Geometric Series: A New Solution to the Dog Problem

ERIC Educational Resources Information Center

Dion, Peter; Ho, Anthony

2013-01-01

This article describes what is often referred to as the dog, beetle, mice, ant, or turtle problem. Solutions to this problem exist, some being variations of each other, which involve mathematics of a wide range of complexity. Herein, the authors describe the intuitive solution and the calculus solution and then offer a completely new solution…

Running from Iliotibial Band Syndrome: A Guide for Preventing Overuse Injuries

ERIC Educational Resources Information Center

Ramsey, Codi A.

2016-01-01

Iliotbial band syndrome (ITBS) is an overuse injury that affects distance runners and produces a large amount of frustration (and pain) to the runner, coaches and trainers. Treatments for ITBS vary widely and no known cures exist. Many running experts and physicians have prescribed several variations of training programs designed to help runners…

Review of in-service moisture and temperature conditions in wood-frame buildings

Treesearch

Samuel V. Glass; Anton TenWolde

2007-01-01

This literature review reports in-service moisture and temperature conditions of floor, wall, and roof members of wood-frame buildings and exposed wood decks and permanent wood foundations. A wide variation exists in reported wood moisture content, spanning a range from as low as 2% to well above 30%. Relevant studies are summarized, and measured values of wood...

Improved gas thrust bearings

NASA Technical Reports Server (NTRS)

Anderson, W. J.; Etsion, I.

1979-01-01

Two variations of gas-lubricated thrust bearings extend substantially load-carrying range over existing gas bearings. Dual-Action Gas Thrust Bearing's load-carrying capacity is more than ninety percent greater than that of single-action bearing over range of compressibility numbers. Advantages of Cantilever-mounted Thrust Bearing are greater tolerance to dirt ingestion, good initial lift-off characteristics, and operational capability over wide temperature range.

Dynamics of Agglutinin-Like Sequence (ALS) Protein Localization on the Surface of Candida Albicans

ERIC Educational Resources Information Center

Coleman, David Andrew

2009-01-01

The ALS gene family encodes large cell-surface glycoproteins associated with "C. albicans" pathogenesis. Als proteins are thought to act as adhesin molecules binding to host tissues. Wide variation in expression levels among the ALS genes exists and is related to cell morphology and environmental conditions. "ALS1," "ALS3," and "ALS4" are three of…

Ethical considerations in design of a study to evaluate a US Food and Drug Administration-approved indication: antivenom versus placebo for copperhead envenomation.

PubMed

Gerardo, Charles J; Lavonas, Eric J; McKinney, Ross E

2014-10-01

In 2000, the US Food and Drug Administration approved CroFab(®) Crotalidae Polyvalent Immune Fab, ovine (FabAV), which had received orphan drug designation, for use in patients with minimal to moderate North American crotaline envenomations including copperhead snakes. As existing evidence on the effectiveness of FabAV for this indication is limited, wide practice variation in its use exists. In order to provide more definitive clinical evidence as to the role of this treatment, a new randomized, placebo-controlled trial of FabAV specifically for copperhead bites was initiated. In light of the existing US Food and Drug Administration approval, ethical considerations of participation in this trial have been raised. We discuss the ethical principles pertinent to this randomized, placebo-controlled trial with placebo arm. We apply an accepted framework for ethical research to this trial. Due to the evidence gap in the literature, wide-ranging treatment recommendations by medical experts, and broad practice variation, clinical equipoise exists in the treatment of copperhead envenomation with FabAV. The impact of this clinical equipoise on the value and scientific validity of the trial is discussed. The trial's risk-benefit ratio is also considered. Potential risks to the patients are minimized as the protocol includes a plan for rescue therapy in the event that patients progress to severe envenomation symptoms. Overall, risks are further minimized by the inclusion of an interim analysis with stopping rules based on demonstrated efficacy should the therapy clearly prove to be beneficial. Although a post-marketing clinical study of this nature is unusual for an approved indication, this trial adheres to all ethical preconditions found in existing guidelines for clinical research involving human subjects. © The Author(s) 2014.

Wide variation in cardiopulmonary resuscitation interruption intervals among commercially available automated external defibrillators may affect survival despite high defibrillation efficacy.

PubMed

Snyder, David; Morgan, Carl

2004-09-01

Recent studies have associated interruptions of cardiopulmonary resuscitation imposed by automated external defibrillators (AEDs) with poor resuscitation outcome. In particular, the "hands-off" interval between precordial compressions and subsequent defibrillation shock has been implicated. We sought to determine the range of variation among current-generation AEDs with respect to this characteristic. Seven AEDs from six manufacturers were characterized via stopwatch and arrhythmia simulator with respect to the imposed hands-off interval. All AEDs were equipped with new batteries, and measurements were repeated five times for each AED. A wide variation in the hands-off interval between precordial compressions and shock delivery was observed, ranging from 5.2 to 28.4 secs, with only one AED achieving an interruption of <10 secs. Laboratory and clinical data suggest that this range of variation could be responsible for a more than two-fold variation in patient resuscitation success, an effect that far exceeds any defibrillation efficacy differences that may hypothetically exist. In addition to defibrillation waveform and dose, researchers should consider the hands-off cardiopulmonary resuscitation interruption interval between cardiopulmonary resuscitation and subsequent defibrillation shock to be an important covariate of outcome in resuscitation studies. Defibrillator design should minimize this interval to avoid potential adverse consequences on patient survival.

Solar generated quasi-biennial geomagnetic variation

NASA Technical Reports Server (NTRS)

Sugiura, M.; Poros, D. J.

1977-01-01

The existence of highly correlated quasi-biennial variations in the geomagnetic field and in solar activity is demonstrated. The analysis uses a numerical filter technique applied to monthly averages of the geomagnetic horizontal component and of the Zurich relative sunspot number. Striking correlations are found between the quasi-biennial geomagnetic variations determined from several magnetic observatories located at widely different longitudes, indicating a worldwide nature of the obtained variation. The correlation coefficient between the filtered Dst index and the filtered relative sunspot number is found to be -0.79 at confidence level greater than 99% with a time-lag of 4 months, with solar activity preceding the Dst variation. The correlation between the unfiltered data of Dst and of the sunspot number is also high with a similar time-lag. Such a timelag has not been discussed in the literature, and a further study is required to establish the mode of sun-earth relationship that gives this time delay.

Scaling and universality in heart rate variability distributions

NASA Technical Reports Server (NTRS)

Rosenblum, M. G.; Peng, C. K.; Mietus, J. E.; Havlin, S.; Stanley, H. E.; Goldberger, A. L.

1998-01-01

We find that a universal homogeneous scaling form describes the distribution of cardiac variations for a group of healthy subjects, which is stable over a wide range of time scales. However, a similar scaling function does not exist for a group with a common cardiopulmonary instability associated with sleep apnea. Subtle differences in the distributions for the day- and night-phase dynamics for healthy subjects are detected.

Scaling and universality in heart rate variability distributions

NASA Astrophysics Data System (ADS)

Ivanov, P. Ch; Rosenblum, M. G.; Peng, C.-K.; Mietus, J. E.; Havlin, S.; Stanley, H. E.; Goldberger, A. L.

We find that a universal homogeneous scaling form describes the distributions of cardiac variations for a group of healthy subjects, which is stable over a wide range of time scales. However, a similar scaling function does not exist for a group with a common cardiopulmonary instability associated with sleep apnea. Subtle differences in the distributions for the day- and night-phase dynamics for healthy subjects are detected.

Individual variation in cone photoreceptor density in house sparrows: implications for between-individual differences in visual resolution and chromatic contrast.

PubMed

Ensminger, Amanda L; Fernández-Juricic, Esteban

2014-01-01

Between-individual variation has been documented in a wide variety of taxa, especially for behavioral characteristics; however, intra-population variation in sensory systems has not received similar attention in wild animals. We measured a key trait of the visual system, the density of retinal cone photoreceptors, in a wild population of house sparrows (Passer domesticus). We tested whether individuals differed from each other in cone densities given within-individual variation across the retina and across eyes. We further tested whether the existing variation could lead to individual differences in two aspects of perception: visual resolution and chromatic contrast. We found consistent between-individual variation in the densities of all five types of avian cones, involved in chromatic and achromatic vision. Using perceptual modeling, we found that this degree of variation translated into significant between-individual differences in visual resolution and the chromatic contrast of a plumage signal that has been associated with mate choice and agonistic interactions. However, there was no evidence for a relationship between individual visual resolution and chromatic contrast. The implication is that some birds may have the sensory potential to perform "better" in certain visual tasks, but not necessarily in both resolution and contrast simultaneously. Overall, our findings (a) highlight the need to consider multiple individuals when characterizing sensory traits of a species, and (b) provide some mechanistic basis for between-individual variation in different behaviors (i.e., animal personalities) and for testing the predictions of several widely accepted hypotheses (e.g., honest signaling).

Individual Variation in Cone Photoreceptor Density in House Sparrows: Implications for Between-Individual Differences in Visual Resolution and Chromatic Contrast

PubMed Central

Ensminger, Amanda L.; Fernández-Juricic, Esteban

2014-01-01

Between-individual variation has been documented in a wide variety of taxa, especially for behavioral characteristics; however, intra-population variation in sensory systems has not received similar attention in wild animals. We measured a key trait of the visual system, the density of retinal cone photoreceptors, in a wild population of house sparrows (Passer domesticus). We tested whether individuals differed from each other in cone densities given within-individual variation across the retina and across eyes. We further tested whether the existing variation could lead to individual differences in two aspects of perception: visual resolution and chromatic contrast. We found consistent between-individual variation in the densities of all five types of avian cones, involved in chromatic and achromatic vision. Using perceptual modeling, we found that this degree of variation translated into significant between-individual differences in visual resolution and the chromatic contrast of a plumage signal that has been associated with mate choice and agonistic interactions. However, there was no evidence for a relationship between individual visual resolution and chromatic contrast. The implication is that some birds may have the sensory potential to perform “better” in certain visual tasks, but not necessarily in both resolution and contrast simultaneously. Overall, our findings (a) highlight the need to consider multiple individuals when characterizing sensory traits of a species, and (b) provide some mechanistic basis for between-individual variation in different behaviors (i.e., animal personalities) and for testing the predictions of several widely accepted hypotheses (e.g., honest signaling). PMID:25372039

Deterministic and probabilistic analysis of damping device resistance under impact loads from nuclear fuel container drop

NASA Astrophysics Data System (ADS)

Kala, J.; Bajer, M.; Barnat, J.; Smutný, J.

2010-12-01

Pedestrian-induced vibrations are a criterion for serviceability. This loading is significant for light-weight footbridge structures, but was established as a basic loading for the ceilings of various ordinary buildings. Wide variations of this action exist. To verify the different conclusions of various authors, vertical pressure measurements invoked during walking were performed. In the article the approaches of different design codes are also shown.

Genome Variation Map: a data repository of genome variations in BIG Data Center

PubMed Central

Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang

2018-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473

Efficient identification of context dependent subgroups of risk from genome wide association studies

PubMed Central

Dyson, Greg; Sing, Charles F.

2014-01-01

We have developed a modified Patient Rule-Induction Method (PRIM) as an alternative strategy for analyzing representative samples of non-experimental human data to estimate and test the role of genomic variations as predictors of disease risk in etiologically heterogeneous sub-samples. A computational limit of the proposed strategy is encountered when the number of genomic variations (predictor variables) under study is large (> 500) because permutations are used to generate a null distribution to test the significance of a term (defined by values of particular variables) that characterizes a sub-sample of individuals through the peeling and pasting processes. As an alternative, in this paper we introduce a theoretical strategy that facilitates the quick calculation of Type I and Type II errors in the evaluation of terms in the peeling and pasting processes carried out in the execution of a PRIM analysis that are underestimated and non-existent, respectively, when a permutation-based hypothesis test is employed. The resultant savings in computational time makes possible the consideration of larger numbers of genomic variations (an example genome wide association study is given) in the selection of statistically significant terms in the formulation of PRIM prediction models. PMID:24570412

BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations

PubMed Central

Wang, Junbai; Batmanov, Kirill

2015-01-01

Sequence variations in regulatory DNA regions are known to cause functionally important consequences for gene expression. DNA sequence variations may have an essential role in determining phenotypes and may be linked to disease; however, their identification through analysis of massive genome-wide sequencing data is a great challenge. In this work, a new computational pipeline, a Bayesian method for protein–DNA interaction with binding affinity ranking (BayesPI-BAR), is proposed for quantifying the effect of sequence variations on protein binding. BayesPI-BAR uses biophysical modeling of protein–DNA interactions to predict single nucleotide polymorphisms (SNPs) that cause significant changes in the binding affinity of a regulatory region for transcription factors (TFs). The method includes two new parameters (TF chemical potentials or protein concentrations and direct TF binding targets) that are neglected by previous methods. The new method is verified on 67 known human regulatory SNPs, of which 47 (70%) have predicted true TFs ranked in the top 10. Importantly, the performance of BayesPI-BAR, which uses principal component analysis to integrate multiple predictions from various TF chemical potentials, is found to be better than that of existing programs, such as sTRAP and is-rSNP, when evaluated on the same SNPs. BayesPI-BAR is a publicly available tool and is able to carry out parallelized computation, which helps to investigate a large number of TFs or SNPs and to detect disease-associated regulatory sequence variations in the sea of genome-wide noncoding regions. PMID:26202972

Variations in colonoscopy practice in Europe: a multicentre descriptive study (EPAGE).

PubMed

Harris, Jennifer K; Vader, John-Paul; Wietlisbach, Vincent; Burnand, Bernard; Gonvers, Jean-Jacques; Froehlich, Florian

2007-01-01

The volume of colonoscopies performed is increasing and differences in colonoscopy practice over time and between centres have been reported. Examination of current practice is important for bench-marking quality. The objective of this study was to examine variations in colonoscopy practice in endoscopy centres internationally. This observational study prospectively included consecutive patients referred for colonoscopy from 21 centres in 11 countries. Patient, procedure and centre characteristics were collected through questionnaires. Descriptive statistics were performed and the variation between centres while controlling for case-mix was examined. A total of 6004 patients were included in the study. Most colonoscopies (93%; range between centres 70-100%) were performed for diagnostic purposes. The proportion of main indications for colonoscopy showed wide variations between centres, the two most common indications, surveillance and haematochezia, ranging between 7-24% and 5-38%, respectively. High-quality cleansing occurred in 74% (range 51-94%) of patients, and 30% (range 0-100%) of patients received deep sedation. Three-quarters (range 0-100%) of the patients were monitored during colonoscopy, and one-quarter (range 14-35%) underwent polypectomy. Colonoscopy was complete in 89% (range 69-98%) of patients and the median total duration was 20 min (range of centre medians 15-30 min). The variation between centres was not reduced when case-mix was controlled for. This study documented wide variations in colonoscopy practice between centres. Controlling for case-mix did not remove these variations, indicating that centre and procedure characteristics play a role. Centres generally were within the existing guidelines, although there is still some work to be done to ensure that all centres attain the goal of providing high-quality colonoscopy.

Morphological Variation in the Adult Hard Palate and Posterior Pharyngeal Wall

PubMed Central

Lammert, Adam; Proctor, Michael; Narayanan, Shrikanth

2013-01-01

Purpose Adult human vocal tracts display considerable morphological variation across individuals, but the nature and extent of this variation has not been extensively studied for many vocal tract structures. There exists a need to analyze morphological variation and, even more basically, to develop a methodology for morphological analysis of the vocal tract. Such analysis will facilitate fundamental characterization of the speech production system, with broad implications from modeling to explaining inter-speaker variability. Method A data-driven methodology to automatically analyze the extent and variety of morphological variation is proposed and applied to a diverse subject pool of 36 adults. Analysis is focused on two key aspects of vocal tract structure: the midsagittal shape of the hard palate and the posterior pharyngeal wall. Result Palatal morphology varies widely in its degree of concavity, but also in anteriority and sharpness. Pharyngeal wall morphology, by contrast, varies mostly in terms of concavity alone. The distribution of morphological characteristics is complex, and analysis suggests that certain variations may be categorical in nature. Conclusion Major modes of morphological variation are identified, including their relative magnitude, distribution and categorical nature. Implications of these findings for speech articulation strategies and speech acoustics are discussed. PMID:23690566

Hydrological and oceanic excitations to polar motion andlength-of-day variation

NASA Astrophysics Data System (ADS)

Chen, J. L.; Wilson, C. R.; Chao, B. F.; Shum, C. K.; Tapley, B. D.

2000-04-01

Water mass redistributions in the global hydrosphere, including continental water storage change and non-steric sea level change, introduce variations in the hydrological angular momentum (HAM) and the oceanic angular momentum (OAM). Under the conservation of angular momentum, HAM and OAM variations are significant excitation sources of the Earth rotational variations at a wide range of timescales. In this paper, we estimate HAM and OAM variations and their excitations to polar motion and length-of-day variation using soil moisture and snow estimates andnon-steric sea level change determined by TOPEX/Poseidon satellite radar altimeter observations and a simplified steric sea level change model. The results are compared with the variations of polar motion and LOD that are not accounted for by the atmosphere. This study indicates that seasonal continental water storage change provides significant contributions to both polar motion and LOD variation, especially to polar motion X, and the non-steric sea level change is responsible for a major part of the remaining excitations at both seasonal scale and high frequencies, particularly in polar motion Y and LOD. The good correlation between OAM contributions and the remaining excitations shows that large-scale non-tidal mass variation exists in the oceans and can be detected by TOPEX/Poseidon altimeter observations.

Sex Bias Exists in Human Surgical Clinical Research

PubMed Central

Mansukhani, Neel A.; Yoon, Dustin Y.; Teter, Katherine A.; Stubbs, Vanessa C.; Helenowski, Irene B.; Woodruff, Teresa K.; Kibbe, Melina R.

2016-01-01

Importance Sex is a variable that is poorly controlled for in clinical research. Objective Determine if sex bias exists in human surgical clinical research, determine if data are reported and analyzed using sex as an independent variable, and identify specialties where the greatest and least sex biases exist. Design Review and data abstraction from published peer-reviewed manuscripts. Setting All original peer-reviewed manuscripts published in 2011 and 2012 in Annals of Surgery, American Journal of Surgery, JAMA Surgery, Journal of Surgical Research, and Surgery. Main Outcome Measures Study type, location, number and sex of subjects, sex matching, and inclusion of sex-based reporting, statistical analysis, and discussion of data. Results Of 2,347 articles reviewed, 1,668 included human subjects. After excluding 365 articles, 1,303 manuscripts remained: 17 (1%) included only males, 41 (3%) included only females, 1,020 (78%) included males and females, and 225 (17%) did not document the sex of the subjects. While females represent over 50% of the total number of subjects included, considerable variability existed with the number of male, female, and unspecified subjects included among the journals, between US domestic and international studies, and between single versus multi-center studies. For manuscripts included in the study, only 38% reported these data by sex, 33% analyzed these data by sex, and 23% included a discussion of sex-based results. Sex matching of the subjects included in the research was poor, with only 18% of the studies matching the inclusion of both sexes by 80%. Upon analysis of the different surgical specialties, a wide variation in sex-based inclusion, matching, and data reporting existed, with colorectal surgery having the best matching of males and females and cardiac surgery having the worst. Conclusion Our data show that sex bias exists in human surgical clinical research. Few studies included men and women equally, less than one-third performed data analysis by sex, and there was wide variation in inclusion and matching of the sexes among the specialties and the journals reviewed. Because clinical research serves as the foundation for evidence-based medicine, it is imperative that this disparity be addressed so that therapies benefit both sexes. PMID:27551816

Patterns of variation in clutch sizes in a guild of temperate-nesting dabbling ducks

USGS Publications Warehouse

Krapu, G.L.; Reynolds, R.E.; Sargeant, G.A.; Renner, R.W.

2004-01-01

Clutch sizes of temperate-nesting dabbling ducks vary widely within and between years. Biologists have long been interested in why such patterns exist but have had difficulty separating intrinsic effects from environmental influences. In an attempt to gain greater insight into the roles of intrinsic and environmental influences on clutch sizes of dabbling ducks, we compared clutch-size patterns of mallard, northern pintail, gadwall, northern shoveler, and blue-winged teal in North Dakota and South Dakota over a 3-year period. The study was conducted during 1993-1995 when wetland habitat conditions were exceptionally consistent within time intervals but varied widely from the onset to the end of the study. We found that clutch sizes of gadwall and blue-winged teal were significantly smaller at the onset of nesting in 1993, when water conditions remained relatively poor following a 5-year drought (1988-1992), and pintail clutch sizes were larger late in the breeding season in 1993 after wetland conditions became exceptionally productive following heavy rains in late May and June. These findings were associated with gadwall and teal relying primarily on nutrients acquired on the breeding grounds to produce early clutches, and pintails using an exceptionally high proportion of their body lipids to produce early clutches, making this species highly dependent on abundant local sources of lipids for clutches produced later. Mallard, pintail, and shoveler rely largely on endogenous lipids carried to the breeding grounds to produce early clutches, and at least in the years of study, clutch sizes exhibited minimal variation at the onset of nesting. Our findings, when examined in context with existing information, suggest that interspecific variation in clutch sizes results from innate differences in several traits -- including body size, diet, timing of lipid acquisition, and nesting-- that affect the amount of lipid available for egg production. Annual differences in clutch sizes of all five species were not significant when effects of annual variation in nest initiation dates was accounted for, reflecting the key role of environmental influences on intraspecific variation among years.

Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species.

PubMed

West, Claire; James, Stephen A; Davey, Robert P; Dicks, Jo; Roberts, Ian N

2014-07-01

The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the internal transcribed spacer region, frequently used in plant phylogenetics, is now recognized as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analyzed data sets from the Saccharomyces Genome Resequencing Project, characterizing rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterization of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intraspecies phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridization events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multilocus rDNA systems. [concerted evolution; genome hydridisation; phylogenetic analysis; ribosomal DNA; whole genome sequencing; yeast]. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Water as an urban resource and nuisance

USGS Publications Warehouse

Thomas, H.E.; Schneider, William Joseph

1970-01-01

The water resource, which is widely and irregularly distributed on earth, is available to man for such enjoyment and development and use as he sees fit, some use being essential to his existence. Natural variations in the quantity and quality of water are inevitable and, if they cause annoyance or injury to someone, are accepted as one of the hardships that this planet imposes upon its inhabitants; such variations are recognized as "acts of God." However, if any man or society is partly responsible for these variations, which may cause such annoyance or injury, and may become a nuisance (an invasion or disturbance of the rights of others) such a man or society may perhaps be subject to injunctions and damage suits. Legal disputes over water as a nuisance are generally deeply involved with problems of the respective rights of plaintiff and defendant. These respective rights vary among the States.

A Survey on Gas Sensing Technology

PubMed Central

Liu, Xiao; Cheng, Sitian; Liu, Hong; Hu, Sha; Zhang, Daqiang; Ning, Huansheng

2012-01-01

Sensing technology has been widely investigated and utilized for gas detection. Due to the different applicability and inherent limitations of different gas sensing technologies, researchers have been working on different scenarios with enhanced gas sensor calibration. This paper reviews the descriptions, evaluation, comparison and recent developments in existing gas sensing technologies. A classification of sensing technologies is given, based on the variation of electrical and other properties. Detailed introduction to sensing methods based on electrical variation is discussed through further classification according to sensing materials, including metal oxide semiconductors, polymers, carbon nanotubes, and moisture absorbing materials. Methods based on other kinds of variations such as optical, calorimetric, acoustic and gas-chromatographic, are presented in a general way. Several suggestions related to future development are also discussed. Furthermore, this paper focuses on sensitivity and selectivity for performance indicators to compare different sensing technologies, analyzes the factors that influence these two indicators, and lists several corresponding improved approaches. PMID:23012563

Genome-Wide Mapping of Copy Number Variation in Humans: Comparative Analysis of High Resolution Array Platforms

PubMed Central

Haraksingh, Rajini R.; Abyzov, Alexej; Gerstein, Mark; Urban, Alexander E.; Snyder, Michael

2011-01-01

Accurate and efficient genome-wide detection of copy number variants (CNVs) is essential for understanding human genomic variation, genome-wide CNV association type studies, cytogenetics research and diagnostics, and independent validation of CNVs identified from sequencing based technologies. Numerous, array-based platforms for CNV detection exist utilizing array Comparative Genome Hybridization (aCGH), Single Nucleotide Polymorphism (SNP) genotyping or both. We have quantitatively assessed the abilities of twelve leading genome-wide CNV detection platforms to accurately detect Gold Standard sets of CNVs in the genome of HapMap CEU sample NA12878, and found significant differences in performance. The technologies analyzed were the NimbleGen 4.2 M, 2.1 M and 3×720 K Whole Genome and CNV focused arrays, the Agilent 1×1 M CGH and High Resolution and 2×400 K CNV and SNP+CGH arrays, the Illumina Human Omni1Quad array and the Affymetrix SNP 6.0 array. The Gold Standards used were a 1000 Genomes Project sequencing-based set of 3997 validated CNVs and an ultra high-resolution aCGH-based set of 756 validated CNVs. We found that sensitivity, total number, size range and breakpoint resolution of CNV calls were highest for CNV focused arrays. Our results are important for cost effective CNV detection and validation for both basic and clinical applications. PMID:22140474

Genome Variation Map: a data repository of genome variations in BIG Data Center.

PubMed

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2018-01-04

The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The role of interindividual variation in human carcinogenesis.

PubMed

Lai, C; Shields, P G

1999-02-01

The process of chemical carcinogenesis is a complex multistage process initiated by DNA damage in growth control genes. Carcinogens enter the body from a variety of sources, but most require metabolic activation before they can damage DNA. There are multiple protective processes that include detoxification and conjugation, DNA repair and programmed cell death. Most of these functions exhibit wide interindividual variation in the population and thus are thought to affect cancer risk. The role of gene-environment interactions is being explored, and current data indicate that genetic susceptibilities can modify carcinogen exposures from the diet and tobacco smoking, although much more data exist for the latter. This review addresses the relationships of human carcinogenesis to these interindividual differences of phase I, phase II and DNA repair enzymes.

License Plate Recognition System for Indian Vehicles

NASA Astrophysics Data System (ADS)

Sanap, P. R.; Narote, S. P.

2010-11-01

We consider the task of recognition of Indian vehicle number plates (also called license plates or registration plates in other countries). A system for Indian number plate recognition must cope with wide variations in the appearance of the plates. Each state uses its own range of designs with font variations between the designs. Also, vehicle owners may place the plates inside glass covered frames or use plates made of nonstandard materials. These issues compound the complexity of automatic number plate recognition, making existing approaches inadequate. We have developed a system that incorporates a novel combination of image processing and artificial neural network technologies to successfully locate and read Indian vehicle number plates in digital images. Commercial application of the system is envisaged.

Physical Therapy Protocols for Arthroscopic Bankart Repair.

PubMed

DeFroda, Steven F; Mehta, Nabil; Owens, Brett D

Outcomes after arthroscopic Bankart repair can be highly dependent on compliance and participation in physical therapy. Additionally, there are many variations in physician-recommended physical therapy protocols. The rehabilitation protocols of academic orthopaedic surgery departments vary widely despite the presence of consensus protocols. Descriptive epidemiology study. Level 3. Web-based arthroscopic Bankart rehabilitation protocols available online from Accreditation Council for Graduate Medical Education (ACGME)-accredited orthopaedic surgery programs were included for review. Individual protocols were reviewed to evaluate for the presence or absence of recommended therapies, goals for completion of ranges of motion, functional milestones, exercise start times, and recommended time to return to sport. Thirty protocols from 27 (16.4%) total institutions were identified out of 164 eligible for review. Overall, 9 (30%) protocols recommended an initial period of strict immobilization. Variability existed between the recommended time periods for sling immobilization (mean, 4.8 ± 1.8 weeks). The types of exercises and their start dates were also inconsistent. Goals to full passive range of motion (mean, 9.2 ± 2.8 weeks) and full active range of motion (mean, 12.2 ± 2.8 weeks) were consistent with other published protocols; however, wide ranges existed within the reviewed protocols as a whole. Only 10 protocols (33.3%) included a timeline for return to sport, and only 3 (10%) gave an estimate for return to game competition. Variation also existed when compared with the American Society of Shoulder and Elbow Therapists' (ASSET) consensus protocol. Rehabilitation protocols after arthroscopic Bankart repair were found to be highly variable. They also varied with regard to published consensus protocols. This discrepancy may lead to confusion among therapists and patients. This study highlights the importance of attending surgeons being very clear and specific with regard to their physical therapy instructions to patients and therapists.

Individual variation in social aggression and the probability of inheritance: theory and a field test.

PubMed

Cant, Michael A; Llop, Justine B; Field, Jeremy

2006-06-01

Recent theory suggests that much of the wide variation in individual behavior that exists within cooperative animal societies can be explained by variation in the future direct component of fitness, or the probability of inheritance. Here we develop two models to explore the effect of variation in future fitness on social aggression. The models predict that rates of aggression will be highest toward the front of the queue to inherit and will be higher in larger, more productive groups. A third prediction is that, in seasonal animals, aggression will increase as the time available to inherit the breeding position runs out. We tested these predictions using a model social species, the paper wasp Polistes dominulus. We found that rates of both aggressive "displays" (aimed at individuals of lower rank) and aggressive "tests" (aimed at individuals of higher rank) decreased down the hierarchy, as predicted by our models. The only other significant factor affecting aggression rates was date, with more aggression observed later in the season, also as predicted. Variation in future fitness due to inheritance rank is the hidden factor accounting for much of the variation in aggressiveness among apparently equivalent individuals in this species.

A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations

PubMed Central

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A.

2012-01-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure. PMID:22927824

Wide variation in hospital and physician payment rates evidence of provider market power.

PubMed

Ginsburg, Paul B

2010-11-01

Wide variation in private insurer payment rates to hospitals and physicians across and within local markets suggests that some providers, particularly hospitals, have significant market power to negotiate higher-than-competitive prices, according to a new study by the Center for Studying Health System Change (HSC). Looking across eight health care markets--Cleveland; Indianapolis; Los Angeles; Miami; Milwaukee; Richmond, Va.; San Francisco; and rural Wisconsin--average inpatient hospital payment rates of four large national insurers ranged from 147 percent of Medicare in Miami to 210 percent in San Francisco. In extreme cases, some hospitals command almost five times what Medicare pays for inpatient services and more than seven times what Medicare pays for outpatient care. Variation within markets was just as dramatic. For example, the hospital with prices at the 25th percentile of Los Angeles hospitals received 84 percent of Medicare rates for inpatient care, while the hospital with prices at the 75th percentile received 184 percent of Medicare rates. The highest-priced Los Angeles hospital with substantial inpatient claims volume received 418 percent of Medicare. While not as pronounced, significant variation in physician payment rates also exists across and within markets and by specialty. Few would characterize the variation in hospital and physician payment rates found in this study to be consistent with a highly competitive market. Purchasers and public policy makers can address provider market power, or the ability to negotiate higher-than-competitive prices, through two distinct approaches. One is to pursue market approaches to strengthen competitive forces, while the other is to constrain payment rates through regulation.

A quantitative comparison of the similarity between genes and geography in worldwide human populations.

PubMed

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A

2012-08-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure.

tRNA gene copy number variation in humans

PubMed Central

Iben, James R.; Maraia, Richard J.

2014-01-01

The human tRNAome consists of more than 500 interspersed tRNA genes comprising 51 anticodon families of largely unequal copy number. We examined tRNA gene copy number variation (tgCNV) in six individuals; two kindreds of two parents and a child, using high coverage whole genome sequence data. Such differences may be important because translation of some mRNAs is sensitive to the relative amounts of tRNAs and because tRNA competition determines translational efficiency vs. fidelity and production of native vs. misfolded proteins. We identified several tRNA gene clusters with CNV, which in some cases were part of larger iterations. In addition there was an isolated tRNALysCUU gene that was absent as a homozygous deletion in one of the parents. When assessed by semiquantitative PCR in 98 DNA samples representing a wide variety of ethnicities, this allele was found deleted in hetero- or homozygosity in all groups at ~50% frequency. This is the first report of copy number variation of human tRNA genes. We conclude that tgCNV exists at significant levels among individual humans and discuss the results in terms of genetic diversity and prior genome wide association studies (GWAS) that suggest the importance of the ratio of tRNALys isoacceptors in Type-2 diabetes. PMID:24342656

[Variations and simulation of stable isotopes in precipitation in the Heihe River basin].

PubMed

Wu, Jin-Kui; Yang, Qi-Yue; Ding, Yong-Jian; Ye, Bai-Sheng; Zhang, Ming-Quan

2011-07-01

To study the variations of deltaD and delta18O in precipitation, 301 samples were sampled during 2002-2004 in 6 sites in the Heihe River basin, Northwestern China. The deltaD and delta18O values ranged from 59 per thousand to -254 per thousand and 6.5 per thousand to -33.4 per thousand, respectively. This wide range indicated that stable isotopes in precipitation were controlled by different condensation mechanisms as a function of air temperature and varying sources of moisture. delta18O in precipitation had a close positive relationship with the air temperature, i. e., a clear temperature effect existed in this area. At a monthly scale, no precipitation effect existed. On the other hand, a weak precipitation effect still accrued at precipitation events scale. The spatial variation of delta18O showed that the weighted average delta18O values decreased with the increasing altitude of sampling sites at a gradient of -0. 47 per thousand/100m. A regional Meteoric Water Line, deltaD = 7.82 delta18O + 7.63, was nearly identical to the Meteoric Water Line in the Northern China. The results of backward trajectory of each precipitation day at Xishui showed that the moisture of the precipitation in cold season (October to March) mainly originated from the west while the moisture source was more complicated in warm season (April to September). The simulation of seasonal delta18O variation showed that the stable isotope composition of precipitation tended to a clear sine-wave seasonal variation.

Revisiting the variation of clustering coefficient of biological networks suggests new modular structure.

PubMed

Hao, Dapeng; Ren, Cong; Li, Chuanxing

2012-05-01

A central idea in biology is the hierarchical organization of cellular processes. A commonly used method to identify the hierarchical modular organization of network relies on detecting a global signature known as variation of clustering coefficient (so-called modularity scaling). Although several studies have suggested other possible origins of this signature, it is still widely used nowadays to identify hierarchical modularity, especially in the analysis of biological networks. Therefore, a further and systematical investigation of this signature for different types of biological networks is necessary. We analyzed a variety of biological networks and found that the commonly used signature of hierarchical modularity is actually the reflection of spoke-like topology, suggesting a different view of network architecture. We proved that the existence of super-hubs is the origin that the clustering coefficient of a node follows a particular scaling law with degree k in metabolic networks. To study the modularity of biological networks, we systematically investigated the relationship between repulsion of hubs and variation of clustering coefficient. We provided direct evidences for repulsion between hubs being the underlying origin of the variation of clustering coefficient, and found that for biological networks having no anti-correlation between hubs, such as gene co-expression network, the clustering coefficient doesn't show dependence of degree. Here we have shown that the variation of clustering coefficient is neither sufficient nor exclusive for a network to be hierarchical. Our results suggest the existence of spoke-like modules as opposed to "deterministic model" of hierarchical modularity, and suggest the need to reconsider the organizational principle of biological hierarchy.

Geographical genetic structuring and phenotypic variation in the Vellozia hirsuta (Velloziaceae) ochlospecies complex.

PubMed

Barbosa, Ariane R; Fiorini, Cecília F; Silva-Pereira, Viviane; Mello-Silva, Renato; Borba, Eduardo L

2012-09-01

Vellozia hirsuta forms a complex presenting wide morphological and anatomical variation, resulting in five specific names and 14 morpho-anatomical patterns occurring in disjunct populations. We carried out a phylogeographical study to investigate the existence of correlation among the genetic and morphological patterns within this complex, and to determine whether it is composed of various species or should be treated as an ochlospecies, a species having widely polymorphic and weakly polytypic complex variation, with morphological characteristics varying independently. We carried out phylogeographical analyses using cpDNA rpl32F-trnL intergenic region. We found 20 haplotypes in 23 populations sampled. The populations are genetically structured (Φ(ST) = 0.818) into four phylogeographical groups demonstrating geographical structuring but with no correlation with morpho-anatomical patterns. Our analyses do not support recognizing any of the species now synonymized under Vellozia hirsuta. The northern populations were the most genetically differentiated and could be considered a distinct taxon, as they are also morphologically different. It is recommended that Vellozia hirsuta be considered a single enormously variable species. The patterns of variation within V. hirsuta probably are related to climatic changes that occurred during the Pleistocene Epoch in tropical Brazil when reductions in forest cover favored the expansion of V. hirsuta populations into extensive lowland areas. The expansion of forest cover at the end of the glaciations would have again restricted the occurrence of campos rupestres vegetation to high elevations, which constitute the current centers of diversity of this species.

Segmental dynamics of polymers in nanoscopic confinements, as probed by simulations of polymer/layered-silicate nanocomposites.

PubMed

Kuppa, V; Foley, T M D; Manias, E

2003-09-01

In this paper we review molecular modeling investigations of polymer/layered-silicate intercalates, as model systems to explore polymers in nanoscopically confined spaces. The atomic-scale picture, as revealed by computer simulations, is presented in the context of salient results from a wide range of experimental techniques. This approach provides insights into how polymeric segmental dynamics are affected by severe geometric constraints. Focusing on intercalated systems, i.e. polystyrene (PS) in 2 nm wide slit-pores and polyethylene-oxide (PEO) in 1 nm wide slit-pores, a very rich picture for the segmental dynamics is unveiled, despite the topological constraints imposed by the confining solid surfaces. On a local scale, intercalated polymers exhibit a very wide distribution of segmental relaxation times (ranging from ultra-fast to ultra-slow, over a wide range of temperatures). In both cases (PS and PEO), the segmental relaxations originate from the confinement-induced local density variations. Additionally, where there exist special interactions between the polymer and the confining surfaces ( e.g., PEO) more molecular mechanisms are identified.

Genetic Contributions to Disparities in Preterm Birth

PubMed Central

Anum, Emmanuel A.; Springel, Edward H.; Shriver, Mark D.; Strauss, Jerome F.

2008-01-01

Ethnic disparity in preterm delivery between African Americans and European Americans has existed for decades, and is likely the consequence of multiple factors, including socioeconomic status, access to care, environment, and genetics. This review summarizes existing information on genetic variation and its association with preterm birth in African Americans. Candidate gene-based association studies, in which investigators have evaluated particular genes selected primarily because of their potential roles in the process of normal and pathological parturition, provide evidence that genetic contributions from both mother and fetus account for some of the disparity in preterm births. To date, most attention has been focused on genetic variation in pro- and anti-inflammatory cytokine genes and their respective receptors. These genes, particularly the pro-inflammatory cytokine genes and their receptors, are linked to matrix metabolism since these cytokines increase expression of matrix degrading metalloproteinases. However, the role that genetic variants that are different between populations play in preterm birth cannot yet be quantified. Future studies based on genome wide association or admixture mapping may reveal other genes that contribute to disparity in prematurity. PMID:18787421

Eucalyptus applied genomics: from gene sequences to breeding tools.

PubMed

Grattapaglia, Dario; Kirst, Matias

2008-01-01

Eucalyptus is the most widely planted hardwood crop in the tropical and subtropical world because of its superior growth, broad adaptability and multipurpose wood properties. Plantation forestry of Eucalyptus supplies high-quality woody biomass for several industrial applications while reducing the pressure on tropical forests and associated biodiversity. This review links current eucalypt breeding practices with existing and emerging genomic tools. A brief discussion provides a background to modern eucalypt breeding together with some current applications of molecular markers in support of operational breeding. Quantitative trait locus (QTL) mapping and genetical genomics are reviewed and an in-depth perspective is provided on the power of association genetics to dissect quantitative variation in this highly diverse organism. Finally, some challenges and opportunities to integrate genomic information into directional selective breeding are discussed in light of the upcoming draft of the Eucalyptus grandis genome. Given the extraordinary genetic variation that exists in the genus Eucalyptus, the ingenuity of most breeders, and the powerful genomic tools that have become available, the prospects of applied genomics in Eucalyptus forest production are encouraging.

Assessment of Gene-by-Sex Interaction Effect on Bone Mineral Density

PubMed Central

Liu, Ching-Ti; Estrada, Karol; Yerges-Armstrong, Laura M.; Amin, Najaf; Evangelou, Evangelos; Li, Guo; Minster, Ryan L.; Carless, Melanie A.; Kammerer, Candace M.; Oei, Ling; Zhou, Yanhua; Alonso, Nerea; Dailiana, Zoe; Eriksson, Joel; García-Giralt, Natalia; Giroux, Sylvie; Husted, Lise Bjerre; Khusainova, Rita I.; Koromila, Theodora; Kung, Annie WaiChee; Lewis, Joshua R.; Masi, Laura; Mencej-Bedrac, Simona; Nogues, Xavier; Patel, Millan S.; Prezelj, Janez; Richards, J Brent; Sham, Pak Chung; Spector, Timothy; Vandenput, Liesbeth; Xiao, Su-Mei; Zheng, Hou-Feng; Zhu, Kun; Balcells, Susana; Brandi, Maria Luisa; Frost, Morten; Goltzman, David; González-Macías, Jesús; Karlsson, Magnus; Khusnutdinova, Elza K.; Kollia, Panagoula; Langdahl, Bente Lomholt; Ljunggren, Östen; Lorentzon, Mattias; Marc, Janja; Mellström, Dan; Ohlsson, Claes; Olmos, José M.; Ralston, Stuart H.; Riancho, José A.; Rousseau, François; Urreizti, Roser; Van Hul, Wim; Zarrabeitia, María T.; Castano-Betancourt, Martha; Demissie, Serkalem; Grundberg, Elin; Herrera, Lizbeth; Kwan, Tony; Medina-Gómez, Carolina; Pastinen, Tomi; Sigurdsson, Gunnar; Thorleifsson, Gudmar; vanMeurs, Joyce B.J.; Blangero, John; Hofman, Albert; Liu, Yongmei; Mitchell, Braxton D.; O’Connell, Jeffrey R.; Oostra, Ben A.; Rotter, Jerome I; Stefansson, Kari; Streeten, Elizabeth A.; Styrkarsdottir, Unnur; Thorsteinsdottir, Unnur; Tylavsky, Frances A.; Uitterlinden, Andre; Cauley, Jane A.; Harris, Tamara B.; Ioannidis, John P.A.; Psaty, Bruce M.; Robbins, John A; Zillikens, M. Carola; vanDuijn, Cornelia M.; Prince, Richard L.; Karasik, David; Rivadeneira, Fernando; Kiel, Douglas P.; Cupples, L. Adrienne; Hsu, Yi-Hsiang

2012-01-01

Background Sexual dimorphism in various bone phenotypes, including bone mineral density (BMD), is widely observed; however the extent to which genes explain these sex differences is unclear. To identify variants with different effects by sex, we examined gene-by-sex autosomal interactions genome-wide, and performed eQTL analysis and bioinformatics network analysis. Methods We conducted an autosomal genome-wide meta-analysis of gene-by-sex interaction on lumbar spine (LS-) and femoral neck (FN-) BMD, in 25,353 individuals from eight cohorts. In a second stage, we followed up the 12 top SNPs (P<1×10−5) in an additional set of 24,763 individuals. Gene-by-sex interaction and sex-specific effects were examined in these 12 SNPs. Results We detected one novel genome-wide significant interaction associated with LS-BMD at the Chr3p26.1-p25.1 locus, near the GRM7 gene (male effect = 0.02 & p-value = 3.0×10−5; female effect = −0.007 & p-value=3.3×10−2) and eleven suggestive loci associated with either FN- or LS-BMD in discovery cohorts. However, there was no evidence for genome-wide significant (P<5×10−8) gene-by-sex interaction in the joint analysis of discovery and replication cohorts. Conclusion Despite the large collaborative effort, no genome-wide significant evidence for gene-by-sex interaction was found influencing BMD variation in this screen of autosomal markers. If they exist, gene-by-sex interactions for BMD probably have weak effects, accounting for less than 0.08% of the variation in these traits per implicated SNP. PMID:22692763

Prognosis research: why is Dr. Lydgate still waiting?

PubMed

Hemingway, Harry

2006-12-01

Understanding prognosis--the future risk of adverse outcomes among people with existing disease--plays third fiddle behind clinical research into therapeutic interventions and novel diagnostic technologies. Diseases show marked variations in a wide range of prognostic outcomes, yet these variations have seldom been the subject of systematic and sustained epidemiologic and multidisciplinary research. This is important to prioritize hypotheses for testing in intervention studies in groups, and to refine tools for prognostication in individuals. Methodologic standards for the design, conduct, analysis and reporting of prognosis research are required. Training is needed for the clinicians, policymakers, and payers who use prognostic information. Here, arguments detracting from the potential scope of prognosis research are rebutted and misconceptions addressed with the aim of stimulating debate on the evolving role of prognosis research.

Variation in printed handoff documents: Results and recommendations from a multicenter needs assessment.

PubMed

Rosenbluth, Glenn; Bale, James F; Starmer, Amy J; Spector, Nancy D; Srivastava, Rajendu; West, Daniel C; Sectish, Theodore C; Landrigan, Christopher P

2015-08-01

Handoffs of patient care are a leading root cause of medical errors. Standardized techniques exist to minimize miscommunications during verbal handoffs, but studies to guide standardization of printed handoff documents are lacking. To determine whether variability exists in the content of printed handoff documents and to identify key data elements that should be uniformly included in these documents. Pediatric hospitalist services at 9 institutions in the United States and Canada. Sample handoff documents from each institution were reviewed, and structured group interviews were conducted to understand each institution's priorities for written handoffs. An expert panel reviewed all handoff documents and structured group-interview findings, and subsequently made consensus-based recommendations for data elements that were either essential or recommended, including best overall printed handoff practices. Nine sites completed structured group interviews and submitted data. We identified substantial variation in both the structure and content of printed handoff documents. Only 4 of 23 possible data elements (17%) were uniformly present in all sites' handoff documents. The expert panel recommended the following as essential for all printed handoffs: assessment of illness severity, patient summary, action items, situation awareness and contingency plans, allergies, medications, age, weight, date of admission, and patient and hospital service identifiers. Code status and several other elements were also recommended. Wide variation exists in the content of printed handoff documents. Standardizing printed handoff documents has the potential to decrease omissions of key data during patient care transitions, which may decrease the risk of downstream medical errors. © 2015 Society of Hospital Medicine.

Neonatal Intensive Care Unit Safety Culture Varies Widely

PubMed Central

Profit, Jochen; Etchegaray, Jason; Petersen, Laura A; Sexton, J Bryan; Hysong, Sylvia J; Mei, Minghua; Thomas, Eric J

2013-01-01

background Variation in health care delivery and outcomes in NICUs may be partly explained by differences in safety culture. objective To describe NICU caregiver assessments of safety culture, explore the variability within and between NICUs on safety culture domains, and test for association with caregiver characteristics. methods We surveyed NICU caregivers in a convenience sample of 12 hospitals from a single health care system, using the Safety Attitudes Questionnaire (SAQ). The six scales of the SAQ include teamwork climate, safety climate, job satisfaction, stress recognition, perception of management, and working conditions. For each NICU we calculated scale means, standard deviations and percent positives (percent agreement). results We found substantial variation in safety culture domains among participating NICUs. A composite mean score across the six safety culture domains ranged from 56.3 to 77.8 on a 100-point scale and NICUs in the top four NICUs were significantly different from the bottom four (p < .001). Across the six domains, respondent assessments varied widely, but were least positive on perceptions of management (3–80% positive; mean 33.3%) and stress recognition (18–61% positive; mean 41.3%). Comparisons of SAQ scale scores between NICUs and a previously published cohort of adult ICUs generally revealed higher scores for NICUs. Physicians composite scores were 8.2 (p = .04) and 9.5 (p =.02) points higher than nurses and ancillary personnel. conclusion Significant variation and scope for improvement in safety culture exists among this sample of NICUs. The NICU variation was similar to variation in adult ICUs, but NICU scores were generally higher than adult ICU scores. Future studies should validate whether safety culture as measured with the SAQ correlates with clinical and operational outcomes in the NICU setting. PMID:21930691

What we know about the purpose, theoretical foundation, scope and dimensionality of existing self-management measurement tools: A scoping review.

PubMed

Packer, Tanya L; Fracini, America; Audulv, Åsa; Alizadeh, Neda; van Gaal, Betsie G I; Warner, Grace; Kephart, George

2018-04-01

To identify self-report, self-management measures for adults with chronic conditions, and describe their purpose, theoretical foundation, dimensionality (multi versus uni), and scope (generic versus condition specific). A search of four databases (8479 articles) resulted in a scoping review of 28 self-management measures. Although authors identified tools as measures of self-management, wide variation in constructs measured, purpose, and theoretical foundations existed. Subscales on 13 multidimensional tools collectively measure domains of self-management relevant to clients, however no one tool's subscales cover all domains. Viewing self-management as a complex, multidimensional whole, demonstrated that existing measures assess different, related aspects of self-management. Activities and social roles, though important to patients, are rarely measured. Measures with capacity to quantify and distinguish aspects of self-management may promote tailored patient care. In selecting tools for research or assessment, the reason for development, definitions, and theories underpinning the measure should be scrutinized. Our ability to measure self-management must be rigorously mapped to provide comprehensive and system-wide care for clients with chronic conditions. Viewing self-management as a complex whole will help practitioners to understand the patient perspective and their contribution in supporting each individual patient. Copyright © 2017 Elsevier B.V. All rights reserved.

The genetics of exceptional longevity: Insights from centenarians.

PubMed

Santos-Lozano, Alejandro; Santamarina, Ana; Pareja-Galeano, Helios; Sanchis-Gomar, Fabian; Fiuza-Luces, Carmen; Cristi-Montero, Carlos; Bernal-Pino, Aranzazu; Lucia, Alejandro; Garatachea, Nuria

2016-08-01

As the world population ages, so the prevalence increases of individuals aged 100 years or more, known as centenarians. Reaching this age has been described as exceptional longevity (EL) and is attributed to both genetic and environmental factors. Many genetic variations known to affect life expectancy exist in centenarians. This review of studies conducted on centenarians and supercentenarians (older than 110 years) updates knowledge of the impacts on longevity of the twenty most widely investigated single nucleotide polymorphisms (SNPs). Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Prevalence and treatment of depression in Parkinson's disease.

