an intercomparison of multiple gridded statistical downscaling methods

    Science.gov (United States)

    Werner, Arelia T.; Cannon, Alex J.

    2016-04-01

    Gridded statistical downscaling methods are the main means of preparing climate model data to drive distributed hydrological models. Past work on the validation of climate downscaling methods has focused on temperature and precipitation, with less attention paid to the ultimate outputs from hydrological models. Also, as attention shifts towards projections of extreme events, downscaling comparisons now commonly assess methods in terms of climate extremes, but hydrologic extremes are less well explored. Here, we test the ability of gridded downscaling models to replicate historical properties of climate and hydrologic extremes, as measured in terms of temporal sequencing (i.e. correlation tests) and distributional properties (i.e. tests for equality of probability distributions). Outputs from seven downscaling methods - bias correction constructed analogues (BCCA), double BCCA (DBCCA), BCCA with quantile mapping reordering (BCCAQ), bias correction spatial disaggregation (BCSD), BCSD using minimum/maximum temperature (BCSDX), the climate imprint delta method (CI), and bias corrected CI (BCCI) - are used to drive the Variable Infiltration Capacity (VIC) model over the snow-dominated Peace River basin, British Columbia. Outputs are tested using split-sample validation on 26 climate extremes indices (ClimDEX) and two hydrologic extremes indices (3-day peak flow and 7-day peak flow). To characterize observational uncertainty, four atmospheric reanalyses are used as climate model surrogates and two gridded observational data sets are used as downscaling target data. The skill of the downscaling methods generally depended on reanalysis and gridded observational data set. However, CI failed to reproduce the distribution and BCSD and BCSDX the timing of winter 7-day low-flow events, regardless of reanalysis or observational data set. Overall, DBCCA passed the greatest number of tests for the ClimDEX indices, while BCCAQ, which is designed to more accurately resolve event

  18. Application of Extreme Value Theory to Crash Data Analysis.

    Science.gov (United States)

    Xu, Lan; Nusholtz, Guy

    2017-11-01

    A parametric model obtained by fitting a set of data to a function generally uses a procedure such as maximum likelihood or least squares. In general this will generate the best estimate for the distribution of the data overall but will not necessarily generate a reasonable estimation for the tail of the distribution unless the function fitted resembles the underlying distribution function. A distribution function can represent an estimate that is significantly different from the actual tail data, while the bulk of the data is reasonably represented by the central part of the fitted distribution. Extreme value theory can be used to improve the predictive capabilities of the fitted function in the tail region. In this study the peak-over-threshold approach from the extreme value theory was utilized to show that it is possible to obtain a better fit of the tail of a distribution than the procedures that use the entire distribution only. Additional constraints, on the current use of the extreme value approach with respect to the selection of the threshold (an estimate of the beginning of the tail region) that minimize the sensitivity to individual data samples associated with the tail section as well as contamination from the central distribution are used. Once the threshold is determined, the maximum likelihood method was used to fit the exceedances with the Generalized Pareto Distribution to obtain the tail distribution. The approach was then used in the analysis of airbag inflator pressure data from tank tests, crash velocity distribution and mass distribution from the field crash data (NASS). From the examples, the extreme (tail) distributions were better estimated with the Generalized Pareto Distribution, than a single overall distribution, along with the probability of the occurrence for a given extreme value, or a rare observation such as a high speed crash. It was concluded that the peak-over-threshold approach from extreme value theory can be a useful tool in

  19. Syndromic (phenotypic diarrhea in early infancy

    Directory of Open Access Journals (Sweden)