PubMed

Veazey, Connie; Aki, Sahinde Ozlem Erden; Cook, Karon F; Lai, Eugene C; Kunik, Mark E

2005-01-01

Parkinson's disease (PD) is a progressive neurological condition with debilitating symptoms, and depression is a common comorbid condition of this disease. The authors review existing literature on the prevalence and treatment of depression in PD. Prevalence estimates of depression vary widely, ranging from 7%-76%. This variation is due to inconsistent methodology. Treatment options for depression in PD include medication therapy, electroconvulsive therapy (ECT), and psychotherapy. There are few randomized controlled trials of these treatment options. The authors argue for more systematic and controlled research examining both the prevalence and treatment of depression in PD.

Therapy Caps and Variation in Cost of Outpatient Occupational Therapy by Provider, Insurance Status, and Geographic Region.

PubMed

Pergolotti, Mackenzi; Lavery, Jessica; Reeve, Bryce B; Dusetzina, Stacie B

This article describes the cost of occupational therapy by provider, insurance status, and geographic region and the number of visits allowed and out-of-pocket costs under proposed therapy caps. This retrospective, population-based study used Medicare Provider Utilization and Payment Data for occupational therapists billing in 2012 and 2013 (Ns = 3,662 and 3,820, respectively). We examined variations in outpatient occupational therapy services with descriptive statistics and the impact of therapy caps on occupational therapy visits and patient out-of-pocket costs. Differences in cost between occupational and physical therapists were minimal. The most frequently billed service was therapeutic exercises. Wisconsin had the most inflated outpatient costs in both years. Under the proposed therapy cap, patients could receive an evaluation plus 12-14 visits. . Wide variation exists in potential patient out-of-pocket costs for occupational therapy services on the basis of insurance coverage and state. Patients without insurance pay a premium. Copyright © 2018 by the American Occupational Therapy Association, Inc.

Therapy Caps and Variation in Cost of Outpatient Occupational Therapy by Provider, Insurance Status, and Geographic Region

PubMed Central

Pergolotti, Mackenzi; Lavery, Jessica; Reeve, Bryce B.; Dusetzina, Stacie B.

2018-01-01

OBJECTIVE. This article describes the cost of occupational therapy by provider, insurance status, and geographic region and the number of visits allowed and out-of-pocket costs under proposed therapy caps. METHOD. This retrospective, population-based study used Medicare Provider Utilization and Payment Data for occupational therapists billing in 2012 and 2013 (Ns = 3,662 and 3,820, respectively). We examined variations in outpatient occupational therapy services with descriptive statistics and the impact of therapy caps on occupational therapy visits and patient out-of-pocket costs. RESULTS. Differences in cost between occupational and physical therapists were minimal. The most frequently billed service was therapeutic exercises. Wisconsin had the most inflated outpatient costs in both years. Under the proposed therapy cap, patients could receive an evaluation plus 12–14 visits. DISCUSSION. Wide variation exists in potential patient out-of-pocket costs for occupational therapy services on the basis of insurance coverage and state. Patients without insurance pay a premium. PMID:29426383

Common genetic variation drives molecular heterogeneity in human iPSCs.

PubMed

Kilpinen, Helena; Goncalves, Angela; Leha, Andreas; Afzal, Vackar; Alasoo, Kaur; Ashford, Sofie; Bala, Sendu; Bensaddek, Dalila; Casale, Francesco Paolo; Culley, Oliver J; Danecek, Petr; Faulconbridge, Adam; Harrison, Peter W; Kathuria, Annie; McCarthy, Davis; McCarthy, Shane A; Meleckyte, Ruta; Memari, Yasin; Moens, Nathalie; Soares, Filipa; Mann, Alice; Streeter, Ian; Agu, Chukwuma A; Alderton, Alex; Nelson, Rachel; Harper, Sarah; Patel, Minal; White, Alistair; Patel, Sharad R; Clarke, Laura; Halai, Reena; Kirton, Christopher M; Kolb-Kokocinski, Anja; Beales, Philip; Birney, Ewan; Danovi, Davide; Lamond, Angus I; Ouwehand, Willem H; Vallier, Ludovic; Watt, Fiona M; Durbin, Richard; Stegle, Oliver; Gaffney, Daniel J

2017-06-15

Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS cell lines limits their potential use for research and therapy. Here we describe the systematic generation, genotyping and phenotyping of 711 iPS cell lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative. Our study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPS cell phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in iPS cells. In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells.

Common genetic variation drives molecular heterogeneity in human iPSCs

PubMed Central

Leha, Andreas; Afzal, Vackar; Alasoo, Kaur; Ashford, Sofie; Bala, Sendu; Bensaddek, Dalila; Casale, Francesco Paolo; Culley, Oliver J; Danecek, Petr; Faulconbridge, Adam; Harrison, Peter W; Kathuria, Annie; McCarthy, Davis; McCarthy, Shane A; Meleckyte, Ruta; Memari, Yasin; Moens, Nathalie; Soares, Filipa; Mann, Alice; Streeter, Ian; Agu, Chukwuma A; Alderton, Alex; Nelson, Rachel; Harper, Sarah; Patel, Minal; White, Alistair; Patel, Sharad R; Clarke, Laura; Halai, Reena; Kirton, Christopher M; Kolb-Kokocinski, Anja; Beales, Philip; Birney, Ewan; Danovi, Davide; Lamond, Angus I; Ouwehand, Willem H; Vallier, Ludovic; Watt, Fiona M; Durbin, Richard

2017-01-01

Induced pluripotent stem cell (iPSC) technology has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterisation of many existing iPSC lines limits their potential use for research and therapy. Here, we describe the systematic generation, genotyping and phenotyping of 711 iPSC lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative (HipSci: http://www.hipsci.org). Our study outlines the major sources of genetic and phenotypic variation in iPSCs and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPSC phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of rare, genomic copy number mutations that are repeatedly observed in iPSC reprogramming and present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells. PMID:28489815

A new Mumford-Shah total variation minimization based model for sparse-view x-ray computed tomography image reconstruction.

PubMed

Chen, Bo; Bian, Zhaoying; Zhou, Xiaohui; Chen, Wensheng; Ma, Jianhua; Liang, Zhengrong

2018-04-12

Total variation (TV) minimization for the sparse-view x-ray computer tomography (CT) reconstruction has been widely explored to reduce radiation dose. However, due to the piecewise constant assumption for the TV model, the reconstructed images often suffer from over-smoothness on the image edges. To mitigate this drawback of TV minimization, we present a Mumford-Shah total variation (MSTV) minimization algorithm in this paper. The presented MSTV model is derived by integrating TV minimization and Mumford-Shah segmentation. Subsequently, a penalized weighted least-squares (PWLS) scheme with MSTV is developed for the sparse-view CT reconstruction. For simplicity, the proposed algorithm is named as 'PWLS-MSTV.' To evaluate the performance of the present PWLS-MSTV algorithm, both qualitative and quantitative studies were conducted by using a digital XCAT phantom and a physical phantom. Experimental results show that the present PWLS-MSTV algorithm has noticeable gains over the existing algorithms in terms of noise reduction, contrast-to-ratio measure and edge-preservation.

Genotype-Specific Variation in the Structure of Root Fungal Communities Is Related to Chickpea Plant Productivity

PubMed Central

Hamel, Chantal; Gan, Yantai; Tar'an, Bunyamin; Knight, Joan Diane

2015-01-01

Increasing evidence supports the existence of variations in the association of plant roots with symbiotic fungi that can improve plant growth and inhibit pathogens. However, it is unclear whether intraspecific variations in the symbiosis exist among plant cultivars and if they can be used to improve crop productivity. In this study, we determined genotype-specific variations in the association of chickpea roots with soil fungal communities and evaluated the effect of root mycota on crop productivity. A 2-year field experiment was conducted in southwestern Saskatchewan, the central zone of the chickpea growing region of the Canadian prairie. The effects of 13 cultivars of chickpea, comprising a wide range of phenotypes and genotypes, were tested on the structure of root-associated fungal communities based on internal transcribed spacer (ITS) and 18S rRNA gene markers using 454 amplicon pyrosequencing. Chickpea cultivar significantly influenced the structure of the root fungal community. The magnitude of the effect varied with the genotypes evaluated, and effects were consistent across years. For example, the roots of CDC Corrine, CDC Cory, and CDC Anna hosted the highest fungal diversity and CDC Alma and CDC Xena the lowest. Fusarium sp. was dominant in chickpea roots but was less abundant in CDC Corrine than the other cultivars. A bioassay showed that certain of these fungal taxa, including Fusarium species, can reduce the productivity of chickpea, whereas Trichoderma harzianum can increase chickpea productivity. The large variation in the profile of chickpea root mycota, which included growth-promoting and -inhibiting species, supports the possibility of improving the productivity of chickpea by improving its root mycota in chickpea genetic improvement programs using traditional breeding techniques. PMID:25616789

Genome-wide association studies in Africans and African Americans: Expanding the Framework of the Genomics of Human Traits and Disease

PubMed Central

Peprah, Emmanuel; Xu, Huichun; Tekola-Ayele, Fasil; Royal, Charmaine D.

2014-01-01

Genomic research is one of the tools for elucidating the pathogenesis of diseases of global health relevance, and paving the research dimension to clinical and public health translation. Recent advances in genomic research and technologies have increased our understanding of human diseases, genes associated with these disorders, and the relevant mechanisms. Genome-wide association studies (GWAS) have proliferated since the first studies were published several years ago, and have become an important tool in helping researchers comprehend human variation and the role genetic variants play in disease. However, the need to expand the diversity of populations in GWAS has become increasingly apparent as new knowledge is gained about genetic variation. Inclusion of diverse populations in genomic studies is critical to a more complete understanding of human variation and elucidation of the underpinnings of complex diseases. In this review, we summarize the available data on GWAS in recent-African ancestry populations within the western hemisphere (i.e. African Americans and peoples of the Caribbean) and continental African populations. Furthermore, we highlight ways in which genomic studies in populations of recent African ancestry have led to advances in the areas of malaria, HIV, prostate cancer, and other diseases. Finally, we discuss the advantages of conducting GWAS in recent African ancestry populations in the context of addressing existing and emerging global health conditions. PMID:25427668

Watershed boundaries and geographic isolation: patterns of diversification in cutthroat trout from western North America.

PubMed

Loxterman, Janet L; Keeley, Ernest R

2012-03-19

For wide-ranging species, intraspecific variation can occur as a result of reproductive isolation from local adaptive differences or from physical barriers to movement. Cutthroat trout (Oncorhynchus clarkii), a widely distributed fish species from North America, has been divided into numerous putative subspecies largely based on its isolation in different watersheds. In this study, we examined mtDNA sequence variation of cutthroat trout to determine the major phylogenetic lineages of this polytypic species. We use these data as a means of testing whether geographic isolation by watershed boundaries can be a primary factor organizing intraspecific diversification. We collected cutthroat trout from locations spanning almost the entire geographic range of this species and included samples from all major subspecies of cutthroat trout. Based on our analyses, we reveal eight major lineages of cutthroat trout, six of which correspond to subspecific taxonomy commonly used to describe intraspecific variation in this species. The Bonneville cutthroat trout (O. c. utah) and Yellowstone cutthroat trout (O. c. bouvieri) did not form separate monophyletic lineages, but instead formed an intermixed clade. We also document the geographic distribution of a Great Basin lineage of cutthroat trout; a group typically defined as Bonneville cutthroat trout, but it appears more closely related to the Colorado River lineage of cutthroat trout. Our study indicates that watershed boundaries can be an organizing factor isolating genetic diversity in fishes; however, historical connections between watersheds can also influence the template of isolation. Widely distributed species, like cutthroat trout, offer an opportunity to assess where historic watershed connections may have existed, and help explain the current distribution of biological diversity across a landscape.

Watershed boundaries and geographic isolation: patterns of diversification in cutthroat trout from western North America

PubMed Central

2012-01-01

Background For wide-ranging species, intraspecific variation can occur as a result of reproductive isolation from local adaptive differences or from physical barriers to movement. Cutthroat trout (Oncorhynchus clarkii), a widely distributed fish species from North America, has been divided into numerous putative subspecies largely based on its isolation in different watersheds. In this study, we examined mtDNA sequence variation of cutthroat trout to determine the major phylogenetic lineages of this polytypic species. We use these data as a means of testing whether geographic isolation by watershed boundaries can be a primary factor organizing intraspecific diversification. Results We collected cutthroat trout from locations spanning almost the entire geographic range of this species and included samples from all major subspecies of cutthroat trout. Based on our analyses, we reveal eight major lineages of cutthroat trout, six of which correspond to subspecific taxonomy commonly used to describe intraspecific variation in this species. The Bonneville cutthroat trout (O. c. utah) and Yellowstone cutthroat trout (O. c. bouvieri) did not form separate monophyletic lineages, but instead formed an intermixed clade. We also document the geographic distribution of a Great Basin lineage of cutthroat trout; a group typically defined as Bonneville cutthroat trout, but it appears more closely related to the Colorado River lineage of cutthroat trout. Conclusion Our study indicates that watershed boundaries can be an organizing factor isolating genetic diversity in fishes; however, historical connections between watersheds can also influence the template of isolation. Widely distributed species, like cutthroat trout, offer an opportunity to assess where historic watershed connections may have existed, and help explain the current distribution of biological diversity across a landscape. PMID:22429757

Hydrotherapy in burn care: a survey of hydrotherapy practices in the UK and Ireland and literature review.

PubMed

Langschmidt, Jenna; Caine, Paul L; Wearn, Christopher M; Bamford, Amy; Wilson, Yvonne T; Moiemen, Naiem S

2014-08-01

Hydrotherapy is widely used in burns management however there are risks associated with its use, in particular cross-infection. Data regarding indications and techniques in common use is deficient. This study aimed to investigate hydrotherapy practices in the UK and Ireland. A survey of the hydrotherapy practice of major burn care providers was performed by e mail and where necessary, follow up telephone contact. The survey included 28 burn care providers. 27 reported using hydrotherapy. Only 11 (41%) had defined indication criteria with 4 (15%) implementing a specific protocol. Variations in hydrotherapy practice were seen. Hydrotherapy is used nationwide, however considerable variation in practice exists. One area worthy of further consideration is the need for appropriate standards of infection control. Copyright © 2013 Elsevier Ltd and ISBI. All rights reserved.

Anatomic Assessment of Variations in Kambin's Triangle: A Surgical and Cadaver Study.

PubMed

Ozer, Ali Fahir; Suzer, Tuncer; Can, Halil; Falsafi, Mani; Aydin, Murat; Sasani, Mehdi; Oktenoglu, Tunc

2017-04-01

The relationship of exiting root and Kambin's triangle is discussed in this article. Transforaminal endoscopic surgery as the gold standard of less invasive lumbar disc surgeries is performed through Kambin's triangle. Existing root damage is one of the most important complication for this type of surgery. Anatomic variations in Kambin's triangle may be the main reason for nerve root damage during endoscopic lumbar disc surgery. Kambin's triangle was investigated with surgical views and cadaver studies. Thirty-four patients with far lateral disc herniation were treated with an extraforaminal approach under the microscope. On the other hand, 48 Kambin's triangles were dissected on 8 cadavers. Three main types of triangle were identified, and patients were grouped according to these 3 types of the triangle. Only 6 of the 34 patients had type 3 triangles, which is the wide classical triangle described by Kambin; however, 17 patients had type 2, with a narrow space in the triangle, and 11 patients had type 1, with no space inside the triangle. Cadaver results were similar; only 10 of the 48 specimens had the type 3 classical triangle, whereas 23 specimens had type 2, and 15 specimens had type 1 triangles. Our results disclosed narrowed or no space in 82.4% of the patients and 79.2% of the cadavers. We observed that a wide and safe room of the triangle may not be exist in some patients. Therefore, more care must be taken during endoscopic lumbar disc surgery to avoid nerve damage. Copyright © 2017 Elsevier Inc. All rights reserved.

Time-varying BRDFs.

PubMed

Sun, Bo; Sunkavalli, Kalyan; Ramamoorthi, Ravi; Belhumeur, Peter N; Nayar, Shree K

2007-01-01

The properties of virtually all real-world materials change with time, causing their bidirectional reflectance distribution functions (BRDFs) to be time varying. However, none of the existing BRDF models and databases take time variation into consideration; they represent the appearance of a material at a single time instance. In this paper, we address the acquisition, analysis, modeling, and rendering of a wide range of time-varying BRDFs (TVBRDFs). We have developed an acquisition system that is capable of sampling a material's BRDF at multiple time instances, with each time sample acquired within 36 sec. We have used this acquisition system to measure the BRDFs of a wide range of time-varying phenomena, which include the drying of various types of paints (watercolor, spray, and oil), the drying of wet rough surfaces (cement, plaster, and fabrics), the accumulation of dusts (household and joint compound) on surfaces, and the melting of materials (chocolate). Analytic BRDF functions are fit to these measurements and the model parameters' variations with time are analyzed. Each category exhibits interesting and sometimes nonintuitive parameter trends. These parameter trends are then used to develop analytic TVBRDF models. The analytic TVBRDF models enable us to apply effects such as paint drying and dust accumulation to arbitrary surfaces and novel materials.

An Integrative Review of Pain Resource Nurse Programs.

PubMed

Crawford, Cecelia L; Boller, Jan; Jadalla, Ahlam; Cuenca, Emma

2016-01-01

Mismanaged pain challenges health care systems. In the early 1990s, pain resource nurse programs were developed by Ferrell and colleagues. Variations of the model have existed for more than 20 years. While results of these programs have been disseminated, conclusive evidence has not been examined via a synthesis of the literature. A structured systematic search using multiple databases was conducted for research studies published 2005-2012. The search identified 11 studies on effective use of a pain resource nurse and/or a pain resource nurse program. The results revealed wide variations existing in program design, research methodology, practice settings, and reported outcomes. Overall, the strength of the evidence on pain resource nurse programs was determined to range from low to moderate quality for making generalizable conclusions. However, 4 key elements were identified as integral to effective pain resource nurse programs and useful for the program design and development: leadership commitment and active involvement in embedding a culture of effective pain management throughout the organization; addressing staff-related and organization-related challenges and barriers to pain management; a combination of strategies to overcome these barriers; and collaborative multidisciplinary teamwork and communication. Specific recommendations are provided for program implementation. Although the evidence was inconclusive, useful information exists to create the design of effective pain resource nurse programs. Collaborative multisite studies on the long-term effects of pain resource nurse programs are recommended.

Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness.

PubMed

Conomos, Matthew P; Miller, Michael B; Thornton, Timothy A

2015-05-01

Population structure inference with genetic data has been motivated by a variety of applications in population genetics and genetic association studies. Several approaches have been proposed for the identification of genetic ancestry differences in samples where study participants are assumed to be unrelated, including principal components analysis (PCA), multidimensional scaling (MDS), and model-based methods for proportional ancestry estimation. Many genetic studies, however, include individuals with some degree of relatedness, and existing methods for inferring genetic ancestry fail in related samples. We present a method, PC-AiR, for robust population structure inference in the presence of known or cryptic relatedness. PC-AiR utilizes genome-screen data and an efficient algorithm to identify a diverse subset of unrelated individuals that is representative of all ancestries in the sample. The PC-AiR method directly performs PCA on the identified ancestry representative subset and then predicts components of variation for all remaining individuals based on genetic similarities. In simulation studies and in applications to real data from Phase III of the HapMap Project, we demonstrate that PC-AiR provides a substantial improvement over existing approaches for population structure inference in related samples. We also demonstrate significant efficiency gains, where a single axis of variation from PC-AiR provides better prediction of ancestry in a variety of structure settings than using 10 (or more) components of variation from widely used PCA and MDS approaches. Finally, we illustrate that PC-AiR can provide improved population stratification correction over existing methods in genetic association studies with population structure and relatedness. © 2015 WILEY PERIODICALS, INC.

Extreme isotopic variations in the upper mantle: evidence from Ronda

NASA Astrophysics Data System (ADS)

Reisberg, Laurie; Zindler, Alan

1986-12-01

The Ronda Ultramafic Complex in southern Spain represents a piece of the Earth's mantle which has been tectonically emplaced into the crust. Nd and Sr isotopic analyses are presented for leached, hand-picked Cr-diopside separates prepared from 15 rock and 18 river sediment samples from Ronda. These results demonstrate that within this small, contiguous body there exists the entire range of Nd isotopic compositions, and much of the range of Sr compositions, found in rocks derived from the sub-oceanic mantle. The sediment cpx samples show that the average isotopic composition of the massif becomes progressively less "depleted" moving from SW to NE along the long axis of the massif. The rock cpx samples document 143Nd/ 144Nd variations from 0.5129 to 0.5126 and 87Sr/ 86Sr variations from 0.7031 to 0.7039 within a uniform outcrop less than 10 m in extent. Thus, extreme isotopic fluctuations exist over a wide range of wavelengths. Sr and Nd isotopes are generally inversely correlated, forming a trend on a Nd-Sr diagram that sharply crosscuts that of the "mantle array". Many of the 143Nd/ 144Nd values, and all of the Sm/Nd values, from one section of the massif are lower than that SCV015SCV0 of the bulk earth, implying that this region existed, or was influenced by a component which existed, in a LREE-enriched environment for a significant period of time. Among the sediment cpxs there is a positive correlation between 143Nd/ 144Nd and 147Sm/ 144Nd. The rock cpx separates display considerably more scatter. A simple, single-stage differentiation event starting with a uniform mantle source cannot explain these results. At least one episode of mixing with a LREE-enriched component is required. If these results from Ronda are typical of the upper mantle, basalts with different isotopic compositions need not derive from spatially separated mantle sources.

Qualitative and Quantitative Assessment of Four Marketed Formulations of Brahmi

PubMed Central

Saini, Neeti; Mathur, Rajani; Agrawal, S. S.

2012-01-01

This study was conducted with the aim to compare two batches each of four popular commercial formulations of Bacopa monnieri (Brahmi), and report, if any, inter-batch variations. The formulations were procured from local market and analyzed for label specifications, uniformity of weight of capsule, identity, purity and strength parameters (total ash content test, acid insoluble ash content, water soluble extractive, alcohol soluble extractive, loss on drying). Bacoside A, one of the pharmacologically active saponin present in B. monnieri, was quantified in all the formulations using UV-spectrophotometer. In addition each formulation was assessed and compared for variation in biological activity using in vitro test for hemolytic activity using human erythrocytes. The results of the study show that there is a wide variation in the quality and content of herbal drugs marketed by different manufacturers. More importantly this study demonstrates that there exists a bigger challenge of batch-to-batch variation in the quality and content of herbal formulations of the same manufacturer. This challenge of providing standardized formulations is being faced by not any one manufacturing house but by all, and may be attributed firstly to, lack of stringent regulations and secondly to high variability in raw material quality. PMID:23204618

Qualitative and quantitative assessment of four marketed formulations of brahmi.

PubMed

Saini, Neeti; Mathur, Rajani; Agrawal, S S

2012-01-01

This study was conducted with the aim to compare two batches each of four popular commercial formulations of Bacopa monnieri (Brahmi), and report, if any, inter-batch variations. The formulations were procured from local market and analyzed for label specifications, uniformity of weight of capsule, identity, purity and strength parameters (total ash content test, acid insoluble ash content, water soluble extractive, alcohol soluble extractive, loss on drying). Bacoside A, one of the pharmacologically active saponin present in B. monnieri, was quantified in all the formulations using UV-spectrophotometer. In addition each formulation was assessed and compared for variation in biological activity using in vitro test for hemolytic activity using human erythrocytes. The results of the study show that there is a wide variation in the quality and content of herbal drugs marketed by different manufacturers. More importantly this study demonstrates that there exists a bigger challenge of batch-to-batch variation in the quality and content of herbal formulations of the same manufacturer. This challenge of providing standardized formulations is being faced by not any one manufacturing house but by all, and may be attributed firstly to, lack of stringent regulations and secondly to high variability in raw material quality.

From symmetry to asymmetry: Phylogenetic patterns of asymmetry variation in animals and their evolutionary significance

PubMed Central

Palmer, A. Richard

1996-01-01

Phylogenetic analyses of asymmetry variation offer a powerful tool for exploring the interplay between ontogeny and evolution because (i) conspicuous asymmetries exist in many higher metazoans with widely varying modes of development, (ii) patterns of bilateral variation within species may identify genetically and environmentally triggered asymmetries, and (iii) asymmetries arising at different times during development may be more sensitive to internal cytoplasmic inhomogeneities compared to external environmental stimuli. Using four broadly comparable asymmetry states (symmetry, antisymmetry, dextral, and sinistral), and two stages at which asymmetry appears developmentally (larval and postlarval), I evaluated relations between ontogenetic and phylogenetic patterns of asymmetry variation. Among 140 inferred phylogenetic transitions between asymmetry states, recorded from 11 classes in five phyla, directional asymmetry (dextral or sinistral) evolved directly from symmetrical ancestors proportionally more frequently among larval asymmetries. In contrast, antisymmetry, either as an end state or as a transitional stage preceding directional asymmetry, was confined primarily to postlarval asymmetries. The ontogenetic origin of asymmetry thus significantly influences its subsequent evolution. Furthermore, because antisymmetry typically signals an environmentally triggered asymmetry, the phylogenetic transition from antisymmetry to directional asymmetry suggests that many cases of laterally fixed asymmetries evolved via genetic assimilation. PMID:8962039

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data

PubMed Central

Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

2017-01-01

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data—previously only browseable through our FTP site—by focusing on particular samples, populations or data sets of interest. PMID:27638885

Integrative DNA methylation and gene expression analysis to assess the universality of the CpG island methylator phenotype.

PubMed

Moarii, Matahi; Reyal, Fabien; Vert, Jean-Philippe

2015-10-13

The CpG island methylator phenotype (CIMP) was first characterized in colorectal cancer but since has been extensively studied in several other tumor types such as breast, bladder, lung, and gastric. CIMP is of clinical importance as it has been reported to be associated with prognosis or response to treatment. However, the identification of a universal molecular basis to define CIMP across tumors has remained elusive. We perform a genome-wide methylation analysis of over 2000 tumor samples from 5 cancer sites to assess the existence of a CIMP with common molecular basis across cancers. We then show that the CIMP phenotype is associated with specific gene expression variations. However, we do not find a common genetic signature in all tissues associated with CIMP. Our results suggest the existence of a universal epigenetic and transcriptomic signature that defines the CIMP across several tumor types but does not indicate the existence of a common genetic signature of CIMP.

Electrocardiogram transmission - The state of the art.

NASA Technical Reports Server (NTRS)

Firstenberg, A.; Huston, S. W.; Olsen, D. E.; Hahn, P. M.

1971-01-01

A comparative analysis of available clinical EKG telemetry systems was conducted. Although present day electrocardiogram diagnosis requires a high degree of measurement accuracy, there exists wide variations in the performance characteristics of the various telemeters marketed today necessitating careful consideration of specifications prior to procurement. The authors have endeavored to provide the physicians with a clear understanding, in terms of the effects on the electrocardiogram, of the factors he must evaluate in order to ensure high fidelity EKG reproduction. A tabulation of comparative parameter values for each unit obtained from manufacturers' specifications and substantiated by standardized performance tests conducted in our laboratory is presented.

Multistate Lempel-Ziv (MLZ) index interpretation as a measure of amplitude and complexity changes.

PubMed

Sarlabous, Leonardo; Torres, Abel; Fiz, Jose A; Gea, Joaquim; Galdiz, Juan B; Jane, Raimon

2009-01-01

The Lempel-Ziv complexity (LZ) has been widely used to evaluate the randomness of finite sequences. In general, the LZ complexity has been used to determine the complexity grade present in biomedical signals. The LZ complexity is not able to discern between signals with different amplitude variations and similar random components. On the other hand, amplitude parameters, as the root mean square (RMS), are not able to discern between signals with similar power distributions and different random components. In this work, we present a novel method to quantify amplitude and complexity variations in biomedical signals by means of the computation of the LZ coefficient using more than two quantification states, and with thresholds fixed and independent of the dynamic range or standard deviation of the analyzed signal: the Multistate Lempel-Ziv (MLZ) index. Our results indicate that MLZ index with few quantification levels only evaluate the complexity changes of the signal, with high number of levels, the amplitude variations, and with an intermediate number of levels informs about both amplitude and complexity variations. The study performed in diaphragmatic mechanomyographic signals shows that the amplitude variations of this signal are more correlated with the respiratory effort than the complexity variations. Furthermore, it has been observed that the MLZ index with high number of levels practically is not affected by the existence of impulsive, sinusoidal, constant and Gaussian noises compared with the RMS amplitude parameter.

Robust resolution enhancement optimization methods to process variations based on vector imaging model

NASA Astrophysics Data System (ADS)

Ma, Xu; Li, Yanqiu; Guo, Xuejia; Dong, Lisong

2012-03-01

Optical proximity correction (OPC) and phase shifting mask (PSM) are the most widely used resolution enhancement techniques (RET) in the semiconductor industry. Recently, a set of OPC and PSM optimization algorithms have been developed to solve for the inverse lithography problem, which are only designed for the nominal imaging parameters without giving sufficient attention to the process variations due to the aberrations, defocus and dose variation. However, the effects of process variations existing in the practical optical lithography systems become more pronounced as the critical dimension (CD) continuously shrinks. On the other hand, the lithography systems with larger NA (NA>0.6) are now extensively used, rendering the scalar imaging models inadequate to describe the vector nature of the electromagnetic field in the current optical lithography systems. In order to tackle the above problems, this paper focuses on developing robust gradient-based OPC and PSM optimization algorithms to the process variations under a vector imaging model. To achieve this goal, an integrative and analytic vector imaging model is applied to formulate the optimization problem, where the effects of process variations are explicitly incorporated in the optimization framework. The steepest descent algorithm is used to optimize the mask iteratively. In order to improve the efficiency of the proposed algorithms, a set of algorithm acceleration techniques (AAT) are exploited during the optimization procedure.

Variation in clinical decision-making for induction of labour: a qualitative study.

PubMed

Nippita, Tanya A; Porter, Maree; Seeho, Sean K; Morris, Jonathan M; Roberts, Christine L

2017-09-22

Unexplained variation in induction of labour (IOL) rates exist between hospitals, even after accounting for casemix and hospital differences. We aimed to explore factors that influence clinical decision-making for IOL that may be contributing to the variation in IOL rates between hospitals. We undertook a qualitative study involving semi-structured, audio-recorded interviews with obstetricians and midwives. Using purposive sampling, participants known to have diverse opinions on IOL were selected from ten Australian maternity hospitals (based on differences in hospital IOL rate, size, location and case-mix complexities). Transcripts were indexed, coded, and analysed using the Framework Approach to identify main themes and subthemes. Forty-five participants were interviewed (21 midwives, 24 obstetric medical staff). Variations in decision-making for IOL were based on the obstetrician's perception of medical risk in the pregnancy (influenced by the obstetrician's personality and knowledge), their care relationship with the woman, how they involved the woman in decision-making, and resource availability. The role of a 'gatekeeper' in the procedural aspects of arranging an IOL also influenced decision-making. There was wide variation in the clinical decision-making practices of obstetricians and less accountability for decision-making in hospitals with a high IOL rate, with the converse occurring in hospitals with low IOL rates. Improved communication, standardised risk assessment and accountability for IOL offer potential for reducing variation in hospital IOL rates.

Geometric Representations of Condition Queries on Three-Dimensional Vector Fields

NASA Technical Reports Server (NTRS)

Henze, Chris

1999-01-01

Condition queries on distributed data ask where particular conditions are satisfied. It is possible to represent condition queries as geometric objects by plotting field data in various spaces derived from the data, and by selecting loci within these derived spaces which signify the desired conditions. Rather simple geometric partitions of derived spaces can represent complex condition queries because much complexity can be encapsulated in the derived space mapping itself A geometric view of condition queries provides a useful conceptual unification, allowing one to intuitively understand many existing vector field feature detection algorithms -- and to design new ones -- as variations on a common theme. A geometric representation of condition queries also provides a simple and coherent basis for computer implementation, reducing a wide variety of existing and potential vector field feature detection techniques to a few simple geometric operations.

Infection prevention practices in adult intensive care units in a large community hospital system after implementing strategies to reduce health care-associated, methicillin-resistant Staphylococcus aureus infections.

PubMed

Moody, Julia; Septimus, Edward; Hickok, Jason; Huang, Susan S; Platt, Richard; Gombosev, Adrijana; Terpstra, Leah; Avery, Taliser; Lankiewicz, Julie; Perlin, Jonathan B

2013-02-01

A range of strategies and approaches have been developed for preventing health care-associated infections. Understanding the variation in practices among facilities is necessary to improve compliance with existing programs and aid the implementation of new interventions. In 2009, HCA Inc administered an electronic survey to measure compliance with evidence-based infection prevention practices as well as identify variation in products or methods, such as use of special approach technology for central vascular catheters and ventilator care. Responding adult intensive care units (ICUs) were those considering participation in a clinical trial to reduce health care-associated infections. Responses from 99 ICUs in 55 hospitals indicated that many evidenced-based practices were used consistently, including methicillin-resistant Staphylococcus aureus (MRSA) screening and use of contact precautions for MRSA-positive patients. Other practices exhibited wide variability including discontinuation of precautions and use of antimicrobial technology or chlorhexidine patches for central vascular catheters. MRSA decolonization was not a predominant practice in ICUs. In this large, community-based health care system, there was substantial variation in the products and methods to reduce health care-associated infections. Despite system-wide emphasis on basic practices as a precursor to adding special approach technologies, this survey showed that these technologies were commonplace, including in facilities where improvement in basic practices was needed. Copyright © 2013 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

Reliable gene expression analysis by reverse transcription-quantitative PCR: reporting and minimizing the uncertainty in data accuracy.

PubMed

Remans, Tony; Keunen, Els; Bex, Geert Jan; Smeets, Karen; Vangronsveld, Jaco; Cuypers, Ann

2014-10-01

Reverse transcription-quantitative PCR (RT-qPCR) has been widely adopted to measure differences in mRNA levels; however, biological and technical variation strongly affects the accuracy of the reported differences. RT-qPCR specialists have warned that, unless researchers minimize this variability, they may report inaccurate differences and draw incorrect biological conclusions. The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines describe procedures for conducting and reporting RT-qPCR experiments. The MIQE guidelines enable others to judge the reliability of reported results; however, a recent literature survey found low adherence to these guidelines. Additionally, even experiments that use appropriate procedures remain subject to individual variation that statistical methods cannot correct. For example, since ideal reference genes do not exist, the widely used method of normalizing RT-qPCR data to reference genes generates background noise that affects the accuracy of measured changes in mRNA levels. However, current RT-qPCR data reporting styles ignore this source of variation. In this commentary, we direct researchers to appropriate procedures, outline a method to present the remaining uncertainty in data accuracy, and propose an intuitive way to select reference genes to minimize uncertainty. Reporting the uncertainty in data accuracy also serves for quality assessment, enabling researchers and peer reviewers to confidently evaluate the reliability of gene expression data. © 2014 American Society of Plant Biologists. All rights reserved.

Wide variations in blood product transfusion practices among providers who care for patients with acute leukemia in the United States.

PubMed

Pine, Alexander B; Lee, Eun-Ju; Sekeres, Mikkael; Steensma, David P; Zelterman, Daniel; Prebet, Thomas; DeZern, Amy; Komrokji, Rami; Litzow, Mark; Luger, Selina; Stone, Richard; Erba, Harry P; Garcia-Manero, Guillermo; Lee, Alfred I; Podoltsev, Nikolai A; Barbarotta, Lisa; Kasberg, Stephanie; Hendrickson, Jeanne E; Gore, Steven D; Zeidan, Amer M

2017-02-01

Transfusion of blood products is a key component of the supportive management in patients with acute leukemia (AL). However high-quality trial evidence and clinical outcome data to support specific transfusion goals for blood products for patients with AL remain limited leading to diverse transfusion practices. The primary objective of this study was to determine the spectrum of transfusion patterns in a variety of care settings among providers who treat AL patients. A 31-question survey queried providers caring for AL patients about the existence of institutional guidelines for transfusion of blood products, transfusion triggers for hemoglobin (Hb), platelets (PLTs), and fibrinogen in various settings including inpatient and outpatient and before procedures. We analyzed 130 responses and identified divergent transfusion Hb goals in hospitalized and ambulatory patients, fibrinogen goals for cryoprecipitate transfusions, and variation in practice for use of certain PLTs and red blood cell products. The least variable transfusion patterns were reported for PLT goals in thrombocytopenia and in the setting of invasive procedures such as bone marrow biopsy and lumbar punctures. This survey confirmed wide variations in blood product transfusion practices across several clinical scenarios in patients with AL. The findings emphasized the need for large prospective randomized trials to develop standardized evidence-based guidelines for blood product transfusions in patients with AL with the goal of limiting unnecessary transfusions without compromising outcomes. © 2016 AABB.

Assessment of gene-by-sex interaction effect on bone mineral density.

PubMed

Liu, Ching-Ti; Estrada, Karol; Yerges-Armstrong, Laura M; Amin, Najaf; Evangelou, Evangelos; Li, Guo; Minster, Ryan L; Carless, Melanie A; Kammerer, Candace M; Oei, Ling; Zhou, Yanhua; Alonso, Nerea; Dailiana, Zoe; Eriksson, Joel; García-Giralt, Natalia; Giroux, Sylvie; Husted, Lise Bjerre; Khusainova, Rita I; Koromila, Theodora; Kung, Annie Waichee; Lewis, Joshua R; Masi, Laura; Mencej-Bedrac, Simona; Nogues, Xavier; Patel, Millan S; Prezelj, Janez; Richards, J Brent; Sham, Pak Chung; Spector, Timothy; Vandenput, Liesbeth; Xiao, Su-Mei; Zheng, Hou-Feng; Zhu, Kun; Balcells, Susana; Brandi, Maria Luisa; Frost, Morten; Goltzman, David; González-Macías, Jesús; Karlsson, Magnus; Khusnutdinova, Elza K; Kollia, Panagoula; Langdahl, Bente Lomholt; Ljunggren, Osten; Lorentzon, Mattias; Marc, Janja; Mellström, Dan; Ohlsson, Claes; Olmos, José M; Ralston, Stuart H; Riancho, José A; Rousseau, François; Urreizti, Roser; Van Hul, Wim; Zarrabeitia, María T; Castano-Betancourt, Martha; Demissie, Serkalem; Grundberg, Elin; Herrera, Lizbeth; Kwan, Tony; Medina-Gómez, Carolina; Pastinen, Tomi; Sigurdsson, Gunnar; Thorleifsson, Gudmar; Vanmeurs, Joyce Bj; Blangero, John; Hofman, Albert; Liu, Yongmei; Mitchell, Braxton D; O'Connell, Jeffrey R; Oostra, Ben A; Rotter, Jerome I; Stefansson, Kari; Streeten, Elizabeth A; Styrkarsdottir, Unnur; Thorsteinsdottir, Unnur; Tylavsky, Frances A; Uitterlinden, Andre; Cauley, Jane A; Harris, Tamara B; Ioannidis, John Pa; Psaty, Bruce M; Robbins, John A; Zillikens, M Carola; Vanduijn, Cornelia M; Prince, Richard L; Karasik, David; Rivadeneira, Fernando; Kiel, Douglas P; Cupples, L Adrienne; Hsu, Yi-Hsiang

2012-10-01

Sexual dimorphism in various bone phenotypes, including bone mineral density (BMD), is widely observed; however, the extent to which genes explain these sex differences is unclear. To identify variants with different effects by sex, we examined gene-by-sex autosomal interactions genome-wide, and performed expression quantitative trait loci (eQTL) analysis and bioinformatics network analysis. We conducted an autosomal genome-wide meta-analysis of gene-by-sex interaction on lumbar spine (LS) and femoral neck (FN) BMD in 25,353 individuals from 8 cohorts. In a second stage, we followed up the 12 top single-nucleotide polymorphisms (SNPs; p < 1 × 10(-5) ) in an additional set of 24,763 individuals. Gene-by-sex interaction and sex-specific effects were examined in these 12 SNPs. We detected one novel genome-wide significant interaction associated with LS-BMD at the Chr3p26.1-p25.1 locus, near the GRM7 gene (male effect = 0.02 and p = 3.0 × 10(-5) ; female effect = -0.007 and p = 3.3 × 10(-2) ), and 11 suggestive loci associated with either FN- or LS-BMD in discovery cohorts. However, there was no evidence for genome-wide significant (p < 5 × 10(-8) ) gene-by-sex interaction in the joint analysis of discovery and replication cohorts. Despite the large collaborative effort, no genome-wide significant evidence for gene-by-sex interaction was found to influence BMD variation in this screen of autosomal markers. If they exist, gene-by-sex interactions for BMD probably have weak effects, accounting for less than 0.08% of the variation in these traits per implicated SNP. © 2012 American Society for Bone and Mineral Research. Copyright © 2012 American Society for Bone and Mineral Research.

Cross-National Moral Beliefs: The Influence of National Religious Context

PubMed Central

Finke, Roger; Adamczyk, Amy

2014-01-01

International surveys have documented wide variation in religious beliefs and practices across nations, but does this variation in the national religious context make a difference? Building on existing theory we explain why religion should have both micro and macro-level effects on morality not sanctioned by the state and why the effects of religion differ from other forms of culture. Using two international surveys and Hierarchical Linear Modeling Techniques (HLM) we sort out the effects of national context and personal beliefs on morality with and without legal underpinnings. We find that national religious context, the respondent’s age, and religious beliefs and practices are the most consistent predictors of the sexual morality index. For morality sanctioned by the state, however, the effects for personal beliefs and practices are attenuated and the effects of the national religious context are no longer significant. PMID:25097270

Low-frequency sound propagation modeling over a locally-reacting boundary using the parabolic approximation

NASA Technical Reports Server (NTRS)

Robertson, J. S.; Siegman, W. L.; Jacobson, M. J.

1989-01-01

There is substantial interest in the analytical and numerical modeling of low-frequency, long-range atmospheric acoustic propagation. Ray-based models, because of frequency limitations, do not always give an adequate prediction of quantities such as sound pressure or intensity levels. However, the parabolic approximation method, widely used in ocean acoustics, and often more accurate than ray models for lower frequencies of interest, can be applied to acoustic propagation in the atmosphere. Modifications of an existing implicit finite-difference implementation for computing solutions to the parabolic approximation are discussed. A locally-reacting boundary is used together with a one-parameter impedance model. Intensity calculations are performed for a number of flow resistivity values in both quiescent and windy atmospheres. Variations in the value of this parameter are shown to have substantial effects on the spatial variation of the acoustic signal.

Choosing surgical lighting in the LED era.

PubMed

Knulst, Arjan J; Stassen, Laurents P S; Grimbergen, Cornelis A; Dankelman, Jenny

2009-12-01

The aim of this study is to evaluate the illumination characteristics of LED lights objectively to ease the selection of surgical lighting. The illuminance distributions of 5 main and 4 auxiliary lights were measured in 8 clinically relevant scenarios. For each light and scenario, the maximum illuminance E(c) (klux) and the size of the light field d(10) (mm) were computed. The results showed: that large variations for both E(c) (25-160 klux) and d(10) (109-300 mm) existed; that using auxiliary lights reduced both E(c) and d(10) by up to 80% and 30%; that with segmented lights, uneven light distributions occurred; and that with colored LED lights shadow edges on the surgical field became colored. Objective illuminance measurements show a wide variation between lights and a superiority of main over auxiliary lights. Uneven light distributions and colored shadows indicate that LED lights still need to converge to an optimal design.

Interpreting estimates of heritability--a note on the twin decomposition.

PubMed

Stenberg, Anders

2013-03-01

While most outcomes may in part be genetically mediated, quantifying genetic heritability is a different matter. To explore data on twins and decompose the variation is a classical method to determine whether variation in outcomes, e.g. IQ or schooling, originate from genetic endowments or environmental factors. Despite some criticism, the model is still widely used. The critique is generally related to how estimates of heritability may encompass environmental mediation. This aspect is sometimes left implicit by authors even though its relevance for the interpretation is potentially profound. This short note is an appeal for clarity from authors when interpreting the magnitude of heritability estimates. It is demonstrated how disregarding existing theoretical contributions can easily lead to unnecessary misinterpretations and/or controversies. The key arguments are relevant also for estimates based on data of adopted children or from modern molecular genetics research. Copyright © 2012 Elsevier B.V. All rights reserved.

Hospital variation in time to defibrillation after in-hospital cardiac arrest.

PubMed

Chan, Paul S; Nichol, Graham; Krumholz, Harlan M; Spertus, John A; Nallamothu, Brahmajee K

2009-07-27

Delays to defibrillation are associated with worse survival after in-hospital cardiac arrest, but the degree to which hospitals vary in defibrillation response times and hospital predictors of delays remain unknown. Using hierarchical models, we evaluated hospital variation in rates of delayed defibrillation (>2 minutes) and its impact on survival among 7479 adult inpatients with cardiac arrests at 200 hospitals within the National Registry of Cardiopulmonary Resuscitation. Adjusted rates of delayed defibrillation varied substantially among hospitals (range, 2.4%-50.9%), with hospital-level effects accounting for a significant amount of the total variation in defibrillation delays after adjusting for patient factors. We found a 46% greater odds of patients with identical covariates getting delayed defibrillation at one randomly selected hospital compared with another. Among traditional hospital factors evaluated, however, only bed volume (reference category: <200 beds; 200-499 beds: odds ratio [OR], 0.62 [95% confidence interval {CI}, 0.48-0.80]; >or=500 beds: OR, 0.74 [95% CI, 0.53-1.04]) and arrest location (reference category: intensive care unit; telemetry unit: OR, 1.92 [95% CI, 1.65-2.22]; nonmonitored unit: OR, 1.90 [95% CI, 1.61-2.24]) were associated with differences in rates of delayed defibrillation. Wide variation also existed in adjusted hospital rates of survival to discharge (range, 5.3%-49.6%), with higher survival among hospitals in the top-performing quartile for defibrillation time (compared with the bottom quartile: OR for top quartile, 1.41 [95% CI, 1.11-1.77]). Rates of delayed defibrillation vary widely among hospitals but are largely unexplained by traditional hospital factors. Given its association with improved survival, future research is needed to better understand best practices in the delivery of defibrillation at top-performing hospitals.

Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

PubMed Central

Song, Yun S.

2012-01-01

Estimating fine-scale recombination maps of Drosophila from population genomic data is a challenging problem, in particular because of the high background recombination rate. In this paper, a new computational method is developed to address this challenge. Through an extensive simulation study, it is demonstrated that the method allows more accurate inference, and exhibits greater robustness to the effects of natural selection and noise, compared to a well-used previous method developed for studying fine-scale recombination rate variation in the human genome. As an application, a genome-wide analysis of genetic variation data is performed for two Drosophila melanogaster populations, one from North America (Raleigh, USA) and the other from Africa (Gikongoro, Rwanda). It is shown that fine-scale recombination rate variation is widespread throughout the D. melanogaster genome, across all chromosomes and in both populations. At the fine-scale, a conservative, systematic search for evidence of recombination hotspots suggests the existence of a handful of putative hotspots each with at least a tenfold increase in intensity over the background rate. A wavelet analysis is carried out to compare the estimated recombination maps in the two populations and to quantify the extent to which recombination rates are conserved. In general, similarity is observed at very broad scales, but substantial differences are seen at fine scales. The average recombination rate of the X chromosome appears to be higher than that of the autosomes in both populations, and this pattern is much more pronounced in the African population than the North American population. The correlation between various genomic features—including recombination rates, diversity, divergence, GC content, gene content, and sequence quality—is examined using the wavelet analysis, and it is shown that the most notable difference between D. melanogaster and humans is in the correlation between recombination and diversity. PMID:23284288

Case-mix fails to explain variation in mastectomy rates: management of screen-detected breast cancer in a UK region 1997–2003

PubMed Central

Caldon, L J M; Walters, S J; Reed, J A; Murphy, A; Worley, A; Reed, M W R

2004-01-01

Wide variation in the surgical management of breast cancer exists at hospital, regional, national and international level. To demonstrate whether variation in surgical practice observed at aggregate level between breast units persists following adjustment for case-mix, individual patient-level data from the Trent Breast Screening Programme Quality Assurance database (1997–2003) was analysed. Expected case-mix adjusted mastectomy rates were derived by logistic regression using the variables tumour size, site and grade, patient age and year of presentation, employing the region's overall case-mix adjusted practice as the reference population. The region's 11 breast screening units detected 5109 (3989 invasive) surgically managed primary breast cancers over the 6-year period. A total of 1828 mastectomies (Mx) were performed (Mx rate 35.8%, 95% confidence interval: 34.5–37.1%). Significant variation in mastectomy rates were observed between units (range 25–45%, P<0.0001), and persists following case-mix adjustment (P<0.0001). Two-fold variation in observed to expected unit mastectomy rate coefficient is demonstrated overall (range 0.66–1.36), increasing to almost four-fold variation in cancers less than 15 mm diameter (range 0.55–1.95). Significant variation in surgery for screen-detected primary breast cancer is not explained by case-mix. Further research is required to investigate potential patient and professional causative factors. PMID:15611797

Physical-level synthesis for digital lab-on-a-chip considering variation, contamination, and defect.

PubMed

Liao, Chen; Hu, Shiyan

2014-03-01

Microfluidic lab-on-a-chips have been widely utilized in biochemical analysis and human health studies due to high detection accuracy, high timing efficiency, and low cost. The increasing design complexity of lab-on-a-chips necessitates the computer-aided design (CAD) methodology in contrast to the classical manual design methodology. A key part in lab-on-a-chip CAD is physical-level synthesis. It includes the lab-on-a-chip placement and routing, where placement is to determine the physical location and the starting time of each operation and routing is to transport each droplet from the source to the destination. In the lab-on-a-chip design, variation, contamination, and defect need to be considered. This work designs a physical-level synthesis flow which simultaneously considers variation, contamination, and defect of the lab-on-a-chip design. It proposes a maze routing based, variation, contamination, and defect aware droplet routing technique, which is seamlessly integrated into an existing placement technique. The proposed technique improves the placement solution for routing and achieves the placement and routing co-optimization to handle variation, contamination, and defect. The simulation results demonstrate that our technique does not use any defective/contaminated grids, while the technique without considering contamination and defect uses 17.0% of the defective/contaminated grids on average. In addition, our routing variation aware technique significantly improves the average routing yield by 51.2% with only 3.5% increase in completion time compared to a routing variation unaware technique.

COMADRE: a global data base of animal demography.

PubMed

Salguero-Gómez, Roberto; Jones, Owen R; Archer, C Ruth; Bein, Christoph; de Buhr, Hendrik; Farack, Claudia; Gottschalk, Fränce; Hartmann, Alexander; Henning, Anne; Hoppe, Gabriel; Römer, Gesa; Ruoff, Tara; Sommer, Veronika; Wille, Julia; Voigt, Jakob; Zeh, Stefan; Vieregg, Dirk; Buckley, Yvonne M; Che-Castaldo, Judy; Hodgson, David; Scheuerlein, Alexander; Caswell, Hal; Vaupel, James W

2016-03-01

The open-data scientific philosophy is being widely adopted and proving to promote considerable progress in ecology and evolution. Open-data global data bases now exist on animal migration, species distribution, conservation status, etc. However, a gap exists for data on population dynamics spanning the rich diversity of the animal kingdom world-wide. This information is fundamental to our understanding of the conditions that have shaped variation in animal life histories and their relationships with the environment, as well as the determinants of invasion and extinction. Matrix population models (MPMs) are among the most widely used demographic tools by animal ecologists. MPMs project population dynamics based on the reproduction, survival and development of individuals in a population over their life cycle. The outputs from MPMs have direct biological interpretations, facilitating comparisons among animal species as different as Caenorhabditis elegans, Loxodonta africana and Homo sapiens. Thousands of animal demographic records exist in the form of MPMs, but they are dispersed throughout the literature, rendering comparative analyses difficult. Here, we introduce the COMADRE Animal Matrix Database, an open-data online repository, which in its version 1.0.0 contains data on 345 species world-wide, from 402 studies with a total of 1625 population projection matrices. COMADRE also contains ancillary information (e.g. ecoregion, taxonomy, biogeography, etc.) that facilitates interpretation of the numerous demographic metrics that can be derived from its MPMs. We provide R code to some of these examples. We introduce the COMADRE Animal Matrix Database, a resource for animal demography. Its open-data nature, together with its ancillary information, will facilitate comparative analysis, as will the growing availability of databases focusing on other aspects of the rich animal diversity, and tools to query and combine them. Through future frequent updates of COMADRE, and its integration with other online resources, we encourage animal ecologists to tackle global ecological and evolutionary questions with unprecedented sample size. © 2016 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Insights into mammalian biology from the wild house mouse Mus musculus

PubMed Central

Phifer-Rixey, Megan; Nachman, Michael W

2015-01-01

The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system. DOI: http://dx.doi.org/10.7554/eLife.05959.001 PMID:25875302

Genome Wide Analysis of Fatty Acid Desaturation and Its Response to Temperature1[OPEN

PubMed Central

Menard, Guillaume N.; Moreno, Jose Martin; Bryant, Fiona M.; Munoz-Azcarate, Olaya; Hassani-Pak, Keywan; Kurup, Smita

2017-01-01

Plants modify the polyunsaturated fatty acid content of their membrane and storage lipids in order to adapt to changes in temperature. In developing seeds, this response is largely controlled by the activities of the microsomal ω-6 and ω-3 fatty acid desaturases, FAD2 and FAD3. Although temperature regulation of desaturation has been studied at the molecular and biochemical levels, the genetic control of this trait is poorly understood. Here, we have characterized the response of Arabidopsis (Arabidopsis thaliana) seed lipids to variation in ambient temperature and found that heat inhibits both ω-6 and ω-3 desaturation in phosphatidylcholine, leading to a proportional change in triacylglycerol composition. Analysis of the 19 parental accessions of the multiparent advanced generation intercross (MAGIC) population showed that significant natural variation exists in the temperature responsiveness of ω-6 desaturation. A combination of quantitative trait locus (QTL) analysis and genome-wide association studies (GWAS) using the MAGIC population suggests that ω-6 desaturation is largely controlled by cis-acting sequence variants in the FAD2 5′ untranslated region intron that determine the expression level of the gene. However, the temperature responsiveness of ω-6 desaturation is controlled by a separate QTL on chromosome 2. The identity of this locus is unknown, but genome-wide association studies identified potentially causal sequence variants within ∼40 genes in an ∼450-kb region of the QTL. PMID:28108698

Intraspecific Trait Variation and Coordination: Root and Leaf Economics Spectra in Coffee across Environmental Gradients

PubMed Central

Isaac, Marney E.; Martin, Adam R.; de Melo Virginio Filho, Elias; Rapidel, Bruno; Roupsard, Olivier; Van den Meersche, Karel

2017-01-01

Hypotheses on the existence of a universal “Root Economics Spectrum” (RES) have received arguably the least attention of all trait spectra, despite the key role root trait variation plays in resource acquisition potential. There is growing interest in quantifying intraspecific trait variation (ITV) in plants, but there are few studies evaluating (i) the existence of an intraspecific RES within a plant species, or (ii) how a RES may be coordinated with other trait spectra within species, such as a leaf economics spectrum (LES). Using Coffea arabica (Rubiaceae) as a model species, we measured seven morphological and chemical traits of intact lateral roots, which were paired with information on four key LES traits. Field collections were completed across four nested levels of biological organization. The intraspecific trait coefficient of variation (cv) ranged from 25 to 87% with root diameter and specific root tip density showing the lowest and highest cv, respectively. Between 27 and 68% of root ITV was explained by site identity alone for five of the seven traits measured. A single principal component explained 56.2% of root trait covariation, with plants falling along a RES from resource acquiring to conserving traits. Multiple factor analysis revealed significant orthogonal relationships between root and leaf spectra. RES traits were strongly orthogonal with respect to LES traits, suggesting these traits vary independently from one another in response to environmental cues. This study provides among the first evidence that plants from the same species differentiate from one another along an intraspecific RES. We find that in one of the world’s most widely cultivated crops, an intraspecific RES is orthogonal to an intraspecific LES, indicating that above and belowground responses of plants to managed (or natural) environmental gradients are likely to occur independently from one another. PMID:28747919

Contrasting Genomic Diversity in Two Closely Related Postharvest Pathogens: Penicillium digitatum and Penicillium expansum.

PubMed

Julca, Irene; Droby, Samir; Sela, Noa; Marcet-Houben, Marina; Gabaldón, Toni

2015-12-14

Penicillium digitatum and Penicillium expansum are two closely related fungal plant pathogens causing green and blue mold in harvested fruit, respectively. The two species differ in their host specificity, being P. digitatum restricted to citrus fruits and P. expansum able to infect a wide range of fruits after harvest. Although host-specific Penicillium species have been found to have a smaller gene content, it is so far unclear whether these different host specificities impact genome variation at the intraspecific level. Here we assessed genome variation across four P. digitatum and seven P. expansum isolates from geographically distant regions. Our results show very high similarity (average 0.06 SNPs [single nucleotide polymorphism] per kb) between globally distributed isolates of P. digitatum pointing to a recent expansion of a single lineage. This low level of genetic variation found in our samples contrasts with the higher genetic variability observed in the similarly distributed P. expansum isolates (2.44 SNPs per kb). Patterns of polymorphism in P. expansum indicate that recombination exists between genetically diverged strains. Consistent with the existence of sexual recombination and heterothallism, which was unknown for this species, we identified the two alternative mating types in different P. expansum isolates. Patterns of polymorphism in P. digitatum indicate a recent clonal population expansion of a single lineage that has reached worldwide distribution. We suggest that the contrasting patterns of genomic variation between the two species reflect underlying differences in population dynamics related with host specificities and related agricultural practices. It should be noted, however, that this results should be confirmed with a larger sampling of strains, as new strains may broaden the diversity so far found in P. digitatum. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Intraspecific Trait Variation and Coordination: Root and Leaf Economics Spectra in Coffee across Environmental Gradients.

PubMed

Isaac, Marney E; Martin, Adam R; de Melo Virginio Filho, Elias; Rapidel, Bruno; Roupsard, Olivier; Van den Meersche, Karel

2017-01-01

Hypotheses on the existence of a universal "Root Economics Spectrum" (RES) have received arguably the least attention of all trait spectra, despite the key role root trait variation plays in resource acquisition potential. There is growing interest in quantifying intraspecific trait variation (ITV) in plants, but there are few studies evaluating (i) the existence of an intraspecific RES within a plant species, or (ii) how a RES may be coordinated with other trait spectra within species, such as a leaf economics spectrum (LES). Using Coffea arabica (Rubiaceae) as a model species, we measured seven morphological and chemical traits of intact lateral roots, which were paired with information on four key LES traits. Field collections were completed across four nested levels of biological organization. The intraspecific trait coefficient of variation (cv) ranged from 25 to 87% with root diameter and specific root tip density showing the lowest and highest cv, respectively. Between 27 and 68% of root ITV was explained by site identity alone for five of the seven traits measured. A single principal component explained 56.2% of root trait covariation, with plants falling along a RES from resource acquiring to conserving traits. Multiple factor analysis revealed significant orthogonal relationships between root and leaf spectra. RES traits were strongly orthogonal with respect to LES traits, suggesting these traits vary independently from one another in response to environmental cues. This study provides among the first evidence that plants from the same species differentiate from one another along an intraspecific RES. We find that in one of the world's most widely cultivated crops, an intraspecific RES is orthogonal to an intraspecific LES, indicating that above and belowground responses of plants to managed (or natural) environmental gradients are likely to occur independently from one another.

Grading Practices and Distributions Across Internal Medicine Clerkships.

PubMed

Fazio, Sara B; Torre, Dario M; DeFer, Thomas M

2016-01-01

Clerkship evaluation and grading practices vary widely between U.S. medical schools. Grade inflation continues to exist, and grade distribution is likely to be different among U.S. medical schools. Increasing the number of available grades curtails "grade inflation." A national survey of all Clerkship Directors in Internal Medicine members was administered in 2011. The authors assessed key aspects of grading. Response rate was 76%. Among clerkship directors (CDs), 61% of respondents agreed that grade inflation existed in the internal medicine clerkship at their school, and 43% believed that it helped students obtain better residency positions. With respect to grading practices, 79% of CDs define specific behaviors needed to achieve each grade, and 36% specify an ideal grade distribution. In addition, 44% have a trained core faculty responsible for evaluating students, 35% describe formal grading meetings, and 39% use the Reporter-Interpreter-Manager-Educator (RIME) scheme. Grading scales were described as follows: 4% utilize a pass/fail system, 13% a 3-tier (e.g., Honors/Pass/Fail), 45% 4-tier, 35% 5-tier, and 4% 6+-tier system. There was a trend to higher grades with more tiers available. Grade inflation continues in the internal medicine clerkship. Almost half of CDs feel that this practice assists students to obtain better residency positions. A minority of programs have a trained core faculty who are responsible for evaluation. About one third have formal grading meetings and use the RIME system; both have been associated with more robust and balanced grading practices. In particular, there is a wide variation between schools in the percentage of students who are awarded the highest grade, which has implications for residency applications. Downstream users of clinical clerkship grades must be fully aware of these variations in grading in order to appropriately judge medical student performance.

Rates, levels, and determinants of electronic health record system adoption: a study of hospitals in Riyadh, Saudi Arabia.

PubMed

Aldosari, Bakheet

2014-05-01

Outside a small number of OECD countries, little information exists regarding the rates, levels, and determinants of hospital electronic health record (EHR) system adoption. This study examines EHR system adoption in Riyadh, Saudi Arabia. Respondents from 22 hospitals were surveyed regarding the implementation, maintenance, and improvement phases of EHR system adoption. Thirty-seven items were graded on a three-point scale of preparedness/completion. Measured determinants included hospital size, level of care, ownership, and EHR system development team composition. Eleven of the hospitals had implemented fully functioning EHR systems, eight had systems in progress, and three had not adopted a system. Sixteen different systems were being used across the 19 adopting hospitals. Differential adoption levels were positively related to hospital size and negatively to the level of care (secondary versus tertiary). Hospital ownership (nonprofit versus private) and development team composition showed mixed effects depending on the particular adoption phase being considered. Adoption rates compare favourably with those reported from other countries and other districts in Saudi Arabia, but wide variations exist among hospitals in the levels of adoption of individual items. General weaknesses in the implementation phase concern the legacy of paper data systems, including document scanning and data conversion; in the maintenance phase concern updating/maintaining software; and in the improvement phase concern the communication and exchange of health information. This study is the first to investigate the level and determinants of EHR system adoption for public, other nonprofit, and private hospitals in Saudi Arabia. Wide interhospital variations in adoption bear implications for policy-making and funding intervention. Identified areas of weakness require action to increase the degree of adoption and usefulness of EHR systems. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Chrono-nutrition: a review of current evidence from observational studies on global trends in time-of-day of energy intake and its association with obesity.

PubMed

Almoosawi, S; Vingeliene, S; Karagounis, L G; Pot, G K

2016-11-01

The importance of the circadian rhythm in regulating human food intake behaviour and metabolism has long been recognised. However, little is known as to how energy intake is distributed over the day in existing populations, and its potential association with obesity. The present review describes global trends in time-of-day of energy intake in the general population based on data from cross-sectional surveys and longitudinal cohorts. Evidence of the association between time-of-day of energy intake and obesity is also summarised. Overall, there were a limited number of cross-sectional surveys and longitudinal cohorts that provided data on time-of-day of energy intake. In the identified studies, a wide variation in time-of-day of energy intake was observed, with patterns of energy distribution varying greatly by country and geographical area. In relation to obesity, eight cross-sectional surveys and two longitudinal cohorts were identified. The association between time-of-day of energy intake and obesity varied widely, with several studies reporting a positive link between evening energy intake and obesity. In conclusion, the current review summarises global trends in time-of-day of energy intake. The large variations across countries and global regions could have important implications to health, emphasising the need to understand the socio-environmental factors guiding such differences in eating patterns. Evidence of the association between time-of-day of energy intake and BMI also varied. Further larger scale collaborations between various countries and regions are needed to sum data from existing surveys and cohorts, and guide our understanding of the role of chrono-nutrition in health.

Inter- and intraspecific variation in leaf economic traits in wheat and maize

PubMed Central

Hale, Christine E; Cerabolini, Bruno E L; Cornelissen, Johannes H C; Craine, Joseph; Gough, William A; Kattge, Jens; Tirona, Cairan K F

2018-01-01

Abstract Leaf Economics Spectrum (LES) trait variation underpins multiple agroecological processes and many prominent crop yield models. While there are numerous independent studies assessing trait variation in crops, to date there have been no comprehensive assessments of intraspecific trait variation (ITV) in LES traits for wheat and maize: the world’s most widespread crops. Using trait databases and peer-reviewed literature, we compiled over 700 records of specific leaf area (SLA), maximum photosynthetic rates (Amax) and leaf nitrogen (N) concentrations, for wheat and maize. We evaluated intraspecific LES trait variation, and intraspecific trait–environment relationships. While wheat and maize occupy the upper 90th percentile of LES trait values observed across a global species pool, ITV ranged widely across the LES in wheat and maize. Fertilization treatments had strong impacts on leaf N, while plant developmental stage (here standardized as the number of days since planting) had strong impacts on Amax; days since planting, N fertilization and irrigation all influenced SLA. When controlling for these factors, intraspecific responses to temperature and precipitation explained 39.4 and 43.7 % of the variation in Amax and SLA, respectively, but only 5.4 % of the variation in leaf N. Despite a long history of domestication in these species, ITV in wheat and maize among and within cultivars remains large. Intraspecific trait variation is a critical consideration to refine regional to global models of agroecosystem structure, function and food security. Considerable opportunities and benefits exist for consolidating a crop trait database for a wider range of domesticated plant species. PMID:29484152

Inter- and intraspecific variation in leaf economic traits in wheat and maize.

PubMed

Martin, Adam R; Hale, Christine E; Cerabolini, Bruno E L; Cornelissen, Johannes H C; Craine, Joseph; Gough, William A; Kattge, Jens; Tirona, Cairan K F

2018-02-01

Leaf Economics Spectrum (LES) trait variation underpins multiple agroecological processes and many prominent crop yield models. While there are numerous independent studies assessing trait variation in crops, to date there have been no comprehensive assessments of intraspecific trait variation (ITV) in LES traits for wheat and maize: the world's most widespread crops. Using trait databases and peer-reviewed literature, we compiled over 700 records of specific leaf area (SLA), maximum photosynthetic rates ( A max ) and leaf nitrogen (N) concentrations, for wheat and maize. We evaluated intraspecific LES trait variation, and intraspecific trait-environment relationships. While wheat and maize occupy the upper 90th percentile of LES trait values observed across a global species pool, ITV ranged widely across the LES in wheat and maize. Fertilization treatments had strong impacts on leaf N, while plant developmental stage (here standardized as the number of days since planting) had strong impacts on A max ; days since planting, N fertilization and irrigation all influenced SLA. When controlling for these factors, intraspecific responses to temperature and precipitation explained 39.4 and 43.7 % of the variation in A max and SLA, respectively, but only 5.4 % of the variation in leaf N. Despite a long history of domestication in these species, ITV in wheat and maize among and within cultivars remains large. Intraspecific trait variation is a critical consideration to refine regional to global models of agroecosystem structure, function and food security. Considerable opportunities and benefits exist for consolidating a crop trait database for a wider range of domesticated plant species.

The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster.

PubMed

Hunter, Chad M; Huang, Wen; Mackay, Trudy F C; Singh, Nadia D

2016-04-01

Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait.

The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster

PubMed Central

Hunter, Chad M.; Huang, Wen; Mackay, Trudy F. C.; Singh, Nadia D.

2016-01-01

Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait. PMID:27035832

Prevalence of hot flushes and night sweats around the world: a systematic review.

PubMed

Freeman, E W; Sherif, K

2007-06-01

Many studies have evaluated the relationships between ethnicity and culture, prevalence of menopausal symptoms, and attitudes toward them, but few have assessed menopausal symptoms across cultures world-wide. This paper aims to systematically review the prevalence of hot flushes and night sweats, two prevalent symptoms of menopause, across the menopausal stages in different cultures and considers potential explanations for differences in prevalence rates. Sixty-six papers formed the basis for this review. Studies were organized by geographic region, and results are presented for North America, Europe, East Asia, Southeast Asia, Australia, Latin America, South Asia, Middle East, and Africa. Studies were included if they provided quantitative information on the occurrence of hot flushes. This report focuses on hot flushes and night sweats, the most common menopausal symptoms reported in epidemiologic studies. Studies reviewed indicate that vasomotor symptoms are highly prevalent in most societies. The prevalence of these symptoms varies widely and may be influenced by a range of factors, including climate, diet, lifestyle, women's roles, and attitudes regarding the end of reproductive life and aging. Patterns in hot flush prevalence were apparent for menopausal stages and, to a lesser degree, for regional variation. Caregivers should recognize that variations exist and ask patients specific questions about symptoms and their impact on usual functioning.

Mind the gap: genetic manipulation of basicranial growth within synchondroses modulates calvarial and facial shape in mice through epigenetic interactions.

PubMed

Parsons, Trish E; Downey, Charlene M; Jirik, Frank R; Hallgrimsson, Benedikt; Jamniczky, Heather A

2015-01-01

Phenotypic integration patterns in the mammalian skull have long been a focus of intense interest as a result of their suspected influence on the trajectory of hominid evolution. Here we test the hypothesis that perturbation of cartilage growth, which directly affects only the chondrocranium during development, will produce coordinated shape changes in the adult calvarium and face regardless of mechanism. Using two murine models of cartilage undergrowth that target two very different mechanisms, we show that strong reduction in cartilage growth produces a short, wide, and more flexed cranial base. This in turn produces a short, wide face in both models. Cranial base and face are already correlated early in ontogeny, and the relationship between these modules gains structure through postnatal growth and development. These results provide further evidence that there exist physical interactions between developing parts of the phenotype that produce variation at a distance from the actual locus upon which a particular selective pressure is acting. Phenotypic changes observed over the course of evolution may not all require adaptationist explanations; rather, it is likely that a substantial portion of observed phenotypic variation over the history of a clade is not directly adaptive but rather a secondary consequence of some local response to selection.

Microscopic colitis: the tip of the iceberg?

PubMed

Kitchen, Paul A; Levi, A Jonathen; Domizio, Paula; Talbot, Ian C; Forbes, Alastair; Price, Ashley B

2002-11-01

The aims were to determine whether a wide variation exists between hospitals in the diagnosis of microscopic colitis and to assimilate clinical data. Retrospective study of 90 patients with microscopic colitis aged between 16 and 92 years from 11 hospitals in south-east England. A questionnaire was designed to collect relevant data from all patients in whom a new diagnosis of microscopic colitis had been made at the source hospital between January 1990 and December 1996. The inclusion criteria were presentation with watery diarrhoea, a normal endoscopy and a histological report of microscopic colitis. Histology slides were then requested and reviewed. Clinical data were analysed with reference to the confirmed diagnosis. The number of patients diagnosed at each hospital ranged between zero and 30, with a median of six. Sixty-eight patients had histological slides reviewed. The numbers of patients with a final reviewed diagnosis of collagenous colitis, lymphocytic colitis and microscopic colitis, type undesignated, were 37, 18 and seven respectively. In thirty-one patients (34%) there was a recent history of the use of non-steroidal anti-inflammatory drugs. These data confirm that there is wide hospital variation in the diagnosis of microscopic colitis. Furthermore, the small group with the undesignated type may be associated with the use of non-steroidal anti-inflammatory drugs.

Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)

PubMed Central

Moodley, Yoshan; Russo, Isa-Rita M.; Dalton, Desiré L.; Kotzé, Antoinette; Muya, Shadrack; Haubensak, Patricia; Bálint, Boglárka; Munimanda, Gopi K.; Deimel, Caroline; Setzer, Andrea; Dicks, Kara; Herzig-Straschil, Barbara; Kalthoff, Daniela C.; Siegismund, Hans R.; Robovský, Jan; O’Donoghue, Paul; Bruford, Michael W.

2017-01-01

The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species’ once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide genetic structure of historic and modern populations using the largest and most geographically representative sample of black rhinoceroses ever assembled. Using both mitochondrial and nuclear datasets, we described a staggering loss of 69% of the species’ mitochondrial genetic variation, including the most ancestral lineages that are now absent from modern populations. Genetically unique populations in countries such as Nigeria, Cameroon, Chad, Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer exist. We found that the historic range of the West African subspecies (D. b. longipes), declared extinct in 2011, extends into southern Kenya, where a handful of individuals survive in the Masai Mara. We also identify conservation units that will help maintain evolutionary potential. Our results suggest a complete re-evaluation of current conservation management paradigms for the black rhinoceros. PMID:28176810

The local work function: Concept and implications

NASA Astrophysics Data System (ADS)

Wandelt, K.

1997-02-01

The term 'local work function' is now widely applied. The present work discusses the common physical basis of 'photoemission of adsorbed xenon (PAX)' and 'two-photon photonemissionspectroscopy of image potential states' as local work function probes. New examples with bimetallic and defective surfaces are presented which demonstrate the capability of PAX measurements for the characterization of heterogeneous surfaces on an atomic scale. Finally, implications of the existence of short-range variations of the surface potential at surface steps are addressed. In particular, dynamical work function change measurements are a sensitive probe for the step-density at surfaces and, as such, a powerful in-situ method to monitor film growth.

Evaluation and Management of Dehydration in Children.

PubMed

Santillanes, Genevieve; Rose, Emily

2018-05-01

The article discusses the evaluation of dehydration in children and reviews the literature on physical findings of dehydration. Pediatric dehydration is a common problem in emergency departments and wide practice variation in treatment exists. Dehydration can be treated with oral, nasogastric, subcutaneous, or intravenous fluids. Although oral rehydration is underutilized in the United States, most children with dehydration can be successfully rehydrated via the oral route. Selection of oral rehydration solution and techniques for successful oral rehydration are presented. Appropriate selection and rate of administration of intravenous fluids are also discussed for isonatremic, hyponatremic, and hypernatremic dehydration. Copyright © 2017 Elsevier Inc. All rights reserved.

Effect of in-material losses on terahertz absorption, transmission, and reflection in photonic crystals made of polar dielectrics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Serebryannikov, Andriy E., E-mail: andser@amu.edu.pl; Nanotechnology Research Center—NANOTAM, Bilkent University, 06800 Ankara; Nojima, S.

2015-10-07

The effect of the material absorption factor on terahertz absorption (A), transmittance (T), and reflectance (R) for slabs of PhC that comprise rods made of GaAs, a polar dielectric, is studied. The main goal was to illustrate how critical a choice of the absorption factor for simulations is and to indicate the importance of the possible modification of the absorption ability by using either active or lossy impurities. The spectra of A, T, and R are strongly sensitive to the location of the polaritonic gap with respect to the photonic pass and stop bands connected with periodicity that enables themore » efficient combination of the effects of material and structural parameters. It will be shown that the spectra can strongly depend on the utilized value of the material absorption factor. In particular, both narrow and wide absorption bands may appear owing to a variation of the material parameters with a frequency in the vicinity of the polaritonic gap. The latter are often achieved at wideband suppression of transmission, so that an ultra-wide stop band can appear as a result of adjustment of the stop bands having different origin. The results obtained at simultaneous variation of the absorption factor and frequency, and angle of incidence and frequency, indicate the possibility of the existence of wide ranges of tolerance, in which the basic features do remain. This allows for mitigating the accuracy requirements for the absorption factor in simulations and promises the efficient absorption of nonmonochromatic waves and beams with a wide angular spectrum. Suppression of narrowband effects in transmission is demonstrated at rather large values of the absorption factor, when they appear due to either the defect modes related to structural defects or dispersion inspired variations of the material parameters in the vicinity of the polaritonic gap. Comparison with auxiliary structures helps one to detect the common features and differences of homogeneous slabs and slabs of a PhC, which are made of GaAs.« less

Piracetam in the treatment of cortical myoclonus.

PubMed

Genton, P; Guerrini, R; Remy, C

1999-03-01

This paper reviews existing publications on the use of piracetam for the treatment of cortical myoclonus of various etiologies and includes the personal experience of the authors in progressive myoclonus epilepsy. Two double-blind comparisons with placebo provided results which allow recommendations for the dosage and usage of piracetam in cortical myoclonus. Wide individual variation (7-24g daily) exists in dosage requirements but responses are dose-related so that dosage should be increased until an optimum effect is obtained. Tolerability after long-term use of piracetam in high dosage has been very good and without toxicity or serious adverse effects. Side effects have been occasional, mild and transient. The authors present their experience of 12 patients with progressive myoclonus epilepsy in whom the administration of up to 45 g piracetam daily, when added to existing anti-epileptic treatment, caused marked and sometimes spectacular improvement and was without significant adverse effects. Improvement was maintained for up to 7 years. The use of piracetam for disabling cortical myoclonus of any etiology, either as an addition to existing antimyoclonic drugs or as monotherapy, may bring about profound improvement in disability and quality of life. Piracetam should be considered a first-line drug for the treatment of cortical myoclonus.

Real-Time Closed Loop Modulated Turbine Cooling

NASA Technical Reports Server (NTRS)

Shyam, Vikram; Culley, Dennis E.; Eldridge, Jeffrey; Jones, Scott; Woike, Mark; Cuy, Michael

2014-01-01

It has been noted by industry that in addition to dramatic variations of temperature over a given blade surface, blade-to-blade variations also exist despite identical design. These variations result from manufacturing variations, uneven wear and deposition over the life of the part as well as limitations in the uniformity of coolant distribution in the baseline cooling design. It is proposed to combine recent advances in optical sensing, actuation, and film cooling concepts to develop a workable active, closed-loop modulated turbine cooling system to improve by 10 to 20 the turbine thermal state over the flight mission, to improve engine life and to dramatically reduce turbine cooling air usage and aircraft fuel burn. A reduction in oxides of nitrogen (NOx) can also be achieved by using the excess coolant to improve mixing in the combustor especially for rotorcraft engines. Recent patents filed by industry and universities relate to modulating endwall cooling using valves. These schemes are complex, add weight and are limited to the endwalls. The novelty of the proposed approach is twofold 1) Fluidic diverters that have no moving parts are used to modulate cooling and can operate under a wide range of conditions and environments. 2) Real-time optical sensing to map the thermal state of the turbine has never been attempted in realistic engine conditions.

Priming as a Motivating Factor in Sociophonetic Variation and Change.

PubMed

Clark, Lynn

2018-04-24

Understanding how and why pronunciations vary and change has been a dominant theme in variationist sociolinguistics (Labov, , ). Linguistic variability has also been an area of focus in psychology and cognitive science. Work from these two fields has shown that where variation exists in language, an alternative form, once used, persists in working memory and has a greater chance of reuse (Bock, ; Bock & Loebell, ; Branigan, Pickering, & Cleland, ). While there have been efforts to connect priming research with sociolinguistics at the level of grammar (Poplack, ; Travis, ), there has been less work which explicitly considers the potential role of priming as a motivating factor in accent variation and change. This paper explores the role of priming in a socially conditioned sound change. There are two main findings: (a) phonetic variants with the same voicing tend to cluster together in naturally occurring speech and (b) repetition of phonetic form interacts with widely attested sociolinguistic predictors of variation. I argue that there are benefits to both cognitive science and sociolinguistics from this synergy: Incorporating research from cognitive science into sociolinguistics provides us with a better understanding of the factors underpinning a sound change in progress; incorporating insights from sociolinguistics into cognitive science shows that priming does not always operate in the same way for all speakers. Copyright © 2018 Cognitive Science Society, Inc.

Is variation management included in regional healthcare governance systems? Some proposals from Italy.

PubMed

Nuti, Sabina; Seghieri, Chiara

2014-01-01

The Italian National Health System, which follows a Beveridge model, provides universal healthcare coverage through general taxation. Universal coverage provides uniform healthcare access to citizens and is the characteristic usually considered the added value of a welfare system financed by tax revenues. Nonetheless, wide differences in practice patterns, health outcomes and regional usages of resources that cannot be justified by differences in patient needs have been demonstrated to exist. Beginning with the experience of the health care system of the Tuscany region (Italy), this study describes the first steps of a long-term approach to proactively address the issue of geographic variation in healthcare. In particular, the study highlights how the unwarranted variation management has been addressed in a region with a high degree of managerial control over the delivery of health care and a consolidated performance evaluation system, by first, considering it a high priority objective and then by actively integrating it into the regional planning and control mechanism. The implications of this study can be useful to policy makers, professionals and managers, and will contribute to the understanding of how the management of variation can be implemented with performance measurements and financial incentives. Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.

PubMed

Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

2017-01-04

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

SNP discovery by high-throughput sequencing in soybean

PubMed Central

2010-01-01

Background With the advance of new massively parallel genotyping technologies, quantitative trait loci (QTL) fine mapping and map-based cloning become more achievable in identifying genes for important and complex traits. Development of high-density genetic markers in the QTL regions of specific mapping populations is essential for fine-mapping and map-based cloning of economically important genes. Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation existing between any diverse genotypes that are usually used for QTL mapping studies. The massively parallel sequencing technologies (Roche GS/454, Illumina GA/Solexa, and ABI/SOLiD), have been widely applied to identify genome-wide sequence variations. However, it is still remains unclear whether sequence data at a low sequencing depth are enough to detect the variations existing in any QTL regions of interest in a crop genome, and how to prepare sequencing samples for a complex genome such as soybean. Therefore, with the aims of identifying SNP markers in a cost effective way for fine-mapping several QTL regions, and testing the validation rate of the putative SNPs predicted with Solexa short sequence reads at a low sequencing depth, we evaluated a pooled DNA fragment reduced representation library and SNP detection methods applied to short read sequences generated by Solexa high-throughput sequencing technology. Results A total of 39,022 putative SNPs were identified by the Illumina/Solexa sequencing system using a reduced representation DNA library of two parental lines of a mapping population. The validation rates of these putative SNPs predicted with low and high stringency were 72% and 85%, respectively. One hundred sixty four SNP markers resulted from the validation of putative SNPs and have been selectively chosen to target a known QTL, thereby increasing the marker density of the targeted region to one marker per 42 K bp. Conclusions We have demonstrated how to quickly identify large numbers of SNPs for fine mapping of QTL regions by applying massively parallel sequencing combined with genome complexity reduction techniques. This SNP discovery approach is more efficient for targeting multiple QTL regions in a same genetic population, which can be applied to other crops. PMID:20701770

Rigorous ILT optimization for advanced patterning and design-process co-optimization

NASA Astrophysics Data System (ADS)

Selinidis, Kosta; Kuechler, Bernd; Cai, Howard; Braam, Kyle; Hoppe, Wolfgang; Domnenko, Vitaly; Poonawala, Amyn; Xiao, Guangming

2018-03-01

Despite the large difficulties involved in extending 193i multiple patterning and the slow ramp of EUV lithography to full manufacturing readiness, the pace of development for new technology node variations has been accelerating. Multiple new variations of new and existing technology nodes have been introduced for a range of device applications; each variation with at least a few new process integration methods, layout constructs and/or design rules. This had led to a strong increase in the demand for predictive technology tools which can be used to quickly guide important patterning and design co-optimization decisions. In this paper, we introduce a novel hybrid predictive patterning method combining two patterning technologies which have each individually been widely used for process tuning, mask correction and process-design cooptimization. These technologies are rigorous lithography simulation and inverse lithography technology (ILT). Rigorous lithography simulation has been extensively used for process development/tuning, lithography tool user setup, photoresist hot-spot detection, photoresist-etch interaction analysis, lithography-TCAD interactions/sensitivities, source optimization and basic lithography design rule exploration. ILT has been extensively used in a range of lithographic areas including logic hot-spot fixing, memory layout correction, dense memory cell optimization, assist feature (AF) optimization, source optimization, complex patterning design rules and design-technology co-optimization (DTCO). The combined optimization capability of these two technologies will therefore have a wide range of useful applications. We investigate the benefits of the new functionality for a few of these advanced applications including correction for photoresist top loss and resist scumming hotspots.

Comparison of Two Devices for Intraoperative Portal Venous Flow Measurement in Living-Donor Liver Transplantation: Transit Time Ultrasound and Conventional Doppler Ultrasound.

PubMed

Wang, H-K; Chen, C-Y; Lin, N-C; Liu, C-S; Loong, C-C; Lin, Y-H; Lai, Y-C; Chiou, H-J

2018-05-01

Intraoperative portal venous flow measurement provides surgeons with instant guidance for portal flow modulation during living-donor liver transplantation (LDLT). In this study, we compared the agreement of portal flow measurement obtained by 2 devices: transit time ultrasound (TTU) and conventional Doppler ultrasound (CDU). Fifty-four recipients of LDLT underwent intraoperative measurement of portal flow after completion of vascular anastomosis of the implanted partial liver graft. Both TTU and CDU were used concurrently. Agreement of TTU and CDU was assessed by intraclass correlation coefficient using a model of 2-way random effects, absolute agreement, and single measurement. A Bland-Altman plot was applied to assess the variability between the 2 devices. The mean, median, and range of portal venous flow was 1456, 1418, and 117 to 2776 mL/min according to TTU; and 1564, 1566, and 119 to 3216 mL/min according to CDU. The intraclass correlation coefficient of portal venous flow between TTU and CDU was 0.68 (95% confidence interval, 0.51-0.80). The Bland-Altman plots revealed an average variation of 4.8% between TTU and CDU but with a rather wide 95% confidence interval of variation ranging from -57.7% to 67.4%. Intraoperative TTU and CDU showed moderate agreement in portal flow measurement. However, a relatively wide range of variation exists between TTU and CDU, indicating that data obtained from the 2 devices may not be interchangeable. Copyright © 2018 Elsevier Inc. All rights reserved.

Random Positional Variation Among the Skull, Mandible, and Cervical Spine With Treatment Progression During Head-and-Neck Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahn, Peter H.; Ahn, Andrew I.; Lee, C. Joe

2009-02-01

Purpose: With 54{sup o} of freedom from the skull to mandible to C7, ensuring adequate immobilization for head-and-neck radiotherapy (RT) is complex. We quantify variations in skull, mandible, and cervical spine movement between RT sessions. Methods and Materials: Twenty-three sequential head-and-neck RT patients underwent serial computed tomography. Patients underwent planned rescanning at 11, 22, and 33 fractions for a total of 93 scans. Coordinates of multiple bony elements of the skull, mandible, and cervical spine were used to calculate rotational and translational changes of bony anatomy compared with the original planning scan. Results: Mean translational and rotational variations on rescanningmore » were negligible, but showed a wide range. Changes in scoliosis and lordosis of the cervical spine between fractions showed similar variability. There was no correlation between positional variation and fraction number and no strong correlation with weight loss or skin separation. Semi-independent rotational and translation movement of the skull in relation to the lower cervical spine was shown. Positioning variability measured by means of vector displacement was largest in the mandible and lower cervical spine. Conclusions: Although only small overall variations in position between head-and-neck RT sessions exist on average, there is significant random variation in patient positioning of the skull, mandible, and cervical spine elements. Such variation is accentuated in the mandible and lower cervical spine. These random semirigid variations in positioning of the skull and spine point to a need for improved immobilization and/or confirmation of patient positioning in RT of the head and neck.« less

Raman spectroscopy, "big data", and local heterogeneity of solid state synthesized lithium titanate

NASA Astrophysics Data System (ADS)

Pelegov, Dmitry V.; Slautin, Boris N.; Gorshkov, Vadim S.; Zelenovskiy, Pavel S.; Kiselev, Evgeny A.; Kholkin, Andrei L.; Shur, Vladimir Ya.

2017-04-01

Existence of defects is an inherent property of real materials. Due to an explicit correlation between defects concentration and conductivity, it is important to understand the level and origins of the structural heterogeneity for any particulate electrode material. Poor conductive lithium titanate Li4Ti5O12 (LTO), widely used in batteries for grids and electric buses, needs it like no one else. In this work, structural heterogeneity of compacted lithium titanate is measured locally in 100 different points by conventional micro-Raman technique, characterized in terms of variation of Raman spectra parameters and interpreted using our version of "big data" analysis. This very simple approach with automated measurement and treatment has allowed us to demonstrate inherent heterogeneity of solid-state synthesized LTO and attribute it to the existence of lithium and oxygen vacancies. The proposed approach can be used as a fast, convenient, and cost-effective defects-probing tool for a wide range of materials with defects-sensitive properties. In case of LTO, such an approach can be used to increase its charge/discharge rates by synthesis of materials with controlled nonstoichiometry. New approaches to solid state synthesis of LTO, suitable for high-power applications, will help to significantly reduce the costs of batteries for heavy-duty electric vehicles and smart-grids.

Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders and/or congenital anomalies.

PubMed

Willemsen, Marjolein H; de Leeuw, Nicole; de Brouwer, Arjan P M; Pfundt, Rolph; Hehir-Kwa, Jayne Y; Yntema, Helger G; Nillesen, Willy M; de Vries, Bert B A; van Bokhoven, Hans; Kleefstra, Tjitske

2012-11-01

Genome-wide array studies are now routinely being used in the evaluation of patients with cognitive disorders (CD) and/or congenital anomalies (CA). Therefore, inevitably each clinician is confronted with the challenging task of the interpretation of copy number variations detected by genome-wide array platforms in a diagnostic setting. Clinical interpretation of autosomal copy number variations is already challenging, but assessment of the clinical relevance of copy number variations of the X-chromosome is even more complex. This study provides an overview of the X-Chromosome copy number variations that we have identified by genome-wide array analysis in a large cohort of 4407 male and female patients. We have made an interpretation of the clinical relevance of each of these copy number variations based on well-defined criteria and previous reports in literature and databases. The prevalence of X-chromosome copy number variations in this cohort was 57/4407 (∼1.3%), of which 15 (0.3%) were interpreted as (likely) pathogenic. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Simulations of a epidemic model with parameters variation analysis for the dengue fever

NASA Astrophysics Data System (ADS)

Jardim, C. L. T. F.; Prates, D. B.; Silva, J. M.; Ferreira, L. A. F.; Kritz, M. V.

2015-09-01

Mathematical models can be widely found in the literature for describing and analyzing epidemics. The models that use differential equations to represent mathematically such description are specially sensible to parameters involved in the modelling. In this work, an already developed model, called SIR, is analyzed when applied to a scenario of a dengue fever epidemic. Such choice is powered by the existence of useful tools presented by a variation of this original model, which allow an inclusion of different aspects of the dengue fever disease, as its seasonal characteristics, the presence of more than one strain of the vector and of the biological factor of cross-immunity. The analysis and results interpretation are performed through numerical solutions of the model in question, and a special attention is given to the different solutions generated by the use of different values for the parameters present in this model. Slight variations are performed either dynamically or statically in those parameters, mimicking hypothesized changes in the biological scenario of this simulation and providing a source of evaluation of how those changes would affect the outcomes of the epidemic in a population.

Image ratio features for facial expression recognition application.

PubMed

Song, Mingli; Tao, Dacheng; Liu, Zicheng; Li, Xuelong; Zhou, Mengchu

2010-06-01

Video-based facial expression recognition is a challenging problem in computer vision and human-computer interaction. To target this problem, texture features have been extracted and widely used, because they can capture image intensity changes raised by skin deformation. However, existing texture features encounter problems with albedo and lighting variations. To solve both problems, we propose a new texture feature called image ratio features. Compared with previously proposed texture features, e.g., high gradient component features, image ratio features are more robust to albedo and lighting variations. In addition, to further improve facial expression recognition accuracy based on image ratio features, we combine image ratio features with facial animation parameters (FAPs), which describe the geometric motions of facial feature points. The performance evaluation is based on the Carnegie Mellon University Cohn-Kanade database, our own database, and the Japanese Female Facial Expression database. Experimental results show that the proposed image ratio feature is more robust to albedo and lighting variations, and the combination of image ratio features and FAPs outperforms each feature alone. In addition, we study asymmetric facial expressions based on our own facial expression database and demonstrate the superior performance of our combined expression recognition system.

Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale.

PubMed

Liu, Siyang; Huang, Shujia; Rao, Junhua; Ye, Weijian; Krogh, Anders; Wang, Jun

2015-01-01

Comprehensive recognition of genomic variation in one individual is important for understanding disease and developing personalized medication and treatment. Many tools based on DNA re-sequencing exist for identification of single nucleotide polymorphisms, small insertions and deletions (indels) as well as large deletions. However, these approaches consistently display a substantial bias against the recovery of complex structural variants and novel sequence in individual genomes and do not provide interpretation information such as the annotation of ancestral state and formation mechanism. We present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variation and novel sequence from population-scale de novo genome assemblies up to nucleotide resolution. Application of AsmVar to several human de novo genome assemblies captures a wide spectrum of structural variants and novel sequences present in the human population in high sensitivity and specificity. Our method provides a direct solution for investigating structural variants and novel sequences from de novo genome assemblies, facilitating the construction of population-scale pan-genomes. Our study also highlights the usefulness of the de novo assembly strategy for definition of genome structure.

Accurate landmarking of three-dimensional facial data in the presence of facial expressions and occlusions using a three-dimensional statistical facial feature model.

PubMed

Zhao, Xi; Dellandréa, Emmanuel; Chen, Liming; Kakadiaris, Ioannis A

2011-10-01

Three-dimensional face landmarking aims at automatically localizing facial landmarks and has a wide range of applications (e.g., face recognition, face tracking, and facial expression analysis). Existing methods assume neutral facial expressions and unoccluded faces. In this paper, we propose a general learning-based framework for reliable landmark localization on 3-D facial data under challenging conditions (i.e., facial expressions and occlusions). Our approach relies on a statistical model, called 3-D statistical facial feature model, which learns both the global variations in configurational relationships between landmarks and the local variations of texture and geometry around each landmark. Based on this model, we further propose an occlusion classifier and a fitting algorithm. Results from experiments on three publicly available 3-D face databases (FRGC, BU-3-DFE, and Bosphorus) demonstrate the effectiveness of our approach, in terms of landmarking accuracy and robustness, in the presence of expressions and occlusions.

PoMo: An Allele Frequency-Based Approach for Species Tree Estimation

PubMed Central

De Maio, Nicola; Schrempf, Dominik; Kosiol, Carolin

2015-01-01

Incomplete lineage sorting can cause incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data. We extend this model to perform efficient estimation of species trees. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele frequency based. We show that PoMo is well suited for genome-wide species tree estimation and that on such data it is more accurate than previous approaches. PMID:26209413

Polar Mesospheric Clouds (PMCs) Observed by the Ozone Monitoring Instrument (OMI) on Aura

NASA Technical Reports Server (NTRS)

DeLand, Matthew T.; Shettle, Eric P.; Levelt, Pieternel F.; Kowalewski, Matthew G.

2010-01-01

Backscattered ultraviolet (BUV) instruments designed for measuring stratospheric ozone profiles have proven to be robust tools for observing polar mesospheric clouds (PMCs). These measurements are available for more than 30 years, and have been used to demonstrate the existence of long-term variations in PMC occurrence frequency and brightness. The Ozone Monitoring Instrument (OMI) on the EOS Aura satellite provides new and improved capabilities for PMC characterization. OMI uses smaller pixels than previous BUV instruments, which increases its ability to identify PMCs and discern more spatial structure, and its wide cross-track viewing swath provides full polar coverage up to 90 latitude every day in both hemispheres. This cross-track coverage allows the evolution of PMC regions to be followed over several consecutive orbits. Localized PMC variations determined from OMI measurements are consistent with coincident SBUV/2 measurements. Nine seasons of PMC observations from OMI are now available, and clearly demonstrate the advantages of these measurements for PMC analysis.

Markov-modulated Markov chains and the covarion process of molecular evolution.

PubMed

Galtier, N; Jean-Marie, A

2004-01-01

The covarion (or site specific rate variation, SSRV) process of biological sequence evolution is a process by which the evolutionary rate of a nucleotide/amino acid/codon position can change in time. In this paper, we introduce time-continuous, space-discrete, Markov-modulated Markov chains as a model for representing SSRV processes, generalizing existing theory to any model of rate change. We propose a fast algorithm for diagonalizing the generator matrix of relevant Markov-modulated Markov processes. This algorithm makes phylogeny likelihood calculation tractable even for a large number of rate classes and a large number of states, so that SSRV models become applicable to amino acid or codon sequence datasets. Using this algorithm, we investigate the accuracy of the discrete approximation to the Gamma distribution of evolutionary rates, widely used in molecular phylogeny. We show that a relatively large number of classes is required to achieve accurate approximation of the exact likelihood when the number of analyzed sequences exceeds 20, both under the SSRV and among site rate variation (ASRV) models.

Cross-National Variations in Student Employment and Academic Performance: The Roles of National Context and International Law*

PubMed Central

Byun, Soo-yong; Henck, Adrienne; Post, David

2014-01-01

Most existing research indicates that working students perform more poorly than do full-time students on standardized achievement tests. However, we know there are wide international variations in this gap. This article shows that national and international contexts help to explain the gap in the academic performance between working and non-working middle-school students. We combined data from the 2003 Trends in International Mathematics and Science Study (TIMSS) eighth-grade assessment with the country specific information on socioeconomic and educational conditions, as well as the timing of each country's ratification of an international treaty regulating child labor. Our multilevel analyses show that, while student employment was generally negatively associated with academic performance, this negative association is smaller in countries that by 1995 had ratified the International Labour Organization's Convention No. 138 on child labor. These findings highlight the role of national and international policy in structuring the consequences of student employment for academic performance. PMID:25632163

Microscopic theory of vortex interaction in two-band superconductors and type-1.5 superconductivity

NASA Astrophysics Data System (ADS)

Silaev, Mihail; Babaev, Egor

2011-03-01

In the framework of self-consistent microscopic theory we study the structure and interaction of vortices in two-gap superconductor taking into account the interband Josephson coupling. The asymptotical behavior of order parameter densities and magnetic field is studied analytically within the microscopic theory at low temperature. At higher temperatures, results consistent with Ginzburg-Landau theory are obtained. It is shown that under quite general conditions and in a wide temperature ranges (in particular outside the validity of the Ginzburg-Landau theory) there can exist an additional characteristic length scale of the order parameter density variation which exceeds the London penetration length of magnetic field due to the multi-component nature of superconducting state. Such behavior of order parameter density variation leads to the attractive long-range and repulsive short-range interaction between vortices. Supported by NSF CAREER Award DMR-0955902, Knut and Alice Wallenberg Foundation through the Royal Swedish Academy of Sciences and Swedish Research Council, ''Dynasty'' foundation and Russian Foundation for Basic Research.

Novel active contour model based on multi-variate local Gaussian distribution for local segmentation of MR brain images

NASA Astrophysics Data System (ADS)

Zheng, Qiang; Li, Honglun; Fan, Baode; Wu, Shuanhu; Xu, Jindong

2017-12-01

Active contour model (ACM) has been one of the most widely utilized methods in magnetic resonance (MR) brain image segmentation because of its ability of capturing topology changes. However, most of the existing ACMs only consider single-slice information in MR brain image data, i.e., the information used in ACMs based segmentation method is extracted only from one slice of MR brain image, which cannot take full advantage of the adjacent slice images' information, and cannot satisfy the local segmentation of MR brain images. In this paper, a novel ACM is proposed to solve the problem discussed above, which is based on multi-variate local Gaussian distribution and combines the adjacent slice images' information in MR brain image data to satisfy segmentation. The segmentation is finally achieved through maximizing the likelihood estimation. Experiments demonstrate the advantages of the proposed ACM over the single-slice ACM in local segmentation of MR brain image series.

Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants.