    Bodemer Christine

    2008-02-01

    Full Text Available Abstract Syndromic diarrhea (SD, also known as phenotypic diarrhea (PD or tricho-hepato-enteric syndrome (THE, is a congenital enteropathy presenting with early-onset of severe diarrhea requiring parenteral nutrition (PN. To date, no epidemiological data are available. The estimated prevalence is approximately 1/300,000–400,000 live births in Western Europe. Ethnic origin does not appear to be associated with SD. Infants are born small for gestational age and present with facial dysmorphism including prominent forehead and cheeks, broad nasal root and hypertelorism. Hairs are woolly, easily removed and poorly pigmented. Severe and persistent diarrhea starts within the first 6 months of life (≤ 1 month in most cases and is accompanied by severe malabsorption leading to early and relentless protein energy malnutrition with failure to thrive. Liver disease affects about half of patients with extensive fibrosis or cirrhosis. There is currently no specific biochemical profile, though a functional T-cell immune deficiency with defective antibody production was reported. Microscopic analysis of the hair show twisted hair (pili torti, aniso- and poilkilotrichosis, and trichorrhexis nodosa. Histopathological analysis of small intestine biopsy shows non-specific villous atrophy with low or no mononuclear cell infiltration of the lamina propria, and no specific histological abnormalities involving the epithelium. The etiology remains unknown. The frequent association of the disorder with parental consanguinity and/or affected siblings suggests a genetic origin with an autosomal recessive mode of transmission. Early management consists of total PN. Some infants have a rather milder phenotype with partial PN dependency or require only enteral feeding. Prognosis of this syndrome is poor, but most patients now survive, and about half of the patients may be weaned from PN at adolescence, but experience failure to thrive and final short stature. Disease name

  20. Predictable Phenotypes of Antibiotic Resistance Mutations.

    Science.gov (United States)

    Knopp, M; Andersson, D I

    2018-05-15

    Antibiotic-resistant bacteria represent a major threat to our ability to treat bacterial infections. Two factors that determine the evolutionary success of antibiotic resistance mutations are their impact on resistance level and the fitness cost. Recent studies suggest that resistance mutations commonly show epistatic interactions, which would complicate predictions of their stability in bacterial populations. We analyzed 13 different chromosomal resistance mutations and 10 host strains of Salmonella enterica and Escherichia coli to address two main questions. (i) Are there epistatic interactions between different chromosomal resistance mutations? (ii) How does the strain background and genetic distance influence the effect of chromosomal resistance mutations on resistance and fitness? Our results show that the effects of combined resistance mutations on resistance and fitness are largely predictable and that epistasis remains rare even when up to four mutations were combined. Furthermore, a majority of the mutations, especially target alteration mutations, demonstrate strain-independent phenotypes across different species. This study extends our understanding of epistasis among resistance mutations and shows that interactions between different resistance mutations are often predictable from the characteristics of the individual mutations. IMPORTANCE The spread of antibiotic-resistant bacteria imposes an urgent threat to public health. The ability to forecast the evolutionary success of resistant mutants would help to combat dissemination of antibiotic resistance. Previous studies have shown that the phenotypic effects (fitness and resistance level) of resistance mutations can vary substantially depending on the genetic context in which they occur. We conducted a broad screen using many different resistance mutations and host strains to identify potential epistatic interactions between various types of resistance mutations and to determine the effect of strain

  1. Phenotype-Driven Plasma Biobanking Strategies and Methods

    Directory of Open Access Journals (Sweden)

    Erica A. Bowton

    2015-05-01

    Full Text Available Biobank development and integration with clinical data from electronic medical record (EMR databases have enabled recent strides in genomic research and personalized medicine. BioVU, Vanderbilt’s DNA biorepository linked to de-identified clinical EMRs, has proven fruitful in its capacity to extensively appeal to numerous areas of biomedical and clinical research, supporting the discovery of genotype-phenotype interactions. Expanding on experiences in BioVU creation and development, we have recently embarked on a parallel effort to collect plasma in addition to DNA from blood specimens leftover after routine clinical testing at Vanderbilt. This initiative offers expanded utility of BioVU by combining proteomic and metabolomic approaches with genomics and/or clinical outcomes, widening the breadth for potential research and subsequent future impact on clinical care. Here, we describe the considerations and components involved in implementing a plasma biobank program from a feasibility assessment through pilot sample collection.

  2. Surface roughness control by extreme ultraviolet (EUV) radiation

    Science.gov (United States)

    Ahad, Inam Ul; Obeidi, Muhannad Ahmed; Budner, Bogusław; Bartnik, Andrzej; Fiedorowicz, Henryk; Brabazon, Dermot

    2017-10-01

    Surface roughness control of polymeric materials is often desirable in various biomedical engineering applications related to biocompatibility control, separation science and surface wettability control. In this study, Polyethylene terephthalate (PET) polymer films were irradiated with Extreme ultraviolet (EUV) photons in nitrogen environment and investigations were performed on surface roughness modification via EUV exposure. The samples were irradiated at 3 mm and 4 mm distance from the focal spot to investigate the effect of EUV fluence on topography. The topography of the EUV treated PET samples were studied by AFM. The detailed scanning was also performed on the sample irradiated at 3 mm. It was observed that the average surface roughness of PET samples was increased from 9 nm (pristine sample) to 280 nm and 253 nm for EUV irradiated samples. Detailed AFM studies confirmed the presence of 1.8 mm wide period U-shaped channels in EUV exposed PET samples. The walls of the channels were having FWHM of about 0.4 mm. The channels were created due to translatory movements of the sample in horizontal and transverse directions during the EUV exposure. The increased surface roughness is useful for many applications. The nanoscale channels fabricated by EUV exposure could be interesting for microfluidic applications based on lab-on-a-chip (LOC) devices.