PubMed

Anderson, Justin E; Michno, Jean-Michel; Kono, Thomas J Y; Stec, Adrian O; Campbell, Benjamin W; Curtin, Shaun J; Stupar, Robert M

2016-05-12

The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants, and five genetically transformed plants developed through Agrobacterium based transformation methods. On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the rates observed between cultivars. Structural variants in transgenic plants, while rare, occurred adjacent to the transgenes, and at unlinked loci on different chromosomes. DNA repair junctions at both transgenic and unlinked sites were consistent with sequence microhomology across breakpoints. The single nucleotide substitution rates were modest in both fast neutron and transformed plants, exhibiting fewer than 100 substitutions genome-wide, while inter-cultivar comparisons identified over one-million single nucleotide polymorphisms. Overall, these patterns provide a fresh perspective on the genomic variation associated with high-energy induced mutagenesis and genetically transformed plants. The genetic transformation process infrequently results in novel genetic variation and these rare events are analogous to genetic variants occurring spontaneously, already present in the existing germplasm, or induced through other types of mutagenesis. It remains unclear how broadly these results can be applied to other crops or transformation methods.

Early Paleogene Orbital Variations in Atmospheric CO2 and New Astronomical Solutions

NASA Astrophysics Data System (ADS)

Zeebe, R. E.

2017-12-01

Geologic records across the globe show prominent variations on orbital time scales during numerous epochs going back hundreds of millions of years. The origin of the Milankovic cycles are variations in orbital parameters of the bodies of the Solar System. On long time scales, the orbital variations can not be computed analytically because of the chaotic nature of the Solar System. Thus, numerical solutions are used to estimate changes in, e.g., Earth's orbital parameters in the past. The orbital solutions represent the backbone of cyclostratigraphy and astrochronology, now widely used in geology and paleoclimatology. Hitherto only two solutions for Earth's eccentricity appear to be used in paleoclimate studies, provided by two different groups that integrated the full Solar System equations over the past >100 Myr. In this presentation, I will touch on the basic physics behind, and present new results of, accurate Solar System integrations for Earth's eccentricity over the past hundred million years. I will discuss various limitations within the framework of the present simulations and compare the results to existing solutions. Furthermore, I will present new results from practical applications of such orbital solutions, including effects of orbital forcing on coupled climate- and carbon cycle variations. For instance, we have recently revealed a mechanism for a large lag between changes in carbon isotope ratios and eccentricity at the 400-kyr period, which has been observed in Paleocene, Oligocene, and Miocene sections. Finally, I will present the first estimates of orbital-scale variations in atmospheric CO2 during the early Paleogene.

Feedback from video for virtual reality Navigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsap, L V

2000-10-27

Important preconditions for wide acceptance of virtual reality (VR) systems include their comfort, ease and naturalness to use. Most existing trackers super from discomfort-related issues. For example, body-based trackers (hand controllers, joysticks, helmet attachments, etc.) restrict spontaneity and naturalness of motion, while ground-based devices (e.g., hand controllers) limit the workspace by literally binding an operator to the ground. There are similar problems with controls. This paper describes using real-time video with registered depth information (from a commercially available camera) for virtual reality navigation. Camera-based setup can replace cumbersome trackers. The method includes selective depth processing for increased speed, and amore » robust skin-color segmentation for accounting illumination variations.« less

AAFE man-made noise experiment project. Volume 1: Introduction experiment definition and requirements

NASA Technical Reports Server (NTRS)

1974-01-01

An experiment was conducted to measure and map the man-made radio frequency emanations which exist at earth orbital altitudes. The major objectives of the program are to develop a complete conceptual experiment and developmental hardware for the collection and processing of data required to produce meaningful statistics on man-made noise level variations as functions of time, frequency, and geographic location. A wide dispersion measurement receiver mounted in a spacecraft operating in a specialized orbit is used to obtain the data. A summary of the experiment designs goals and constraints is provided. The recommended orbit for the spacecraft is defined. The characteristics of the receiver and the antennas are analyzed.

The Minor fall, the Major lift: inferring emotional valence of musical chords through lyrics

PubMed Central

Kolchinsky, Artemy; Dhande, Nakul; Park, Kengjeun

2017-01-01

We investigate the association between musical chords and lyrics by analysing a large dataset of user-contributed guitar tablatures. Motivated by the idea that the emotional content of chords is reflected in the words used in corresponding lyrics, we analyse associations between lyrics and chord categories. We also examine the usage patterns of chords and lyrics in different musical genres, historical eras and geographical regions. Our overall results confirm a previously known association between Major chords and positive valence. We also report a wide variation in this association across regions, genres and eras. Our results suggest possible existence of different emotional associations for other types of chords. PMID:29291089

Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm.

PubMed

Abdurakhmonov, I Y; Kohel, R J; Yu, J Z; Pepper, A E; Abdullaev, A A; Kushanov, F N; Salakhutdinov, I B; Buriev, Z T; Saha, S; Scheffler, B E; Jenkins, J N; Abdukarimov, A

2008-12-01

The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still 'lagging' cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11-12% of SSR loci pairs revealed a significant LD. At the significance threshold (r(2)>/=0.1), a genome-wide average of LD declines within the genetic distance at <10 cM in the landrace stocks germplasm and >30 cM in variety germplasm. Genome wide LD at r(2)>/=0.2 was reduced on average to approximately 1-2 cM in the landrace stock germplasm and 6-8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and stratification existing in cotton germplasm resources. The number of SSR markers associated with fiber quality traits in diverse cotton germplasm, which broadly covered many historical meiotic events, should be useful to effectively exploit potentially new genetic variation by using MAS programs.

Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation.

PubMed

Gao, Lexuan; Geng, Yupeng; Li, Bo; Chen, Jiakuan; Yang, Ji

2010-11-01

Alternanthera philoxeroides (alligator weed) is an invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation in its introduced range. The mechanisms underpinning the wide range of phenotypic variation and rapid adaptation to novel and changing environments remain uncharacterized. In this study, we examined the epigenetic variation and its correlation with phenotypic variation in plants exposed to natural and manipulated environmental variability. Genome-wide methylation profiling using methylation-sensitive amplified fragment length polymorphism (MSAP) revealed considerable DNA methylation polymorphisms within and between natural populations. Plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent a genome-wide epigenetic reprogramming in response to different treatments. Methylation alterations associated with response to different water availability were detected in 78.2% (169/216) of common garden induced polymorphic sites, demonstrating the environmental sensitivity and flexibility of the epigenetic regulatory system. These data provide evidence of the correlation between epigenetic reprogramming and the reversible phenotypic response of alligator weed to particular environmental factors. © 2010 Blackwell Publishing Ltd.

A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes

PubMed Central

Dimkpa, Stanley O. N.; Lahari, Zobaida; Shrestha, Roshi; Douglas, Alex; Gheysen, Godelieve; Price, Adam H.

2016-01-01

The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists, so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions. Accessions Khao Pahk Maw and LD 24 appeared to be resistant, which was confirmed in large pot experiments where no galls were observed. Detailed observations on these two accessions revealed no nematodes inside the roots 2 days after inoculation and very few females after 17 days (5 in Khao Pahk Maw and <1 in LD 24, in comparison with >100 in the susceptible controls). These two cultivars appear ideal donors for breeding root-knot nematode resistance. A genome-wide association study revealed 11 quantitative trait loci, two of which are close to epistatic loci detected in the Bala x Azucena population. The discussion highlights a small number of candidate genes worth exploring further, in particular many genes with lectin domains and genes on chromosome 11 with homology to the Hordeum Mla locus. PMID:26552884

Rapid Response Team composition, resourcing and calling criteria in Australia.

PubMed

Jones, Daryl; Drennan, Kelly; Hart, Graeme K; Bellomo, Rinaldo; Web, Steven A R

2012-05-01

Rapid Response Teams (RRTs) have been introduced into at least 60% of Intensive Care Unit (ICU) - equipped Australian hospitals to review deteriorating ward patients. Most studies have assessed their impact on patient outcome and less information exists on team composition or aspects of their calling criteria. We obtained information on team composition, resourcing and details of activation criteria from 39 of 108 (36.1%) RRT-equipped Australian hospitals. We found that all 39 teams operated 24/7 (h/days), but only 10 (25.6%) had received additional funding for the service. Although 38/39 teams, were physician-led medical emergency teams, in 7 (17.9%) sites the most senior member would be unlikely to have advanced airway skills. Three quarters of calling criteria were structured into "ABCD", and approximately 40% included cardiac and/or respiratory arrest as a calling criterion. Thresholds for calling criteria varied widely (particularly for respiratory rate and heart rate), as did the wording of the worried/concerned criterion. There was also wide variation in the number and nature of additional activation criteria. Our findings imply the likelihood of significant practice variation in relation to RRT composition, staff skill set and activation criteria between hospitals. We recommend improved resourcing of RRTs, training of the team members, and consideration for improved standardisation of calling criteria across institutions. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Allele-Specific Methylation Occurs at Genetic Variants Associated with Complex Disease

PubMed Central

Hutchinson, John N.; Raj, Towfique; Fagerness, Jes; Stahl, Eli; Viloria, Fernando T.; Gimelbrant, Alexander; Seddon, Johanna; Daly, Mark; Chess, Andrew; Plenge, Robert

2014-01-01

We hypothesize that the phenomenon of allele-specific methylation (ASM) may underlie the phenotypic effects of multiple variants identified by Genome-Wide Association studies (GWAS). We evaluate ASM in a human population and document its genome-wide patterns in an initial screen at up to 380,678 sites within the genome, or up to 5% of the total genomic CpGs. We show that while substantial inter-individual variation exists, 5% of assessed sites show evidence of ASM in at least six samples; the majority of these events (81%) are under genetic influence. Many of these cis-regulated ASM variants are also eQTLs in peripheral blood mononuclear cells and monocytes and/or in high linkage-disequilibrium with variants linked to complex disease. Finally, focusing on autoimmune phenotypes, we extend this initial screen to confirm the association of cis-regulated ASM with multiple complex disease-associated variants in an independent population using next-generation bisulfite sequencing. These four variants are implicated in complex phenotypes such as ulcerative colitis and AIDS progression disease (rs10491434), Celiac disease (rs2762051), Crohn's disease, IgA nephropathy and early-onset inflammatory bowel disease (rs713875) and height (rs6569648). Our results suggest cis-regulated ASM may provide a mechanistic link between the non-coding genetic changes and phenotypic variation observed in these diseases and further suggests a route to integrating DNA methylation status with GWAS results. PMID:24911414

A rapid generalized least squares model for a genome-wide quantitative trait association analysis in families.

PubMed

Li, Xiang; Basu, Saonli; Miller, Michael B; Iacono, William G; McGue, Matt

2011-01-01

Genome-wide association studies (GWAS) using family data involve association analyses between hundreds of thousands of markers and a trait for a large number of related individuals. The correlations among relatives bring statistical and computational challenges when performing these large-scale association analyses. Recently, several rapid methods accounting for both within- and between-family variation have been proposed. However, these techniques mostly model the phenotypic similarities in terms of genetic relatedness. The familial resemblances in many family-based studies such as twin studies are not only due to the genetic relatedness, but also derive from shared environmental effects and assortative mating. In this paper, we propose 2 generalized least squares (GLS) models for rapid association analysis of family-based GWAS, which accommodate both genetic and environmental contributions to familial resemblance. In our first model, we estimated the joint genetic and environmental variations. In our second model, we estimated the genetic and environmental components separately. Through simulation studies, we demonstrated that our proposed approaches are more powerful and computationally efficient than a number of existing methods are. We show that estimating the residual variance-covariance matrix in the GLS models without SNP effects does not lead to an appreciable bias in the p values as long as the SNP effect is small (i.e. accounting for no more than 1% of trait variance). Copyright © 2011 S. Karger AG, Basel.

Case-mix analysis and variation in rates of non-surgical treatment of older women with operable breast cancer.

PubMed

Morgan, J; Richards, P; Ward, S; Francis, M; Lawrence, G; Collins, K; Reed, M; Wyld, L

2015-08-01

Non-surgical management of older women with oestrogen receptor (ER)-positive operable breast cancer is common in the UK, with up to 40 per cent of women aged over 70 years receiving primary endocrine therapy. Although this may be appropriate for frailer patients, for some it may result in treatment failure, contributing to the poor outcomes seen in this age group. Wide variation in the rates of non-operative management of breast cancer in older women exists across the UK. Case mix may explain some of this variation in practice. Data from two UK regional cancer registries were analysed to determine whether variation in treatment observed between 2002 and 2010 at hospital and clinician level persisted after adjustment for case mix. Expected case mix-adjusted surgery rates were derived by logistic regression using the variables age, proxy Charlson co-morbidity score, deprivation quintile, method of cancer detection, tumour size, stage, grade and node status. Data on 17,129 women aged 70 years or more with ER-positive operable breast cancer were analysed. There was considerable variation in rates of surgery at both hospital and clinician level. Despite adjusting for case mix, this variation persisted at hospital level, although not at clinician level. This study demonstrates variation in selection criteria for older women for operative treatment of early breast cancer, indicating that some older women may be undertreated or overtreated, and may partly explain the inferior disease outcomes in this age group. It emphasizes the urgent need for evidence-based guidelines for treatment selection criteria in older women with breast cancer. © 2015 BJS Society Ltd Published by John Wiley & Sons Ltd.

Nuclear DNA contents of Echinchloa crus-galli and its Gaussian relationships with environments

NASA Astrophysics Data System (ADS)

Li, Dan-Dan; Lu, Yong-Liang; Guo, Shui-Liang; Yin, Li-Ping; Zhou, Ping; Lou, Yu-Xia

2017-02-01

Previous studies on plant nuclear DNA content variation and its relationships with environmental gradients produced conflicting results. We speculated that the relationships between nuclear DNA content of a widely-distributed species and its environmental gradients might be non-linear if it was sampled in a large geographical gradient. Echinochloa crus-galli (L.) P. Beauv. is a worldwide species, but without documents on its intraspecific variation of nuclear DNA content. Our objectives are: 1) to detect intraspecific variation scope of E. crus-galli in its nuclear DNA content, and 2) to testify whether nuclear DNA content of the species changes with environmental gradients following Gaussian models if its populations were sampled in a large geographical gradient. We collected seeds of 36 Chinese populations of E. crus-galli across a wide geographical gradient, and sowed them in a homogeneous field to get their offspring to determine their nuclear DNA content. We analyzed the relationships of nuclear DNA content of these populations with latitude, longitude, and nineteen bioclimatic variables by using Gaussian and linear models. (1) Nuclear DNA content varied from 2.113 to 2.410 pg among 36 Chinese populations of E. crus-galli, with a mean value of 2.256 pg. (2) Gaussian correlations of nuclear DNA content (y) with geographical gradients were detected, with latitude (x) following y = 2.2923*e -(x - 24.9360)2/2*63.79452 (r = 0.546, P < 0.001), and with longitude (x) following y = 2.2933*e -(x - 116.1801)2/2*44.74502 (r = 0.672, P < 0.001). (3) Among the nineteen bioclimatic variables, except temperature isothermality, precipitations of the wettest month, the wettest quarter and the warmest quarter, the others could be better fit with nuclear DNA content by using Gaussian models than by linear models. There exists intra-specific variation among 36 Chinese populations of E. crus-galli, Gaussian models could be applied to fit the correlations of its Nuclear DNA content with geographical and most bioclimatic gradients.

Copy number variation of individual cattle genomes using next-generation sequencing

USDA-ARS?s Scientific Manuscript database

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one ...

Copy number variation of individual cattle genomes using next-generation sequencing

USDA-ARS?s Scientific Manuscript database

Copy Number Variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often difficult to track. Using a read depth approach based on next generation sequencing, we examined genome-wide copy number differences among five taurine (three Angu...

Intraspecific Variation of Eysarcoris guttigerus (Hemiptera: Pentatomidae) in Japanese Southwest Population Based on Mitochondrial DNA

PubMed Central

Yamaji, Takuya; Ishikawa, Tadashi; Nomura, Masashi

2016-01-01

The white-spotted globular bug Eysarcoris guttigerus (Thunberg) (Hemiptera: Pentatomidae) is widely distributed in East Asia and the Pacific region. In Japan, the species is found in grassy or composite weeds in the western area of the main islands and Ryukyu Islands of Japan. One notable characteristic of the Eysarcoris genus is the two white spots on the scutellum. This is not the case with the Ishigaki Island population, however, which sports red spots instead of white, suggesting that intraspecific variation exists in the species. Therefore, we investigated intraspecific variation in E. guttigerus using mitochondrial NADH dehydrogenase subunit 2 (ND2), cytochrome oxidase subunit 1 (CO1), cytochrome b (Cytb), tRNA-Serine (tRNAser), NADH dehydrogenase subunit 1 (ND1), and 16S ribosomal RNA (16SrRNA) genes from 13 populations of Japan. The obtained maximum likelihood phylogenetic tree was divided into three groups—Group 1: Mainland, Group 2: Central Ryukyu Islands (Okinawa-Amamioshima Islands), and Group 3: South Ryukyu Islands (Ishigaki Island). The Ishigaki population was significantly separated from the other populations with consistent differences in spot color. The estimated period of divergence between the Ishigaki population and the other populations was consistent with the period of formation of the Kerama Gap in the Ryukyu arc. Thus, the process of formation of the Kerama Gap may have influenced the intraspecific variation of E. guttigerus. PMID:26798143

Satellite orbit and data sampling requirements

NASA Technical Reports Server (NTRS)

Rossow, William

1993-01-01

Climate forcings and feedbacks vary over a wide range of time and space scales. The operation of non-linear feedbacks can couple variations at widely separated time and space scales and cause climatological phenomena to be intermittent. Consequently, monitoring of global, decadal changes in climate requires global observations that cover the whole range of space-time scales and are continuous over several decades. The sampling of smaller space-time scales must have sufficient statistical accuracy to measure the small changes in the forcings and feedbacks anticipated in the next few decades, while continuity of measurements is crucial for unambiguous interpretation of climate change. Shorter records of monthly and regional (500-1000 km) measurements with similar accuracies can also provide valuable information about climate processes, when 'natural experiments' such as large volcanic eruptions or El Ninos occur. In this section existing satellite datasets and climate model simulations are used to test the satellite orbits and sampling required to achieve accurate measurements of changes in forcings and feedbacks at monthly frequency and 1000 km (regional) scale.

Variation in neoadjuvant chemotherapy utilization for epithelial ovarian cancer at high volume hospitals in the United States and associated survival.

PubMed

Barber, Emma L; Dusetzina, Stacie B; Stitzenberg, Karyn B; Rossi, Emma C; Gehrig, Paola A; Boggess, John F; Garrett, Joanne M

2017-06-01

To estimate variation in the use of neoadjuvant chemotherapy by high volume hospitals and to determine the association between hospital utilization of neoadjuvant chemotherapy and survival. We identified incident cases of stage IIIC or IV epithelial ovarian cancer in the National Cancer Database from 2006 to 2012. Inclusion criteria were treatment at a high volume hospital (>20 cases/year) and treatment with both chemotherapy and surgery. A logistic regression model was used to predict receipt of neoadjuvant chemotherapy based on case-mix predictors (age, comorbidities, stage etc). Hospitals were categorized by the observed-to-expected ratio for neoadjuvant chemotherapy use as low, average, or high utilization hospitals. Survival analysis was performed. We identified 11,574 patients treated at 55 high volume hospitals. Neoadjuvant chemotherapy was used for 21.6% (n=2494) of patients and use varied widely by hospital, from 5%-55%. High utilization hospitals (n=1910, 10 hospitals) had a median neoadjuvant chemotherapy rate of 39% (range 23-55%), while low utilization hospitals (n=2671, 14 hospitals) had a median rate of 10% (range 5-17%). For all ovarian cancer patients adjusting for clinical and socio-demographic factors, treatment at a hospital with average or high neoadjuvant chemotherapy utilization was associated with a decreased rate of death compared to treatment at a low utilization hospital (HR 0.90 95% CI 0.83-0.97 and HR 0.85 95% CI 0.75-0.95). Wide variation exists in the utilization of neoadjuvant chemotherapy to treat stage IIIC and IV epithelial ovarian cancer even among high volume hospitals. Patients treated at hospitals with low rates of neoadjuvant chemotherapy utilization experience decreased survival. Copyright © 2017 Elsevier Inc. All rights reserved.

Variation in Neoadjuvant Chemotherapy Utilization for Epithelial Ovarian Cancer at High Volume Hospitals in the United States and Associated Survival

PubMed Central

Barber, Emma L; Dusetzina, Stacie B; Stitzenberg, Karyn B; Rossi, Emma C; Gehrig, Paola A; Boggess, John F; Garrett, Joanne M

2017-01-01

Objective To estimate variation in the use of neoadjuvant chemotherapy by high volume hospitals and to determine the association between hospital utilization of neoadjuvant chemotherapy and survival. Methods We identified incident cases of stage IIIC or IV epithelial ovarian cancer in the National Cancer Database from 2006–2012. Inclusion criteria were treatment at a high volume hospital (>20 cases/yr) and treatment with both chemotherapy and surgery. A logistic regression model was used to predict receipt of neoadjuvant chemotherapy based on case-mix predictors (age, comorbidities, stage etc). Hospitals were categorized by the observed-to-expected ratio for neoadjuvant chemotherapy use as low, average, or high utilization hospitals. Survival analysis was performed. Results We identified 11,574 patients treated at 55 high volume hospitals. Neoadjuvant chemotherapy was used for 21.6% (n=2494) of patients and use varied widely by hospital, from 5%–55%. High utilization hospitals (n=1910, 10 hospitals) had a median neoadjuvant chemotherapy rate of 39% (range 23–55%), while low utilization hospitals (n=2671, 14 hospitals) had a median rate of 10% (range 5–17%). For all ovarian cancer patients adjusting for clinical and socio-demographic factors, treatment at a hospital with average or high neoadjuvant chemotherapy utilization was associated with a decreased rate of death compared to treatment at a low utilization hospital (HR 0.90 95%CI 0.83–0.97 and HR 0.85 95%CI 0.75–0.95). Conclusions Wide variation exists in the utilization of neoadjuvant chemotherapy to treat stage IIIC and IV epithelial ovarian cancer even among high volume hospitals. Patients treated at hospitals with low rates of neoadjuvant chemotherapy utilization experience decreased survival. PMID:28366545

Evidence for a link between mortality in acute COPD and hospital type and resources.

PubMed

Roberts, C M; Barnes, S; Lowe, D; Pearson, M G

2003-11-01

The 1997 BTS/RCP national audit of acute care of chronic obstructive pulmonary disease (COPD) found wide variations in mortality between hospitals which were only partially explained by known audit indicators of outcome. It was hypothesised that some of the unexplained variation may result from differences in hospital type, organisation and resources. This pilot study examined the hypothesis as a factor to be included in a future national audit programme. Thirty hospitals in England and Wales were randomly selected by geographical region and hospital type (teaching, large district general hospital (DGH), small DGH). Data on process and outcome of care (death and length of stay) were collected retrospectively at 90 days on all prospectively identified COPD admissions over an 8 week period. Each centre completed a questionnaire relating to organisation and resources available for the care of COPD patients. Eleven teaching hospitals, nine large DGHs, and 10 small DGHs provided data on 1274 cases. Mortality was high (14%) with wide variation between centres (IQR 9-19%). Small DGHs had a higher mortality (17.5%) than teaching hospitals (11.9%) and large DGHs (11.2%). When corrected for confounding factors, an excess of deaths in small DGHs was still observed (OR 1.56 (CI 1.04 to 2.35)) v teaching hospitals. Analysis of resource and organisational factors suggested higher mortality was associated with fewer doctors (OR 1.5) and with fewer patients being under the care of a specialist physician (OR 1.8). Small DGHs had fewest resources. Significant differences in mortality may exist between hospital types. The findings justify further study in a proposed national audit.

Evidence for a link between mortality in acute COPD and hospital type and resources

PubMed Central

Roberts, C; Barnes, S; Lowe, D; Pearson, M

2003-01-01

Background: The 1997 BTS/RCP national audit of acute care of chronic obstructive pulmonary disease (COPD) found wide variations in mortality between hospitals which were only partially explained by known audit indicators of outcome. It was hypothesised that some of the unexplained variation may result from differences in hospital type, organisation and resources. This pilot study examined the hypothesis as a factor to be included in a future national audit programme. Methods: Thirty hospitals in England and Wales were randomly selected by geographical region and hospital type (teaching, large district general hospital (DGH), small DGH). Data on process and outcome of care (death and length of stay) were collected retrospectively at 90 days on all prospectively identified COPD admissions over an 8 week period. Each centre completed a questionnaire relating to organisation and resources available for the care of COPD patients. Results: Eleven teaching hospitals, nine large DGHs, and 10 small DGHs provided data on 1274 cases. Mortality was high (14%) with wide variation between centres (IQR 9–19%). Small DGHs had a higher mortality (17.5%) than teaching hospitals (11.9%) and large DGHs (11.2%). When corrected for confounding factors, an excess of deaths in small DGHs was still observed (OR 1.56 (CI 1.04 to 2.35)) v teaching hospitals. Analysis of resource and organisational factors suggested higher mortality was associated with fewer doctors (OR 1.5) and with fewer patients being under the care of a specialist physician (OR 1.8). Small DGHs had fewest resources. Conclusion: Significant differences in mortality may exist between hospital types. The findings justify further study in a proposed national audit. PMID:14586045

Travel and tropical medicine practice among infectious disease practitioners.

PubMed

Streit, Judy A; Marano, Cinzia; Beekmann, Susan E; Polgreen, Philip M; Moore, Thomas A; Brunette, Gary W; Kozarsky, Phyllis E

2012-01-01

Infectious disease specialists who evaluate international travelers before or after their trips need skills to prevent, recognize, and treat an increasingly broad range of infectious diseases. Wide variation exists in training and percentage effort among providers of this care. In parallel, there may be variations in approach to pre-travel consultation and the types of travel-related illness encountered. Aggregate information from travel-medicine providers may reveal practice patterns and novel trends in infectious illness acquired through travel. The 1,265 members of the Infectious Disease Society of America's Emerging Infections Network were queried by electronic survey about their training in travel medicine, resources used, pre-travel consultations, and evaluation of ill-returning travelers. The survey also captured information on whether any of 10 particular conditions had been diagnosed among ill-returning travelers, and if these diagnoses were perceived to be changing in frequency. A majority of respondents (69%) provided both pre-travel counseling and post-travel evaluations, with significant variation in the numbers of such consultations. A majority of all respondents (61%) reported inadequate training in travel medicine during their fellowship years. However, a majority of recent graduates (55%) reported adequate preparation. Diagnoses of malaria, traveler's diarrhea, and typhoid fever were reported by the most respondents (84, 71, and 53%, respectively). The percent effort dedicated to pre-travel evaluation and care of the ill-returning traveler vary widely among infectious disease specialists, although a majority participate in these activities. On the basis of respondents' self-assessment, recent fellowship training is reported to equip graduates with better skills in these areas than more remote training. Ongoing monitoring of epidemiologic trends of travel-related illness is warranted. © 2012 International Society of Travel Medicine.

Existence of evolutionary variational solutions via the calculus of variations

NASA Astrophysics Data System (ADS)

Bögelein, Verena; Duzaar, Frank; Marcellini, Paolo

In this paper we introduce a purely variational approach to time dependent problems, yielding the existence of global parabolic minimizers, that is ∫0T ∫Ω [uṡ∂tφ+f(x,Du)] dx dt⩽∫0T ∫Ω f(x,Du+Dφ) dx dt, whenever T>0 and φ∈C0∞(Ω×(0,T),RN). For the integrand f:Ω×R→[0,∞] we merely assume convexity with respect to the gradient variable and coercivity. These evolutionary variational solutions are obtained as limits of maps depending on space and time minimizing certain convex variational functionals. In the simplest situation, with some growth conditions on f, the method provides the existence of global weak solutions to Cauchy-Dirichlet problems of parabolic systems of the type ∂tu-divDξf(x,Du)=0 in Ω×(0,∞).

Genetic structure and diversity of the selfing model grass Brachypodium stacei (Poaceae) in Western Mediterranean: out of the Iberian Peninsula and into the islands.

PubMed

Shiposha, Valeriia; Catalán, Pilar; Olonova, Marina; Marques, Isabel

2016-01-01

Annual Mediterranean species of the genus Brachypodium are promising model plants for energy crops since their selfing nature and short-life cycles are an advantage in breeding programs. The false brome, B. distachyon, has already been sequenced and new genomic initiatives have triggered the de-novo genome sequencing of its close relatives such as B. stacei, a species that was until recently mistaken for B. distachyon. However, the success of these initiatives hinges on detailed knowledge about the distribution of genetic variation within and among populations for the effective use of germplasm in a breeding program. Understanding population genetic diversity and genetic structure is also an important prerequisite for designing effective experimental populations for genomic wide studies. However, population genetic data are still limited in B. stacei. We therefore selected and amplified 10 nuclear microsatellite markers to depict patterns of population structure and genetic variation among 181 individuals from 19 populations of B. stacei occurring in its predominant range, the western Mediterranean area: mainland Iberian Peninsula, continental Balearic Islands and oceanic Canary Islands. Our genetic results support the occurrence of a predominant selfing system with extremely high levels of homozygosity across the analyzed populations. Despite the low level of genetic variation found, two different genetic clusters were retrieved, one clustering all SE Iberian mainland populations and the island of Minorca and another one grouping all S Iberian mainland populations, the Canary Islands and all Majorcan populations except one that clustered with the former group. These results, together with a high sharing of alleles (89%) suggest different colonization routes from the mainland Iberian Peninsula into the islands. A recent colonization scenario could explain the relatively low levels of genetic diversity and low number of alleles found in the Canary Islands populations while older colonization events are hypothesized to explain the high genetic diversity values found in the Majorcan populations. Our study provides widely applicable information about geographical patterns of genetic variation in B. stacei. Among others, the genetic pattern and the existence of local alleles will need to be adequately reflected in the germplasm collection of B. stacei for efficient genome wide association studies.

Genetic structure and diversity of the selfing model grass Brachypodium stacei (Poaceae) in Western Mediterranean: out of the Iberian Peninsula and into the islands

PubMed Central

Shiposha, Valeriia; Catalán, Pilar; Olonova, Marina

2016-01-01

Annual Mediterranean species of the genus Brachypodium are promising model plants for energy crops since their selfing nature and short-life cycles are an advantage in breeding programs. The false brome, B. distachyon, has already been sequenced and new genomic initiatives have triggered the de-novo genome sequencing of its close relatives such as B. stacei, a species that was until recently mistaken for B. distachyon. However, the success of these initiatives hinges on detailed knowledge about the distribution of genetic variation within and among populations for the effective use of germplasm in a breeding program. Understanding population genetic diversity and genetic structure is also an important prerequisite for designing effective experimental populations for genomic wide studies. However, population genetic data are still limited in B. stacei. We therefore selected and amplified 10 nuclear microsatellite markers to depict patterns of population structure and genetic variation among 181 individuals from 19 populations of B. stacei occurring in its predominant range, the western Mediterranean area: mainland Iberian Peninsula, continental Balearic Islands and oceanic Canary Islands. Our genetic results support the occurrence of a predominant selfing system with extremely high levels of homozygosity across the analyzed populations. Despite the low level of genetic variation found, two different genetic clusters were retrieved, one clustering all SE Iberian mainland populations and the island of Minorca and another one grouping all S Iberian mainland populations, the Canary Islands and all Majorcan populations except one that clustered with the former group. These results, together with a high sharing of alleles (89%) suggest different colonization routes from the mainland Iberian Peninsula into the islands. A recent colonization scenario could explain the relatively low levels of genetic diversity and low number of alleles found in the Canary Islands populations while older colonization events are hypothesized to explain the high genetic diversity values found in the Majorcan populations. Our study provides widely applicable information about geographical patterns of genetic variation in B. stacei. Among others, the genetic pattern and the existence of local alleles will need to be adequately reflected in the germplasm collection of B. stacei for efficient genome wide association studies. PMID:27651993

Short communication: Genetic variants of Sarcocystis cruzi in infected Malaysian cattle based on 18S rDNA.

PubMed

Ng, Yit Han; Fong, Mun Yik; Subramaniam, Vellayan; Shahari, Shahhaziq; Lau, Yee Ling

2015-12-01

Sarcocystis species are pathogenic parasites that infect a wide range of animals, including cattle. A high prevalence of cattle sarcocystosis has been reported worldwide, but its status is unknown in Malaysia. This study focused on utilizing 18S rDNA to identify Sarcocystis species in Malaysian cattle and to determine their genetic variants. In this study, only Sarcocystis cruzi was detected in Malaysian cattle. The intra-species S. cruzi phylogenetic tree analysis and principal coordinate analysis (PCoA), respectively displayed two minor groups among the parasite isolates. This finding was supported by high Wright FST value (FST=0.647). The definitive hosts (dogs) may play a fundamental role in the development of S. cruzi genetic variants. Additionally, the existence of microheterogeneity within the S. cruzi merozoites and/or distinct genetic variants arisen from independent merozoites in mature sarcocysts, possibly contributed to the existence of intra-species variations within the population. Copyright © 2015 Elsevier Ltd. All rights reserved.

Arsenic removal by solar-driven membrane distillation: modeling and experimental investigation with a new flash vaporization module.

PubMed

Pa, Parimal; Manna, Ajay Kumar; Linnanen, Lassi

2013-01-01

A modeling and simulation study was carried out on a new flux-enhancing and solar-driven membrane distillation module for removal of arsenic from contaminated groundwater. The developed new model was validated with rigorous experimental investigations using arsenic-contaminated groundwater. By incorporating flash vaporization dynamics, the model turned out to be substantially different from the existing direct contact membrane distillation models and could successfully predict (with relative error of only 0.042 and a Willmott d-index of 0.997) the performance of such an arsenic removal unit where the existing models exhibited wide variation with experimental findings in the new design. The module with greater than 99% arsenic removal efficiency and greater than 50 L/m2 x h flux could be implemented in arsenic-affected villages in Southeast Asian countries with abundant solar energy, and thus could give relief to millions of affected people. These encouraging results will raise scale-up confidence.

Mapping local variation in educational attainment across Africa

NASA Astrophysics Data System (ADS)

Graetz, Nicholas; Friedman, Joseph; Osgood-Zimmerman, Aaron; Burstein, Roy; Biehl, Molly H.; Shields, Chloe; Mosser, Jonathan F.; Casey, Daniel C.; Deshpande, Aniruddha; Earl, Lucas; Reiner, Robert C.; Ray, Sarah E.; Fullman, Nancy; Levine, Aubrey J.; Stubbs, Rebecca W.; Mayala, Benjamin K.; Longbottom, Joshua; Browne, Annie J.; Bhatt, Samir; Weiss, Daniel J.; Gething, Peter W.; Mokdad, Ali H.; Lim, Stephen S.; Murray, Christopher J. L.; Gakidou, Emmanuela; Hay, Simon I.

2018-03-01

Educational attainment for women of reproductive age is linked to reduced child and maternal mortality, lower fertility and improved reproductive health. Comparable analyses of attainment exist only at the national level, potentially obscuring patterns in subnational inequality. Evidence suggests that wide disparities between urban and rural populations exist, raising questions about where the majority of progress towards the education targets of the Sustainable Development Goals is occurring in African countries. Here we explore within-country inequalities by predicting years of schooling across five by five kilometre grids, generating estimates of average educational attainment by age and sex at subnational levels. Despite marked progress in attainment from 2000 to 2015 across Africa, substantial differences persist between locations and sexes. These differences have widened in many countries, particularly across the Sahel. These high-resolution, comparable estimates improve the ability of decision-makers to plan the precisely targeted interventions that will be necessary to deliver progress during the era of the Sustainable Development Goals.

Species trees for the tree swallows (Genus Tachycineta): an alternative phylogenetic hypothesis to the mitochondrial gene tree.

PubMed

Dor, Roi; Carling, Matthew D; Lovette, Irby J; Sheldon, Frederick H; Winkler, David W

2012-10-01

The New World swallow genus Tachycineta comprises nine species that collectively have a wide geographic distribution and remarkable variation both within- and among-species in ecologically important traits. Existing phylogenetic hypotheses for Tachycineta are based on mitochondrial DNA sequences, thus they provide estimates of a single gene tree. In this study we sequenced multiple individuals from each species at 16 nuclear intron loci. We used gene concatenated approaches (Bayesian and maximum likelihood) as well as coalescent-based species tree inference to reconstruct phylogenetic relationships of the genus. We examined the concordance and conflict between the nuclear and mitochondrial trees and between concatenated and coalescent-based inferences. Our results provide an alternative phylogenetic hypothesis to the existing mitochondrial DNA estimate of phylogeny. This new hypothesis provides a more accurate framework in which to explore trait evolution and examine the evolution of the mitochondrial genome in this group. Copyright © 2012 Elsevier Inc. All rights reserved.

Utilisation of rheumatology care services in Germany: the case of physical therapy and self-help groups.

PubMed

Thieme, Holm; Borgetto, Bernhard

2012-01-01

Physical Therapy (PT) and self-help groups (SHG) are important components of health care in rheumatic diseases. The utilisation of PT and SHG by patients with rheumatic diseases may be influenced by several factors. The aim of this study is to summarize the evidence on PT and SHG utilisation of patients with rheumatic diseases in Germany. We systematically searched the MEDLINE-database for studies that evaluated the utilisation and factors that possibly influence the utilisation of PT and SHG. Eight studies were found for PT-utilisation and one for SHG-utilisation. Between 25 and 59 percent of patients with rheumatic diseases received PT services. Several individual and contextual factors that may influence the utilisation could be identified. In conclusion, evidence exists for wide variations in the utilisation of PT services and an underuse of such services among patients with rheumatic diseases in Germany. By contrast, little evidence exists on the utilisation of SHG.

Focal colors across languages are representative members of color categories.

PubMed

Abbott, Joshua T; Griffiths, Thomas L; Regier, Terry

2016-10-04

Focal colors, or best examples of color terms, have traditionally been viewed as either the underlying source of cross-language color-naming universals or derived from category boundaries that vary widely across languages. Existing data partially support and partially challenge each of these views. Here, we advance a position that synthesizes aspects of these two traditionally opposed positions and accounts for existing data. We do so by linking this debate to more general principles. We show that best examples of named color categories across 112 languages are well-predicted from category extensions by a statistical model of how representative a sample is of a distribution, independently shown to account for patterns of human inference. This model accounts for both universal tendencies and variation in focal colors across languages. We conclude that categorization in the contested semantic domain of color may be governed by principles that apply more broadly in cognition and that these principles clarify the interplay of universal and language-specific forces in color naming.

Focal colors across languages are representative members of color categories

PubMed Central

Abbott, Joshua T.; Griffiths, Thomas L.; Regier, Terry

2016-01-01

Focal colors, or best examples of color terms, have traditionally been viewed as either the underlying source of cross-language color-naming universals or derived from category boundaries that vary widely across languages. Existing data partially support and partially challenge each of these views. Here, we advance a position that synthesizes aspects of these two traditionally opposed positions and accounts for existing data. We do so by linking this debate to more general principles. We show that best examples of named color categories across 112 languages are well-predicted from category extensions by a statistical model of how representative a sample is of a distribution, independently shown to account for patterns of human inference. This model accounts for both universal tendencies and variation in focal colors across languages. We conclude that categorization in the contested semantic domain of color may be governed by principles that apply more broadly in cognition and that these principles clarify the interplay of universal and language-specific forces in color naming. PMID:27647896

Interspecific variation in prey capture behavior by co-occurring Nepenthes pitcher plants

PubMed Central

Chin, Lijin; Chung, Arthur YC; Clarke, Charles

2014-01-01

Pitcher plants of the genus Nepenthes capture a wide range of arthropod prey for nutritional benefit, using complex combinations of visual and olfactory signals and gravity-driven pitfall trapping mechanisms. In many localities throughout Southeast Asia, several Nepenthes different species occur in mixed populations. Often, the species present at any given location have strongly divergent trap structures and preliminary surveys indicate that different species trap different combinations of arthropod prey, even when growing at the same locality. On this basis, it has been proposed that co-existing Nepenthes species may be engaged in niche segregation with regards to arthropod prey, avoiding direct competition with congeners by deploying traps that have modifications that enable them to target specific prey types. We examined prey capture among 3 multi-species Nepenthes populations in Borneo, finding that co-existing Nepenthes species do capture different combinations of prey, but that significant interspecific variations in arthropod prey combinations can often be detected only at sub-ordinal taxonomic ranks. In all lowland Nepenthes species examined, the dominant prey taxon is Formicidae, but montane Nepenthes trap few (or no) ants and 2 of the 3 species studied have evolved to target alternative sources of nutrition, such as tree shrew feces. Using similarity and null model analyses, we detected evidence for niche segregation with regards to formicid prey among 5 lowland, sympatric Nepenthes species in Sarawak. However, we were unable to determine whether these results provide support for the niche segregation hypothesis, or whether they simply reflect unquantified variation in heterogeneous habitats and/or ant communities in the study sites. These findings are used to propose improvements to the design of field experiments that seek to test hypotheses about targeted prey capture patterns in Nepenthes. PMID:24481246

Interspecific variation in prey capture behavior by co-occurring Nepenthes pitcher plants: evidence for resource partitioning or sampling-scheme artifacts?

PubMed

Chin, Lijin; Chung, Arthur Y C; Clarke, Charles

2014-01-01

Pitcher plants of the genus Nepenthes capture a wide range of arthropod prey for nutritional benefit, using complex combinations of visual and olfactory signals and gravity-driven pitfall trapping mechanisms. In many localities throughout Southeast Asia, several Nepenthes different species occur in mixed populations. Often, the species present at any given location have strongly divergent trap structures and preliminary surveys indicate that different species trap different combinations of arthropod prey, even when growing at the same locality. On this basis, it has been proposed that co-existing Nepenthes species may be engaged in niche segregation with regards to arthropod prey, avoiding direct competition with congeners by deploying traps that have modifications that enable them to target specific prey types. We examined prey capture among 3 multi-species Nepenthes populations in Borneo, finding that co-existing Nepenthes species do capture different combinations of prey, but that significant interspecific variations in arthropod prey combinations can often be detected only at sub-ordinal taxonomic ranks. In all lowland Nepenthes species examined, the dominant prey taxon is Formicidae, but montane Nepenthes trap few (or no) ants and 2 of the 3 species studied have evolved to target alternative sources of nutrition, such as tree shrew feces. Using similarity and null model analyses, we detected evidence for niche segregation with regards to formicid prey among 5 lowland, sympatric Nepenthes species in Sarawak. However, we were unable to determine whether these results provide support for the niche segregation hypothesis, or whether they simply reflect unquantified variation in heterogeneous habitats and/or ant communities in the study sites. These findings are used to propose improvements to the design of field experiments that seek to test hypotheses about targeted prey capture patterns in Nepenthes.

Predicting nitrogen loading with land-cover composition: how can watershed size affect model performance?

PubMed

Zhang, Tao; Yang, Xiaojun

2013-01-01

Watershed-wide land-cover proportions can be used to predict the in-stream non-point source pollutant loadings through regression modeling. However, the model performance can vary greatly across different study sites and among various watersheds. Existing literature has shown that this type of regression modeling tends to perform better for large watersheds than for small ones, and that such a performance variation has been largely linked with different interwatershed landscape heterogeneity levels. The purpose of this study is to further examine the previously mentioned empirical observation based on a set of watersheds in the northern part of Georgia (USA) to explore the underlying causes of the variation in model performance. Through the combined use of the neutral landscape modeling approach and a spatially explicit nutrient loading model, we tested whether the regression model performance variation over the watershed groups ranging in size is due to the different watershed landscape heterogeneity levels. We adopted three neutral landscape modeling criteria that were tied with different similarity levels in watershed landscape properties and used the nutrient loading model to estimate the nitrogen loads for these neutral watersheds. Then we compared the regression model performance for the real and neutral landscape scenarios, respectively. We found that watershed size can affect the regression model performance both directly and indirectly. Along with the indirect effect through interwatershed heterogeneity, watershed size can directly affect the model performance over the watersheds varying in size. We also found that the regression model performance can be more significantly affected by other physiographic properties shaping nitrogen delivery effectiveness than the watershed land-cover heterogeneity. This study contrasts with many existing studies because it goes beyond hypothesis formulation based on empirical observations and into hypothesis testing to explore the fundamental mechanism.

Increased mortality associated with EMS transport of gunshot wound victims when compared to private vehicle transport.

PubMed

Zafar, Syed Nabeel; Haider, Adil H; Stevens, Kent A; Ray-Mazumder, Nik; Kisat, Mehreen T; Schneider, Eric B; Chi, Albert; Galvagno, Samuel M; Cornwell, Edward E; Efron, David T; Haut, Elliott R

2014-09-01

Recent studies suggest that mode of transport affects survival in penetrating trauma patients. We hypothesised that there is wide variation in transport mode for patients with gunshot wounds (GSW) and there may be a mortality difference for GSW patients transported by emergency medical services (EMS) vs. private vehicle (PV). We studied adult (≥16 years) GSW patients in the National Trauma Data Bank (2007-2010). Level 1 and 2 trauma centres (TC) receiving ≥50 GSW patients per year were included. Proportions of patients arriving by each transport mode for each TC were examined. In-hospital mortality was compared between the two groups, PV and EMS, using multivariable regression analyses. Models were adjusted for patient demographics, injury severity, and were adjusted for clustering by facility. 74,187 GSW patients were treated at 182 TCs. The majority (76%) were transported by EMS while 12.6% were transported by PV. By individual TC, the proportion of patients transported by each category varied widely: EMS (median 78%, interquartile range (IQR) 66-85%), PV (median 11%, IQR 7-17%), or others (median 7%, IQR 2-18%). Unadjusted mortality was significantly different between PV and EMS (2.1% vs. 9.7%, p<0.001). Multivariable analysis demonstrated that EMS transported patients had a greater than twofold odds of dying when compared to PV (OR=2.0, 95% CI 1.73-2.35). Wide variation exists in transport mode for GSW patients across the United States. Mortality may be higher for GSW patients transported by EMS when compared to private vehicle transport. Further studies should be performed to examine this question. Copyright © 2014 Elsevier Ltd. All rights reserved.

Clopidogrel pharmacokinetics and pharmacodynamics vary widely despite exclusion or control of polymorphisms (CYP2C19, ABCB1, PON1), noncompliance, diet, smoking, co-medications (including proton pump inhibitors), and pre-existent variability in platelet function.

PubMed

Frelinger, Andrew L; Bhatt, Deepak L; Lee, Ronald D; Mulford, Darcy J; Wu, Jingtao; Nudurupati, Sai; Nigam, Anu; Lampa, Michael; Brooks, Julie K; Barnard, Marc R; Michelson, Alan D

2013-02-26

This study sought to determine whether known genetic, drug, dietary, compliance, and lifestyle factors affecting clopidogrel absorption and metabolism fully account for the variability in clopidogrel pharmacokinetics and pharmacodynamics. Platelet inhibition by clopidogrel is highly variable. Patients with reduced inhibition have increased risk for major adverse cardiovascular events. Identification of factors contributing to clopidogrel's variable response is needed to improve platelet inhibition and reduce risk for cardiovascular events. Healthy subjects (n = 160; ages 20 to 53 years; homozygous CYP2C19 extensive metabolizer genotype; no nicotine for 6 weeks, prescription drugs for 4 weeks, over-the-counter drugs for 2 weeks, and no caffeine or alcohol for 72 h; confined; restricted diet) received clopidogrel 75 mg/day for 9 days, at which time clopidogrel pharmacokinetic and pharmacodynamic endpoints were measured. At steady-state, clopidogrel active metabolite (clopidogrel(AM)) pharmacokinetics varied widely between subjects (coefficients of variation [CVs] 33.8% and 40.2% for clopidogrel(AM) area under the time-concentration curve and peak plasma concentration, respectively). On-treatment vasodilator stimulated phosphoprotein P2Y(12) platelet reactivity index (PRI), maximal platelet aggregation (MPA) to adenosine phosphate, and VerifyNow P2Y12 platelet response units (PRU) also varied widely (CVs 32% to 53%). All identified factors together accounted for only 18% of intersubject variation in pharmacokinetic parameters and 32% to 64% of intersubject variation in PRI, MPA, and PRU. High on-treatment platelet reactivity was present in 45% of subjects. Clopidogrel pharmacokinetics and pharmacodynamics vary widely despite rigorous exclusion or control of known disease, polymorphisms (CYP2C19, CYP3A5, ABCB1, PON1), noncompliance, co-medications, diet, smoking, alcohol, demographics, and pre-treatment platelet hyperreactivity. Thus, as yet unidentified factors contribute to high on-treatment platelet reactivity with its known increased risk of major adverse cardiovascular events. (A Study of the Effects of Multiple Doses of Dexiansoprazole, Lansoprazole, Omeprazole or Esomeprazole on the Pharmacokinetics and Pharmacodynamics of Clopidogrel in Healthy Participants: NCT00942175). Copyright © 2013 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Genome-wide interactions with dairy intake for body mass index in adults of European descent

USDA-ARS?s Scientific Manuscript database

Body weight responds variably to the intake of dairy foods. Genetic variation may contribute to inter-individual variability in associations between body weight and dairy consumption. We conducted a genome-wide interaction study to discover genetic variants that account for variation in BMI in the c...

Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

USDA-ARS?s Scientific Manuscript database

Copy number variation (CNV) is an important type of genetic variation contributing to phenotypic differences among mammals and may serve as an alternative molecular marker to single nucleotide polymorphism (SNP) for genome-wide association study (GWAS). Recently, GWAS analysis using CNV has been app...

Assessment of current practice and barriers to antimicrobial prophylaxis in peritoneal dialysis patients.