  3. Phenotypic Changes in Different Spinach Varieties Grown and Selected under Organic Conditions

    Directory of Open Access Journals (Sweden)

    Nicolas Schermann

    2011-09-01

    Full Text Available Organic and low-input agriculture needs flexible varieties that can buffer environmental stress and adapt to the needs of farmers. We implemented an experiment to investigate the evolutionary capacities of a sample of spinach (Spinacia oleracea L. population varieties for a number of phenotypic traits. Three farmers cultivated, selected and multiplied one or several populations over two years on their farms. The third year, the versions of the varieties cultivated and selected by the different farmers were compared to the original seed lots they had been given. After two cycles of cultivation and on-farm mass selection, all the observed varieties showed significant phenotypic changes (differences between the original version and the version cultivated by farmers for morphological and phenological traits. When the divergence among versions within varieties was studied, the results show that the varieties conserved their identity, except for one variety, which evolved in such a way that it may now be considered two different varieties. The heterogeneity of the population varieties was assessed in comparison with a commercial F1 hybrid used as control, and we found no specific differences in phenotypic diversity between the hybrid and population varieties. The phenotypic changes shown by the population varieties in response to on-farm cultivation and selection could be useful for the development of specific adaptation. These results call into question the current European seed legislation and the requirements of phenotypic stability for conservation varieties.

  4. Using Dendritic Heat Maps to Simultaneously Display Genotype Divergence with Phenotype Divergence.

    Science.gov (United States)

    Kellom, Matthew; Raymond, Jason

    2016-01-01

    The advancement of techniques to visualize and analyze large-scale sequencing datasets is an area of active research and is rooted in traditional techniques such as heat maps and dendrograms. We introduce dendritic heat maps that display heat map results over aligned DNA sequence clusters for a range of clustering cutoffs. Dendritic heat maps aid in visualizing the effects of group differences on clustering hierarchy and relative abundance of sampled sequences. Here, we artificially generate two separate datasets with simplified mutation and population growth procedures with GC content group separation to use as example phenotypes. In this work, we use the term phenotype to represent any feature by which groups can be separated. These sequences were clustered in a fractional identity range of 0.75 to 1.0 using agglomerative minimum-, maximum-, and average-linkage algorithms, as well as a divisive centroid-based algorithm. We demonstrate that dendritic heat maps give freedom to scrutinize specific clustering levels across a range of cutoffs, track changes in phenotype inequity across multiple levels of sequence clustering specificity, and easily visualize how deeply rooted changes in phenotype inequity are in a dataset. As genotypes diverge in sample populations, clusters are shown to break apart into smaller clusters at higher identity cutoff levels, similar to a dendrogram. Phenotype divergence, which is shown as a heat map of relative abundance bin response, may or may not follow genotype divergences. This joined view highlights the relationship between genotype and phenotype divergence for treatment groups. We discuss the minimum-, maximum-, average-, and centroid-linkage algorithm approaches to building dendritic heat maps and make a case for the divisive "top-down" centroid-based clustering methodology as being the best option visualize the effects of changing factors on clustering hierarchy and relative abundance.

  5. Using Dendritic Heat Maps to Simultaneously Display Genotype Divergence with Phenotype Divergence.

    Directory of Open Access Journals (Sweden)