PubMed

Campbell, Denise J; Brown, Fiona G; Craig, Jonathan C; Gallagher, Martin P; Johnson, David W; Kirkland, Geoffrey S; Kumar, Subramanian K; Lim, Wai H; Ranganathan, Dwarakanathan; Saweirs, Walaa; Sud, Kamal; Toussaint, Nigel D; Walker, Rowan G; Williams, Lesley A; Yehia, Maha; Mudge, David W

2016-04-01

Existing Australasian and international guidelines outline antibiotic and antifungal measures to prevent the development of treatment-related infection in peritoneal dialysis (PD) patients. Practice patterns and rates of PD-related infection vary widely across renal units in Australia and New Zealand and are known to vary significantly from guideline recommendations, resulting in PD technique survival rates that are lower than those achieved in many other countries. The aim of this study was to determine if there is an association between current practice and PD-related infection outcomes and to identify the barriers and enablers to good clinical practice. This is a multicentre network study involving eight PD units in Australia and New Zealand, with a focus on adherence to guideline recommendations on antimicrobial prophylaxis in PD patients. Current practice was established by asking the PD unit heads to respond to a short survey about practice/protocols/policies and a 'process map' was constructed following a face-to-face interview with the primary PD nurse at each unit. The perceived barriers/enablers to adherence to the relevant guideline recommendations were obtained from the completion of 'cause and effect' diagrams by the nephrologist and PD nurse at each unit. Data on PD-related infections were obtained for the period 1 January 2011 to 31 December 2011. Perceived barriers that may result in reduced adherence to guideline recommendations included lack of knowledge, procedural lapses, lack of a centralized patient database, patients with non-English speaking background, professional concern about antibiotic resistance, medication cost and the inability of nephrologists and infectious diseases staff to reach consensus on unit protocols. The definitions of PD-related infections used by some units varied from those recommended by the International Society for Peritoneal Dialysis, particularly with exit-site infection (ESI). Wide variations were observed in the rates of ESI (0.06-0.53 episodes per patient-year) and peritonitis (0.31-0.86 episodes per patient-year). Despite the existence of strongly evidence-based guideline recommendations, there was wide variation in adherence to these recommendations between PD units which might contribute to PD-related infection rates, which varied widely between units. Although individual patient characteristics may account for some of this variability, inconsistencies in the processes of care to prevent infection in PD patients also play a role. © The Author 2015. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

Weather-based forecasts of California crop yields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lobell, D B; Cahill, K N; Field, C B

2005-09-26

Crop yield forecasts provide useful information to a range of users. Yields for several crops in California are currently forecast based on field surveys and farmer interviews, while for many crops official forecasts do not exist. As broad-scale crop yields are largely dependent on weather, measurements from existing meteorological stations have the potential to provide a reliable, timely, and cost-effective means to anticipate crop yields. We developed weather-based models of state-wide yields for 12 major California crops (wine grapes, lettuce, almonds, strawberries, table grapes, hay, oranges, cotton, tomatoes, walnuts, avocados, and pistachios), and tested their accuracy using cross-validation over themore » 1980-2003 period. Many crops were forecast with high accuracy, as judged by the percent of yield variation explained by the forecast, the number of yields with correctly predicted direction of yield change, or the number of yields with correctly predicted extreme yields. The most successfully modeled crop was almonds, with 81% of yield variance captured by the forecast. Predictions for most crops relied on weather measurements well before harvest time, allowing for lead times that were longer than existing procedures in many cases.« less

Existing methods for improving the accuracy of digital-to-analog converters

NASA Astrophysics Data System (ADS)

Eielsen, Arnfinn A.; Fleming, Andrew J.

2017-09-01

The performance of digital-to-analog converters is principally limited by errors in the output voltage levels. Such errors are known as element mismatch and are quantified by the integral non-linearity. Element mismatch limits the achievable accuracy and resolution in high-precision applications as it causes gain and offset errors, as well as harmonic distortion. In this article, five existing methods for mitigating the effects of element mismatch are compared: physical level calibration, dynamic element matching, noise-shaping with digital calibration, large periodic high-frequency dithering, and large stochastic high-pass dithering. These methods are suitable for improving accuracy when using digital-to-analog converters that use multiple discrete output levels to reconstruct time-varying signals. The methods improve linearity and therefore reduce harmonic distortion and can be retrofitted to existing systems with minor hardware variations. The performance of each method is compared theoretically and confirmed by simulations and experiments. Experimental results demonstrate that three of the five methods provide significant improvements in the resolution and accuracy when applied to a general-purpose digital-to-analog converter. As such, these methods can directly improve performance in a wide range of applications including nanopositioning, metrology, and optics.

Organic metamorphism in the Lower Mississippian-Upper Devonian Bakken shales. Part 1: Rock-Eval pyrolysis and vitrinite reflectance.

USGS Publications Warehouse

Price, L.C.; Daws, T.; Pawlewicz, M.

1986-01-01

The Williston basin is an intracratonic basin extending across parts of several states, principally North Dakota, on the US/Canadian frontier. A sequence of up to 16 000 ft of Phanerozoic rocks exists in the basin; the Bakken formation is a relatively thin clastic unit composed of three members, of which the middle one is a black shale. Both core chip and cutting chip samples from a series of widely-distributed well locations were taken for laboratory analysis. Pyrolysis data showed 'wide variations' in maturity indices in samples from equivalent depths at different well locations. This suggests that a number of different palaeoheat-flow regimes have existed in the basin, resulting in the optimization of hydrocarbon formation processes at varying depths at different localities. The vitrinite reflectance profiles presented illustrate the expected trend of linearly-increasing maturity with depth to around 6500 ft. Between 6700 and 10 000 ft, however, this trend is interrupted by two 'reversals'. It is suggested that these reversals are due to suppression of the vitrinite reflectance values in samples with high concentrations of H-rich organic matter, and that they may therefore be associated with transitions from 'terrestrial-derived' to marine-depositional conditions. Consequently, the precise identification of the thresholds of intense hydrocarbon generation within the basin is problematic.-J.M.H.

Is there a species spectrum within the world-wide leaf economics spectrum? Major variations in leaf functional traits in the Mediterranean sclerophyll Quercus ilex.

PubMed

Niinemets, Ulo

2015-01-01

The leaf economics spectrum is a general concept describing coordinated variation in foliage structural, chemical and physiological traits across resource gradients. Yet, within this concept,the role of within-species variation, including ecotypic and plastic variation components, has been largely neglected. This study hypothesized that there is a within-species economics spectrum within the general spectrum in the evergreen sclerophyll Quercus ilex which dominates low resource ecosystems over an exceptionally wide range. An extensive database of foliage traits covering the full species range was constructed, and improved filtering algorithms were developed. Standardized data filtering was deemed absolutely essential as additional variation sources can result in trait variation of 10–300%,blurring the broad relationships. Strong trait variation, c. two-fold for most traits to up to almost an order of magnitude, was uncovered.Although the Q. ilex spectrum is part of the general spectrum, within-species trait and climatic relationships in this species partly differed from the overall spectrum. Contrary to world-wide trends, Q. ilex does not necessarily have a low nitrogen content per mass and can increase photosynthetic capacity with increasing foliage robustness. This study argues that the within-species economics spectrum needs to be considered in regional- to biome-level analyses.

Analysis of copy number variations among cattle breeds

USDA-ARS?s Scientific Manuscript database

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in the modern domesticated cattle using array comparative genomic hybridization (array CGH) and quanti...

Characterization of Genome-Wide Variation in Four-Row Wax, a Waxy Maize Landrace with a Reduced Kernel Row Phenotype

PubMed Central

Liu, Hanmei; Wang, Xuewen; Wei, Bin; Wang, Yongbin; Liu, Yinghong; Zhang, Junjie; Hu, Yufeng; Yu, Guowu; Li, Jian; Xu, Zhanbin; Huang, Yubi

2016-01-01

In southwest China, some maize landraces have long been isolated geographically, and have phenotypes that differ from those of widely grown cultivars. These landraces may harbor rich genetic variation responsible for those phenotypes. Four-row Wax is one such landrace, with four rows of kernels on the cob. We resequenced the genome of Four-row Wax, obtaining 50.46 Gb sequence at 21.87× coverage, then identified and characterized 3,252,194 SNPs, 213,181 short InDels (1–5 bp) and 39,631 structural variations (greater than 5 bp). Of those, 312,511 (9.6%) SNPs were novel compared to the most detailed haplotype map (HapMap) SNP database of maize. Characterization of variations in reported kernel row number (KRN) related genes and KRN QTL regions revealed potential causal mutations in fea2, td1, kn1, and te1. Genome-wide comparisons revealed abundant genetic variations in Four-row Wax, which may be associated with environmental adaptation. The sequence and SNP variations described here enrich genetic resources of maize, and provide guidance into study of seed numbers for crop yield improvement. PMID:27242868

Abundance differences among globular-cluster giants: Primordial versus evolutionary scenarios

NASA Astrophysics Data System (ADS)

Kraft, Robert P.

1994-06-01

Contrary to historical expectation, stars within a given globular cluster often exhibit wide variations in the abundance of C, N, and O as well as certain light metals, particularly Na and Al. Owing to flux limitations, studies have been confined to evolved stars, especially giants, but in few instances variations have been detected among main-sequence stars. Among giants, the variations are of two kinds. The abundances of C and N are often anticorrelated, and in the limited number of cases in which both have been measured, O and N abundances have also often proved to be anticorrelated (Pilachowski 1988; Sneden et al. 1991; Brown et al. 1991; Kraft et al. 1992). Following pioneering work by Cohen (1978) and Peterson (1980), strong evidence has recently emerged for the existence of a significant global anticorrelation between O and Na abundances (Drake et al. 1992, Kraft et al. 1993). The observations are discussed in terms of contrasting hypotheses: evolutionary versus primordial. In the former, the variations are attributed to the dredgeup of material that has been processed through the CNO cycle in the globular-cluster stars themselves. In the latter, the variations are attributed to primordial chemical inhomogeneities in the material out of which the cluster stars were formed, the composition of these 'clumps' having been determined by nuclear processing in a prior generation of more massive stars. Observational evidence supporting each of these scenarios is cited. Recent studies of stellar rotation among horizontal branch stars in certain clusters (Peterson et al. 1994) as well as new calculations of Na-23 and Al-27 production in the CNO processing regions of evolving low-mass giants (Langer et al. 1993) lend fresh support to the evolutionary hypothesis. However, such calculations do not explain the variation of C and N abundances found among cluster main-sequence stars (Suntzeff 1989; Briley et al. 1991) which therefore seem explicable only on the basis of a primordial scenario. Among mildly metal-poor giants, i.e., those in the range from solar metallicity to (Fe/H) approximately -1, recent observational evidence suggesting the existence of a substructure in the (el/Fe) ratios of the heavier alpha elements, e.g., Si, Mg, Ca, and Ti, is discussed. The possible influence of this effect on the interpretation of the integrated spectra of extragalactic globular clusters and E galaxies is noted.

Novel genetic capacitors and potentiators for the natural genetic variation of sensory bristles and their trait specificity in Drosophila melanogaster.

PubMed

Takahashi, Kazuo H

2015-11-01

Cryptic genetic variation (CGV) is defined as the genetic variation that has little effect on phenotypic variation under a normal condition, but contributes to heritable variation under environmental or genetic perturbations. Genetic buffering systems that suppress the expression of CGV and store it in a population are called genetic capacitors, and the opposite systems are called genetic potentiators. One of the best-known candidates for a genetic capacitor and potentiator is the molecular chaperone protein, HSP90, and one of its characteristics is that it affects the genetic variation in various morphological traits. However, it remains unclear whether the wide-ranging effects of HSP90 on a broad range of traits are a general feature of genetic capacitors and potentiators. In the current study, I searched for novel genetic capacitors and potentiators for quantitative bristle traits of Drosophila melanogaster and then investigated the trait specificity of their genetic buffering effect. Three bristle traits of D. melanogaster were used as the target traits, and the genomic regions with genetic buffering effects were screened using the 61 genomic deficiencies examined previously for genetic buffering effects in wing shape. As a result, four and six deficiencies with significant effects on increasing and decreasing the broad-sense heritability of the bristle traits were identified, respectively. Of the 18 deficiencies with significant effects detected in the current study and/or by the previous study, 14 showed trait-specific effects, and four affected the genetic buffering of both bristle traits and wing shape. This suggests that most genetic capacitors and potentiators exert trait-specific effects, but that general capacitors and potentiators with effects on multiple traits also exist. © 2015 John Wiley & Sons Ltd.

Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence

PubMed Central

Iskow, Rebecca C.; Austermann, Christian; Scharer, Christopher D.; Raj, Towfique; Boss, Jeremy M.; Sunyaev, Shamil; Price, Alkes; Stranger, Barbara; Simon, Viviana; Lee, Charles

2013-01-01

Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10−15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human–Neandertal divergence and is evolving under balancing selection, especially among European populations. PMID:23593015

CaGLK2 regulates natural variation of chlorophyll content and fruit color in pepper fruit.

PubMed

Brand, Arnon; Borovsky, Yelena; Hill, Theresa; Rahman, Khalis Afnan Abdul; Bellalou, Aharon; Van Deynze, Allen; Paran, Ilan

2014-10-01

We provide multiple evidences that CaGLK2 underlies a quantitative trait locus controlling natural variation in chlorophyll content and immature fruit color of pepper via modulating chloroplast compartment size. Pepper fruit quality is attributed to a variety of traits, affecting visual appearance, flavor, chemical composition and nutritional value. Among the quality traits, fruit color is of primary importance because the pigments that confer color are associated with nutrition, health and flavor. Although gene models have been proposed for qualitative aspects of fruit color, large natural variation in quantitative pigment content and fruit color exists in pepper. However, its genetic basis is largely unknown which hampers its utilization for plant improvement. We studied the role of GLK2, a GOLDEN2-like transcription factor that regulates chloroplast development in controlling natural variation for chlorophyll content and immature fruit color of pepper. The role of GLK2 in regulating fruit development has been studied previously in tomato using ectopic expression and the uniform ripening mutant analyses. However, pepper provides a unique opportunity to further study the function of this gene because of the wide natural variation of fruit colors in this species. Segregation, sequencing and expression analyses indicated that pepper GLK2 (CaGLK2) corresponds to the recently reported pc10 QTL that controls chloroplast development and chlorophyll content in pepper. CaGLK2 exerts its effect on chloroplast compartment size predominantly during immature fruit development. We show that the genetic background, sequence variation and expression pattern confer a complex and multi-level regulation of CaGLK2 and fruit color in Capsicum. The positive effect on fruit quality predominantly at the green stage conferred by CaGLK2 can be utilized to breed green pepper varieties with improved nutritional values and taste.

Dissection of complex adult traits in a mouse synthetic population.

PubMed

Burke, David T; Kozloff, Kenneth M; Chen, Shu; West, Joshua L; Wilkowski, Jodi M; Goldstein, Steven A; Miller, Richard A; Galecki, Andrzej T

2012-08-01

Finding the causative genetic variations that underlie complex adult traits is a significant experimental challenge. The unbiased search strategy of genome-wide association (GWAS) has been used extensively in recent human population studies. These efforts, however, typically find only a minor fraction of the genetic loci that are predicted to affect variation. As an experimental model for the analysis of adult polygenic traits, we measured a mouse population for multiple phenotypes and conducted a genome-wide search for effector loci. Complex adult phenotypes, related to body size and bone structure, were measured as component phenotypes, and each subphenotype was associated with a genomic spectrum of candidate effector loci. The strategy successfully detected several loci for the phenotypes, at genome-wide significance, using a single, modest-sized population (N = 505). The effector loci each explain 2%-10% of the measured trait variation and, taken together, the loci can account for over 25% of a trait's total population variation. A replicate population (N = 378) was used to confirm initially observed loci for one trait (femur length), and, when the two groups were merged, the combined population demonstrated increased power to detect loci. In contrast to human population studies, our mouse genome-wide searches find loci that individually explain a larger fraction of the observed variation. Also, the additive effects of our detected mouse loci more closely match the predicted genetic component of variation. The genetic loci discovered are logical candidates for components of the genetic networks having evolutionary conservation with human biology.

Genome-wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds

USDA-ARS?s Scientific Manuscript database

Copy number variations (CNVs) are large insertions, deletions or duplications in the genome that vary between members of a species and are known to affect a wide variety of phenotypic traits. In this study, we identified CNVs in a population of bulls using low coverage next-generation sequence data....

Parabolic Systems with p, q-Growth: A Variational Approach

NASA Astrophysics Data System (ADS)

Bögelein, Verena; Duzaar, Frank; Marcellini, Paolo

2013-10-01

We consider the evolution problem associated with a convex integrand {f : {R}^{Nn}to [0,infty)} satisfying a non-standard p, q-growth assumption. To establish the existence of solutions we introduce the concept of variational solutions. In contrast to weak solutions, that is, mappings {u\\colon Ω_T to {R}^n} which solve partial_tu-div Df(Du)=0 weakly in {Ω_T}, variational solutions exist under a much weaker assumption on the gap q - p. Here, we prove the existence of variational solutions provided the integrand f is strictly convex and 2n/n+2 < p le q < p+1. These variational solutions turn out to be unique under certain mild additional assumptions on the data. Moreover, if the gap satisfies the natural stronger assumption 2le p le q < p+ minbig \\{1,4/n big \\}, we show that variational solutions are actually weak solutions. This means that solutions u admit the necessary higher integrability of the spatial derivative Du to satisfy the parabolic system in the weak sense, that is, we prove that uin L^q_locbig(0,T; W^{1,q}_loc(Ω,{R}^N)big).

Analysis of copy number variations reveals differences among cattle breeds

USDA-ARS?s Scientific Manuscript database

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in the modern domesticated cattle using array comparative genomic hybridization (array CGH) and quanti...

The existence results and Tikhonov regularization method for generalized mixed variational inequalities in Banach spaces

NASA Astrophysics Data System (ADS)

Wang, Min

2017-06-01

This paper aims to establish the Tikhonov regularization method for generalized mixed variational inequalities in Banach spaces. For this purpose, we firstly prove a very general existence result for generalized mixed variational inequalities, provided that the mapping involved has the so-called mixed variational inequality property and satisfies a rather weak coercivity condition. Finally, we establish the Tikhonov regularization method for generalized mixed variational inequalities. Our findings extended the results for the generalized variational inequality problem (for short, GVIP( F, K)) in R^n spaces (He in Abstr Appl Anal, 2012) to the generalized mixed variational inequality problem (for short, GMVIP(F,φ , K)) in reflexive Banach spaces. On the other hand, we generalized the corresponding results for the generalized mixed variational inequality problem (for short, GMVIP(F,φ ,K)) in R^n spaces (Fu and He in J Sichuan Norm Univ (Nat Sci) 37:12-17, 2014) to reflexive Banach spaces.

Methodological variations and their effects on reported medication administration error rates.

PubMed

McLeod, Monsey Chan; Barber, Nick; Franklin, Bryony Dean

2013-04-01

Medication administration errors (MAEs) are a problem, yet methodological variation between studies presents a potential barrier to understanding how best to increase safety. Using the UK as a case-study, we systematically summarised methodological variations in MAE studies, and their effects on reported MAE rates. Nine healthcare databases were searched for quantitative observational MAE studies in UK hospitals. Methodological variations were analysed and meta-analysis of MAE rates performed using studies that used the same definitions. Odds ratios (OR) were calculated to compare MAE rates between intravenous (IV) and non-IV doses, and between paediatric and adult doses. We identified 16 unique studies reporting three MAE definitions, 44 MAE subcategories and four different denominators. Overall adult MAE rates were 5.6% of a total of 21 533 non-IV opportunities for error (OE) (95% CI 4.6% to 6.7%) and 35% of a total of 154 IV OEs (95% CI 2% to 68%). MAEs were five times more likely in IV than non-IV doses (pooled OR 5.1; 95% CI 3.5 to 7.5). Including timing errors of ±30 min increased the MAE rate from 27% to 69% of 320 IV doses in one study. Five studies were unclear as to whether the denominator included dose omissions; omissions accounted for 0%-13% of IV doses and 1.8%-5.1% of non-IV doses. Wide methodological variations exist even within one country, some with significant effects on reported MAE rates. We have made recommendations for future MAE studies; these may be applied both within and outside the UK.

Variation in Biomass Composition Components among Forage, Biomass, Sorghum-Sudangrass, and Sweet Sorghum Types

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stefaniak, T. R.; Dahlberg, J. A.; Bean, B. W.

2012-07-01

Alternative biomass sources must be developed if the United States is to meet the goal in the U.S. Energy Security Act of 2007 to derive 30% of its petroleum from renewable sources, and several different biomass crops are currently in development. Sorghum [Sorghum bicolor (L.) Moench] is one such crop that will be an important feedstock source for biofuel production. As composition influences productivity, there exists a need to understand the range in composition observed within the crop. The goal of this research was to assess the range in dietary fiber composition observed within different types of biomass sorghums. Amore » total of 152 sorghum samples were divided into the four end-use types of sorghum: biomass, forage, sorghum-sudangrass, and sweet. These samples were analyzed chemically using dietary fiber analysis performed at the National Renewable Energy Laboratory using published protocols. Significant variation among the groups was detected for glucan and ash. Positive and highly significant correlations were detected between structural carbohydrates in the biomass and sweet sorghums while many of these correlations were negative or not significant in the forage and sorghum-sudangrass types. In addition, a wide range of variation was present within each group indicating that there is potential to manipulate the composition of the crop.« less

Drivers of protogynous sex change differ across spatial scales.

PubMed

Taylor, Brett M

2014-01-22

The influence of social demography on sex change schedules in protogynous reef fishes is well established, yet effects across spatial scales (in particular, the magnitude of natural variation relative to size-selective fishing effects) are poorly understood. Here, I examine variation in timing of sex change for exploited parrotfishes across a range of environmental, anthropogenic and geographical factors. Results were highly dependent on spatial scale. Fishing pressure was the most influential factor determining length at sex change at the within-island scale where a wide range of anthropogenic pressure existed. Sex transition occurred at smaller sizes where fishing pressure was high. Among islands, however, differences were overwhelmingly predicted by reefal-scale structural features, a pattern evident for all species examined. For the most abundant species, Chlorurus spilurus, length at sex change increased at higher overall densities and greater female-to-male sex ratios at all islands except where targeted by fishermen; here the trend was reversed. This implies differing selective pressures on adult individuals can significantly alter sex change dynamics, highlighting the importance of social structure, demography and the selective forces structuring populations. Considerable life-history responses to exploitation were observed, but results suggest potential fishing effects on demography may be obscured by natural variation at biogeographic scales.

The episode of genetic drift defining the migration of humans out of Africa is derived from a large east African population size.

PubMed

Elhassan, Nuha; Gebremeskel, Eyoab Iyasu; Elnour, Mohamed Ali; Isabirye, Dan; Okello, John; Hussien, Ayman; Kwiatksowski, Dominic; Hirbo, Jibril; Tishkoff, Sara; Ibrahim, Muntaser E

2014-01-01

Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount.

Hsp90 prevents phenotypic variation by suppressing the mutagenic activity of transposons.

PubMed

Specchia, Valeria; Piacentini, Lucia; Tritto, Patrizia; Fanti, Laura; D'Alessandro, Rosalba; Palumbo, Gioacchino; Pimpinelli, Sergio; Bozzetti, Maria P

2010-02-04

The canalization concept describes the resistance of a developmental process to phenotypic variation, regardless of genetic and environmental perturbations, owing to the existence of buffering mechanisms. Severe perturbations, which overcome such buffering mechanisms, produce altered phenotypes that can be heritable and can themselves be canalized by a genetic assimilation process. An important implication of this concept is that the buffering mechanism could be genetically controlled. Recent studies on Hsp90, a protein involved in several cellular processes and development pathways, indicate that it is a possible molecular mechanism for canalization and genetic assimilation. In both flies and plants, mutations in the Hsp90-encoding gene induce a wide range of phenotypic abnormalities, which have been interpreted as an increased sensitivity of different developmental pathways to hidden genetic variability. Thus, Hsp90 chaperone machinery may be an evolutionarily conserved buffering mechanism of phenotypic variance, which provides the genetic material for natural selection. Here we offer an additional, perhaps alternative, explanation for proposals of a concrete mechanism underlying canalization. We show that, in Drosophila, functional alterations of Hsp90 affect the Piwi-interacting RNA (piRNA; a class of germ-line-specific small RNAs) silencing mechanism leading to transposon activation and the induction of morphological mutants. This indicates that Hsp90 mutations can generate new variation by transposon-mediated 'canonical' mutagenesis.

Welding of high chromium steels

NASA Technical Reports Server (NTRS)

Miller, W B

1928-01-01

A brief description is given of different groups of high chromium steels (rustless iron and stainless steels) according to their composition and more generally accepted names. The welding procedure for a given group will be much the same regardless of the slight variations in chemical composition which may exist within a certain group. Information is given for the tensile properties (yield point and ultimate strength) of metal sheets and welds before and after annealing on coupons one and one-half inches wide. Since welds in rustless iron containing 16 to 18 percent chromium and 7 to 12 percent nickel show the best combination of strength and ductility in the 'as welded' or annealed condition, it is considered the best alloy to use for welded construction.

The safe and responsible disposal of unused controlled drugs.

PubMed

Ahmed, Iftikhar; Majeed, Amer

There are well-defined legal requirements for the safe storage, handling and disposal of controlled drugs (CDs): The Misuse of Drugs Act 1971, and Safer Management of Controlled Drugs (Department of Health, 2007). Clinical staff involved in the prescription and administration of CDs to patients are responsible and accountable for the appropriate disposal of these drugs because of the risk of substance abuse. A review of current practice, as followed by staff involved in the use and disposal of CDs, has been evaluated in a multi-centre audit. This audit showed that a wide variation in attitude towards disposal of CDs exists among medical and non-medical staff, and that the sample hospitals are falling short of meeting proposed standards.

Is there a protocol in experimental skin wounds in rats using low-level diode laser therapy (LLDLT) combining or not red and infrared wavelengths? Systematic review.

PubMed

de Lima, Fernando José Camello; de Oliveira Neto, Olavo Barbosa; Barbosa, Fabiano Timbó; do Nascimento Galvão, Ailton Mota; Ramos, Fernando Wagner Silva; de Lima, Christiane Calheiros Farias; de Sousa Rodrigues, Célio Fernando

2016-05-01

A systematic review addressing experiments with healing of skin wounds in rats using LLDLT with different active means seeking to identify a pattern in adjustments such as laser wavelength, power and fluency and analysing wound healing parameters, such as wound area, presence of fibroblasts, angiogenesis, leukocyte infiltration, epithelial coverage and antibacterial effect. It was perceived that a protocol does not exist in view of the wide variation in the use of power (9 to 500 mW) and fluency (1 to 60 J/cm2); however, between the different wavelengths, the highlight was the combined use of red and infrared wavelengths showing better results than when used alone.

Development of performance criteria for advanced Viking seismic experiments

NASA Technical Reports Server (NTRS)

1972-01-01

The characteristics and requirements of the seismic instrument for mapping the internal structure of the planet Mars are briefly described. The types of signals expected to exist are microseismic background generated by wind and pressure variations and thermal effects, disturbances of or in the landed vehicle, signals caused by faulting and volcanic activity, and signals due to meteoritic impacts. The advanced instrument package should include a short-period vertical component system, a long-period or wide-band 3-component system, a high frequency vertical component system, and a system for detection and rejection of lander noises. The Viking '75, Surveyor, and Apollo systems are briefly described as potential instruments to be considered for modification. Data processing and control systems are also summarized.

A method for surface topography measurement using a new focus function based on dual-tree complex wavelet transform

NASA Astrophysics Data System (ADS)

Li, Shimiao; Guo, Tong; Yuan, Lin; Chen, Jinping

2018-01-01

Surface topography measurement is an important tool widely used in many fields to determine the characteristics and functionality of a part or material. Among existing methods for this purpose, the focus variation method has proved high performance particularly in large slope scenarios. However, its performance depends largely on the effectiveness of focus function. This paper presents a method for surface topography measurement using a new focus measurement function based on dual-tree complex wavelet transform. Experiments are conducted on simulated defocused images to prove its high performance in comparison with other traditional approaches. The results showed that the new algorithm has better unimodality and sharpness. The method was also verified by measuring a MEMS micro resonator structure.

Variation in National ACGME Case Log Data for Pediatric Orthopaedic Fellowships: Are Fellow Coding Practices Responsible?

PubMed

McClure, Philip K; Woiczik, Marcella; Karol, Lori; Sankar, Wudbhav N

The introduction of the 80-hour work week for Accreditation Council for Graduate Medical Education (ACGME) accredited fellowship programs initiated many efforts to optimize surgical training. One particular area of interest is on recording and tracking surgical experiences. The current standard is logging cases based on Current Procedural Terminology codes, which are primarily designed for billing. Proposed guidelines from the ACGME regarding logging exist, but their implementation is unknown, as is the variation in case volume across fellowship programs. The purpose of this study was to investigate variability in the national case log data, and explore potential sources of variation using fellow surveys. National ACGME case log data for pediatric orthopaedic fellowships from 2012 to 2015 were reviewed, with particular attention to the domains of spine, pelvis/hip, arthroscopy, trauma, and other (which includes clubfoot casting). To explore potential sources of case log variability, a survey on case logging behavior was distributed to all pediatric orthopaedic fellows for the academic year 2015 to 2016. Reported experiences based on ACGME case logs varied widely between fellows with percentage difference of up to 100% in all areas. Similarly, wide variability is present in coding practices of pediatric orthopaedic fellows, who often lack formal education on the topic of appropriate coding/logging. In the survey, hypothetical case scenarios had an absolute difference in recorded codes of up to 13 and a percentage difference of up to 100%. ACGME case log data for pediatric orthopaedic fellowships demonstrates wide variability in reported surgical experiences. This variability may be due, in part, to differences in logging practices by individual fellows. This observation makes meaningful interpretation of national data on surgical volume challenging. Proposed surgical experience minimums should be interpreted in light of these data, and may not be advisable unless accompanied by standardized and specific guidelines for case log entry. Efforts to optimize training in the post 80-hour era will require accurate data to serve as a starting point for future educational efforts.

Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy.

PubMed

Heinig, Matthias; Adriaens, Michiel E; Schafer, Sebastian; van Deutekom, Hanneke W M; Lodder, Elisabeth M; Ware, James S; Schneider, Valentin; Felkin, Leanne E; Creemers, Esther E; Meder, Benjamin; Katus, Hugo A; Rühle, Frank; Stoll, Monika; Cambien, François; Villard, Eric; Charron, Philippe; Varro, Andras; Bishopric, Nanette H; George, Alfred L; Dos Remedios, Cristobal; Moreno-Moral, Aida; Pesce, Francesco; Bauerfeind, Anja; Rüschendorf, Franz; Rintisch, Carola; Petretto, Enrico; Barton, Paul J; Cook, Stuart A; Pinto, Yigal M; Bezzina, Connie R; Hubner, Norbert

2017-09-14

Genetic variation is an important determinant of RNA transcription and splicing, which in turn contributes to variation in human traits, including cardiovascular diseases. Here we report the first in-depth survey of heart transcriptome variation using RNA-sequencing in 97 patients with dilated cardiomyopathy and 108 non-diseased controls. We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls, affecting known as well as novel dilated cardiomyopathy genes. Moreover, we show a widespread effect of genetic variation on the regulation of transcription, isoform usage, and allele-specific expression. Systematic annotation of genome-wide association SNPs identifies 60 functional candidate genes for heart phenotypes, representing 20% of all published heart genome-wide association loci. Focusing on the dilated cardiomyopathy phenotype we found that eQTL variants are also enriched for dilated cardiomyopathy genome-wide association signals in two independent cohorts. RNA transcription, splicing, and allele-specific expression are each important determinants of the dilated cardiomyopathy phenotype and are controlled by genetic factors. Our results represent a powerful resource for the field of cardiovascular genetics.

Meta-analysis of sex-specific genome-wide association studies.

PubMed

Magi, Reedik; Lindgren, Cecilia M; Morris, Andrew P

2010-12-01

Despite the success of genome-wide association studies, much of the genetic contribution to complex human traits is still unexplained. One potential source of genetic variation that may contribute to this "missing heritability" is that which differs in magnitude and/or direction between males and females, which could result from sexual dimorphism in gene expression. Such sex-differentiated effects are common in model organisms, and are becoming increasingly evident in human complex traits through large-scale male- and female-specific meta-analyses. In this article, we review the methodology for meta-analysis of sex-specific genome-wide association studies, and propose a sex-differentiated test of association with quantitative or dichotomous traits, which allows for heterogeneity of allelic effects between males and females. We perform detailed simulations to compare the power of the proposed sex-differentiated meta-analysis with the more traditional "sex-combined" approach, which is ambivalent to gender. The results of this study highlight only a small loss in power for the sex-differentiated meta-analysis when the allelic effects of the causal variant are the same in males and females. However, over a range of models of heterogeneity in allelic effects between genders, our sex-differentiated meta-analysis strategy offers substantial gains in power, and thus has the potential to discover novel loci contributing effects to complex human traits with existing genome-wide association data. © 2010 Wiley-Liss, Inc.

Timing of anticoagulant re-initiation following intracerebral hemorrhage in mechanical heart valves: Survey of neurosurgeons and thrombosis experts.

PubMed

AlKherayf, Fahad; Xu, Yan; Westwick, Harrison; Moldovan, Ioana Doina; Wells, Philip S

2017-03-01

While oral anticoagulation (OAC) is universally indicated for patients with mechanical heart valves (MHVs), OAC resumption following anticoagulant-associated intracerebral hemorrhage (ICH) is an area of uncertainty. We sought to determine the practice preferences of North American neurosurgeons and thrombosis experts on optimal timing of OAC re-initiation. A cross-sectional survey was disseminated to North American members of the American Association of Neurological Surgeons and the International Society for Thrombosis and Haemostasis. Demographic factors, as well as a clinical scenario with 14 modifiable clinical risk factors were included in the survey. 504 physicians completed our survey (response rate 34.3%). Majority of participants were affiliated with academic centres, and managed≤10 ICH patients with MHV per year. There was wide distribution in response in optimal timing for OAC resumption following an ICH: 59% and 60% preferred to re-start OAC between 3 and 14 days following the hemorrhagic event (median of 6-7 days). Smaller hemorrhages (<30cm 2 ). CHADS 2 score ≥2, concomitant venous thromboembolism, mitral valve prosthesis, caged-ball valves and multiple valves prompted earlier OAC resumption. Wide variation in the current practice of neurosurgeons and thrombosis specialists exist when they encounter patients with ICH and MHV, though decisions were influenced by patient- and valve-related factors. As our observed variation likely reflects the immense gap in current evidence, prospective randomized trials in this population are therefore urgently needed. Copyright © 2017 Elsevier B.V. All rights reserved.

A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes.

PubMed

Dimkpa, Stanley O N; Lahari, Zobaida; Shrestha, Roshi; Douglas, Alex; Gheysen, Godelieve; Price, Adam H

2016-02-01

The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists, so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions. Accessions Khao Pahk Maw and LD 24 appeared to be resistant, which was confirmed in large pot experiments where no galls were observed. Detailed observations on these two accessions revealed no nematodes inside the roots 2 days after inoculation and very few females after 17 days (5 in Khao Pahk Maw and <1 in LD 24, in comparison with >100 in the susceptible controls). These two cultivars appear ideal donors for breeding root-knot nematode resistance. A genome-wide association study revealed 11 quantitative trait loci, two of which are close to epistatic loci detected in the Bala x Azucena population. The discussion highlights a small number of candidate genes worth exploring further, in particular many genes with lectin domains and genes on chromosome 11 with homology to the Hordeum Mla locus. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

The feasibility of universal DLP-to-risk conversion coefficients for body CT protocols

NASA Astrophysics Data System (ADS)

Li, Xiang; Samei, Ehsan; Segars, W. Paul; Paulson, Erik K.; Frush, Donald P.

2011-03-01

The effective dose associated with computed tomography (CT) examinations is often estimated from dose-length product (DLP) using scanner-independent conversion coefficients. Such conversion coefficients are available for a small number of examinations, each covering an entire region of the body (e.g., head, neck, chest, abdomen and/or pelvis). Similar conversion coefficients, however, do not exist for examinations that cover a single organ or a sub-region of the body, as in the case of a multi-phase liver examination. In this study, we extended the DLP-to-effective dose conversion coefficient (k factor) to a wide range of body CT protocols and derived the corresponding DLP-to-cancer risk conversion coefficient (q factor). An extended cardiactorso (XCAT) computational model was used, which represented a reference adult male patient. A range of body CT protocols used in clinical practice were categorized based on anatomical regions examined into 10 protocol classes. A validated Monte Carlo program was used to estimate the organ dose associated with each protocol class. Assuming the reference model to be 20 years old, effective dose and risk index (an index of the total risk for cancer incidence) were then calculated and normalized by DLP to obtain the k and q factors. The k and q factors varied across protocol classes; the coefficients of variation were 28% and 9%, respectively. The small variation exhibited by the q factor suggested the feasibility of universal q factors for a wide range of body CT protocols.

Paramecium putrinum (Ciliophora, Protozoa): the first insight into the variation of two DNA fragments - molecular support for the existence of cryptic species.

PubMed

Tarcz, Sebastian; Rautian, Maria; Potekhin, Alexey; Sawka, Natalia; Beliavskaya, Alexandra; Kiselev, Andrey; Nekrasova, Irina; Przyboś, Ewa

2014-04-01

Paramecium putrinum (Claparede & Lachmann 1858) is one of the smallest (80-140 μm long) species of the genus Paramecium. Although it commonly occurs in freshwater reservoirs, no molecular studies of P. putrinum have been conducted to date. Herein we present an assessment of molecular variation in 27 strains collected from widely separated populations by using two selected DNA fragments (ITS1-5.8S-ITS2-5'LSU rDNA and COI mtDNA). Both the trees and haplotype networks reconstructed for both genome fragments show that the studied strains of P. putrinum form five main haplogroups. The mean distance between the studied strains is p-distance=0.007/0.068 (rDNA/COI) and exhibits similar variability as that between P. bursaria syngens. Based on these data, one could hypothesize that the clusters revealed in the present study may correspond to previously reported syngens and that there are at least five cryptic species within P. putrinum. Copyright © 2014 Elsevier Inc. All rights reserved.

The temperature size rule in arthropods: independent of macro-environmental variables but size dependent.

PubMed

Klok, C Jaco; Harrison, Jon F

2013-10-01

Temperature is a key factor that affects the rates of growth and development in animals, which ultimately determine body size. Although not universal, a widely documented and poorly understood pattern is the inverse relationship between the temperature at which an ectothermic animal is reared and its body size (temperature size rule [TSR]). The proximate and ultimate mechanisms for the TSR remain unclear. To explore possible explanations for the TSR, we tested for correlations between the magnitude/direction of the TSR and latitude, temperature, elevation, habitat, availability of oxygen, capacity for flight, and taxonomic grouping in 98 species/populations of arthropods. The magnitude and direction of the TSR was not correlated with any of the macro-environmental variables we examined, supporting the generality of the TSR. However, body size affected the magnitude and direction of the TSR, with smaller arthropods more likely to demonstrate a classic TSR. Considerable variation among species exists in the TSR, suggesting either strong interactions with nutrition, or selection based on microclimatic or seasonal variation not captured in classic macro-environmental variables.

Multitasking operating systems for microprocessors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cramer, T.

1981-01-01

Microprocessors, because of their low cost, low power consumption, and small size, have caused an explosion in the number of innovative computer applications. Although there is a great deal of variation in microprocessor applications software, there is relatively little variation in the operating-system-level software from one application to the next. Nonetheless, operating system software, especially when multitasking is involved, can be very time consuming and expensive to develop. The major microprocessor manufacturers have acknowledged the need for operating systems in microprocessor applications and are now supplying real-time multitasking operating system software that is adaptable to a wide variety of usermore » systems. Use of this existing operating system software will decrease the number of redundant operating system development efforts, thus freeing programmers to work on more creative and productive problems. This paper discusses the basic terminology and concepts involved with multitasking operating systems. It is intended to provide a general understanding of the subject, so that the reader will be prepared to evaluate specific operating system software according to his or her needs. 2 references.« less

A germline JAK2 SNP is associated with predisposition to the development of JAK2V617F-positive myeloproliferative neoplasms

PubMed Central

Kilpivaara, Outi; Mukherjee, Semanti; Schram, Alison M; Wadleigh, Martha; Mullally, Ann; Ebert, Benjamin L; Bass, Adam; Marubayashi, Sachie; Heguy, Adriana; Garcia-Manero, Guillermo; Kantarjian, Hagop; Offit, Kenneth; Stone, Richard M; Gilliland, D Gary; Klein, Robert J; Levine, Ross L

2013-01-01

Polycythemia vera, essential thrombocythemia and primary myelofibrosis are myeloproliferative neoplasms (MPN) characterized by multilineage clonal hematopoiesis1–5. Given that the identical somatic activating mutation in the JAK2 tyrosine kinase gene (JAK2V617F) is observed in most individuals with polycythemia vera, essential thrombocythemia and primary myelofibrosis6–10, there likely are additional genetic events that contribute to the pathogenesis of these phenotypically distinct disorders. Moreover, family members of individuals with MPN are at higher risk for the development of MPN, consistent with the existence of MPN predisposition loci11. We hypothesized that germline variation contributes to MPN predisposition and phenotypic pleiotropy. Genome-wide analysis identified an allele in the JAK2 locus (rs10974944) that predisposes to the development of JAK2V617F-positive MPN, as well as three previously unknown MPN modifier loci. We found that JAK2V617F is preferentially acquired in cis with the predisposition allele. These data suggest that germline variation is an important contributor to MPN phenotype and predisposition. PMID:19287384

The low noise limit in gene expression

DOE PAGES

Dar, Roy D.; Weinberger, Leor S.; Cox, Chris D.; ...

2015-10-21

Protein noise measurements are increasingly used to elucidate biophysical parameters. Unfortunately noise analyses are often at odds with directly measured parameters. Here we show that these inconsistencies arise from two problematic analytical choices: (i) the assumption that protein translation rate is invariant for different proteins of different abundances, which has inadvertently led to (ii) the assumption that a large constitutive extrinsic noise sets the low noise limit in gene expression. While growing evidence suggests that transcriptional bursting may set the low noise limit, variability in translational bursting has been largely ignored. We show that genome-wide systematic variation in translational efficiencymore » can-and in the case of E. coli does-control the low noise limit in gene expression. Therefore constitutive extrinsic noise is small and only plays a role in the absence of a systematic variation in translational efficiency. Lastly, these results show the existence of two distinct expression noise patterns: (1) a global noise floor uniformly imposed on all genes by expression bursting; and (2) high noise distributed to only a select group of genes.« less

Heritabilities of Directional Asymmetry in the Fore- and Hindlimbs of Rabbit Fetuses

PubMed Central

Breno, Matteo; Bots, Jessica; Van Dongen, Stefan

2013-01-01

Directional asymmetry (DA), where at the population level symmetry differs from zero, has been reported in a wide range of traits and taxa, even for traits in which symmetry is expected to be the target of selection such as limbs or wings. In invertebrates, DA has been suggested to be non-adaptive. In vertebrates, there has been a wealth of research linking morphological asymmetry to behavioural lateralisation. On the other hand, the prenatal expression of DA and evidences for quantitative genetic variation for asymmetry may suggest it is not solely induced by differences in mechanic loading between sides. We estimate quantitative genetic variation of fetal limb asymmetry in a large dataset of rabbits. Our results showed a low but highly significant level of DA that is partially under genetic control for all traits, with forelimbs displaying higher levels of asymmetry. Genetic correlations were positive within limbs, but negative across bones of fore and hind limbs. Environmental correlations were positive for all, but smaller across fore and hind limbs. We discuss our results in light of the existence and maintenance of DA in locomotory traits. PMID:24130770

Fast propagation of electromagnetic fields through graded-index media.

PubMed

Zhong, Huiying; Zhang, Site; Shi, Rui; Hellmann, Christian; Wyrowski, Frank

2018-04-01

Graded-index (GRIN) media are widely used for modeling different situations: some components are designed considering GRIN modulation, e.g., multi-mode fibers, optical lenses, or acousto-optical modulators; on the other hand, there are other components where the refractive-index variation is undesired due to, e.g., stress or heating; and finally, some effects in nature are characterized by a GRIN variation, like turbulence in air or biological tissues. Modeling electromagnetic fields propagating in GRIN media is then of high importance for optical simulation and design. Though ray tracing can be used to evaluate some basic effects in GRIN media, the field properties are not considered and evaluated. The general physical optics techniques, like finite element method or finite difference time domain, can be used to calculate fields in GRIN media, but they need great numerical effort or may even be impractical for large-scale components. Therefore, there still exists a demand for a fast physical optics model of field propagation through GRIN media on a large scale, which will be explored in this paper.

Wide variation in payments for Medicare beneficiary oncology services suggests room for practice-level improvement.

PubMed

Clough, Jeffrey D; Patel, Kavita; Riley, Gerald F; Rajkumar, Rahul; Conway, Patrick H; Bach, Peter B

2015-04-01

In recent years many policy makers have recommended alternative payment models in medical oncology in order to reduce costs and improve patient outcomes. Yet information on how oncology practices differ in their use of key service categories is limited. We measured annual payments for key service categories delivered to fee-for-service Medicare beneficiaries receiving care from 1,534 medical oncology practices in 2011-12. In 2012, differences in payments per beneficiary at the seventy-fifth-percentile practice compared to the twenty-fifth-percentile practice were $3,866 for chemotherapy (including administration and supportive care drugs), $1,872 for acute medical hospitalizations, and $439 for advanced imaging. Supportive care drugs, bevacizumab, and positron-emission tomography accounted for the greatest percentage of variation. Average practice payments for service categories were highly correlated across years but not correlated with each other, which suggests that service categories may be affected by different physician practice characteristics. These differences, even when clinical guidelines exist, demonstrate the potential for quality improvement that could be accelerated through alternative payment models. Project HOPE—The People-to-People Health Foundation, Inc.

Genome-wide copy number variant analysis in Holstein cattle reveals variants associated with 10 production traits including residual feed intake and dry matter intake

USDA-ARS?s Scientific Manuscript database

Copy number variation (CNV) is an important type of genetic variation contributing to phenotypic differences among mammals and may serve as an alternative molecular marker to single nucleotide polymorphism (SNP) for genome-wide association study (GWAS). Recently, GWAS analysis using CNV has been app...

Class-Wide Positive Behavior Support and Group Contingencies: Examining a Positive Variation of the Good Behavior Game

ERIC Educational Resources Information Center

Wright, Robert A.; McCurdy, Barry L.

2012-01-01

The Good Behavior Game (GBG) is a powerful group contingency with a history of documented empirical support. The purpose of this study was to compare two interdependent group contingencies, the GBG and a positive variation, the Caught Being Good Game (CBGG), in a school implementing school-wide positive behavior support. A kindergarten and…

Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae

PubMed Central

Neymotin, Benjamin; Ettorre, Victoria; Gresham, David

2016-01-01

Degradation of mRNA contributes to variation in transcript abundance. Studies of individual mRNAs have shown that both cis and trans factors affect mRNA degradation rates. However, the factors underlying transcriptome-wide variation in mRNA degradation rates are poorly understood. We investigated the contribution of different transcript properties to transcriptome-wide degradation rate variation in the budding yeast, Saccharomyces cerevisiae, using multiple regression analysis. We find that multiple transcript properties are significantly associated with variation in mRNA degradation rates, and that a model incorporating these properties explains ∼50% of the genome-wide variance. Predictors of mRNA degradation rates include transcript length, ribosome density, biased codon usage, and GC content of the third position in codons. To experimentally validate these factors, we studied individual transcripts expressed from identical promoters. We find that decreasing ribosome density by mutating the first translational start site of a transcript increases its degradation rate. Using coding sequence variants of green fluorescent protein (GFP) that differ only at synonymous sites, we show that increased GC content of the third position of codons results in decreased rates of mRNA degradation. Thus, in steady-state conditions, a large fraction of genome-wide variation in mRNA degradation rates is determined by inherent properties of transcripts, many of which are related to translation, rather than specific regulatory mechanisms. PMID:27633789

Variation in US outpatient antibiotic prescribing quality measures according to health plan and geography.

PubMed

Roberts, Rebecca M; Hicks, Lauri A; Bartoces, Monina

2016-08-01

Antibiotic prescribing has become increasingly viewed as an issue related to patient safety and quality of care. The objective of this study was to better understand the differences between health plan reporting and the geographic variation seen in quality measures related to antibiotic use. We focused on 3 measures from the Healthcare Effectiveness Data and Information Set (HEDIS) related to antibiotic prescribing and testing to guide antibiotic prescribing. We analyzed data for 3 relevant measures for the years 2008 to 2012, including only commercial health plans. We analyzed the following 3 HEDIS measures: 1) "Appropriate Testing for Children With Pharyngitis," 2) "Appropriate Treatment for Children With Upper Respiratory Infections," and 3) "Avoidance of Antibiotic Treatment in Adults With Acute Bronchitis." Out of these 3 measures, health plans consistently performed poorly on the adult bronchitis measure. Performance was better on the 2 measures focused on the pediatric population. We also saw geographic variation between measures when looking at Census divisions across all years. There is wide variation between individual health plan performance on the measures related to antibiotic use. Geographic differences were also observed on these measures, with health plans in the South Central Census division performing worse than other parts of the country. Stakeholders, such as public health, advocacy groups, foundations, and professional societies, interested in improving the quality of care that patients receive related to antibiotic use in the outpatient setting should consider how existing measures and working with health plans could be used to improve prescribing.

A comparison of current practice patterns of US dermatologists versus published guidelines for the biopsy, initial management, and follow up of patients with primary cutaneous melanoma.

PubMed

Farberg, Aaron S; Rigel, Darrell S

2016-12-01

Guidelines exist for the management of cutaneous malignant melanoma, but their adoption, prevalence, and impact have not yet been determined. To determine current melanoma clinical management practices of US dermatologists and the variance from guidelines that might exist. A cross-sectional e-mail survey study assessing preferred biopsy methods for lesions suspicious for melanoma, margins used for excision, and recommended follow-up intervals were sent to 6177 US dermatologists (540 responding). The representative nature of the responding subset was verified by comparing their demographics to that from the American Academy of Dermatology (AAD) membership. Management varied from published guidelines. Shave biopsy (35%) was the most commonly used method followed by narrow excisional biopsy (31%), saucerization/scoop shave (12%), punch (11%), and wide excision (3%). Excisional margins narrower than recommended were noted and follow-up intervals varied. There were significant management differences noted for dermatologists by practice setting and by years in practice. The impact of patient history, lesion anatomic site, and size of lesion were not assessed. Recall and nonresponder sampling bias may exist. Variations in dermatologists' approaches to melanoma management and variance from current guidelines suggest that a knowledge gap may exist representing an educational opportunity. However, emerging data may also justify deviations from existing guidelines, suggesting a reassessment of the guidelines may be indicated. Copyright © 2016 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.