    Matthew Kellom

    Full Text Available The advancement of techniques to visualize and analyze large-scale sequencing datasets is an area of active research and is rooted in traditional techniques such as heat maps and dendrograms. We introduce dendritic heat maps that display heat map results over aligned DNA sequence clusters for a range of clustering cutoffs. Dendritic heat maps aid in visualizing the effects of group differences on clustering hierarchy and relative abundance of sampled sequences. Here, we artificially generate two separate datasets with simplified mutation and population growth procedures with GC content group separation to use as example phenotypes. In this work, we use the term phenotype to represent any feature by which groups can be separated. These sequences were clustered in a fractional identity range of 0.75 to 1.0 using agglomerative minimum-, maximum-, and average-linkage algorithms, as well as a divisive centroid-based algorithm. We demonstrate that dendritic heat maps give freedom to scrutinize specific clustering levels across a range of cutoffs, track changes in phenotype inequity across multiple levels of sequence clustering specificity, and easily visualize how deeply rooted changes in phenotype inequity are in a dataset. As genotypes diverge in sample populations, clusters are shown to break apart into smaller clusters at higher identity cutoff levels, similar to a dendrogram. Phenotype divergence, which is shown as a heat map of relative abundance bin response, may or may not follow genotype divergences. This joined view highlights the relationship between genotype and phenotype divergence for treatment groups. We discuss the minimum-, maximum-, average-, and centroid-linkage algorithm approaches to building dendritic heat maps and make a case for the divisive "top-down" centroid-based clustering methodology as being the best option visualize the effects of changing factors on clustering hierarchy and relative abundance.

  6. Extreme learning machines 2013 algorithms and applications

    CERN Document Server

    Toh, Kar-Ann; Romay, Manuel; Mao, Kezhi

    2014-01-01

    In recent years, ELM has emerged as a revolutionary technique of computational intelligence, and has attracted considerable attentions. An extreme learning machine (ELM) is a single layer feed-forward neural network alike learning system, whose connections from the input layer to the hidden layer are randomly generated, while the connections from the hidden layer to the output layer are learned through linear learning methods. The outstanding merits of extreme learning machine (ELM) are its fast learning speed, trivial human intervene and high scalability.   This book contains some selected papers from the International Conference on Extreme Learning Machine 2013, which was held in Beijing China, October 15-17, 2013. This conference aims to bring together the researchers and practitioners of extreme learning machine from a variety of fields including artificial intelligence, biomedical engineering and bioinformatics, system modelling and control, and signal and image processing, to promote research and discu...

  7. Extremal vacuum black holes in higher dimensions

    International Nuclear Information System (INIS)

    Figueras, Pau; Lucietti, James; Rangamani, Mukund; Kunduri, Hari K.

    2008-01-01

    We consider extremal black hole solutions to the vacuum Einstein equations in dimensions greater than five. We prove that the near-horizon geometry of any such black hole must possess an SO(2,1) symmetry in a special case where one has an enhanced rotational symmetry group. We construct examples of vacuum near-horizon geometries using the extremal Myers-Perry black holes and boosted Myers-Perry strings. The latter lead to near-horizon geometries of black ring topology, which in odd spacetime dimensions have the correct number of rotational symmetries to describe an asymptotically flat black object. We argue that a subset of these correspond to the near-horizon limit of asymptotically flat extremal black rings. Using this identification we provide a conjecture for the exact 'phase diagram' of extremal vacuum black rings with a connected horizon in odd spacetime dimensions greater than five.

  8. Models and Inference for Multivariate Spatial Extremes

    KAUST Repository

    Vettori, Sabrina

    2017-01-01

    The development of flexible and interpretable statistical methods is necessary in order to provide appropriate risk assessment measures for extreme events and natural disasters. In this thesis, we address this challenge by contributing

  9. Atomic collisions under extreme conditions in space

    International Nuclear Information System (INIS)

    Itikawa, Yukikazu

    1987-01-01

    In space, atoms and molecules are often placed under the extreme conditions which are very difficult to be realized on Earth. For instance, extremely hot and dense plasmas are found in and around various stellar objects (e.g., neutron stars) on one hand and extremely cold and diffuse gases prevail in interstellar space on the other. There is so strong a magnetic field that electron clouds in atoms and molecules are distorted. The study of atomic collisions under the extreme conditions is not only helpful in understanding the astrophysical environment but also reveals new aspects of the physics of atoms and molecules. This paper is an invitation to the study. (References are not exhaustive but only provide a clue with which more details can be found.) (author)

  10. Statistics of extremes theory and applications

    CERN Document Server

    Beirlant, Jan; Segers, Johan; Teugels, Jozef; De Waal, Daniel; Ferro, Chris

    2006-01-01

    Research in the statistical analysis of extreme values has flourished over the past decade: new probability models, inference and data analysis techniques have been introduced; and new application areas have been explored. Statistics of Extremes comprehensively covers a wide range of models and application areas, including risk and insurance: a major area of interest and relevance to extreme value theory. Case studies are introduced providing a good balance of theory and application of each model discussed, incorporating many illustrated examples and plots of data. The last part of the book covers some interesting advanced topics, including  time series, regression, multivariate and Bayesian modelling of extremes, the use of which has huge potential.  

  11. Hidden conformal symmetry of extremal black holes

    International Nuclear Information System (INIS)

    Chen Bin; Long Jiang; Zhang Jiaju

    2010-01-01

    We study the hidden conformal symmetry of extremal black holes. We introduce a new set of conformal coordinates to write the SL(2,R) generators. We find that the Laplacian of the scalar field in many extremal black holes, including Kerr(-Newman), Reissner-Nordstrom, warped AdS 3 , and null warped black holes, could be written in terms of the SL(2,R) quadratic Casimir. This suggests that there exist dual conformal field theory (CFT) descriptions of these black holes. From the conformal coordinates, the temperatures of the dual CFTs could be read directly. For the extremal black hole, the Hawking temperature is vanishing. Correspondingly, only the left (right) temperature of the dual CFT is nonvanishing, and the excitations of the other sector are suppressed. In the probe limit, we compute the scattering amplitudes of the scalar off the extremal black holes and find perfect agreement with the CFT prediction.

  12. Automaton Rover for Extreme Environments, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Extreme environments abound in the solar system and include the radiation around Jupiter, high surface temperatures on Mercury and Venus, and hot, high pressure...

  13. GGCX-Associated Phenotypes: An Overview in Search of Genotype-Phenotype Correlations

    Directory of Open Access Journals (Sweden)

    Eva Y. G. De Vilder

    2017-01-01

    Full Text Available Gamma-carboxylation, performed by gamma-glutamyl carboxylase (GGCX, is an enzymatic process essential for activating vitamin K-dependent proteins (VKDP with important functions in various biological processes. Mutations in the encoding GGCX gene are associated with multiple phenotypes, amongst which vitamin K-dependent coagulation factor deficiency (VKCFD1 is best known. Other patients have skin, eye, heart or bone manifestations. As genotype–phenotype correlations were never described, literature was systematically reviewed in search of patients with at least one GGCX mutation with a phenotypic description, resulting in a case series of 47 patients. Though this number was too low for statistically valid correlations—a frequent problem in orphan diseases—we demonstrate the crucial role of the horizontally transferred transmembrane domain in developing cardiac and bone manifestations. Moreover, natural history suggests ageing as the principal determinant to develop skin and eye symptoms. VKCFD1 symptoms seemed more severe in patients with both mutations in the same protein domain, though this could not be linked to a more perturbed coagulation factor function. Finally, distinct GGCX functional domains might be dedicated to carboxylation of very specific VKDP. In conclusion, this systematic review suggests that there indeed may be genotype–phenotype correlations for GGCX-related phenotypes, which can guide patient counseling and management.

  14. International Conference on Extreme Learning Machines 2014

    CERN Document Server

    Mao, Kezhi; Cambria, Erik; Man, Zhihong; Toh, Kar-Ann

    2015-01-01

    This book contains some selected papers from the International Conference on Extreme Learning Machine 2014, which was held in Singapore, December 8-10, 2014. This conference brought together the researchers and practitioners of Extreme Learning Machine (ELM) from a variety of fields to promote research and development of “learning without iterative tuning”.  The book covers theories, algorithms and applications of ELM. It gives the readers a glance of the most recent advances of ELM.  

  15. Extreme Ultraviolet Explorer Bright Source List

    Science.gov (United States)

    Malina, Roger F.; Marshall, Herman L.; Antia, Behram; Christian, Carol A.; Dobson, Carl A.; Finley, David S.; Fruscione, Antonella; Girouard, Forrest R.; Hawkins, Isabel; Jelinsky, Patrick

    1994-01-01

    Initial results from the analysis of the Extreme Ultraviolet Explorer (EUVE) all-sky survey (58-740 A) and deep survey (67-364 A) are presented through the EUVE Bright Source List (BSL). The BSL contains 356 confirmed extreme ultraviolet (EUV) point sources with supporting information, including positions, observed EUV count rates, and the identification of possible optical counterparts. One-hundred twenty-six sources have been detected longward of 200 A.