Different Places, Different Stories: A Study of Spatial Heterogeneity of County-Level Fertility in China

PubMed Central

Wang, Donghui; Chi, Guangqing

2018-01-01

Background China has been characterized by persistently low fertility rates since the 1990s. Existing literature has examined the relationships of fertility levels with social, economic, and policy-related determinants. However, the possible spatial variations in these relationships have not been investigated. Objective The purpose of this study is to examine the potential spatially varying relationships between county-level fertility rates and policy and socioeconomic factors in China. Methods Using geocoded 2010 county-level census data, this study adopts the geographically weighted regression (GWR) method to identify place-specific relationships between county-level total fertility rate (TFR) and socioeconomics and policy-related factors. Conclusions We find relationships between TFR and widely used social, economic, and policy-related factors (rural Hukou, ethnic minority, female education, net migration rate, poor living standard, sex ratio at birth, and fertility policy compliance ratio) vary spatially in terms of the direction, strength, and magnitude. The spatial variation is largely due to the difference in local characteristics. The differences and the complexities of localities cannot be told by a single story of either government intervention or socioeconomic development. Contribution This study extends the existing fertility research in China by explicitly recognizing the spatial heterogeneity in the impacts of policy and socioeconomic factors on the local fertility rate. This study sets the stage for future research that will contextually analyze varying fertility rates at the sub-national level in China and other countries. PMID:29593449

Firefighter Hand Anthropometry and Structural Glove Sizing: A New Perspective.

PubMed

Hsiao, Hongwei; Whitestone, Jennifer; Kau, Tsui-Ying; Hildreth, Brooke

2015-12-01

We evaluated the current use and fit of structural firefighting gloves and developed an improved sizing scheme that better accommodates the U.S. firefighter population. Among surveys, 24% to 30% of men and 31% to 62% of women reported experiencing problems with the fit or bulkiness of their structural firefighting gloves. An age-, race/ethnicity-, and gender-stratified sample of 863 male and 88 female firefighters across the United States participated in the study. Fourteen hand dimensions relevant to glove design were measured. A cluster analysis of the hand dimensions was performed to explore options for an improved sizing scheme. The current national standard structural firefighting glove-sizing scheme underrepresents firefighter hand size range and shape variation. In addition, mismatch between existing sizing specifications and hand characteristics, such as hand dimensions, user selection of glove size, and the existing glove sizing specifications, is significant. An improved glove-sizing plan based on clusters of overall hand size and hand/finger breadth-to-length contrast has been developed. This study presents the most up-to-date firefighter hand anthropometry and a new perspective on glove accommodation. The new seven-size system contains narrower variations (standard deviations) for almost all dimensions for each glove size than the current sizing practices. The proposed science-based sizing plan for structural firefighting gloves provides a step-forward perspective (i.e., including two women hand model-based sizes and two wide-palm sizes for men) for glove manufacturers to advance firefighter hand protection. © 2015, Human Factors and Ergonomics Society.

Qualitative variation of photolabelled benzodiazepine receptors in different species.

PubMed

Hebebrand, J; Friedl, W; Lentes, K U; Propping, P

1986-01-01

In order to examine whether species differences of benzodiazepine receptor subunits exist, we compared the fluorographic pattern of photoaffinity labelled subunits after SDS-PAGE in five species: fish, frog, chicken, mouse and calf. Each species showed a distinct pattern of specifically labelled proteins. We conclude that species variation of benzodiazepine receptor does indeed exist.

A wide-band fiber optic frequency distribution system employing thermally controlled phase compensation

NASA Technical Reports Server (NTRS)

Johnson, Dean; Calhoun, Malcolm; Sydnor, Richard; Lutes, George

1993-01-01

An active wide-band fiber optic frequency distribution system employing a thermally controlled phase compensator to stabilize phase variations induced by environmental temperature changes is described. The distribution system utilizes bidirectional dual wavelength transmission to provide optical feedback of induced phase variations of 100 MHz signals propagating along the distribution cable. The phase compensation considered differs from earlier narrow-band phase compensation designs in that it uses a thermally controlled fiber delay coil rather than a VCO or phase modulation to compensate for induced phase variations. Two advantages of the wide-band system over earlier designs are (1) that it provides phase compensation for all transmitted frequencies, and (2) the compensation is applied after the optical interface rather than electronically ahead of it as in earlier schemes. Experimental results on the first prototype shows that the thermal stabilizer reduces phase variations and Allan deviation by a factor of forty over an equivalent uncompensated fiber optic distribution system.

Maintenance of phenotypic variation: repeatibility, heritability, and size-dependent processes in a wild brook trout population

Treesearch

Benjamin H. Letcher; Jason A Coombs; Keith H. Nislow

2011-01-01

Phenotypic variation in body size can result from within-cohort variation in birth dates, among-individual growth variation and size-selective processes. We explore the relative effects of these processes on the maintenance of wide observed body size variation in stream-dwelling brook trout (Salvelinus fontinalis). Based on the analyses of multiple...

A Variational Reduction and the Existence of a Fully Localised Solitary Wave for the Three-Dimensional Water-Wave Problem with Weak Surface Tension

NASA Astrophysics Data System (ADS)

Buffoni, Boris; Groves, Mark D.; Wahlén, Erik

2017-12-01

Fully localised solitary waves are travelling-wave solutions of the three- dimensional gravity-capillary water wave problem which decay to zero in every horizontal spatial direction. Their existence has been predicted on the basis of numerical simulations and model equations (in which context they are usually referred to as `lumps'), and a mathematically rigorous existence theory for strong surface tension (Bond number {β} greater than {1/3} ) has recently been given. In this article we present an existence theory for the physically more realistic case {0 < β < 1/3} . A classical variational principle for fully localised solitary waves is reduced to a locally equivalent variational principle featuring a perturbation of the functional associated with the Davey-Stewartson equation. A nontrivial critical point of the reduced functional is found by minimising it over its natural constraint set.

A Variational Reduction and the Existence of a Fully Localised Solitary Wave for the Three-Dimensional Water-Wave Problem with Weak Surface Tension

NASA Astrophysics Data System (ADS)

Buffoni, Boris; Groves, Mark D.; Wahlén, Erik

2018-06-01

Fully localised solitary waves are travelling-wave solutions of the three- dimensional gravity-capillary water wave problem which decay to zero in every horizontal spatial direction. Their existence has been predicted on the basis of numerical simulations and model equations (in which context they are usually referred to as `lumps'), and a mathematically rigorous existence theory for strong surface tension (Bond number {β} greater than {1/3}) has recently been given. In this article we present an existence theory for the physically more realistic case {0 < β < 1/3}. A classical variational principle for fully localised solitary waves is reduced to a locally equivalent variational principle featuring a perturbation of the functional associated with the Davey-Stewartson equation. A nontrivial critical point of the reduced functional is found by minimising it over its natural constraint set.

Genetics of Genome-Wide Recombination Rate Evolution in Mice from an Isolated Island.

PubMed

Wang, Richard J; Payseur, Bret A

2017-08-01

Recombination rate is a heritable quantitative trait that evolves despite the fundamentally conserved role that recombination plays in meiosis. Differences in recombination rate can alter the landscape of the genome and the genetic diversity of populations. Yet our understanding of the genetic basis of recombination rate evolution in nature remains limited. We used wild house mice ( Mus musculus domesticus ) from Gough Island (GI), which diverged recently from their mainland counterparts, to characterize the genetics of recombination rate evolution. We quantified genome-wide autosomal recombination rates by immunofluorescence cytology in spermatocytes from 240 F 2 males generated from intercrosses between GI-derived mice and the wild-derived inbred strain WSB/EiJ. We identified four quantitative trait loci (QTL) responsible for inter-F 2 variation in this trait, the strongest of which had effects that opposed the direction of the parental trait differences. Candidate genes and mutations for these QTL were identified by overlapping the detected intervals with whole-genome sequencing data and publicly available transcriptomic profiles from spermatocytes. Combined with existing studies, our findings suggest that genome-wide recombination rate divergence is not directional and its evolution within and between subspecies proceeds from distinct genetic loci. Copyright © 2017 by the Genetics Society of America.

Genome-wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection.

PubMed

Bandillo, Nonoy B; Lorenz, Aaron J; Graef, George L; Jarquin, Diego; Hyten, David L; Nelson, Randall L; Specht, James E

2017-07-01

Genome-wide association (GWA) has been used as a tool for dissecting the genetic architecture of quantitatively inherited traits. We demonstrate here that GWA can also be highly useful for detecting many major genes governing categorically defined phenotype variants that exist for qualitatively inherited traits in a germplasm collection. Genome-wide association mapping was applied to categorical phenotypic data available for 10 descriptive traits in a collection of ∼13,000 soybean [ (L.) Merr.] accessions that had been genotyped with a 50,000 single nucleotide polymorphism (SNP) chip. A GWA on a panel of accessions of this magnitude can offer substantial statistical power and mapping resolution, and we found that GWA mapping resulted in the identification of strong SNP signals for 24 classical genes as well as several heretofore unknown genes controlling the phenotypic variants in those traits. Because some of these genes had been cloned, we were able to show that the narrow GWA mapping SNP signal regions that we detected for the phenotypic variants had chromosomal bp spans that, with just one exception, overlapped the bp region of the cloned genes, despite local variation in SNP number and nonuniform SNP distribution in the chip set. Copyright © 2017 Crop Science Society of America.

Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer

PubMed Central

Wang, Yufei; McKay, James D.; Rafnar, Thorunn; Wang, Zhaoming; Timofeeva, Maria; Broderick, Peter; Zong, Xuchen; Laplana, Marina; Wei, Yongyue; Han, Younghun; Lloyd, Amy; Delahaye-Sourdeix, Manon; Chubb, Daniel; Gaborieau, Valerie; Wheeler, William; Chatterjee, Nilanjan; Thorleifsson, Gudmar; Sulem, Patrick; Liu, Geoffrey; Kaaks, Rudolf; Henrion, Marc; Kinnersley, Ben; Vallée, Maxime; LeCalvez-Kelm, Florence; Stevens, Victoria L.; Gapstur, Susan M.; Chen, Wei V.; Zaridze, David; Szeszenia-Dabrowska, Neonilia; Lissowska, Jolanta; Rudnai, Peter; Fabianova, Eleonora; Mates, Dana; Bencko, Vladimir; Foretova, Lenka; Janout, Vladimir; Krokan, Hans E.; Gabrielsen, Maiken Elvestad; Skorpen, Frank; Vatten, Lars; Njølstad, Inger; Chen, Chu; Goodman, Gary; Benhamou, Simone; Vooder, Tonu; Valk, Kristjan; Nelis, Mari; Metspalu, Andres; Lener, Marcin; Lubiński, Jan; Johansson, Mattias; Vineis, Paolo; Agudo, Antonio; Clavel-Chapelon, Francoise; Bueno-de-Mesquita, H.Bas; Trichopoulos, Dimitrios; Khaw, Kay-Tee; Johansson, Mikael; Weiderpass, Elisabete; Tjønneland, Anne; Riboli, Elio; Lathrop, Mark; Scelo, Ghislaine; Albanes, Demetrius; Caporaso, Neil E.; Ye, Yuanqing; Gu, Jian; Wu, Xifeng; Spitz, Margaret R.; Dienemann, Hendrik; Rosenberger, Albert; Su, Li; Matakidou, Athena; Eisen, Timothy; Stefansson, Kari; Risch, Angela; Chanock, Stephen J.; Christiani, David C.; Hung, Rayjean J.; Brennan, Paul; Landi, Maria Teresa; Houlston, Richard S.; Amos, Christopher I.

2014-01-01

We conducted imputation to the 1000 Genomes Project of four genome-wide association studies of lung cancer in populations of European ancestry (11,348 cases and 15,861 controls) and genotyped an additional 10,246 cases and 38,295 controls for follow-up. We identified large-effect genome-wide associations for squamous lung cancer with the rare variants of BRCA2-K3326X (rs11571833; odds ratio [OR]=2.47, P=4.74×10−20) and of CHEK2-I157T (rs17879961; OR=0.38 P=1.27×10−13). We also showed an association between common variation at 3q28 (TP63; rs13314271; OR=1.13, P=7.22×10−10) and lung adenocarcinoma previously only reported in Asians. These findings provide further evidence for inherited genetic susceptibility to lung cancer and its biological basis. Additionally, our analysis demonstrates that imputation can identify rare disease-causing variants having substantive effects on cancer risk from pre-existing GWAS data. PMID:24880342

Can skull form predict the shape of the temporomandibular joint? A study using geometric morphometrics on the skulls of wolves and domestic dogs.

PubMed

Curth, Stefan; Fischer, Martin S; Kupczik, Kornelius

2017-11-01

The temporomandibular joint (TMJ) conducts and restrains masticatory movements between the mammalian cranium and the mandible. Through this functional integration, TMJ morphology in wild mammals is strongly correlated with diet, resulting in a wide range of TMJ variations. However, in artificially selected and closely related domestic dogs, dietary specialisations between breeds can be ruled out as a diversifying factor although they display an enormous variation in TMJ morphology. This raises the question of the origin of this variation. Here we hypothesise that, even in the face of reduced functional demands, TMJ shape in dogs can be predicted by skull form; i.e. that the TMJ is still highly integrated in the dog skull. If true, TMJ variation in the dog would be a plain by-product of the enormous cranial variation in dogs and its genetic causes. We addressed this hypothesis using geometric morphometry on a data set of 214 dog and 60 wolf skulls. We digitized 53 three-dimensional landmarks of the skull and the TMJ on CT-based segmentations and compared (1) the variation between domestic dog and wolf TMJs (via principal component analysis) and (2) the pattern of covariation of skull size, flexion and rostrum length with TMJ shape (via regression of centroid size on shape and partial least squares analyses). We show that the TMJ in domestic dogs is significantly more diverse than in wolves: its shape covaries significantly with skull size, flexion and rostrum proportions in patterns which resemble those observed in primates. Similar patterns in canids, which are carnivorous, and primates, which are mostly frugivorous imply the existence of basic TMJ integration patterns which are independent of dietary adaptations. However, only limited amounts of TMJ variation in dogs can be explained by simple covariation with overall skull geometry. This implies that the final TMJ shape is gained partially independently of the rest of the skull. Copyright © 2017 Elsevier GmbH. All rights reserved.

Patient Handoffs between Emergency Department and Inpatient Physicians: A Qualitative Study to Inform Standardization of Practice and Organization Theory

ERIC Educational Resources Information Center

Hilligoss, Phillip Brian

2011-01-01

This dissertation is motivated by two problems. First, existing literature characterizes patient handoff as an information transfer activity in which safety and quality are compromised by practice variation. This has prompted a movement to standardize practice. However, existing research has not closely examined how practice variations may be…

An Application of Variational Theory to an Integrated Walrasian Model of Exchange, Consumption and Production

NASA Astrophysics Data System (ADS)

Donato, M. B.; Milasi, M.; Vitanza, C.

2010-09-01

An existence result of a Walrasian equilibrium for an integrated model of exchange, consumption and production is obtained. The equilibrium model is characterized in terms of a suitable generalized quasi-variational inequality; so the existence result comes from an original technique which takes into account tools of convex and set-valued analysis.

Geographical variation in the periodicity of gypsy moth outbreaks

Treesearch

Derek M. Johnson; Andrew M. Liebhold; Ottar N. Bj& #248rnstad

2006-01-01

The existence of periodic oscillations in populations of forest Lepidoptera is well known. While information exists on how the periods of oscillations vary among different species, there is little prior evidence of variation in periodicity within the range of a single Lepidopteran species. The exotic gypsy moth is an introduced foliage-feeding insect in North America....

Geographic variation in lumbar diskectomy: a protocol for evaluation.

PubMed

Barron, M; Kazandjian, V A

1992-03-01

In 1989 the Maryland Hospital Association (MHA) began developing a protocol related to lumbar diskectomy, a procedure with widely reported geographic variation in its use. The MHA's Laminectomy Advisory Committee drafted three criteria for performance of lumbar diskectomy and also developed a data-collection instrument with which the eight hospitals participating in a pilot study could abstract the necessary data from medical records. Both individual hospital and aggregate results showed wide variation in compliance with the criteria. These findings suggest research and development activities such as refinement of the data-collection instrument, use of the protocol for bench-marking, further investigation of clinical and other determinants of rate variation, and study of the effect of new diagnostic technology on utilization rates for this procedure.

Functional associations between support use and forelimb shape in strepsirrhines and their relevance to inferring locomotor behavior in early primates.

PubMed

Fabre, Anne-Claire; Marigó, Judit; Granatosky, Michael C; Schmitt, Daniel

2017-07-01

The evolution of primates is intimately linked to their initial invasion of an arboreal environment. However, moving and foraging in this milieu creates significant mechanical challenges related to the presence of substrates differing in their size and orientation. It is widely assumed that primates are behaviorally and anatomically adapted to movement on specific substrates, but few explicit tests of this relationship in an evolutionary context have been conducted. Without direct tests of form-function relationships in living primates it is impossible to reliably infer behavior in fossil taxa. In this study, we test a hypothesis of co-variation between forelimb morphology and the type of substrates used by strepsirrhines. If associations between anatomy and substrate use exist, these can then be applied to better understand limb anatomy of extinct primates. The co-variation between each forelimb long bone and the type of substrate used was studied in a phylogenetic context. Our results show that despite the presence of significant phylogenetic signal for each long bone of the forelimb, clear support use associations are present. A strong co-variation was found between the type of substrate used and the shape of the radius, with and without taking phylogeny into account, whereas co-variation was significant for the ulna only when taking phylogeny into account. Species that use a thin branch milieu show radii that are gracile and straight and have a distal articular shape that allows for a wide range of movements. In contrast, extant species that commonly use large supports show a relatively robust and curved radius with an increased surface area available for forearm and hand muscles in pronated posture. These results, especially for the radius, support the idea that strepsirrhine primates exhibit specific skeletal adaptations associated with the supports that they habitually move on. With these robust associations in hand it will be possible to explore the same variables in extinct early primates and primate relatives and thus improve the reliability of inferences concerning substrate use in early primates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa

PubMed Central

Doddapaneni, Harshavardhan; Yao, Jiqiang; Lin, Hong; Walker, M Andrew; Civerolo, Edwin L

2006-01-01

Background The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine, citrus and many other plant species. Despite its economic impact, relatively little is known about the genomic variations among strains isolated from different hosts and their influence on the population genetics of this pathogen. With the availability of genome sequence information for four strains, it is now possible to perform genome-wide analyses to identify and categorize such DNA variations and to understand their influence on strain functional divergence. Results There are 1,579 genes and 194 non-coding homologous sequences present in the genomes of all four strains, representing a 76. 2% conservation of the sequenced genome. About 60% of the X. fastidiosa unique sequences exist as tandem gene clusters of 6 or more genes. Multiple alignments identified 12,754 SNPs and 14,449 INDELs in the 1528 common genes and 20,779 SNPs and 10,075 INDELs in the 194 non-coding sequences. The average SNP frequency was 1.08 × 10-2 per base pair of DNA and the average INDEL frequency was 2.06 × 10-2 per base pair of DNA. On an average, 60.33% of the SNPs were synonymous type while 39.67% were non-synonymous type. The mutation frequency, primarily in the form of external INDELs was the main type of sequence variation. The relative similarity between the strains was discussed according to the INDEL and SNP differences. The number of genes unique to each strain were 60 (9a5c), 54 (Dixon), 83 (Ann1) and 9 (Temecula-1). A sub-set of the strain specific genes showed significant differences in terms of their codon usage and GC composition from the native genes suggesting their xenologous origin. Tandem repeat analysis of the genomic sequences of the four strains identified associations of repeat sequences with hypothetical and phage related functions. Conclusion INDELs and strain specific genes have been identified as the main source of variations among strains, with individual strains showing different rates of genome evolution. Based on these genome comparisons, it appears that the Pierce's disease strain Temecula-1 genome represents the ancestral genome of the X. fastidiosa. Results of this analysis are publicly available in the form of a web database. PMID:16948851

New technologies provide insights into genetic basis of psychiatric disorders and explain their co-morbidity.

PubMed

Rudan, Igor

2010-06-01

The completion of Human Genome Project and the "HapMap" project was followed by translational activities from companies within the private sector. This led to the introduction of genome-wide scans based on hundreds of thousands of single nucleotide polymorphysms (SNP). These scans were based on common genetic variants in human populations. This new and powerful technology was then applied to the existing DNA-based datasets with information on psychiatric disorders. As a result, an unprecedented amount of novel scientific insights related to the underlying biology and genetics of psychiatric disorders was obtained. The dominant design of these studies, so called "genome-wide association studies" (GWAS), used statistical methods which minimized the risk of false positive reports and provided much greater power to detect genotype-phenotype associations. All findings were entirely data-driven rather than hypothesis-driven, which often made it difficult for researchers to understand or interpret the findings. Interestingly, this work in genetics is indicating how non-specific some genes are for psychiatric disorders, having associations in common for schizophrenia, bipolar disorder and autism. This suggests that the earlier stages of psychiatric disorders may be multi-valent and that early detection, coupled with a clearer understanding of the environmental factors, may allow prevention. At the present time, the rich "harvest" from GWAS still has very limited power to predict the variation in psychiatric disease status at individual level, typically explaining less than 5% of the total risk variance. The most recent studies of common genetic variation implicated the role of major histocompatibility complex in schizophrenia and other disorders. They also provided molecular evidence for a substantial polygenic component to the risk of psychiatric diseases, involving thousands of common alleles of very small effect. The studies of structural genetic variation, such as copy number variants (CNV), coupled with the efforts targeting rare genetic variation (using the emerging whole-genome "deep" sequencing technologies) will become the area of the greatest interest in the field of genetic epidemiology. This will be complemented by the studies of epigenetic phoenomena, changes of expression at a large scale and understanding gene-gene interactions in complex networks using systems biology approaches. A deeper understanding of the underlying biology of psychiatric disorders is essential to improve diagnoses and therapies of these diseases. New technologies - genome-wide association studies, imaging and the optical manipulation of neural circuits - are promising to provide novel insights and lead to new treatments.

Comparison of alternative approaches for analysing multi-level RNA-seq data

PubMed Central

Mohorianu, Irina; Bretman, Amanda; Smith, Damian T.; Fowler, Emily K.; Dalmay, Tamas

2017-01-01

RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D. melanogaster that we used here. We investigated the power of existing approaches for quality checking mRNA-seq data and explored additional, quantitative quality checks. To accommodate nested, multi-level experimental designs, we incorporated sample layout into our analyses. We employed a subsampling without replacement-based normalization and an identification of DE that accounted for the hierarchy and amplitude of effect sizes within samples, then evaluated the resulting differential expression call in comparison to existing approaches. In a final step to test for broader applicability, we applied our approaches to a published set of H. sapiens mRNA-seq samples, The dataset-tailored methods improved sample comparability and delivered a robust prediction of subtle gene expression changes. The proposed approaches have the potential to improve key steps in the analysis of RNA-seq data by incorporating the structure and characteristics of biological experiments. PMID:28792517

Source-Free Exchange-Correlation Magnetic Fields in Density Functional Theory.

PubMed

Sharma, S; Gross, E K U; Sanna, A; Dewhurst, J K

2018-03-13

Spin-dependent exchange-correlation energy functionals in use today depend on the charge density and the magnetization density: E xc [ρ, m]. However, it is also correct to define the functional in terms of the curl of m for physical external fields: E xc [ρ,∇ × m]. The exchange-correlation magnetic field, B xc , then becomes source-free. We study this variation of the theory by uniquely removing the source term from local and generalized gradient approximations to the functional. By doing so, the total Kohn-Sham moments are improved for a wide range of materials for both functionals. Significantly, the moments for the pnictides are now in good agreement with experiment. This source-free method is simple to implement in all existing density functional theory codes.

Eco-efficiency of solid waste management in Welsh SMEs

NASA Astrophysics Data System (ADS)

Sarkis, Joseph; Dijkshoorn, Jeroen

2005-11-01

This paper provides an efficiency analysis of practices in Solid Waste Management of manufacturing companies in Wales. We apply data envelopment analysis (DEA) to a data set compiled during the National Waste Survey Wales 2003. We explore the relative performance of small and medium sized manufacturing enterprises (SME; 10-250 employees) in Wales. We determine the technical and scale environmental and economic efficiencies of these organizations. Our evaluation focuses on empirical data collected from companies in a wide diversity of manufacturing industries throughout Wales. We find significant differences in industry and size efficiencies. We also find correlations that exist among environmental and economic efficiencies. These variations show that improvements can be made using benchmarks from similar and different size industries. Further pursuit of an investigation of possible reasons for these differences is recommended.

Adaptive Correlation Model for Visual Tracking Using Keypoints Matching and Deep Convolutional Feature.

PubMed

Li, Yuankun; Xu, Tingfa; Deng, Honggao; Shi, Guokai; Guo, Jie

2018-02-23

Although correlation filter (CF)-based visual tracking algorithms have achieved appealing results, there are still some problems to be solved. When the target object goes through long-term occlusions or scale variation, the correlation model used in existing CF-based algorithms will inevitably learn some non-target information or partial-target information. In order to avoid model contamination and enhance the adaptability of model updating, we introduce the keypoints matching strategy and adjust the model learning rate dynamically according to the matching score. Moreover, the proposed approach extracts convolutional features from a deep convolutional neural network (DCNN) to accurately estimate the position and scale of the target. Experimental results demonstrate that the proposed tracker has achieved satisfactory performance in a wide range of challenging tracking scenarios.

Evaluation and integration of disparate classification systems for clefts of the lip

PubMed Central

Wang, Kathie H.; Heike, Carrie L.; Clarkson, Melissa D.; Mejino, Jose L. V.; Brinkley, James F.; Tse, Raymond W.; Birgfeld, Craig B.; Fitzsimons, David A.; Cox, Timothy C.

2014-01-01

Orofacial clefting is a common birth defect with wide phenotypic variability. Many systems have been developed to classify cleft patterns to facilitate diagnosis, management, surgical treatment, and research. In this review, we examine the rationale for different existing classification schemes and determine their inter-relationships, as well as strengths and deficiencies for subclassification of clefts of the lip. The various systems differ in how they describe and define attributes of cleft lip (CL) phenotypes. Application and analysis of the CL classifications reveal discrepancies that may result in errors when comparing studies that use different systems. These inconsistencies in terminology, variable levels of subclassification, and ambiguity in some descriptions may confound analyses and impede further research aimed at understanding the genetics and etiology of clefts, development of effective treatment options for patients, as well as cross-institutional comparisons of outcome measures. Identification and reconciliation of discrepancies among existing systems is the first step toward creating a common standard to allow for a more explicit interpretation that will ultimately lead to a better understanding of the causes and manifestations of phenotypic variations in clefting. PMID:24860508

Seasonal and interannual variability of surface CDOM in the South China Sea associated with El Niño

NASA Astrophysics Data System (ADS)

Ma, Jinfeng; Zhan, Haigang; Du, Yan

2011-04-01

Satellite imagery of SeaWiFS from October 1997 to November 2007 is used to investigate the dominant seasonal and interannual variations of the surface light absorption due to Colored Dissolved Organic Materials (CDOM) in the South China Sea (SCS). Results show that the spatial distribution of CDOM mimics the major features of the SCS basin-scale circulation. High values of CDOM are found in upwelling regions like southeast of Vietnam in summer and northwest of Luzon in winter. At a basin scale, CDOM is high in winter when upwelling is strong, solar shortwave radiation and stratification weak, and vertical mixing intense. Opposite conditions exist in spring and summer. Interannual variability of the basin-wide CDOM is characterized by abnormal troughs during the El Niño events. A strong relationship exists between the time series of the first EOF mode (for both winter and summer) and Niño 3.4 Index. Associations of these events with climatic and hydrographic properties (i.e. wind forcing, solar shortwave radiation, Ekman pumping, vertical mixing, sea surface height and temperature) are discussed.

Worldwide Mycotoxins Exposure in Pig and Poultry Feed Formulations

PubMed Central

Guerre, Philippe

2016-01-01

The purpose of this review is to present information about raw materials that can be used in pig and poultry diets and the factors responsible for variations in their mycotoxin contents. The levels of mycotoxins in pig and poultry feeds are calculated based on mycotoxin contamination levels of the raw materials with different diet formulations, to highlight the important role the stage of production and the raw materials used can have on mycotoxins levels in diets. Our analysis focuses on mycotoxins for which maximum tolerated levels or regulatory guidelines exist, and for which sufficient contamination data are available. Raw materials used in feed formulation vary considerably depending on the species of animal, and the stage of production. Mycotoxins are secondary fungal metabolites whose frequency and levels also vary considerably depending on the raw materials used and on the geographic location where they were produced. Although several reviews of existing data and of the literature on worldwide mycotoxin contamination of food and feed are available, the impact of the different raw materials used on feed formulation has not been widely studied. PMID:27886128

Plant leaf traits, canopy processes, and global atmospheric chemistry interactions.

NASA Astrophysics Data System (ADS)

Guenther, A. B.

2017-12-01

Plants produce and emit a diverse array of volatile metabolites into the atmosphere that participate in chemical reactions that influence distributions of air pollutants and short-lived climate forcers including organic aerosol, ozone and methane. It is now widely accepted that accurate estimates of these emissions are required as inputs for regional air quality and global climate models. Predicting these emissions is complicated by the large number of volatile organic compounds, driving variables (e.g., temperature, solar radiation, abiotic and biotic stresses) and processes operating across a range of scales. Modeling efforts to characterize emission magnitude and variations will be described along with an assessment of the observations available for parameterizing and evaluating these models including discussion of the limitations and challenges associated with existing model approaches. A new approach for simulating canopy scale organic emissions on regional to global scales will be described and compared with leaf, canopy and regional scale flux measurements. The importance of including additional compounds and processes as well as improving estimates of existing ones will also be discussed.

Hidden levels of phylodiversity in Antarctic green algae: further evidence for the existence of glacial refugia

PubMed Central

De Wever, Aaike; Leliaert, Frederik; Verleyen, Elie; Vanormelingen, Pieter; Van der Gucht, Katleen; Hodgson, Dominic A.; Sabbe, Koen; Vyverman, Wim

2009-01-01

Recent data revealed that metazoans such as mites and springtails have persisted in Antarctica throughout several glacial–interglacial cycles, which contradicts the existing paradigm that terrestrial life was wiped out by successive glacial events and that the current inhabitants are recent colonizers. We used molecular phylogenetic techniques to study Antarctic microchlorophyte strains isolated from lacustrine habitats from maritime and continental Antarctica. The 14 distinct chlorophycean and trebouxiophycean lineages observed point to a wide phylogenetic diversity of apparently endemic Antarctic lineages at different taxonomic levels. This supports the hypothesis that long-term survival took place in glacial refugia, resulting in a specific Antarctic flora. The majority of the lineages have estimated ages between 17 and 84 Ma and probably diverged from their closest relatives around the time of the opening of Drake Passage (30–45 Ma), while some lineages with longer branch lengths have estimated ages that precede the break-up of Gondwana. The variation in branch length and estimated age points to several independent but rare colonization events. PMID:19625320

Endodontic treatment of a mandibular second premolar with three root canals.

PubMed

Aguiar, Carlos; Mendes, Daniela; Câmara, Andréa; Figueiredo, Jose

2010-03-01

The purpose of this case report is to describe a nonsurgical endodontic treatment of a mandibular left second premolar with two separate roots and three distinct root canals. In endodontics, the possible existence of extra canals must be considered before endodontic treatment is instituted. A wide morphological variation of the root canal system is known to exist. A 36-year-old male patient was referred for endodontic treatment on the left mandibular second premolar. Radiographic examination of the involved tooth revealed an unusual, complex root canal anatomy. There was an irregular root morphology consisting of two distinct roots and three canals. This case report describes the successful nonsurgical endodontic treatment of a mandibular left second premolar with two separate roots and three distinct root canals filled using size 35 Thermafil gutta-percha carriers and AH Plus sealer. On the one-year follow-up radiograph, the tooth was asymptomatic, confirming adequate healing with no complications. Even in a tooth with an extremely complex root canal morphology, conventional endodontic treatment without surgical intervention can result in adequate healing without any complications.

Variation in monitoring and treatment policies for intracranial hypertension in traumatic brain injury: a survey in 66 neurotrauma centers participating in the CENTER-TBI study.

PubMed

Cnossen, Maryse C; Huijben, Jilske A; van der Jagt, Mathieu; Volovici, Victor; van Essen, Thomas; Polinder, Suzanne; Nelson, David; Ercole, Ari; Stocchetti, Nino; Citerio, Giuseppe; Peul, Wilco C; Maas, Andrew I R; Menon, David; Steyerberg, Ewout W; Lingsma, Hester F

2017-09-06

No definitive evidence exists on how intracranial hypertension should be treated in patients with traumatic brain injury (TBI). It is therefore likely that centers and practitioners individually balance potential benefits and risks of different intracranial pressure (ICP) management strategies, resulting in practice variation. The aim of this study was to examine variation in monitoring and treatment policies for intracranial hypertension in patients with TBI. A 29-item survey on ICP monitoring and treatment was developed on the basis of literature and expert opinion, and it was pilot-tested in 16 centers. The questionnaire was sent to 68 neurotrauma centers participating in the Collaborative European Neurotrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study. The survey was completed by 66 centers (97% response rate). Centers were mainly academic hospitals (n = 60, 91%) and designated level I trauma centers (n = 44, 67%). The Brain Trauma Foundation guidelines were used in 49 (74%) centers. Approximately 90% of the participants (n = 58) indicated placing an ICP monitor in patients with severe TBI and computed tomographic abnormalities. There was no consensus on other indications or on peri-insertion precautions. We found wide variation in the use of first- and second-tier treatments for elevated ICP. Approximately half of the centers were classified as using a relatively aggressive approach to ICP monitoring and treatment (n = 32, 48%), whereas the others were considered more conservative (n = 34, 52%). Substantial variation was found regarding monitoring and treatment policies in patients with TBI and intracranial hypertension. The results of this survey indicate a lack of consensus between European neurotrauma centers and provide an opportunity and necessity for comparative effectiveness research.

A simple temperature-based method to estimate heterogeneous frozen ground within a distributed watershed model

NASA Astrophysics Data System (ADS)

Follum, Michael L.; Niemann, Jeffrey D.; Parno, Julie T.; Downer, Charles W.

2018-05-01

Frozen ground can be important to flood production and is often heterogeneous within a watershed due to spatial variations in the available energy, insulation by snowpack and ground cover, and the thermal and moisture properties of the soil. The widely used continuous frozen ground index (CFGI) model is a degree-day approach and identifies frozen ground using a simple frost index, which varies mainly with elevation through an elevation-temperature relationship. Similarly, snow depth and its insulating effect are also estimated based on elevation. The objective of this paper is to develop a model for frozen ground that (1) captures the spatial variations of frozen ground within a watershed, (2) allows the frozen ground model to be incorporated into a variety of watershed models, and (3) allows application in data sparse environments. To do this, we modify the existing CFGI method within the gridded surface subsurface hydrologic analysis watershed model. Among the modifications, the snowpack and frost indices are simulated by replacing air temperature (a surrogate for the available energy) with a radiation-derived temperature that aims to better represent spatial variations in available energy. Ground cover is also included as an additional insulator of the soil. Furthermore, the modified Berggren equation, which accounts for soil thermal conductivity and soil moisture, is used to convert the frost index into frost depth. The modified CFGI model is tested by application at six test sites within the Sleepers River experimental watershed in Vermont. Compared to the CFGI model, the modified CFGI model more accurately captures the variations in frozen ground between the sites, inter-annual variations in frozen ground depths at a given site, and the occurrence of frozen ground.

A Survey and Study of the Risk Behavior of the DoD Workforce

DTIC Science & Technology

2012-10-25

new technology , criticality to the mission, and so forth. However, a finding from the research is that there was a wide variation in responses to the...obsolescence, new technology , criticality to the mission, and so forth. However, a finding from the research is that there was a wide variation in...Active Risk Manager AT&L ................. Acquisition, Technology , and Logistics BLRIP ............... Beyond Low Rate Initial

Development of Multistep and Degenerate Variational Integrators for Applications in Plasma Physics

NASA Astrophysics Data System (ADS)

Ellison, Charles Leland

Geometric integrators yield high-fidelity numerical results by retaining conservation laws in the time advance. A particularly powerful class of geometric integrators is symplectic integrators, which are widely used in orbital mechanics and accelerator physics. An important application presently lacking symplectic integrators is the guiding center motion of magnetized particles represented by non-canonical coordinates. Because guiding center trajectories are foundational to many simulations of magnetically confined plasmas, geometric guiding center algorithms have high potential for impact. The motivation is compounded by the need to simulate long-pulse fusion devices, including ITER, and opportunities in high performance computing, including the use of petascale resources and beyond. This dissertation uses a systematic procedure for constructing geometric integrators --- known as variational integration --- to deliver new algorithms for guiding center trajectories and other plasma-relevant dynamical systems. These variational integrators are non-trivial because the Lagrangians of interest are degenerate - the Euler-Lagrange equations are first-order differential equations and the Legendre transform is not invertible. The first contribution of this dissertation is that variational integrators for degenerate Lagrangian systems are typically multistep methods. Multistep methods admit parasitic mode instabilities that can ruin the numerical results. These instabilities motivate the second major contribution: degenerate variational integrators. By replicating the degeneracy of the continuous system, degenerate variational integrators avoid parasitic mode instabilities. The new methods are therefore robust geometric integrators for degenerate Lagrangian systems. These developments in variational integration theory culminate in one-step degenerate variational integrators for non-canonical magnetic field line flow and guiding center dynamics. The guiding center integrator assumes coordinates such that one component of the magnetic field is zero; it is shown how to construct such coordinates for nested magnetic surface configurations. Additionally, collisional drag effects are incorporated in the variational guiding center algorithm for the first time, allowing simulation of energetic particle thermalization. Advantages relative to existing canonical-symplectic and non-geometric algorithms are numerically demonstrated. All algorithms have been implemented as part of a modern, parallel, ODE-solving library, suitable for use in high-performance simulations.

Identification of species and genetic variation in Taenia isolates from human and swine of North India.

PubMed

Singh, Satyendra K; Prasad, Kashi N; Singh, Aloukick K; Gupta, Kamlesh K; Chauhan, Ranjeet S; Singh, Amrita; Singh, Avinash; Rai, Ravi P; Pati, Binod K

2016-10-01

Taenia solium is the major cause of taeniasis and cysticercosis/neurocysticercosis (NCC) in the developing countries including India, but the existence of other Taenia species and genetic variation have not been studied in India. So, we studied the existence of different Taenia species, and sequence variation in Taenia isolates from human (proglottids and cysticerci) and swine (cysticerci) in North India. Amplification of cytochrome c oxidase subunit 1 gene (cox1) was done by polymerase chain reaction (PCR) followed by sequencing and phylogenetic analysis. We identified two species of Taenia i.e. T. solium and Taenia asiatica in our isolates. T. solium isolates showed similarity with Asian genotype and nucleotide variations from 0.25 to 1.01 %, whereas T. asiatica displayed nucleotide variations ranged from 0.25 to 0.5 %. These findings displayed the minimal genetic variations in North Indian isolates of T. solium and T. asiatica.

P450 GENETIC VARIATION: IMPLICATIONS FOR ENVIRONMENTAL AND WORKPLACE EXPOSURE

EPA Science Inventory

The Cytochrome P450 array detoxifies many chemicals by catalyzing the conversion of mostly hydrophobic chemicals into more hydrophilic forms that can subsequently be excreted by the body. Human genetic variation in the genes for these enzymes produces wide variations in the abili...

Common Genetic Variant in VIT Is Associated with Human Brain Asymmetry.

PubMed

Tadayon, Sayed H; Vaziri-Pashkam, Maryam; Kahali, Pegah; Ansari Dezfouli, Mitra; Abbassian, Abdolhossein

2016-01-01

Brain asymmetry varies across individuals. However, genetic factors contributing to this normal variation are largely unknown. Here we studied variation of cortical surface area asymmetry in a large sample of subjects. We performed principal component analysis (PCA) to capture correlated asymmetry variation across cortical regions. We found that caudal and rostral anterior cingulate together account for a substantial part of asymmetry variation among individuals. To find SNPs associated with this subset of brain asymmetry variation we performed a genome-wide association study followed by replication in an independent cohort. We identified one SNP (rs11691187) that had genome-wide significant association (P Combined = 2.40e-08). The rs11691187 is in the first intron of VIT. In a follow-up analysis, we found that VIT gene expression is associated with brain asymmetry in six donors of the Allen Human Brain Atlas. Based on these findings we suggest that VIT contributes to normal brain asymmetry variation. Our results can shed light on disorders associated with altered brain asymmetry.

Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis.

PubMed

Kooke, Rik; Kruijer, Willem; Bours, Ralph; Becker, Frank; Kuhn, André; van de Geest, Henri; Buntjer, Jaap; Doeswijk, Timo; Guerra, José; Bouwmeester, Harro; Vreugdenhil, Dick; Keurentjes, Joost J B

2016-04-01

Quantitative traits in plants are controlled by a large number of genes and their interaction with the environment. To disentangle the genetic architecture of such traits, natural variation within species can be explored by studying genotype-phenotype relationships. Genome-wide association studies that link phenotypes to thousands of single nucleotide polymorphism markers are nowadays common practice for such analyses. In many cases, however, the identified individual loci cannot fully explain the heritability estimates, suggesting missing heritability. We analyzed 349 Arabidopsis accessions and found extensive variation and high heritabilities for different morphological traits. The number of significant genome-wide associations was, however, very low. The application of genomic prediction models that take into account the effects of all individual loci may greatly enhance the elucidation of the genetic architecture of quantitative traits in plants. Here, genomic prediction models revealed different genetic architectures for the morphological traits. Integrating genomic prediction and association mapping enabled the assignment of many plausible candidate genes explaining the observed variation. These genes were analyzed for functional and sequence diversity, and good indications that natural allelic variation in many of these genes contributes to phenotypic variation were obtained. For ACS11, an ethylene biosynthesis gene, haplotype differences explaining variation in the ratio of petiole and leaf length could be identified. © 2016 American Society of Plant Biologists. All Rights Reserved.

Variation in Pediatric Organ Donor Management Practices Among US Organ Procurement Organizations.

PubMed

Ream, Robert S; Armbrecht, Eric S

2018-03-01

Reports of actual pediatric organ donor management practice among US organ procurement organizations are sparse, and the use of standardized management guidelines is unknown. A recent consensus statement from the Society of Critical Care Medicine, the American College of Chest Physicians, and the Association of Organ Procurement Organizations offers guidelines for the management of the pediatric organ donor. To describe the use of guidelines and routine practices in the management of the pediatric organ donor with respect to hemodynamics, lung and ventilator management, fluid and electrolytes, hormonal replacement therapy, the use of blood products, thermoregulation, and prophylactic antibiotics. Cross-sectional observational study using a survey and follow-up telephone interview with respondents from all 58 US organ procurement organizations. All 58 US Organ Procurement Organizations participated. A majority employed written guidelines for the management of pediatric donor hemodynamics, thermoregulation, fluids, and electrolytes. Management of blood products, the lung, and mechanical ventilation were less commonly committed to written guidelines, but common practices were described. All used various forms of hormonal replacement therapy and the majority administered empiric antibiotic therapy. Wide variation was observed in the management of the lung, mechanical ventilation, and glycemic control. Most OPOs used forms of standardized donor management for the pediatric organ donor although variation in the content of that management exists. Barriers to an evidence-based approach to the pediatric donor need to be determined and addressed.

Intraspecific variation of a dominant grass and local adaptation in reciprocal garden communities along a US Great Plains’ precipitation gradient: implications for grassland restoration with climate change

PubMed Central

Johnson, Loretta C; Olsen, Jacob T; Tetreault, Hannah; DeLaCruz, Angel; Bryant, Johnny; Morgan, Theodore J; Knapp, Mary; Bello, Nora M; Baer, Sara G; Maricle, Brian R

2015-01-01

Identifying suitable genetic stock for restoration often employs a ‘best guess’ approach. Without adaptive variation studies, restoration may be misguided. We test the extent to which climate in central US grasslands exerts selection pressure on a foundation grass big bluestem (Andropogon gerardii), widely used in restorations, and resulting in local adaptation. We seeded three regional ecotypes of A. gerardii in reciprocal transplant garden communities across 1150 km precipitation gradient. We measured ecological responses over several timescales (instantaneous gas exchange, medium-term chlorophyll absorbance, and long-term responses of establishment and cover) in response to climate and biotic factors and tested if ecotypes could expand range. The ecotype from the driest region exhibited greatest cover under low rainfall, suggesting local adaptation under abiotic stress. Unexpectedly, no evidence for cover differences between ecotypes exists at mesic sites where establishment and cover of all ecotypes were low, perhaps due to strong biotic pressures. Expression of adaptive differences is strongly environment specific. Given observed adaptive variation, the most conservative restoration strategy would be to plant the local ecotype, especially in drier locations. With superior performance of the most xeric ecotype under dry conditions and predicted drought, this ecotype may migrate eastward, naturally or with assistance in restorations. PMID:26240607

Somaclonal variation: a morphogenetic and biochemical analysis of Mandevilla velutina cultured cells.

PubMed

Maraschin, M; Sugui, J A; Wood, K V; Bonham, C; Buchi, D F; Cantao, M P; Carobrez, S G; Araujo, P S; Peixoto, M L; Verpoorte, R; Fontana, J D

2002-06-01

Cell cultures of Mandevilla velutina have proved to be an interesting production system for biomass and secondary metabolites able to inhibit the hypotensive activity of bradykinin, a nonapeptide generated in plasma during tissue trauma. The crude ethyl acetate extract of cultured cells contains about 31- to 79-fold more potent anti-bradykinin compounds (e.g., velutinol A) than that obtained with equivalent extracts of tubers. Somaclonal variation may be an explanation for the wide range of inhibitor activity found in the cell cultures. The heterogeneity concerning morphology, differentiation, carbon dissimilation, and velutinol A production in M. velutina cell cultures is reported. Cell cultures showed an asynchronous growth and cells in distinct developmental stages. Meristematic cells were found as the major type, with several morphological variations. Cell aggregates consisting only of meristematic cells, differentiated cells containing specialized cell structures such as functional chloroplasts (cytodifferentiation) and cells with embryogenetic characteristics were observed. The time course for sucrose metabolism indicated cell populations with significant differences in growth and metabolic rates, with the highest biomass-producing cell line showing a cell cycle 60% shorter and a metabolic rate 33.6% higher than the control (F2 cell population). MALDI-TOF mass spectrometric analysis of velutinol A in selected cell lines demonstrated the existence of velutinol A producing and nonproducing somaclones. These results point to a high genetic heterogeneity in general and also in terms of secondary metabolite content.

Intraspecific variation of a dominant grass and local adaptation in reciprocal garden communities along a US Great Plains' precipitation gradient: implications for grassland restoration with climate change.

PubMed

Johnson, Loretta C; Olsen, Jacob T; Tetreault, Hannah; DeLaCruz, Angel; Bryant, Johnny; Morgan, Theodore J; Knapp, Mary; Bello, Nora M; Baer, Sara G; Maricle, Brian R

2015-08-01

Identifying suitable genetic stock for restoration often employs a 'best guess' approach. Without adaptive variation studies, restoration may be misguided. We test the extent to which climate in central US grasslands exerts selection pressure on a foundation grass big bluestem (Andropogon gerardii), widely used in restorations, and resulting in local adaptation. We seeded three regional ecotypes of A. gerardii in reciprocal transplant garden communities across 1150 km precipitation gradient. We measured ecological responses over several timescales (instantaneous gas exchange, medium-term chlorophyll absorbance, and long-term responses of establishment and cover) in response to climate and biotic factors and tested if ecotypes could expand range. The ecotype from the driest region exhibited greatest cover under low rainfall, suggesting local adaptation under abiotic stress. Unexpectedly, no evidence for cover differences between ecotypes exists at mesic sites where establishment and cover of all ecotypes were low, perhaps due to strong biotic pressures. Expression of adaptive differences is strongly environment specific. Given observed adaptive variation, the most conservative restoration strategy would be to plant the local ecotype, especially in drier locations. With superior performance of the most xeric ecotype under dry conditions and predicted drought, this ecotype may migrate eastward, naturally or with assistance in restorations.

Geographical origin of Amazonian freshwater fishes fingerprinted by ⁸⁷Sr/⁸⁶Sr ratios on fish otoliths and scales.

PubMed

Pouilly, Marc; Point, David; Sondag, Francis; Henry, Manuel; Santos, Roberto V

2014-08-19

Calcified structures such as otoliths and scales grow continuously throughout the lifetime of fishes. The geochemical variations present in these biogenic structures are particularly relevant for studying fish migration and origin. In order to investigate the potential of the (87)Sr/(86)Sr ratio as a precise biogeochemical tag in Amazonian fishes, we compared this ratio between the water and fish otoliths and scales of two commercial fish species, Hoplias malabaricus and Schizodon fasciatus, from three major drainage basins of the Amazon: the Madeira, Solimões, and Tapajós rivers, displaying contrasted (87)Sr/(86)Sr ratios. A comparison of the (87)Sr/(86)Sr ratios between the otoliths and scales of the same individuals revealed similar values and were very close to the Sr isotopic composition of the local river where they were captured. This indicates, first, the absence of Sr isotopic fractionation during biological uptake and incorporation into calcified structures and, second, that scales may represent an interesting nonlethal alternative for (87)Sr/(86)Sr ratio measurements in comparison to otoliths. Considering the wide range of (87)Sr/(86)Sr variations that exist across Amazonian rivers, we used variations of (87)Sr/(86)Sr to discriminate fish origin at the basin level, as well as at the sub-basin level between the river and savannah lakes of the Beni River (Madeira basin).

Genetic variation of drought tolerance in Pinus pinaster at three hierarchical levels: a comparison of induced osmotic stress and field testing.

PubMed

Gaspar, Maria João; Velasco, Tania; Feito, Isabel; Alía, Ricardo; Majada, Juan

2013-01-01

Understanding the survival capacity of forest trees to periods of severe water stress could improve knowledge of the adaptive potential of different species under future climatic scenarios. In long lived organisms, like forest trees, the combination of induced osmotic stress treatments and field testing can elucidate the role of drought tolerance during the early stages of establishment, the most critical in the life of the species. We performed a Polyethylene glycol-osmotic induced stress experiment and evaluated two common garden experiments (xeric and mesic sites) to test for survival and growth of a wide range clonal collection of Maritime pine. This study demonstrates the importance of additive vs non additive effects for drought tolerance traits in Pinus pinaster, and shows differences in parameters determining the adaptive trajectories of populations and family and clones within populations. The results show that osmotic adjustment plays an important role in population variation, while biomass allocation and hydric content greatly influence survival at population level. Survival in the induced osmotic stress experiment presented significant correlations with survival in the xeric site, and height growth at the mesic site, at population level, indicating constraints of adaptation for those traits, while at the within population level no significant correlation existed. These results demonstrate that population differentiation and within population genetic variation for drought tolerance follow different patterns.

Genetic Variation of Drought Tolerance in Pinus pinaster at Three Hierarchical Levels: A Comparison of Induced Osmotic Stress and Field Testing

PubMed Central

Gaspar, Maria João; Velasco, Tania; Feito, Isabel; Alía, Ricardo; Majada, Juan

2013-01-01

Understanding the survival capacity of forest trees to periods of severe water stress could improve knowledge of the adaptive potential of different species under future climatic scenarios. In long lived organisms, like forest trees, the combination of induced osmotic stress treatments and field testing can elucidate the role of drought tolerance during the early stages of establishment, the most critical in the life of the species. We performed a Polyethylene glycol-osmotic induced stress experiment and evaluated two common garden experiments (xeric and mesic sites) to test for survival and growth of a wide range clonal collection of Maritime pine. This study demonstrates the importance of additive vs non additive effects for drought tolerance traits in Pinus pinaster, and shows differences in parameters determining the adaptive trajectories of populations and family and clones within populations. The results show that osmotic adjustment plays an important role in population variation, while biomass allocation and hydric content greatly influence survival at population level. Survival in the induced osmotic stress experiment presented significant correlations with survival in the xeric site, and height growth at the mesic site, at population level, indicating constraints of adaptation for those traits, while at the within population level no significant correlation existed. These results demonstrate that population differentiation and within population genetic variation for drought tolerance follow different patterns. PMID:24223885

Between-centre variability in transfer function analysis, a widely used method for linear quantification of the dynamic pressure–flow relation: The CARNet study

PubMed Central

Meel-van den Abeelen, Aisha S.S.; Simpson, David M.; Wang, Lotte J.Y.; Slump, Cornelis H.; Zhang, Rong; Tarumi, Takashi; Rickards, Caroline A.; Payne, Stephen; Mitsis, Georgios D.; Kostoglou, Kyriaki; Marmarelis, Vasilis; Shin, Dae; Tzeng, Yu-Chieh; Ainslie, Philip N.; Gommer, Erik; Müller, Martin; Dorado, Alexander C.; Smielewski, Peter; Yelicich, Bernardo; Puppo, Corina; Liu, Xiuyun; Czosnyka, Marek; Wang, Cheng-Yen; Novak, Vera; Panerai, Ronney B.; Claassen, Jurgen A.H.R.

2014-01-01

Transfer function analysis (TFA) is a frequently used method to assess dynamic cerebral autoregulation (CA) using spontaneous oscillations in blood pressure (BP) and cerebral blood flow velocity (CBFV). However, controversies and variations exist in how research groups utilise TFA, causing high variability in interpretation. The objective of this study was to evaluate between-centre variability in TFA outcome metrics. 15 centres analysed the same 70 BP and CBFV datasets from healthy subjects (n = 50 rest; n = 20 during hypercapnia); 10 additional datasets were computer-generated. Each centre used their in-house TFA methods; however, certain parameters were specified to reduce a priori between-centre variability. Hypercapnia was used to assess discriminatory performance and synthetic data to evaluate effects of parameter settings. Results were analysed using the Mann–Whitney test and logistic regression. A large non-homogeneous variation was found in TFA outcome metrics between the centres. Logistic regression demonstrated that 11 centres were able to distinguish between normal and impaired CA with an AUC > 0.85. Further analysis identified TFA settings that are associated with large variation in outcome measures. These results indicate the need for standardisation of TFA settings in order to reduce between-centre variability and to allow accurate comparison between studies. Suggestions on optimal signal processing methods are proposed. PMID:24725709

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple.

PubMed

Urrestarazu, Jorge; Muranty, Hélène; Denancé, Caroline; Leforestier, Diane; Ravon, Elisa; Guyader, Arnaud; Guisnel, Rémi; Feugey, Laurence; Aubourg, Sébastien; Celton, Jean-Marc; Daccord, Nicolas; Dondini, Luca; Gregori, Roberto; Lateur, Marc; Houben, Patrick; Ordidge, Matthew; Paprstein, Frantisek; Sedlak, Jiri; Nybom, Hilde; Garkava-Gustavsson, Larisa; Troggio, Michela; Bianco, Luca; Velasco, Riccardo; Poncet, Charles; Théron, Anthony; Moriya, Shigeki; Bink, Marco C A M; Laurens, François; Tartarini, Stefano; Durel, Charles-Eric

2017-01-01

Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.

Longitudinal trends and cross-sectional analysis of English national hospital antibacterial use over 5 years (2008-13): working towards hospital prescribing quality measures.

PubMed

Cooke, Jonathan; Stephens, Peter; Ashiru-Oredope, Diane; Charani, Esmita; Dryden, Mathew; Fry, Carole; Hand, Kieran; Holmes, Alison; Howard, Philip; Johnson, Alan P; Livermore, David M; Mansell, Paula; McNulty, Cliodna A M; Wellsteed, Sally; Hopkins, Susan; Sharland, Mike

2015-01-01

There is global concern that antimicrobial resistance is a major threat to healthcare. Antimicrobial use is a primary driver of resistance but little information exists about the variation in antimicrobial use in individual hospitals in England over time or comparative use between hospitals. The objective of this study was to collate, analyse and report issue data from pharmacy records of 158 National Health Service (NHS) acute hospitals. This was a cohort study of inpatient antibacterial use in acute hospitals in England analysed over 5 years through a data warehouse from IMS Health, a leading provider of information, services and technology for the healthcare industry. Around 98% of NHS hospitals were included in a country with a population of 50 million residents. There was a dramatic change in the usage of different groups of antibacterials between 2009 and 2013 with a marked reduction in the use of first-generation cephalosporins by 24.7% and second-generation cephalosporins by 41%, but little change in the use of third-generation cephalosporins (+5.7%) and fluoroquinolones (+1.6%). In contrast, use of co-amoxiclav, carbapenems and piperacillin/tazobactam increased by 60.1%, 61.4% and 94.8%, respectively. There was wide variation in the total and relative amounts of antibacterials used between individual hospitals. Longitudinal analysis of antibacterial use demonstrated remarkable changes in NHS hospitals, probably reflecting governmental and professional guidance to mitigate the risk of Clostridium difficile infection. The wide variation in usage between individual hospitals suggests potential for quality improvement and benchmarking. Quality measures of optimal hospital antimicrobial prescribing need urgent development and validation to support antimicrobial stewardship initiatives. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Temporal patterns in adult salmon migration timing across southeast Alaska

USGS Publications Warehouse

Kovach, Ryan P.; Ellison, Stephen; Pyare, Sanjay; Tallmon, David

2015-01-01

Pacific salmon migration timing can drive population productivity, ecosystem dynamics, and human harvest. Nevertheless, little is known about long-term variation in salmon migration timing for multiple species across broad regions. We used long-term data for five Pacific salmon species throughout rapidly warming southeast Alaska to describe long-term changes in salmon migration timing, interannual phenological synchrony, relationships between climatic variation and migratory timing, and to test whether long-term changes in migration timing are related to glaciation in headwater streams. Temporal changes in the median date of salmon migration timing varied widely across species. Most sockeye populations are migrating later over time (11 of 14), but pink, chum, and especially coho populations are migrating earlier than they did historically (16 of 19 combined). Temporal trends in duration and interannual variation in migration timing were highly variable across species and populations. The greatest temporal shifts in the median date of migration timing were correlated with decreases in the duration of migration timing, suggestive of a loss of phenotypic variation due to natural selection. Pairwise interannual correlations in migration timing varied widely but were generally positive, providing evidence for weak region-wide phenological synchrony. This synchrony is likely a function of climatic variation, as interannual variation in migration timing was related to climatic phenomenon operating at large- (Pacific decadal oscillation), moderate- (sea surface temperature), and local-scales (precipitation). Surprisingly, the presence or the absence of glaciers within a watershed was unrelated to long-term shifts in phenology. Overall, there was extensive heterogeneity in long-term patterns of migration timing throughout this climatically and geographically complex region, highlighting that future climatic change will likely have widely divergent impacts on salmon migration timing. Although salmon phenological diversity will complicate future predictions of migration timing, this variation likely acts as a major contributor to population and ecosystem resiliency in southeast Alaska.

A survey of copy number variation in the porcine genome detected from whole-genome sequence

USDA-ARS?s Scientific Manuscript database

An important challenge to post-genomic biology is relating observed phenotypic variation to the underlying genotypic variation. Genome-wide association studies (GWAS) have made thousands of connections between single nucleotide polymorphisms (SNPs) and phenotypes, implicating regions of the genome t...

Variable expression of molecular markers in juvenile nasopharyngeal angiofibroma.

PubMed

Mishra, A; Pandey, A; Mishra, S C

2017-09-01

Molecular categorisation may explain the wide variation in the clinical characteristics of juvenile nasopharyngeal angiofibroma. Variations in molecular markers in juvenile nasopharyngeal angiofibroma in an Indian population were investigated and compared with global reports. Variable molecular marker expression was demonstrated at the regional and global levels. A wide variation in molecular characteristics is evident. Molecular data have been reported for only 11 countries, indicating a clear geographical bias. Only 58 markers have been studied, and most are yet to be validated. Research into the molecular epidemiology of juvenile nasopharyngeal angiofibroma is still in its infancy. Although the molecular variation is not well understood, data obtained so far have prompted important research questions. Hence, multicentre collaborative molecular studies are needed to establish the aetiopathogenesis and establish molecular surrogates for clinical characteristics.

Using a Learning Collaborative Strategy With Office-based Practices to Increase Access and Improve Quality of Care for Patients With Opioid Use Disorders.

PubMed

Nordstrom, Benjamin R; Saunders, Elizabeth C; McLeman, Bethany; Meier, Andrea; Xie, Haiyi; Lambert-Harris, Chantal; Tanzman, Beth; Brooklyn, John; King, Gregory; Kloster, Nels; Lord, Clifton Frederick; Roberts, William; McGovern, Mark P

2016-01-01

Rapidly escalating rates of heroin and prescription opioid use have been widely observed in rural areas across the United States. Although US Food and Drug Administration-approved medications for opioid use disorders exist, they are not routinely accessible to patients. One medication, buprenorphine, can be prescribed by waivered physicians in office-based practice settings, but practice patterns vary widely. This study explored the use of a learning collaborative method to improve the provision of buprenorphine in the state of Vermont. We initiated a learning collaborative with 4 cohorts of physician practices (28 total practices). The learning collaborative consisted of a series of 4 face-to-face and 5 teleconference sessions over 9 months. Practices collected and reported on 8 quality-improvement data measures, which included the number of patients prescribed buprenorphine, and the percent of unstable patients seen weekly. Changes from baseline to 8 months were examined using a p-chart and logistic regression methodology. Physician engagement in the learning collaborative was favorable across all 4 cohorts (85.7%). On 6 of the 7 quality-improvement measures, there were improvements from baseline to 8 months. On 4 measures, these improvements were statistically significant (P < 0.001). Importantly, practice variation decreased over time on all measures. The number of patients receiving medication increased only slightly (3.4%). Results support the effectiveness of a learning collaborative approach to engage physicians, modestly improve patient access, and significantly reduce practice variation. The strategy is potentially generalizable to other systems and regions struggling with this important public health problem.

Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays.

PubMed

Wang, Yanan; Tang, Zhonglin; Sun, Yaqi; Wang, Hongyang; Wang, Chao; Yu, Shaobo; Liu, Jing; Zhang, Yu; Fan, Bin; Li, Kui; Liu, Bang

2014-01-01

Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.

Analysis of Genome-Wide Copy Number Variations in Chinese Indigenous and Western Pig Breeds by 60 K SNP Genotyping Arrays

PubMed Central

Sun, Yaqi; Wang, Hongyang; Wang, Chao; Yu, Shaobo; Liu, Jing; Zhang, Yu; Fan, Bin; Li, Kui; Liu, Bang

2014-01-01

Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs. PMID:25198154

The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine

PubMed Central

Yusuf, Leeban; Anderson, Ainan I J; Pirooznia, Mehdi; Arnellos, Dimitrios; Vilshansky, Gregory; Ercal, Gunes; Lu, Yontao; Webster, Teresa; Baird, Michael L; Esposito, Umberto

2017-01-01

Abstract The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation, drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity. We thereby aimed to design the Diversity of REcent and Ancient huMan (DREAM)—an all-inclusive microarray that would allow both identification of known associations and exploration of standing questions in genetic anthropology, forensics, and personalized medicine. DREAM includes probes to interrogate ancestry informative markers obtained from over 450 human populations, over 200 ancient genomes, and 10 archaic hominins. DREAM can identify 94% and 61% of all known Y and mitochondrial haplogroups, respectively, and was vetted to avoid interrogation of clinically relevant markers. To demonstrate its capabilities, we compared its FST distributions with those of the 1000 Genomes Project and commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, DREAM’s autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. DREAM performances are further illustrated in biogeographical, identical by descent, and copy number variation analyses. In summary, with approximately 800,000 markers spanning nearly 2,000 genes, DREAM is a useful tool for genetic anthropology, forensic, and personalized medicine studies. PMID:29165562

Coevolutionary dynamics of phenotypic diversity and contingent cooperation

PubMed Central

Wang, Long

2017-01-01

Phenotypic diversity is considered beneficial to the evolution of contingent cooperation, in which cooperators channel their help preferentially towards others of similar phenotypes. However, it remains largely unclear how phenotypic variation arises in the first place and thus leads to the construction of phenotypic complexity. Here we propose a mathematical model to study the coevolutionary dynamics of phenotypic diversity and contingent cooperation. Unlike previous models, our model does not assume any prescribed level of phenotypic diversity, but rather lets it be an evolvable trait. Each individual expresses one phenotype at a time and only the phenotypes expressed are visible to others. Moreover, individuals can differ in their potential of phenotypic variation, which is characterized by the number of distinct phenotypes they can randomly switch to. Each individual incurs a cost proportional to the number of potentially expressible phenotypes so as to retain phenotypic variation and expression. Our results show that phenotypic diversity coevolves with contingent cooperation under a wide range of conditions and that there exists an optimal level of phenotypic diversity best promoting contingent cooperation. It pays for contingent cooperators to elevate their potential of phenotypic variation, thereby increasing their opportunities of establishing cooperation via novel phenotypes, as these new phenotypes serve as secret tags that are difficult for defector to discover and chase after. We also find that evolved high levels of phenotypic diversity can occasionally collapse due to the invasion of defector mutants, suggesting that cooperation and phenotypic diversity can mutually reinforce each other. Thus, our results provide new insights into better understanding the coevolution of cooperation and phenotypic diversity. PMID:28141806

Variation in esophageal physiology testing in clinical practice: Results from an international survey.

PubMed

Sweis, R; Heinrich, H; Fox, M

2018-03-01

Advances in clinical measurement of esophageal motility and function have improved the assessment of swallowing disorders and reflux symptoms. Variation in data acquisition, analysis, and reporting exists and impacts on diagnosis and management. This study examined variation in esophageal manometry methodology between institutions to establish the status in current practice. A structured survey was distributed through international NGM societies using an Internet-based platform. Questions explored infrastructure, technology, analysis, and reporting. Responses were received from 91 centers from 29 countries. Eighteen (20%) centers used "conventional" manometry, 75 (82%) high-resolution manometry, and 53 (58%) HR impedance manometry. All centers documented motility for single water swallows. The Chicago Classification was applied by 65 (71.4%) centers. In contrast, analysis of EGJ morphology varied widely. Adjunctive testing was often applied: multiple rapid swallows (77%), rapid drink challenge (77%), single solid swallows (63%), and a standard test meal (18%). Of 86 (94.5%) units that offered pH impedance (pH-Z) studies, approximately half (53.5%) performed tests on acid-suppressant medication in patients with a high pretest probability (eg, erosive esophagitis). Most (75.6%) centers manually reviewed every reflux event. Others examined pH-Z data only prior to symptoms. To assess symptom association with reflux events, 73.6% centers analyzed each symptom separately, whereas 29.7% centers pooled symptoms. There is marked variation in the data acquisition, analysis, and reporting of esophageal manometry studies. Further efforts to improve quality and uniformity in testing and reporting are required. This survey provides information upon which best-practice guidelines can be developed. © 2017 John Wiley & Sons Ltd.

Seeking order amidst chaos: a systematic review of classification systems for causes of stillbirth and neonatal death, 2009-2014.

PubMed

Leisher, Susannah Hopkins; Teoh, Zheyi; Reinebrant, Hanna; Allanson, Emma; Blencowe, Hannah; Erwich, Jan Jaap; Frøen, J Frederik; Gardosi, Jason; Gordijn, Sanne; Gülmezoglu, A Metin; Heazell, Alexander E P; Korteweg, Fleurisca; Lawn, Joy; McClure, Elizabeth M; Pattinson, Robert; Smith, Gordon C S; Tunçalp, Ӧzge; Wojcieszek, Aleena M; Flenady, Vicki

2016-10-05

Each year, about 5.3 million babies die in the perinatal period. Understanding of causes of death is critical for prevention, yet there is no globally acceptable classification system. Instead, many disparate systems have been developed and used. We aimed to identify all systems used or created between 2009 and 2014, with their key features, including extent of alignment with the International Classification of Diseases (ICD) and variation in features by region, to inform the World Health Organization's development of a new global approach to classifying perinatal deaths. A systematic literature review (CINAHL, EMBASE, Medline, Global Health, and PubMed) identified published and unpublished studies and national reports describing new classification systems or modifications of existing systems for causes of perinatal death, or that used or tested such systems, between 2009 and 2014. Studies reporting ICD use only were excluded. Data were independently double-extracted (except from non-English publications). Subgroup analyses explored variation by extent and region. Eighty-one systems were identified as new, modifications of existing systems, or having been used between 2009 and 2014, with an average of ten systems created/modified each year. Systems had widely varying characteristics: (i) comprehensiveness (40 systems classified both stillbirths and neonatal deaths); (ii) extent of use (systems were created in 28 countries and used in 40; 17 were created for national use; 27 were widely used); (iii) accessibility (three systems available in e-format); (iv) underlying cause of death (64 systems required a single cause of death); (v) reliability (10 systems tested for reliability, with overall Kappa scores ranging from .35-.93); and (vi) ICD alignment (17 systems used ICD codes). Regional databases were not searched, so system numbers may be underestimated. Some non-differential misclassification of systems was possible. The plethora of systems in use, and continuing system development, hamper international efforts to improve understanding of causes of death. Recognition of the features of currently used systems, combined with a better understanding of the drivers of continued system creation, may help the development of a truly effective global system.

Tourmaline mineralization in the Barberton greenstone belt, South Africa: early Archean metasomatism by evaporite-derived boron.

PubMed

Byerly, G R; Palmer, M R

1991-05-01

Tourmaline-rich rocks are common in the low-grade, interior portions of the Barberton greenstone belt of South Africa, where shallow-marine sediments and underlying altered basaltic and komatiitic lavas contain up to 50% tourmaline. The presence of tourmaline-bearing rip-up clasts, intraformational tourmaline pebbles and tourmaline-coated grains indicate that boron mineralization was a low-temperature, surficial process. The association of these lithologies with stromatolites, evaporites, and shallow-water sedimentary structures and the virtual absence of tourmaline in correlative deep-water facies rocks in the greenstone belt strengthens this model. Five tourmaline-bearing lithologic groups (basalts, komatiites, evaporite-bearing sediments, stromatolitic sediments, and quartz veins) are distinguished based on field, petrographic, and geochemical criteria. Individual tourmaline crystals within these lithologies show internal chemical and textural variations that reflect continued growth through intervals of change in bulk-rock and fluid composition accompanying one or more metasomatic events. Large single-crystal variations exist in Fe/Mg, Al/Fe, and alkali-site vacancies. A wide range in tourmaline composition exists in rocks altered from similar protoliths, but tourmalines in sediments and lavas have similar compositional variations. Boron-isotope analyses of the tourmalines suggest that the boron enrichment in these rocks has a major marine evaporitic component. Sediments with gypsum pseudomorphs and lavas altered at low temperatures by shallow-level brines have the highest delta 11B values (+2.2 to -1.9%); lower delta 11B values of late quartz veins (-3.7 to -5.7%) reflect intermediate temperature, hydrothermal remobilization of evaporitic boron. The delta 11B values of tourmaline-rich stromatolitic sediments (-9.8 and -10.5%) are consistent with two-stage boron enrichment, in which earlier marine evaporitic boron was hydrothermally remobilized and vented in shallow-marine or subaerial sites, mineralizing algal stromatolites. The stromatolite-forming algae preferentially may have lived near the sites of hydrothermal discharge in Archean times.

Genetic variation in the USDA Chamaecrista fasciculata collection

USDA-ARS?s Scientific Manuscript database

Germplasm collections serve as critical repositories of genetic variation. Characterizing genetic diversity in existing collections is necessary to maximize their utility and to guide future collecting efforts. We have used AFLP markers to characterize genetic variation in the USDA germplasm collect...

Epigenetic Variation in Monozygotic Twins: A Genome-Wide Analysis of DNA Methylation in Buccal Cells

PubMed Central

van Dongen, Jenny; Ehli, Erik A.; Slieker, Roderick C.; Bartels, Meike; Weber, Zachary M.; Davies, Gareth E.; Slagboom, P. Eline; Heijmans, Bastiaan T.; Boomsma, Dorret I.

2014-01-01

DNA methylation is one of the most extensively studied epigenetic marks in humans. Yet, it is largely unknown what causes variation in DNA methylation between individuals. The comparison of DNA methylation profiles of monozygotic (MZ) twins offers a unique experimental design to examine the extent to which such variation is related to individual-specific environmental influences and stochastic events or to familial factors (DNA sequence and shared environment). We measured genome-wide DNA methylation in buccal samples from ten MZ pairs (age 8–19) using the Illumina 450k array and examined twin correlations for methylation level at 420,921 CpGs after QC. After selecting CpGs showing the most variation in the methylation level between subjects, the mean genome-wide correlation (rho) was 0.54. The correlation was higher, on average, for CpGs within CpG islands (CGIs), compared to CGI shores, shelves and non-CGI regions, particularly at hypomethylated CpGs. This finding suggests that individual-specific environmental and stochastic influences account for more variation in DNA methylation in CpG-poor regions. Our findings also indicate that it is worthwhile to examine heritable and shared environmental influences on buccal DNA methylation in larger studies that also include dizygotic twins. PMID:24802513

Geomorphic expression of strike-slip faults: field observations vs. analog experiments: preliminary results

NASA Astrophysics Data System (ADS)

Hsieh, S. Y.; Neubauer, F.; Genser, J.

2012-04-01

The aim of this project is to study the surface expression of strike-slip faults with main aim to find rules how these structures can be extrapolated to depth. In the first step, several basic properties of the fault architecture are in focus: (1) Is it possible to define the fault architecture by studying surface structures of the damage zone vs. the fault core, particularly the width of the damage zone? (2) Which second order structures define the damage zone of strike-slip faults, and how relate these to such reported in basement fault strike-slip analog experiments? (3) Beside classical fault bend structures, is there a systematic along-strike variation of the damage zone width and to which properties relates the variation of the damage zone width. We study the above mentioned properties on the dextral Altyn fault, which is one of the largest strike-slip on Earth with the advantage to have developed in a fully arid climate. The Altyn fault includes a ca. 250 to 600 m wide fault valley, usually with the trace of actual fault in its center. The fault valley is confined by basement highs, from which alluvial fans develop towards the center of the fault valley. The active fault trace is marked by small scale pressure ridges and offset of alluvial fans. The fault valley confining basement highs are several kilometer long and ca. 0.5 to 1 km wide and confined by rotated dextral anti-Riedel faults and internally structured by a regular fracture pattern. Dextral anti-Riedel faults are often cut by Riedel faults. Consequently, the Altyn fault comprises a several km wide damage zone. The fault core zone is a barrier to fluid flow, and the few springs of the region are located on the margin of the fault valley implying the fractured basement highs as the reservoir. Consequently, the southern Silk Road was using the Altyn fault valley. The preliminary data show that two or more orders of structures exist. Small-scale develop during a single earthquake. These finally accumulate to a several 100 m wide fault core, which is in part exposed at surface to arid climate and a km wide damage zone. The basic structures of analog experiments can be well transferred to nature, although along strike changes are common due to fault bending and fracture failure of country rocks.

Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation

USDA-ARS?s Scientific Manuscript database

Genomic structural variations, including segmental duplications (SD) and copy number variations (CNV), contribute significantly to individual health and disease in primates and rodents. As a part of the bovine genome annotation effort, we performed the first genome-wide analysis of SD in cattle usin...

Genetic variation in California oaks

Treesearch

Constance I. Millar; Diane L. Delany; Lawrence A. Riggs

1990-01-01

In forestry the importance of genetic variation for successful reproduction, survival and growth has been widely documented for commercial conifers; until recently, little genetic work has been done on the California oaks. Even before the nature of genetic variation was scientifically investigated, its importance was suspected in operational forestry. Many failures of...

Genomic Diversity in Pig (Sus scrofa) and its Comparison with Human and other Livestock

PubMed Central

Zhang, Chunyan; Plastow, Graham

2011-01-01

We have reviewed the current pig (Sus scrofa) genomic diversity within and between sites and compared them with human and other livestock. The current Porcine 60K single nucleotide polymorphism (SNP) panel has an average SNP distance in a range of 30 - 40 kb. Most of genetic variation was distributed within populations, and only a small proportion of them existed between populations. The average heterozygosity was lower in pig than in human and other livestock. Genetic inbreeding coefficient (FIS), population differentiation (FST), and Nei’s genetic distance between populations were much larger in pig than in human and other livestock. Higher average genetic distance existed between European and Asian populations than between European or between Asian populations. Asian breeds harboured much larger variability and higher average heterozygosity than European breeds. The samples of wild boar that have been analyzed displayed more extensive genetic variation than domestic breeds. The average linkage disequilibrium (LD) in improved pig breeds extended to 1 - 3 cM, much larger than that in human (~ 30 kb) and cattle (~ 100 kb), but smaller than that in sheep (~ 10 cM). European breeds showed greater LD that decayed more slowly than Asian breeds. We briefly discuss some processes for maintaining genomic diversity in pig, including migration, introgression, selection, and drift. We conclude that, due to the long time of domestication, the pig possesses lower heterozygosity, higher FIS, and larger LD compared with human and cattle. This implies that a smaller effective population size and less informative markers are needed in pig for genome wide association studies. PMID:21966252

Firefighter Hand Anthropometry and Structural Glove Sizing: A New Perspective

PubMed Central

Hsiao, Hongwei; Whitestone, Jennifer; Kau, Tsui-Ying; Hildreth, Brooke

2015-01-01

Objective We evaluated the current use and fit of structural firefighting gloves and developed an improved sizing scheme that better accommodates the U.S. firefighter population. Background Among surveys, 24% to 30% of men and 31% to 62% of women reported experiencing problems with the fit or bulkiness of their structural firefighting gloves. Method An age-, race/ethnicity-, and gender-stratified sample of 863 male and 88 female firefighters across the United States participated in the study. Fourteen hand dimensions relevant to glove design were measured. A cluster analysis of the hand dimensions was performed to explore options for an improved sizing scheme. Results The current national standard structural firefighting glove-sizing scheme underrepresents firefighter hand size range and shape variation. In addition, mismatch between existing sizing specifications and hand characteristics, such as hand dimensions, user selection of glove size, and the existing glove sizing specifications, is significant. An improved glove-sizing plan based on clusters of overall hand size and hand/finger breadth-to-length contrast has been developed. Conclusion This study presents the most up-to-date firefighter hand anthropometry and a new perspective on glove accommodation. The new seven-size system contains narrower variations (standard deviations) for almost all dimensions for each glove size than the current sizing practices. Application The proposed science-based sizing plan for structural firefighting gloves provides a step-forward perspective (i.e., including two women hand model–based sizes and two wide-palm sizes for men) for glove manufacturers to advance firefighter hand protection. PMID:26169309

Opposing Forces of A/T-Biased Mutations and G/C-Biased Gene Conversions Shape the Genome of the Nematode Pristionchus pacificus

PubMed Central

Weller, Andreas M.; Rödelsperger, Christian; Eberhardt, Gabi; Molnar, Ruxandra I.; Sommer, Ralf J.

2014-01-01

Base substitution mutations are a major source of genetic novelty and mutation accumulation line (MAL) studies revealed a nearly universal AT bias in de novo mutation spectra. While a comparison of de novo mutation spectra with the actual nucleotide composition in the genome suggests the existence of general counterbalancing mechanisms, little is known about the evolutionary and historical details of these opposing forces. Here, we correlate MAL-derived mutation spectra with patterns observed from population resequencing. Variation observed in natural populations has already been subject to evolutionary forces. Distinction between rare and common alleles, the latter of which are close to fixation and of presumably older age, can provide insight into mutational processes and their influence on genome evolution. We provide a genome-wide analysis of de novo mutations in 22 MALs of the nematode Pristionchus pacificus and compare the spectra with natural variants observed in resequencing of 104 natural isolates. MALs show an AT bias of 5.3, one of the highest values observed to date. In contrast, the AT bias in natural variants is much lower. Specifically, rare derived alleles show an AT bias of 2.4, whereas common derived alleles close to fixation show no AT bias at all. These results indicate the existence of a strong opposing force and they suggest that the GC content of the P. pacificus genome is in equilibrium. We discuss GC-biased gene conversion as a potential mechanism acting against AT-biased mutations. This study provides insight into genome evolution by combining MAL studies with natural variation. PMID:24414549

Isozyme variation in wild and cultivated pineapple

USDA-ARS?s Scientific Manuscript database

Isozyme variation was studied in 161 accessions of pineapple including four species of Ananas and one of Pseudananas. Six enzyme systems (ADH, GPI, PGM, SKDH, TPI, UGPP) involving seven putative loci revealed 35 electromorphs . Considerable variation exists within and between species of Ananas. Sixt...

Variations in achievement of evidence-based, high-impact quality indicators in general practice: An observational study

PubMed Central

West, Robert; Rushforth, Bruno; Stokes, Tim; Glidewell, Liz; Carder, Paul; Faulkner, Simon; Foy, Robbie

2017-01-01

Background There are widely recognised variations in the delivery and outcomes of healthcare but an incomplete understanding of their causes. There is a growing interest in using routinely collected ‘big data’ in the evaluation of healthcare. We developed a set of evidence-based ‘high impact’ quality indicators (QIs) for primary care and examined variations in achievement of these indicators using routinely collected data in the United Kingdom (UK). Methods Cross-sectional analysis of routinely collected, electronic primary care data from a sample of general practices in West Yorkshire, UK (n = 89). The QIs covered aspects of care (including processes and intermediate clinical outcomes) in relation to diabetes, hypertension, atrial fibrillation, myocardial infarction, chronic kidney disease (CKD) and ‘risky’ prescribing combinations. Regression models explored the impact of practice and patient characteristics. Clustering within practice was accounted for by including a random intercept for practice. Results Median practice achievement of the QIs ranged from 43.2% (diabetes control) to 72.2% (blood pressure control in CKD). Considerable between-practice variation existed for all indicators: the difference between the highest and lowest performing practices was 26.3 percentage points for risky prescribing and 100 percentage points for anticoagulation in atrial fibrillation. Odds ratios associated with the random effects for practices emphasised this; there was a greater than ten-fold difference in the likelihood of achieving the hypertension indicator between the lowest and highest performing practices. Patient characteristics, in particular age, gender and comorbidity, were consistently but modestly associated with indicator achievement. Statistically significant practice characteristics were identified less frequently in adjusted models. Conclusions Despite various policy and improvement initiatives, there are enduring inappropriate variations in the delivery of evidence-based care. Much of this variation is not explained by routinely collected patient or practice variables, and is likely to be attributable to differences in clinical and organisational behaviour. PMID:28704407

Spatial and temporal variation of body size among early Homo.

PubMed

Will, Manuel; Stock, Jay T

2015-05-01

The estimation of body size among the earliest members of the genus Homo (2.4-1.5Myr [millions of years ago]) is central to interpretations of their biology. It is widely accepted that Homo ergaster possessed increased body size compared with Homo habilis and Homo rudolfensis, and that this may have been a factor involved with the dispersal of Homo out of Africa. The study of taxonomic differences in body size, however, is problematic. Postcranial remains are rarely associated with craniodental fossils, and taxonomic attributions frequently rest upon the size of skeletal elements. Previous body size estimates have been based upon well-preserved specimens with a more reliable species assessment. Since these samples are small (n < 5) and disparate in space and time, little is known about geographical and chronological variation in body size within early Homo. We investigate temporal and spatial variation in body size among fossils of early Homo using a 'taxon-free' approach, considering evidence for size variation from isolated and fragmentary postcranial remains (n = 39). To render the size of disparate fossil elements comparable, we derived new regression equations for common parameters of body size from a globally representative sample of hunter-gatherers and applied them to available postcranial measurements from the fossils. The results demonstrate chronological and spatial variation but no simple temporal or geographical trends for the evolution of body size among early Homo. Pronounced body size increases within Africa take place only after hominin populations were established at Dmanisi, suggesting that migrations into Eurasia were not contingent on larger body sizes. The primary evidence for these marked changes among early Homo is based upon material from Koobi Fora after 1.7Myr, indicating regional size variation. The significant body size differences between specimens from Koobi Fora and Olduvai support the cranial evidence for at least two co-existing morphotypes in the Early Pleistocene of eastern Africa. Copyright © 2015 Elsevier Ltd. All rights reserved.

A principle of organization which facilitates broad Lamarckian-like adaptations by improvisation.

PubMed

Soen, Yoav; Knafo, Maor; Elgart, Michael

2015-12-02

During the lifetime of an organism, every individual encounters many combinations of diverse changes in the somatic genome, epigenome and microbiome. This gives rise to many novel combinations of internal failures which are unique to each individual. How any individual can tolerate this high load of new, individual-specific scenarios of failure is not clear. While stress-induced plasticity and hidden variation have been proposed as potential mechanisms of tolerance, the main conceptual problem remains unaddressed, namely: how largely non-beneficial random variation can be rapidly and safely organized into net benefits to every individual. We propose an organizational principle which explains how every individual can alleviate a high load of novel stressful scenarios using many random variations in flexible and inherently less harmful traits. Random changes which happen to reduce stress, benefit the organism and decrease the drive for additional changes. This adaptation (termed 'Adaptive Improvisation') can be further enhanced, propagated, stabilized and memorized when beneficial changes reinforce themselves by auto-regulatory mechanisms. This principle implicates stress not only in driving diverse variations in cells tissues and organs, but also in organizing these variations into adaptive outcomes. Specific (but not exclusive) examples include stress reduction by rapid exchange of mobile genetic elements (or exosomes) in unicellular, and rapid changes in the symbiotic microorganisms of animals. In all cases, adaptive changes can be transmitted across generations, allowing rapid improvement and assimilation in a few generations. We provide testable predictions derived from the hypothesis. The hypothesis raises a critical, but thus far overlooked adaptation problem and explains how random variation can self-organize to confer a wide range of individual-specific adaptations beyond the existing outcomes of natural selection. It portrays gene regulation as an inseparable synergy between natural selection and adaptation by improvisation. The latter provides a basis for Lamarckian adaptation that is not limited to a specific mechanism and readily accounts for the remarkable resistance of tumors to treatment.

Variation in Structure and Process of Care in Traumatic Brain Injury: Provider Profiles of European Neurotrauma Centers Participating in the CENTER-TBI Study.

PubMed

Cnossen, Maryse C; Polinder, Suzanne; Lingsma, Hester F; Maas, Andrew I R; Menon, David; Steyerberg, Ewout W

2016-01-01

The strength of evidence underpinning care and treatment recommendations in traumatic brain injury (TBI) is low. Comparative effectiveness research (CER) has been proposed as a framework to provide evidence for optimal care for TBI patients. The first step in CER is to map the existing variation. The aim of current study is to quantify variation in general structural and process characteristics among centers participating in the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study. We designed a set of 11 provider profiling questionnaires with 321 questions about various aspects of TBI care, chosen based on literature and expert opinion. After pilot testing, questionnaires were disseminated to 71 centers from 20 countries participating in the CENTER-TBI study. Reliability of questionnaires was estimated by calculating a concordance rate among 5% duplicate questions. All 71 centers completed the questionnaires. Median concordance rate among duplicate questions was 0.85. The majority of centers were academic hospitals (n = 65, 92%), designated as a level I trauma center (n = 48, 68%) and situated in an urban location (n = 70, 99%). The availability of facilities for neuro-trauma care varied across centers; e.g. 40 (57%) had a dedicated neuro-intensive care unit (ICU), 36 (51%) had an in-hospital rehabilitation unit and the organization of the ICU was closed in 64% (n = 45) of the centers. In addition, we found wide variation in processes of care, such as the ICU admission policy and intracranial pressure monitoring policy among centers. Even among high-volume, specialized neurotrauma centers there is substantial variation in structures and processes of TBI care. This variation provides an opportunity to study effectiveness of specific aspects of TBI care and to identify best practices with CER approaches.

Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies.

PubMed

Willing, Eva-Maria; Bentzen, Paul; van Oosterhout, Cock; Hoffmann, Margarete; Cable, Joanne; Breden, Felix; Weigel, Detlef; Dreyer, Christine

2010-03-01

Adaptation of guppies (Poecilia reticulata) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole-genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome-wide picture of standing natural variation in populations, genome-wide SNP data are rarely available for wild vertebrates. Here we use genetically mapped SNP markers to comprehensively survey genetic variation within and among naturally occurring guppy populations from a wide geographic range in Trinidad and Venezuela. Results from three different clustering methods, Neighbor-net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and largely with previously hypothesized patterns of historical colonization. Within major drainages (Caroni, Oropouche and Northern), populations are genetically similar, but those in different geographic regions are highly divergent from one another, with some indications of ancient shared polymorphisms. Clear genomic signatures of a previous introduction experiment were seen, and we detected additional potential admixture events. Headwater populations were significantly less heterozygous than downstream populations. Pairwise F(ST) values revealed marked differences in allele frequencies among populations from different regions, and also among populations within the same region. F(ST) outlier methods indicated some regions of the genome as being under directional selection. Overall, this study demonstrates the power of a genome-wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations.

Genome-wide association implicates numerous genes and pleiotropy underlying ecological trait variation in natural populations of Populus trichocarpa

DOE Office of Scientific and Technical Information (OSTI.GOV)

McKown, Athena; Klapste, Jaroslav; Guy, Robert

2014-01-01

To uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa Torr. & Gray) from natural populations throughout western North America. Extensive information from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34K Populus SNP array) of all accessions were used for gene discovery in a genome-wide association study (GWAS).

Deep Hashing for Scalable Image Search.

PubMed

Lu, Jiwen; Liong, Venice Erin; Zhou, Jie

2017-05-01

In this paper, we propose a new deep hashing (DH) approach to learn compact binary codes for scalable image search. Unlike most existing binary codes learning methods, which usually seek a single linear projection to map each sample into a binary feature vector, we develop a deep neural network to seek multiple hierarchical non-linear transformations to learn these binary codes, so that the non-linear relationship of samples can be well exploited. Our model is learned under three constraints at the top layer of the developed deep network: 1) the loss between the compact real-valued code and the learned binary vector is minimized, 2) the binary codes distribute evenly on each bit, and 3) different bits are as independent as possible. To further improve the discriminative power of the learned binary codes, we extend DH into supervised DH (SDH) and multi-label SDH by including a discriminative term into the objective function of DH, which simultaneously maximizes the inter-class variations and minimizes the intra-class variations of the learned binary codes with the single-label and multi-label settings, respectively. Extensive experimental results on eight widely used image search data sets show that our proposed methods achieve very competitive results with the state-of-the-arts.

A crustal seismic velocity model for the UK, Ireland and surrounding seas

USGS Publications Warehouse

Kelly, A.; England, R.W.; Maguire, Peter K.H.

2007-01-01

A regional model of the 3-D variation in seismic P-wave velocity structure in the crust of NW Europe has been compiled from wide-angle reflection/refraction profiles. Along each 2-D profile a velocity-depth function has been digitised at 5 km intervals. These 1-D velocity functions were mapped into three dimensions using ordinary kriging with weights determined to minimise the difference between digitised and interpolated values. An analysis of variograms of the digitised data suggested a radial isotropic weighting scheme was most appropriate. Horizontal dimensions of the model cells are optimised at 40 ?? 40 km and the vertical dimension at 1 km. The resulting model provides a higher resolution image of the 3-D variation in seismic velocity structure of the UK, Ireland and surrounding areas than existing models. The construction of the model through kriging allows the uncertainty in the velocity structure to be assessed. This uncertainty indicates the high density of data required to confidently interpolate the crustal velocity structure, and shows that for this region the velocity is poorly constrained for large areas away from the input data. ?? 2007 The Authors Journal compilation ?? 2007 RAS.

Fine structure of the landers fault zone: Segmentation and the rupture process

USGS Publications Warehouse

Li, Y.-G.; Vidale, J.E.; Aki, K.; Marone, C.J.; Lee, W.H.K.

1994-01-01

Observations and modeling of 3- to 6-hertz seismic shear waves trapped within the fault zone of the 1992 Landers earthquake series allow the fine structure and continuity of the zone to be evaluated. The fault, to a depth of at least 12 kilometers, is marked by a zone 100 to 200 meters wide where shear velocity is reduced by 30 to 50 percent. This zone forms a seismic waveguide that extends along the southern 30 kilometers of the Landers rupture surface and ends at the fault bend about 18 kilometers north of the main shock epicenter. Another fault plane waveguide, disconnected from the first, exists along the northern rupture surface. These observations, in conjunction with surface slip, detailed seismicity patterns, and the progression of rupture along the fault, suggest that several simple rupture planes were involved in the Landers earthquake and that the inferred rupture front hesitated or slowed at the location where the rupture jumped from one to the next plane. Reduction in rupture velocity can tentatively be attributed to fault plane complexity, and variations in moment release can be attributed to variations in available energy.

Impact of host cell variation on the neutralization of HIV-1 in vitro.

PubMed

Polonis, Victoria R; Schuitemaker, Hanneke; Bunnik, Evelien M; Brown, Bruce K; Scarlatti, Gabriella

2009-09-01

In this review we present current advances in our understanding of HIV-1 neutralization assays that employ primary cell types, as compared with those that utilize cell lines and the newer, more standardized pseudovirus assays. A commentary on the challenges of standardizing in-vitro neutralization assays using primary cells is included. The data from reporter cell line neutralization assays may agree with results observed in primary cells; however, exceptions have recently been reported. Multiple variables exist in primary cell assays using peripheral blood mononuclear cells from HIV-seronegative donors; in-vitro neutralization titers can vary significantly based on the donor cells used for assay targets and for virus propagation. Thus, more research is required to achieve validated primary cell neutralization assays. HIV-vaccine-induced antibody performance in the current neutralization assays may function as a 'gatekeeper' for HIV-1 subunit vaccine advancement. Development of standardized platforms for reproducible measurement of in-vitro neutralization is therefore a high priority. Given the considerable variation in results obtained from some widely applied HIV neutralization platforms, parallel evaluation of new antibodies using different host cells for assay targets, as well as virus propagation, is recommended until immune correlates of protection are identified.

Genetic variability of garlic accessions as revealed by agro-morphological traits evaluated under different environments.

PubMed

Hoogerheide, E S S; Azevedo Filho, J A; Vencovsky, R; Zucchi, M I; Zago, B W; Pinheiro, J B

2017-05-31

The cultivated garlic (Allium sativum L.) displays a wide phenotypic diversity, which is derived from natural mutations and phenotypic plasticity, due to dependence on soil type, moisture, latitude, altitude and cultural practices, leading to a large number of cultivars. This study aimed to evaluate the genetic variability shown by 63 garlic accessions belonging to Instituto Agronômico de Campinas and the Escola Superior de Agricultura "Luiz de Queiroz" germplasm collections. We evaluated ten quantitative characters in experimental trials conducted under two localities of the State of São Paulo: Monte Alegre do Sul and Piracicaba, during the agricultural year of 2007, in a randomized blocks design with five replications. The Mahalanobis distance was used to measure genetic dissimilarities. The UPGMA method and Tocher's method were used as clustering procedures. Results indicated significant variation among accessions (P < 0.01) for all evaluated characters, except for the percentage of secondary bulb growth in MAS, indicating the existence of genetic variation for bulb production, and germplasm evaluation considering different environments is more reliable for the characterization of the genotypic variability among garlic accessions, since it diminishes the environmental effects in the clustering of genotypes.

Endoscopy and polyps-diagnostic and therapeutic advances in management

PubMed Central

Steele, Scott R; Johnson, Eric K; Champagne, Bradley; Davis, Brad; Lee, Sang; Rivadeneira, David; Ross, Howard; Hayden, Dana A; Maykel, Justin A

2013-01-01

Despite multiple efforts aimed at early detection through screening, colon cancer remains the third leading cause of cancer-related deaths in the United States, with an estimated 51000 deaths during 2013 alone. The goal remains to identify and remove benign neoplastic polyps prior to becoming invasive cancers. Polypoid lesions of the colon vary widely from hyperplastic, hamartomatous and inflammatory to neoplastic adenomatous growths. Although these lesions are all benign, they are common, with up to one-quarter of patients over 60 years old will develop pre-malignant adenomatous polyps. Colonoscopy is the most effective screening tool to detect polyps and colon cancer, although several studies have demonstrated missed polyp rates from 6%-29%, largely due to variations in polyp size. This number can be as high as 40%, even with advanced (> 1 cm) adenomas. Other factors including sub-optimal bowel preparation, experience of the endoscopist, and patient anatomical variations all affect the detection rate. Additional challenges in decision-making exist when dealing with more advanced, and typically larger, polyps that have traditionally required formal resection. In this brief review, we will explore the recent advances in polyp detection and therapeutic options. PMID:23885138

An overview of the model integration process: From pre ...

EPA Pesticide Factsheets

Integration of models requires linking models which can be developed using different tools, methodologies, and assumptions. We performed a literature review with the aim of improving our understanding of model integration process, and also presenting better strategies for building integrated modeling systems. We identified five different phases to characterize integration process: pre-integration assessment, preparation of models for integration, orchestration of models during simulation, data interoperability, and testing. Commonly, there is little reuse of existing frameworks beyond the development teams and not much sharing of science components across frameworks. We believe this must change to enable researchers and assessors to form complex workflows that leverage the current environmental science available. In this paper, we characterize the model integration process and compare integration practices of different groups. We highlight key strategies, features, standards, and practices that can be employed by developers to increase reuse and interoperability of science software components and systems. The paper provides a review of the literature regarding techniques and methods employed by various modeling system developers to facilitate science software interoperability. The intent of the paper is to illustrate the wide variation in methods and the limiting effect the variation has on inter-framework reuse and interoperability. A series of recommendation

A photometric function of planetary surfaces for gourmets

NASA Astrophysics Data System (ADS)

Shkuratov, Yuriy; Korokhin, Viktor; Shevchenko, Vasilij; Mikhalchenko, Olga; Belskaya, Irina; Kaydash, Vadym; Videen, Gorden; Zubko, Evgenij; Velikodsky, Yuriy

2018-03-01

A new photometric model with small number of parameters is presented. The model is based on an assumption that there exist such surfaces for which spatial brightness variations caused by small topography undulations can be reproduced exactly by corresponding spatial variations of albedo. This indistinguishability results in a differential equation suggesting a new photometric function that generalizes, in particular, the Akimov disk-function. Our model provides excellent fits in a wide phase-angle range for integral observations of asteroids of different albedos. We also carried out fitting to integral observations of the Moon and Mercury, confirming difficulties in describing Mercury's phase function at large phase angles, which were also found for the Hapke model. Comparisons of global latitude and longitude trends with our model calculations have shown good coincidence for the Moon. To retrieve the lunar trends, we use the phase-ratio technique, applying it to our telescope observations. Mapping the model parameters using LROC WAC data were carried out for a region comprising the Reiner Gamma formation. This mapping allows us to calculate phase-ratio images of the region, showing at large phase angles systematically steeper phase curves of young craters and smaller steepness for the very Reiner Gamma formation.

Evolutionary heritage influences Amazon tree ecology.