  16. Injuries in an Extreme Conditioning Program

    OpenAIRE

    Aune, Kyle T.; Powers, Joseph M.

    2016-01-01

    Background: Extreme conditioning programs (ECPs) are fitness training regimens relying on aerobic, plyometric, and resistance training exercises, often with high levels of intensity for a short duration of time. These programs have grown rapidly in popularity in recent years, but science describing the safety profile of these programs is lacking. Hypothesis: The rate of injury in the extreme conditioning program is greater than the injury rate of weightlifting and the majority of injuries occ...

  17. International Conference on Extreme Learning Machine 2015

    CERN Document Server

    Mao, Kezhi; Wu, Jonathan; Lendasse, Amaury; ELM 2015; Theory, Algorithms and Applications (I); Theory, Algorithms and Applications (II)

    2016-01-01

    This book contains some selected papers from the International Conference on Extreme Learning Machine 2015, which was held in Hangzhou, China, December 15-17, 2015. This conference brought together researchers and engineers to share and exchange R&D experience on both theoretical studies and practical applications of the Extreme Learning Machine (ELM) technique and brain learning. This book covers theories, algorithms ad applications of ELM. It gives readers a glance of the most recent advances of ELM. .

  18. Prevention of Lower Extremity Injuries in Basketball

    Science.gov (United States)

    Taylor, Jeffrey B.; Ford, Kevin R.; Nguyen, Anh-Dung; Terry, Lauren N.; Hegedus, Eric J.

    2015-01-01

    Context: Lower extremity injuries are common in basketball, yet it is unclear how prophylactic interventions affect lower extremity injury incidence rates. Objective: To analyze the effectiveness of current lower extremity injury prevention programs in basketball athletes, focusing on injury rates of (1) general lower extremity injuries, (2) ankle sprains, and (3) anterior cruciate ligament (ACL) tears. Data Sources: PubMed, MEDLINE, CINAHL, SPORTDiscus, and the Cochrane Register of Controlled Trials were searched in January 2015. Study Selection: Studies were included if they were randomized controlled or prospective cohort trials, contained a population of competitive basketball athletes, and reported lower extremity injury incidence rates specific to basketball players. In total, 426 individual studies were identified. Of these, 9 met the inclusion criteria. One other study was found during a hand search of the literature, resulting in 10 total studies included in this meta-analysis. Study Design: Systematic review and meta-analysis. Level of Evidence: Level 2. Data Extraction: Details of the intervention (eg, neuromuscular vs external support), size of control and intervention groups, and number of injuries in each group were extracted from each study. Injury data were classified into 3 groups based on the anatomic diagnosis reported (general lower extremity injury, ankle sprain, ACL rupture). Results: Meta-analyses were performed independently for each injury classification. Results indicate that prophylactic programs significantly reduced the incidence of general lower extremity injuries (odds ratio [OR], 0.69; 95% CI, 0.57-0.85; P basketball athletes. Conclusion: In basketball players, prophylactic programs may be effective in reducing the risk of general lower extremity injuries and ankle sprains, yet not ACL injuries. PMID:26502412

  19. Test fields cannot destroy extremal black holes

    International Nuclear Information System (INIS)

    Natário, José; Queimada, Leonel; Vicente, Rodrigo

    2016-01-01

    We prove that (possibly charged) test fields satisfying the null energy condition at the event horizon cannot overspin/overcharge extremal Kerr–Newman or Kerr–Newman–anti de Sitter black holes, that is, the weak cosmic censorship conjecture cannot be violated in the test field approximation. The argument relies on black hole thermodynamics (without assuming cosmic censorship), and does not depend on the precise nature of the fields. We also discuss generalizations of this result to other extremal black holes. (paper)

  20. Preconditioned iterations to calculate extreme eigenvalues

    Energy Technology Data Exchange (ETDEWEB)

    Brand, C.W.; Petrova, S. [Institut fuer Angewandte Mathematik, Leoben (Austria)

    1994-12-31

    Common iterative algorithms to calculate a few extreme eigenvalues of a large, sparse matrix are Lanczos methods or power iterations. They converge at a rate proportional to the separation of the extreme eigenvalues from the rest of the spectrum. Appropriate preconditioning improves the separation of the eigenvalues. Davidson`s method and its generalizations exploit this fact. The authors examine a preconditioned iteration that resembles a truncated version of Davidson`s method with a different preconditioning strategy.