PubMed

Coelho de Souza, Fernanda; Dexter, Kyle G; Phillips, Oliver L; Brienen, Roel J W; Chave, Jerome; Galbraith, David R; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E O C; Araujo-Murakami, Alejandro; Arets, Eric J M M; Aymard C, Gerardo A; Baraloto, Christopher; Barroso, Jorcely G; Bonal, Damien; Boot, Rene G A; Camargo, José L C; Comiskey, James A; Valverde, Fernando Cornejo; de Camargo, Plínio B; Di Fiore, Anthony; Elias, Fernando; Erwin, Terry L; Feldpausch, Ted R; Ferreira, Leandro; Fyllas, Nikolaos M; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N; Killeen, Timothy J; Laurance, William F; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S; Marimon-Junior, Ben H; Mendoza, Casimiro; Morandi, Paulo; Neill, David A; Vargas, Percy Núñez; Oliveira, Edmar A; Lenza, Eddie; Palacios, Walter A; Peñuela-Mora, Maria C; Pipoly, John J; Pitman, Nigel C A; Prieto, Adriana; Quesada, Carlos A; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P; Silveira, Marcos; Stropp, Juliana; Ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M F; van der Meer, Peter J; Vasquez, Rodolfo V; Vieira, Simone A; Vilanova, Emilio; Vos, Vincent A; Wang, Ophelia; Young, Kenneth R; Zagt, Roderick J; Baker, Timothy R

2016-12-14

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. © 2016 The Authors.

Isoenzyme variation in Melipona rufiventris (Hymenoptera: Apidae, Meliponina) in Minas Gerais State, Brazil.

PubMed

Costa, Ronaldo Guimarães; Tavares, Mara Garcia; Dias, Luiz Antonio dos Santos; Campos, Lucio Antonio de Oliveira

2005-02-01

The stingless bee Melipona rufiventris is an important pollinator in several Brazilian ecosystems. Originally widely distributed in Minas Gerais (MG) state, this species is becoming very rare. Therefore this species was included in the endangered species list of MG. We used isoenzyme data for a better understanding of the genetic structure of several M. rufiventris colonies. Samples of 35 colonies were collected from 12 localities and evaluated by nine enzymatic systems, which yielded 17 loci. M. rufiventris genetic variation was found to be low, typical of an endangered species. The proportion of polymorphic loci was 5.88% in both ecosystems. Only Est-4 was polymorphic in colonies from the Forest and Mdh-1 in colonies from the Cerrado. The expected heterozygosity ranged from 0.0068 in the Cerrado to 0.0078 in the Forest. Despite this, enzyme electrophoretic analyses provided a good idea of the diversity between samples from Cerrado and Forest which reinforce the existence of two different "forms" of M. rufiventris in MG, one present in the Cerrado and the other in Forest. This information is of great importance for the conservation of M. rufiventris in MG.

Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata

PubMed Central

Aplasca, Andrea C.; Iverson, John B.; Welch, Mark E.; Colosimo, Giuliano

2016-01-01

The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata) is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each). However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp) and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations. PMID:26989628

Evolutionary heritage influences Amazon tree ecology

PubMed Central

Coelho de Souza, Fernanda; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J. W.; Chave, Jerome; Galbraith, David R.; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R. Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E. O. C.; Araujo-Murakami, Alejandro; Arets, Eric J. M. M.; Aymard C, Gerardo A.; Baraloto, Christopher; Barroso, Jorcely G.; Bonal, Damien; Boot, Rene G. A.; Camargo, José L. C.; Comiskey, James A.; Valverde, Fernando Cornejo; de Camargo, Plínio B.; Di Fiore, Anthony; Erwin, Terry L.; Feldpausch, Ted R.; Ferreira, Leandro; Fyllas, Nikolaos M.; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N.; Killeen, Timothy J.; Laurance, William F.; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E.; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S.; Marimon-Junior, Ben H.; Mendoza, Casimiro; Morandi, Paulo; Neill, David A.; Vargas, Percy Núñez; Oliveira, Edmar A.; Lenza, Eddie; Palacios, Walter A.; Peñuela-Mora, Maria C.; Pipoly, John J.; Pitman, Nigel C. A.; Prieto, Adriana; Quesada, Carlos A.; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P.; Silveira, Marcos; ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M. F.; van der Meer, Peter J.; Vasquez, Rodolfo V.; Vieira, Simone A.; Vilanova, Emilio; Vos, Vincent A.; Wang, Ophelia; Young, Kenneth R.; Zagt, Roderick J.; Baker, Timothy R.

2016-01-01

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. PMID:27974517

The World Health Organization World Mental Health Survey Initiative.

PubMed

Kessler, Ronald C; Haro, Josep Maria; Heeringa, Steven G; Pennell, Beth-Ellen; Ustün, T Bedirhan

2006-01-01

To present an overview of the World Health Organization World Mental Health (WMH) Survey Initiative. The discussion draws on knowledge gleaned from the authors' participation as principals in WMH. WMH has carried out community epidemiological surveys in more than two dozen countries with more than 200,000 completed interviews. Additional surveys are in progress. Clinical reappraisal studies embedded in WMH surveys have been used to develop imputation rules to adjust prevalence estimates for within- and between-country variation in accuracy. WMH interviews include detailed information about sub-threshold manifestations to address the problem of rigid categorical diagnoses not applying equally to all countries. Investigations are now underway of targeted substantive issues. Despite inevitable limitations imposed by existing diagnostic systems and variable expertise in participating countries, WMH has produced an unprecedented amount of high-quality data on the general population cross-national epidemiology of mental disorders. WMH collaborators are in thoughtful and subtle investigations of cross-national variation in validity of diagnostic assessments and a wide range of important substantive topics. Recognizing that WMH is not definitive, finally, insights from this round of surveys are being used to carry out methodological studies aimed at improving the quality of future investigations.

He nui na ala e hiki aku ai: Factors Influencing Phonetic Variation in the Hawaiian Word "keia"

ERIC Educational Resources Information Center

Drager, Katie; Comstock, Bethany Kaleialohapau'ole Chun; Kneubuhl, Hina Puamohala

2017-01-01

Apart from a handful of studies (e.g., Kinney 1956), linguists know little about what variation exists in Hawaiian and what factors constrain the variation. In this paper, we present an analysis of phonetic variation in the word "keia," meaning "this," examining the social, linguistic, and probabilistic factors that constrain…

Detection of artifacts from high energy bursts in neonatal EEG.

PubMed

Bhattacharyya, Sourya; Biswas, Arunava; Mukherjee, Jayanta; Majumdar, Arun Kumar; Majumdar, Bandana; Mukherjee, Suchandra; Singh, Arun Kumar

2013-11-01

Detection of non-cerebral activities or artifacts, intermixed within the background EEG, is essential to discard them from subsequent pattern analysis. The problem is much harder in neonatal EEG, where the background EEG contains spikes, waves, and rapid fluctuations in amplitude and frequency. Existing artifact detection methods are mostly limited to detect only a subset of artifacts such as ocular, muscle or power line artifacts. Few methods integrate different modules, each for detection of one specific category of artifact. Furthermore, most of the reference approaches are implemented and tested on adult EEG recordings. Direct application of those methods on neonatal EEG causes performance deterioration, due to greater pattern variation and inherent complexity. A method for detection of a wide range of artifact categories in neonatal EEG is thus required. At the same time, the method should be specific enough to preserve the background EEG information. The current study describes a feature based classification approach to detect both repetitive (generated from ECG, EMG, pulse, respiration, etc.) and transient (generated from eye blinking, eye movement, patient movement, etc.) artifacts. It focuses on artifact detection within high energy burst patterns, instead of detecting artifacts within the complete background EEG with wide pattern variation. The objective is to find true burst patterns, which can later be used to identify the Burst-Suppression (BS) pattern, which is commonly observed during newborn seizure. Such selective artifact detection is proven to be more sensitive to artifacts and specific to bursts, compared to the existing artifact detection approaches applied on the complete background EEG. Several time domain, frequency domain, statistical features, and features generated by wavelet decomposition are analyzed to model the proposed bi-classification between burst and artifact segments. A feature selection method is also applied to select the feature subset producing highest classification accuracy. The suggested feature based classification method is executed using our recorded neonatal EEG dataset, consisting of burst and artifact segments. We obtain 78% sensitivity and 72% specificity as the accuracy measures. The accuracy obtained using the proposed method is found to be about 20% higher than that of the reference approaches. Joint use of the proposed method with our previous work on burst detection outperforms reference methods on simultaneous burst and artifact detection. As the proposed method supports detection of a wide range of artifact patterns, it can be improved to incorporate the detection of artifacts within other seizure patterns and background EEG information as well. © 2013 Elsevier Ltd. All rights reserved.

Allozyme variation in spineless Pejibaye (Bactris gasipaes Kunth)

USDA-ARS?s Scientific Manuscript database

Isozyme variation was studied in 161 accessions of pineapple including four species of Ananas and one of Pseudananas. Six enzyme systems (ADH, GPI, PGM, SKDH, TPI, UGPP) involving seven putative loci revealed 35 electromorphs . Considerable variation exists within and between species of Ananas. Sixt...

Behavioral Indicators of Legal and Illegal Gun Carrying

DTIC Science & Technology

2015-05-01

wide variety of handguns , in a wide variety of sizes and shapes, made of a wide variety of materials , and this variation is likely to have a subtle...Under Clothing/Belt ..................................................................................................... 23 Concealment of Handgun ...in Center of Chest ..................................................................................... 24 Concealment of Handgun in Groin Area with

Foundations of planetary quarantine.

NASA Technical Reports Server (NTRS)

Hall, L. B.; Lyle, R. G.

1971-01-01

Discussion of some of the problems in microbiology and engineering involved in the implementation of planetary quarantine. It is shown that the solutions require new knowledge in both disciplines for success at low cost in terms of both monetary outlay and man's further exploration of the planets. A related problem exists in that engineers are not accustomed to the wide variation of biological data and microbiologists must learn to work and think in more exact terms. Those responsible for formulating or influencing national and international policies must walk a tightrope with delicate balance between unnecessarily stringent requirements for planetary quarantine on the one hand and prevention of contamination on the other. The success of planetary quarantine measures can be assured only by rigorous measures, each checked, rechecked, and triple-checked to make sure that no errors have been made and that no factor has been overlooked.

Results from the CACTI experiment: Air-Cerenkov and particle measurements of PeV air showers at Los Alamos

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paling, S.; Hillas, A.M.; Berley, D.

1997-07-01

An array of six wide angle Cerenkov detectors was constructed amongst the scintillator and muon detectors of the CYGNUS II array at Los Alamos National Laboratory to investigate cosmic ray composition in the PeV region through measurements of the shape of Cerenkov lateral distributions. Data were collected during clear, moonless nights over three observing periods in 1995. Estimates of depths of shower maxima determined from the recorded Cerenkov lateral distributions align well with existing results at higher energies and suggest a mixed to heavy composition in the PeV region with no significant variation observed around the knee. The accuracy ofmore » composition determination is limited by uncertainties in the expected levels of depth of maximum predicted using different Monte-Carlo shower simulation models.« less

Variations of Thermal Pressure for Solids along the Principal Hugoniot

NASA Astrophysics Data System (ADS)

Gong, Zizheng; Yu, Hui; Deng, Liwei; Zhang, Li; Yang, Jinke

2006-07-01

The behavior of thermal pressure PTH for all kinds of solid materials was investigated using the lattice dynamics theory up to 500GPa. The results show that for most metals, ionic crystal and minerals, the thermal pressure is approximately independent on volume, whereas the thermal pressure of a few solids has strong dependence on volume. The volume dependence of thermal pressure has no relation with the chemical bonding type and crystal structure of materials, but is correlated with the Debye temperature ΘD and the second Grüneisen parameter q. The ratio of the thermal pressure to the total pressure (PTH /PTotal) along the Hugoniot keeps constant over a wide compression range, not only for non-porous materials but also for porous materials within certain porosity, which could explain the existence of material constant parameter β along solid Hugoniot.

Innovations in Food Chemistry and Processing to Enhance the Nutrient Profile of the White Potato in All Forms12

PubMed Central

Decker, Eric A.; Ferruzzi, Mario G.

2013-01-01

Potatoes can be an important part of a balanced diet because they are an excellent source of many nutrients, including nutrients that are commonly underconsumed (dietary fiber and potassium). Despite the existence of many positive nutrients in potatoes, the popular press has recently aligned potatoes, and particularly fried potatoes, with an unhealthy diet. This article examines the nutritional content of potatoes and how these nutrients are affected by cooking and other food-processing operations. In addition, it examines how the nutritional content of potatoes is altered by cooking methods and how fried potatoes can have wide variations in fat content depending on the cooking method. Finally, the potential of new food-processing technologies to improve the nutritional content of cooked potatoes is evaluated. PMID:23674803

Genome-wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds

USDA-ARS?s Scientific Manuscript database

Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, are known to be associated with both diseases and phenotypic traits. Deeply sequenced genomes are often u...

On the UV/Optical Variation in NGC 5548: New Evidence Against the Reprocessing Diagram

NASA Astrophysics Data System (ADS)

Zhu, Fei-Fan; Wang, Jun-Xian; Cai, Zhen-Yi; Sun, Yu-Han; Sun, Mou-Yuan; Zhang, Ji-Xian

2018-06-01

The reprocessing scenario is widely adopted in literature to explain the observed tight inter-band correlation and short lags in the UV/optical variations of active galactic nuclei (AGNs). In this work we look into the color variability of the famous Seyfert galaxy NGC 5548 with high-quality Swift multi-band UV/optical light curves. We find the color variation of NGC 5548 is clearly timescale-dependent, in a way that it is more prominent on shorter timescales. This is similar to that previously detected in quasar samples, but for the first time in an individual AGN. We show that while a reprocessing model with strict assumptions on the driving source and the disk size can apparently match the observed light curves and inter-band lags, it fails to reproduce the observed timescale dependency in the color variation. Such discrepancy raises a severe challenge to, and can hardly be reconciled under the widely accepted reprocessing diagram. It also demonstrates that the timescale dependency of the color variation is uniquely powerful in probing the physics behind AGN UV/optical variations.

2D PWV monitoring of a wide and orographically complex area with a low dense GNSS network

NASA Astrophysics Data System (ADS)

Ferrando, Ilaria; Federici, Bianca; Sguerso, Domenico

2018-04-01

This study presents an innovative procedure to monitor the precipitable water vapor (PWV) content of a wide and orographically complex area with low-density networks. The procedure, termed G4M (global navigation satellite system, GNSS, for Meteorology), has been developed in a geographic information system (GIS) environment using the free and open source GRASS GIS software (https://grass.osgeo.org). The G4M input data are zenith total delay estimates obtained from GNSS permanent stations network adjustment and pressure ( P) and temperature ( T) observations using existing infrastructure networks with different geographic distributions in the study area. In spite of the wide sensor distribution, the procedure produces 2D maps with high spatiotemporal resolution (up to 250 m and 6 min) based on a simplified mathematical model including data interpolation, which was conceived by the authors to describe the atmosphere's physics. In addition to PWV maps, the procedure provides ΔPWV and heterogeneity index maps: the former represents PWV variations with respect to a "calm" moment, which are useful for monitoring the PWV evolution; and the latter are promising indicators to localize severe meteorological events in time and space. This innovative procedure is compared with meteorological simulations in this paper; in addition, an application to a severe event that occurred in Genoa (Italy) is presented.[Figure not available: see fulltext.

Clear: Composition of Likelihoods for Evolve and Resequence Experiments.

PubMed

Iranmehr, Arya; Akbari, Ali; Schlötterer, Christian; Bafna, Vineet

2017-06-01

The advent of next generation sequencing technologies has made whole-genome and whole-population sampling possible, even for eukaryotes with large genomes. With this development, experimental evolution studies can be designed to observe molecular evolution "in action" via evolve-and-resequence (E&R) experiments. Among other applications, E&R studies can be used to locate the genes and variants responsible for genetic adaptation. Most existing literature on time-series data analysis often assumes large population size, accurate allele frequency estimates, or wide time spans. These assumptions do not hold in many E&R studies. In this article, we propose a method-composition of likelihoods for evolve-and-resequence experiments (Clear)-to identify signatures of selection in small population E&R experiments. Clear takes whole-genome sequences of pools of individuals as input, and properly addresses heterogeneous ascertainment bias resulting from uneven coverage. Clear also provides unbiased estimates of model parameters, including population size, selection strength, and dominance, while being computationally efficient. Extensive simulations show that Clear achieves higher power in detecting and localizing selection over a wide range of parameters, and is robust to variation of coverage. We applied the Clear statistic to multiple E&R experiments, including data from a study of adaptation of Drosophila melanogaster to alternating temperatures and a study of outcrossing yeast populations, and identified multiple regions under selection with genome-wide significance. Copyright © 2017 by the Genetics Society of America.

Perspectives of methods of laser monitoring of the atmosphere and sea surface

NASA Astrophysics Data System (ADS)

Pashayev, Arif; Tunaboylu, Bahadir; Usta, Metin; Sadixov, Ilham; Allahverdiyev, Kerim

2016-01-01

Laser monitoring (remote sensing) may be considered as the science of collecting and interpreting information about the atmosphere, earth and sea using sensors on earth, on platforms in our atmosphere (airplanes, balloons) or in space (satellites) without being in direct physical contact with them. Remote sensing by LIDARs (Light Identification Detection and Ranging) has wide applications as technique to probe the Earth's atmosphere, ocean and land surfaces. LIDARs are widely used to get knowledge of spatial and temporal variations in meteorological quantities (e.g. temperature, humidity, clouds and aerosol properties) and to monitor the changes in these quantities on different timescales. Subject of the present work is quite wide. It is rather difficult to perform analysis and to provide full knowledge about existing information. In the present work, in addition to the literature data, the information will be provided also about KA-09 aerosol LIDAR developed at the Marmara Research Centre of TÜBITAK (Turkish Scientific and technological Research Council) and also about KA-14 LIDAR developed at the National Aviation Academy of Azerbaijan for remote sensing of contaminations on water surfaces taking place during oil-gas production. The main goal of this paper is to give students insight in different remote sensing instruments and techniques (including their perspectives) that are used for the derivation of meteorological quantities and obtaining the information about water surface.

Novel Loci Associated with PR Interval in a Genome-Wide Association Study of Ten African American Cohorts

PubMed Central

Butler, Anne M.; Yin, Xiaoyan; Evans, Daniel S.; Nalls, Michael A.; Smith, Erin N.; Tanaka, Toshiko; Li, Guo; Buxbaum, Sarah G.; Whitsel, Eric A.; Alonso, Alvaro; Arking, Dan E.; Benjamin, Emelia J.; Berenson, Gerald S.; Bis, Josh C.; Chen, Wei; Deo, Rajat; Ellinor, Patrick T.; Heckbert, Susan R.; Heiss, Gerardo; Hsueh, Wen-Chi; Keating, Brendan J.; Kerr, Kathleen F.; Li, Yun; Limacher, Marian C.; Liu, Yongmei; Lubitz, Steven A.; Marciante, Kristin D.; Mehra, Reena; Meng, Yan A.; Newman, Anne B.; Newton-Cheh, Christopher; North, Kari E.; Palmer, Cameron D.; Psaty, Bruce M.; Quibrera, P. Miguel; Redline, Susan; Reiner, Alex P.; Rotter, Jerome I.; Schnabel, Renate B.; Schork, Nicholas J.; Singleton, Andrew B.; Smith, J. Gustav; Soliman, Elsayed Z.; Srinivasan, Sathanur R.; Zhang, Zhu-ming; Zonderman, Alan B.; Ferrucci, Luigi; Murray, Sarah S.; Evans, Michele K.; Sotoodehnia, Nona; Magnani, Jared W.; Avery, Christy L.

2013-01-01

Background The PR interval (PR) as measured by the resting, standard 12-lead electrocardiogram (ECG) reflects the duration of atrial/atrioventricular nodal depolarization. Substantial evidence exists for a genetic contribution to PR, including genome-wide association studies that have identified common genetic variants at nine loci influencing PR in populations of European and Asian descent. However, few studies have examined loci associated with PR in African Americans. Methods and Results We present results from the largest genome-wide association study to date of PR in 13,415 adults of African descent from ten cohorts. We tested for association between PR (ms) and approximately 2.8 million genotyped and imputed single nucleotide polymorphisms. Imputation was performed using HapMap 2 YRI and CEU panels. Study-specific results, adjusted for global ancestry and clinical correlates of PR, were meta-analyzed using the inverse variance method. Variation in genome-wide test statistic distributions was noted within studies (lambda range: 0.9–1.1), although not after genomic control correction was applied to the overall meta-analysis (lambda: 1.008). In addition to generalizing previously reported associations with MEIS1, SCN5A, ARHGAP24, CAV1, and TBX5 to African American populations at the genome-wide significance level (P<5.0×10−8), we also identified a novel locus: ITGA9, located in a region previously implicated in SCN5A expression. The 3p21 region harboring SCN5A also contained two additional independent secondary signals influencing PR (P<5.0×10−8). Conclusions This study demonstrates the ability to map novel loci in African Americans as well as the generalizability of loci associated with PR across populations of African, European and Asian descent. PMID:23139255

Dental occlusion, body posture and temporomandibular disorders: where we are now and where we are heading for.

PubMed

Manfredini, D; Castroflorio, T; Perinetti, G; Guarda-Nardini, L

2012-06-01

The aim of this investigation was to perform a review of the literature dealing with the issue of relationships between dental occlusion, body posture and temporomandibular disorders (TMD). A search of the available literature was performed to determine what the current evidence is regarding: (i) The physiology of the dental occlusion-body posture relationship, (ii) The relationship of these two topics with TMD and (iii) The validity of the available clinical and instrumental devices (surface electromyography, kinesiography and postural platforms) to measure the dental occlusion-body posture-TMD relationship. The available posturographic techniques and devices have not consistently found any association between body posture and dental occlusion. This outcome is most likely due to the many compensation mechanisms occurring within the neuromuscular system regulating body balance. Furthermore, the literature shows that TMD are not often related to specific occlusal conditions, and they also do not have any detectable relationships with head and body posture. The use of clinical and instrumental approaches for assessing body posture is not supported by the wide majority of the literature, mainly because of wide variations in the measurable variables of posture. In conclusion, there is no evidence for the existence of a predictable relationship between occlusal and postural features, and it is clear that the presence of TMD pain is not related with the existence of measurable occluso-postural abnormalities. Therefore, the use instruments and techniques aiming to measure purported occlusal, electromyographic, kinesiographic or posturographic abnormalities cannot be justified in the evidence-based TMD practice. © 2012 Blackwell Publishing Ltd.

Temporal variations of cosmic rays over a variety of time scales

NASA Technical Reports Server (NTRS)

Jokipii, J. R.; Marti, K.

1986-01-01

The variation of the intensity of Galactic cosmic rays in the inner solar system over a wide variety of time scales is discussed, and the generally accepted physical model which can account quantitatively for these modulations is reviewed. The use of direct measurements and of nuclear reactions to study the temporal intensity variations is summarized. It is demonstrated that all of the observed variations could easily be the result of solar variations on long and short time scales.

Wide-band profile domain pulsar timing analysis

NASA Astrophysics Data System (ADS)

Lentati, L.; Kerr, M.; Dai, S.; Hobson, M. P.; Shannon, R. M.; Hobbs, G.; Bailes, M.; Bhat, N. D. Ramesh; Burke-Spolaor, S.; Coles, W.; Dempsey, J.; Lasky, P. D.; Levin, Y.; Manchester, R. N.; Osłowski, S.; Ravi, V.; Reardon, D. J.; Rosado, P. A.; Spiewak, R.; van Straten, W.; Toomey, L.; Wang, J.; Wen, L.; You, X.; Zhu, X.

2017-04-01

We extend profile domain pulsar timing to incorporate wide-band effects such as frequency-dependent profile evolution and broad-band shape variation in the pulse profile. We also incorporate models for temporal variations in both pulse width and in the separation in phase of the main pulse and interpulse. We perform the analysis with both nested sampling and Hamiltonian Monte Carlo methods. In the latter case, we introduce a new parametrization of the posterior that is extremely efficient in the low signal-to-noise regime and can be readily applied to a wide range of scientific problems. We apply this methodology to a series of simulations, and to between seven and nine years of observations for PSRs J1713+0747, J1744-1134 and J1909-3744 with frequency coverage that spans 700-3600 Mhz. We use a smooth model for profile evolution across the full frequency range, and compare smooth and piecewise models for the temporal variations in dispersion measure (DM). We find that the profile domain framework consistently results in improved timing precision compared to the standard analysis paradigm by as much as 40 per cent for timing parameters. Incorporating smoothness in the DM variations into the model further improves timing precision by as much as 30 per cent. For PSR J1713+0747, we also detect pulse shape variation uncorrelated between epochs, which we attribute to variation intrinsic to the pulsar at a level consistent with previously published analyses. Not accounting for this shape variation biases the measured arrival times at the level of ˜30 ns, the same order of magnitude as the expected shift due to gravitational waves in the pulsar timing band.

TRY – a global database of plant traits

PubMed Central

Kattge, J; Díaz, S; Lavorel, S; Prentice, I C; Leadley, P; Bönisch, G; Garnier, E; Westoby, M; Reich, P B; Wright, I J; Cornelissen, J H C; Violle, C; Harrison, S P; Van Bodegom, P M; Reichstein, M; Enquist, B J; Soudzilovskaia, N A; Ackerly, D D; Anand, M; Atkin, O; Bahn, M; Baker, T R; Baldocchi, D; Bekker, R; Blanco, C C; Blonder, B; Bond, W J; Bradstock, R; Bunker, D E; Casanoves, F; Cavender-Bares, J; Chambers, J Q; Chapin, F S; Chave, J; Coomes, D; Cornwell, W K; Craine, J M; Dobrin, B H; Duarte, L; Durka, W; Elser, J; Esser, G; Estiarte, M; Fagan, W F; Fang, J; Fernández-Méndez, F; Fidelis, A; Finegan, B; Flores, O; Ford, H; Frank, D; Freschet, G T; Fyllas, N M; Gallagher, R V; Green, W A; Gutierrez, A G; Hickler, T; Higgins, S I; Hodgson, J G; Jalili, A; Jansen, S; Joly, C A; Kerkhoff, A J; Kirkup, D; Kitajima, K; Kleyer, M; Klotz, S; Knops, J M H; Kramer, K; Kühn, I; Kurokawa, H; Laughlin, D; Lee, T D; Leishman, M; Lens, F; Lenz, T; Lewis, S L; Lloyd, J; Llusià, J; Louault, F; Ma, S; Mahecha, M D; Manning, P; Massad, T; Medlyn, B E; Messier, J; Moles, A T; Müller, S C; Nadrowski, K; Naeem, S; Niinemets, Ü; Nöllert, S; Nüske, A; Ogaya, R; Oleksyn, J; Onipchenko, V G; Onoda, Y; Ordoñez, J; Overbeck, G; Ozinga, W A; Patiño, S; Paula, S; Pausas, J G; Peñuelas, J; Phillips, O L; Pillar, V; Poorter, H; Poorter, L; Poschlod, P; Prinzing, A; Proulx, R; Rammig, A; Reinsch, S; Reu, B; Sack, L; Salgado-Negret, B; Sardans, J; Shiodera, S; Shipley, B; Siefert, A; Sosinski, E; Soussana, J-F; Swaine, E; Swenson, N; Thompson, K; Thornton, P; Waldram, M; Weiher, E; White, M; White, S; Wright, S J; Yguel, B; Zaehle, S; Zanne, A E; Wirth, C

2011-01-01

Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

PubMed Central

Wang, Jing; Street, Nathaniel R.; Scofield, Douglas G.; Ingvarsson, Pär K.

2016-01-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. PMID:26721855

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

PubMed

Wang, Jing; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

2016-03-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. Copyright © 2016 by the Genetics Society of America.

Estimation of water table based on geomorphologic and geologic conditions using public database of geotechnical information over Japan

NASA Astrophysics Data System (ADS)

Koshigai, Masaru; Marui, Atsunao

Water table provides important information for the evaluation of groundwater resource. Recently, the estimation of water table in wide area is required for effective evaluation of groundwater resources. However, evaluation process is met with difficulties due to technical and economic constraints. Regression analysis for the prediction of groundwater levels based on geomorphologic and geologic conditions is considered as a reliable tool for the estimation of water table of wide area. Data of groundwater levels were extracted from the public database of geotechnical information. It was observed that changes in groundwater level depend on climate conditions. It was also observed and confirmed that there exist variations of groundwater levels according to geomorphologic and geologic conditions. The objective variable of the regression analysis was groundwater level. And the explanatory variables were elevation and the dummy variable consisting of group number. The constructed regression formula was significant according to the determination coefficients and analysis of the variance. Therefore, combining the regression formula and mesh map, the statistical method to estimate the water table based on geomorphologic and geologic condition for the whole country could be established.

Genome Variation Within Triticale in Comparison to its Wheat and Rye Progenitors

USDA-ARS?s Scientific Manuscript database

Genome variation in the intergeneric wheat-rye hybrid triticale (X Triticosecale Wittmack) has been a puzzle to scientists and plant breeders since the first triticale was synthesized. The existence of unexplained genetic variation in triticale as compared to the parents has been a hindrance to bre...

Gravel road paving guidelines.

DOT National Transportation Integrated Search

2016-11-01

The percentage of gravel roads in rural areas in Kansas is higher than most states. A wide variation of traffic volumes : across different regions and variations of local conditions and scenarios present a great challenge for local agencies to determ...

Solar tri-diurnal variation of cosmic rays in a wide range of rigidity

NASA Technical Reports Server (NTRS)

Mori, S.; Ueno, H.; Fujii, Z.; Morishita, I.; Nagashima, K.

1985-01-01

Solar tri-diurnal variations of cosmic rays have been analyzed in a wide range of rigidity, using data from neutron monitors, and the surface and underground muon telescopes for the period 1978-1983. The rigidity spectrum of the anisotropy in space is assumed to be of power-exponential type as (P/gamma P sub o) to the gamma exp (gamma-P/P sub o). By means of the best-fit method between the observed and the expected variations, it is obtained that the spectrum has a peak at P (=gamma P sub o) approx = 90 GV, where gamma=approx 3.0 and P sub o approx. 30 GV. The phase in space of the tri-diurnal variation is also obtained as 7.0 hr (15 hr and 23 hr LT), which is quite different from that of approx. 1 hr. arising from the axisymmetric distribution of cosmic rays with respect to the IMF.

The 27-day versus 13.5-day variations in the solar Lyman-alpha radiation and the radio wave absorption in the lower ionosphere over Europe

NASA Technical Reports Server (NTRS)

Delamorena, B. A.; Lastovicka, Jan; Rapoport, Z. TS.; Alberca, L.

1989-01-01

In order to clarify the question of solar periods in absorption, the pattern was studied of the solar Lyman-alpha radiation (the principal ionizing agent of the lower ionosphere) and of the radio wave absorption at five widely spaced places in Europe. When the solar Lyman-alpha flux variability is very well developed, then it dominates in the lower ionospheric variability. The most pronounced Lyman-alpha variation on time scale day-month is the solar rotation variation (about 27 days). When the Lyman-alpha variability is developed rather poorly, as it is typical for periods dominated by the 13.5 day variability, then the lower ionospheric variability appears to be dominated by variations of meteorological origin. The conclusions hold for all five widely spaced placed in Europe.

Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek’s disease

USDA-ARS?s Scientific Manuscript database

Background: Copy number variation (CNV) is a major source of genome polymorphism that directly contributes to phenotypic variation such as resistance to infectious diseases. Lines 63 and 72 are two highly inbred experimental chicken lines that differ greatly in susceptibility to Marek’s disease (MD)...

Geographic variation in health insurance benefits in Qianjiang District, China: a cross-sectional study.

PubMed

Wu, Yue; Zhang, Liang; Liu, Xuejiao; Ye, Ting; Wang, Yongfei

2018-02-05

Health insurance contributes to reducing the economic burden of disease and improving access to healthcare. In 2016, the Chinese government announced the integration of the New Cooperative Medical Scheme (NCMS) and Urban Resident Basic Medical Insurance (URBMI) to reduce system segmentation. Nevertheless, it was unclear whether there would be any geographic variation in health insurance benefits if the two types of insurance were integrated. The aim of this study was to identify the potential geographic variation in health insurance benefits and the related contributing factors. This cross-sectional study was carried out in Qianjiang District, where the NCMS and URBMI were integrated into Urban and Rural Resident Basic Medical Insurance Scheme (URRBMI) in 2010. All beneficiaries under the URRBMI were hospitalized at least once in 2013, totaling 445,254 persons and 65,877 person-times, were included in this study. Town-level data on health insurance benefits, healthcare utilization, and socioeconomic and geographical characteristics were collected through health insurance system, self-report questionnaires, and the 2014 Statistical Yearbook of Qianjiang District. A simplified Theil index at town level was calculated to measure geographic variation in health insurance benefits. Colored maps were created to visualize the variation in geographic distribution of benefits. The effects of healthcare utilization and socioeconomic and geographical characteristics on geographic variation in health insurance benefits were estimated with a multiple linear regression analysis. Different Theil index values were calculated for different towns, and the Theil index values for compensation by person-times and amount were 2.5028 and 1.8394 in primary healthcare institutions and 1.1466 and 0.9204 in secondary healthcare institutions. Healthcare-seeking behavior and economic factors were positively associated with health insurance benefits in compensation by person-times significantly, meanwhile, geographical accessibility and economic factors had positive effects (p < 0.05). The geographic variation in health insurance benefits widely existed in Qianjiang District and the distribution of health insurance benefits for insured inpatients in primary healthcare institutions was distinctly different from that in secondary healthcare institutions. When combining the NRCM and URMIS in China, the geographical accessibility, healthcare-seeking behavior and economic factors required significant attention.

Aberrant clones: Birth order generates life history diversity in Greater Duckweed, Spirodela polyrhiza.

PubMed

Mejbel, Hebah S; Simons, Andrew M

2018-02-01

Environmental unpredictability is known to result in the evolution of bet-hedging traits. Variable dormancy enhances survival through harsh conditions, and is widely cited as a diversification bet-hedging trait. The floating aquatic plant, Spirodela polyrhiza (Greater Duckweed), provides an opportunity to study diversification because although partially reliable seasonal cues exist, its growing season is subject to an unpredictable and literally "hard" termination when the surface water freezes, and overwinter survival depends on a switch from production of normal daughter fronds to production of dense, sinking "turions" prior to freeze-over. The problem for S. polyrhiza is that diversified dormancy behavior must be generated among clonally produced, genetically identical offspring. Variation in phenology has been observed in the field, but its sources are unknown. Here, we investigate sources of phenological variation in turion production , and test the hypothesis that diversification in turion phenology is generated within genetic lineages through effects of parental birth order. As expected, phenotypic plasticity to temperature is expressed along a thermal gradient; more interestingly, parental birth order was found to have a significant and strong effect on turion phenology: Turions are produced earlier by late birth-order parents. These results hold regardless of whether turion phenology is measured as first turion birth order, time to first turion, or turion frequency. This study addresses a question of current interest on potential mechanisms generating diversification, and suggests that consistent phenotypic differences across birth orders generate life history variation.

Genetic diversity of Candidatus Liberibacter asiaticus based on two hypervariable effector genes in Thailand.

PubMed

Puttamuk, Thamrongjet; Zhou, Lijuan; Thaveechai, Niphone; Zhang, Shouan; Armstrong, Cheryl M; Duan, Yongping

2014-01-01

Huanglongbing (HLB), also known as citrus greening, is one of the most destructive diseases of citrus worldwide. HLB is associated with three species of 'Candidatus Liberibacter' with 'Ca. L. asiaticus' (Las) being the most widely distributed around the world, and the only species detected in Thailand. To understand the genetic diversity of Las bacteria in Thailand, we evaluated two closely-related effector genes, lasAI and lasAII, found within the Las prophages from 239 infected citrus and 55 infected psyllid samples collected from different provinces in Thailand. The results indicated that most of the Las-infected samples collected from Thailand contained at least one prophage sequence with 48.29% containing prophage 1 (FP1), 63.26% containing prophage 2 (FP2), and 19.38% containing both prophages. Interestingly, FP2 was found to be the predominant population in Las-infected citrus samples while Las-infected psyllids contained primarily FP1. The multiple banding patterns that resulted from amplification of lasAI imply extensive variation exists within the full and partial repeat sequence while the single band from lasAII indicates a low amount of variation within the repeat sequence. Phylogenetic analysis of Las-infected samples from 22 provinces in Thailand suggested that the bacterial pathogen may have been introduced to Thailand from China and the Philippines. This is the first report evaluating the genetic variation of a large population of Ca. L. asiaticus infected samples in Thailand using the two effector genes from Las prophage regions.

Colonizing the world in spite of reduced MHC variation

USGS Publications Warehouse

Gangoso, L.; Alcaide, M.; Grande, J.M.; Muñoz, J.; Talbot, Sandra L.; Sonsthagen, Sarah A.; Sage, Kevin; Figuerola, J.

2012-01-01

Reduced immune gene diversity is thought to negatively affect the capacity of organisms to adapt to pathogen challenges, which represent a major force in natural selection. Genes of the Major Histocompatibility Complex (MHC) are the most widely invoked adaptive loci in conservation biology, and have become the most popular genetic markers to investigate pathogen-host interactions in vertebrates. Although MHC genes are the most polymorphic genes described in the vertebrate genome, the extent to which MHC diversity determines the long-term persistence of populations is, unclear and often debated, as recent studies have documented the occurrence of natural populations thriving even after a depletion of MHC diversity caused by genetic drift. Here, we show that some phylogenetically related species belonging to the Falco genus (Aves: Falconidae) present a dramatically low MHC variability that has not precluded, nevertheless, the successful colonization of almost all existing regions and habitats worldwide. We found evidence for two remarkably different patterns of MHC variation within the genus. While kestrels show a high MHC variation according to the general theory, falcons exhibit an ancestrally low intra- and inter-specific MHC allelic diversity. We provide compelling evidence that this pattern is not caused by the degeneration of functional genes into pseudogenes, the inadvertent analyses of paralogous MHC genes, or the devastating action of genetic drift. Instead, our results strongly support the idea of an evolutionary transition driven and maintained by natural selection from primarily highly variable towards low polymorphic, but functional and expressed, MHC genes with species-specific pathogen-recognition capabilities.

Quantitative contrast-enhanced ultrasound imaging: a review of sources of variability

PubMed Central

Tang, M.-X.; Mulvana, H.; Gauthier, T.; Lim, A. K. P.; Cosgrove, D. O.; Eckersley, R. J.; Stride, E.

2011-01-01

Ultrasound provides a valuable tool for medical diagnosis offering real-time imaging with excellent spatial resolution and low cost. The advent of microbubble contrast agents has provided the additional ability to obtain essential quantitative information relating to tissue vascularity, tissue perfusion and even endothelial wall function. This technique has shown great promise for diagnosis and monitoring in a wide range of clinical conditions such as cardiovascular diseases and cancer, with considerable potential benefits in terms of patient care. A key challenge of this technique, however, is the existence of significant variations in the imaging results, and the lack of understanding regarding their origin. The aim of this paper is to review the potential sources of variability in the quantification of tissue perfusion based on microbubble contrast-enhanced ultrasound images. These are divided into the following three categories: (i) factors relating to the scanner setting, which include transmission power, transmission focal depth, dynamic range, signal gain and transmission frequency, (ii) factors relating to the patient, which include body physical differences, physiological interaction of body with bubbles, propagation and attenuation through tissue, and tissue motion, and (iii) factors relating to the microbubbles, which include the type of bubbles and their stability, preparation and injection and dosage. It has been shown that the factors in all the three categories can significantly affect the imaging results and contribute to the variations observed. How these factors influence quantitative imaging is explained and possible methods for reducing such variations are discussed. PMID:22866229

Composition and structure of the shallow subsurface of Ceres revealed by crater morphology

NASA Astrophysics Data System (ADS)

Bland, Michael T.; Raymond, Carol A.; Schenk, Paul M.; Fu, Roger R.; Kneissl, Thomas; Pasckert, Jan Hendrik; Hiesinger, Harry; Preusker, Frank; Park, Ryan S.; Marchi, Simone; King, Scott D.; Castillo-Rogez, Julie C.; Russell, Christopher T.

2016-07-01

Before NASA’s Dawn mission, the dwarf planet Ceres was widely believed to contain a substantial ice-rich layer below its rocky surface. The existence of such a layer has significant implications for Ceres’s formation, evolution, and astrobiological potential. Ceres is warmer than icy worlds in the outer Solar System and, if its shallow subsurface is ice-rich, large impact craters are expected to be erased by viscous flow on short geologic timescales. Here we use digital terrain models derived from Dawn Framing Camera images to show that most of Ceres’s largest craters are several kilometres deep, and are therefore inconsistent with the existence of an ice-rich subsurface. We further show from numerical simulations that the absence of viscous relaxation over billion-year timescales implies a subsurface viscosity that is at least one thousand times greater than that of pure water ice. We conclude that Ceres’s shallow subsurface is no more than 30% to 40% ice by volume, with a mixture of rock, salts and/or clathrates accounting for the other 60% to 70%. However, several anomalously shallow craters are consistent with limited viscous relaxation and may indicate spatial variations in subsurface ice content.

Single-Cell Mass Spectrometry Reveals Changes in Lipid and Metabolite Expression in RAW 264.7 Cells upon Lipopolysaccharide Stimulation

NASA Astrophysics Data System (ADS)

Yang, Bo; Patterson, Nathan Heath; Tsui, Tina; Caprioli, Richard M.; Norris, Jeremy L.

2018-05-01

It has been widely recognized that individual cells that exist within a large population of cells, even if they are genetically identical, can have divergent molecular makeups resulting from a variety of factors, including local environmental factors and stochastic processes within each cell. Presently, numerous approaches have been described that permit the resolution of these single-cell expression differences for RNA and protein; however, relatively few techniques exist for the study of lipids and metabolites in this manner. This study presents a methodology for the analysis of metabolite and lipid expression at the level of a single cell through the use of imaging mass spectrometry on a high-performance Fourier transform ion cyclotron resonance mass spectrometer. This report provides a detailed description of the overall experimental approach, including sample preparation as well as the data acquisition and analysis strategy for single cells. Applying this approach to the study of cultured RAW264.7 cells, we demonstrate that this method can be used to study the variation in molecular expression with cell populations and is sensitive to alterations in that expression that occurs upon lipopolysaccharide stimulation. [Figure not available: see fulltext.

Single-Cell Mass Spectrometry Reveals Changes in Lipid and Metabolite Expression in RAW 264.7 Cells upon Lipopolysaccharide Stimulation

NASA Astrophysics Data System (ADS)

Yang, Bo; Patterson, Nathan Heath; Tsui, Tina; Caprioli, Richard M.; Norris, Jeremy L.

2018-03-01

It has been widely recognized that individual cells that exist within a large population of cells, even if they are genetically identical, can have divergent molecular makeups resulting from a variety of factors, including local environmental factors and stochastic processes within each cell. Presently, numerous approaches have been described that permit the resolution of these single-cell expression differences for RNA and protein; however, relatively few techniques exist for the study of lipids and metabolites in this manner. This study presents a methodology for the analysis of metabolite and lipid expression at the level of a single cell through the use of imaging mass spectrometry on a high-performance Fourier transform ion cyclotron resonance mass spectrometer. This report provides a detailed description of the overall experimental approach, including sample preparation as well as the data acquisition and analysis strategy for single cells. Applying this approach to the study of cultured RAW264.7 cells, we demonstrate that this method can be used to study the variation in molecular expression with cell populations and is sensitive to alterations in that expression that occurs upon lipopolysaccharide stimulation. [Figure not available: see fulltext.

Composition and structure of the shallow subsurface of Ceres revealed by crater morphology

USGS Publications Warehouse

Bland, Michael T.; Carol A. Raymond,; Schenk, Paul M.; Roger R. Fu,; Thomas Kneisl,; Hendrick Pasckert, Jan; Hiesinger, Harald; Frank Preusker,; Ryan S. Park,; Simone Marchi,; Scott King,; Castillo-Rogez, Julie C.; Christopher T. Russell,

2016-01-01

Before NASA’s Dawn mission, the dwarf planet Ceres was widely believed to contain a substantial ice-rich layer below its rocky surface. The existence of such a layer has significant implications for Ceres’s formation, evolution, and astrobiological potential. Ceres is warmer than icy worlds in the outer Solar System and, if its shallow subsurface is ice-rich, large impact craters are expected to be erased by viscous flow on short geologic timescales. Here we use digital terrain models derived from Dawn Framing Camera images to show that most of Ceres’s largest craters are several kilometres deep, and are therefore inconsistent with the existence of an ice-rich subsurface. We further show from numerical simulations that the absence of viscous relaxation over billion-year timescales implies a subsurface viscosity that is at least one thousand times greater than that of pure water ice. We conclude that Ceres’s shallow subsurface is no more than 30% to 40% ice by volume, with a mixture of rock, salts and/or clathrates accounting for the other 60% to 70%. However, several anomalously shallow craters are consistent with limited viscous relaxation and may indicate spatial variations in subsurface ice content.

A novel method for detecting neutralizing antibodies against therapeutic proteins by measuring gene expression.

PubMed

Yu, Yanbin; Piddington, Christopher; Fitzpatrick, Dan; Twomey, Brian; Xu, Ren; Swanson, Steven J; Jing, Shuqian

2006-10-20

The presence of neutralizing antibodies against protein therapeutics is a concern in the biomedical field. Such antibodies not only reduce the efficacy of protein therapeutics, but also impose potential dangers to the patients receiving them. To date, a small number of in vitro cell-based bioassays for detecting neutralizing antibodies against therapeutic proteins have been developed. Most of the existing assays, however, either involve the use of radioactive materials or have limited sensitivities and/or poor specificities. With advances in mRNA profiling and detection techniques, we have established a novel and non-radioactive bioassay system using branched DNA (bDNA) technology for detecting protein-therapeutic neutralizing antibodies in patient serum. Our assay measures the variations of target gene expression that reflect the biologic effect of the therapeutic agent and the capability of the antibodies, if present, to neutralize the therapeutics. Compared with most existing assays, the new assay is more sensitive and specific, and completely eliminates the use of radioactive materials. Application of the new assay system can be widely expanded if new target genes and responding cell lines for other therapeutics are identified or engineered.

Stability of half-metallic behavior with lattice variation for Fe2-xCoxMnAl Heusler alloy

NASA Astrophysics Data System (ADS)

Jain, Vivek Kumar; Lakshmi, N.; Jain, Rakesh

2018-04-01

The electronic structure and magnetic properties with variation of lattice constant for Fe2-xCoxMnAl Heusler alloys have been studied. Total magnetic moments predicted by the Slater Pauling rule is maintained over a wide range of lattice variation for the series. Half metallic ferromagnetic nature with 100% spin polarization is observed for a lattice range from 5.40-5.70 Å, 5.35-5.55 Å, 5.30-5.60 Å and 5.25-5.55 Å respectively for x = 0.5, 1.0 1.5, 2.0. Due to the stability of half metallic character for a wide range of lattice parameters, these alloys are promising, robust materials suitable for spintronics device applications.

A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis.

PubMed

Savary, Romain; Masclaux, Frédéric G; Wyss, Tania; Droh, Germain; Cruz Corella, Joaquim; Machado, Ana Paula; Morton, Joseph B; Sanders, Ian R

2018-01-01

Arbuscular mycorrhizal fungi (AMF; phylum Gomeromycota) associate with plants forming one of the most successful microbe-plant associations. The fungi promote plant diversity and have a potentially important role in global agriculture. Plant growth depends on both inter- and intra-specific variation in AMF. It was recently reported that an unusually large number of AMF taxa have an intercontinental distribution, suggesting long-distance gene flow for many AMF species, facilitated by either long-distance natural dispersal mechanisms or human-assisted dispersal. However, the intercontinental distribution of AMF species has been questioned because the use of very low-resolution markers may be unsuitable to detect genetic differences among geographically separated AMF, as seen with some other fungi. This has been untestable because of the lack of population genomic data, with high resolution, for any AMF taxa. Here we use phylogenetics and population genomics to test for intra-specific variation in Rhizophagus irregularis, an AMF species for which genome sequence information already exists. We used ddRAD sequencing to obtain thousands of markers distributed across the genomes of 81 R. irregularis isolates and related species. Based on 6 888 variable positions, we observed significant genetic divergence into four main genetic groups within R. irregularis, highlighting that previous studies have not captured underlying genetic variation. Despite considerable genetic divergence, surprisingly, the variation could not be explained by geographical origin, thus also supporting the hypothesis for at least one AMF species of widely dispersed AMF genotypes at an intercontinental scale. Such information is crucial for understanding AMF ecology, and how these fungi can be used in an environmentally safe way in distant locations.

Mapping the natural variation in whole bone stiffness and strength across skeletal sites.

PubMed

Schlecht, Stephen H; Bigelow, Erin M R; Jepsen, Karl J

2014-10-01

Traits of the skeletal system are coordinately adjusted to establish mechanical homeostasis in response to genetic and environmental factors. Prior work demonstrated that this 'complex adaptive' process is not perfect, revealing a two-fold difference in whole bone stiffness of the tibia across a population. Robustness (specifically, total cross-sectional area relative to length) varies widely across skeletal sites and between sexes. However, it is unknown whether the natural variation in whole bone stiffness and strength also varies across skeletal sites and between men and women. We tested the hypotheses that: 1) all major long bones of the appendicular skeleton demonstrate inherent, systemic constraints in the degree to which morphological and compositional traits can be adjusted for a given robustness; and 2) these traits covary in a predictable manner independent of body size and robustness. We assessed the functional relationships among robustness, cortical area (Ct.Ar), cortical tissue mineral density (Ct.TMD), and bone strength index (BSI) across the long bones of the upper and lower limbs of 115 adult men and women. All bones showed a significant (p<0.001) positive regression between BSI and robustness after adjusting for body size, with slender bones being 1.7-2.3 times less stiff and strong in men and 1.3-2.8 times less stiff and strong in women compared to robust bones. Our findings are the first to document the natural inter-individual variation in whole bone stiffness and strength that exist within populations and that is predictable based on skeletal robustness for all major long bones. Documenting and further understanding this natural variation in strength may be critical for differentially diagnosing and treating skeletal fragility. Copyright © 2014 Elsevier Inc. All rights reserved.

Epigenetic hereditary transcription profiles III, evidence for an epigenetic network resulting in gender, tissue and age-specific variation in overall transcription

PubMed Central

Simons, Johannes WIM

2009-01-01

Background We have previously shown that deviations from the average transcription profile of a group of functionally related genes are not only heritable, but also demonstrate specific patterns associated with age, gender and differentiation, thereby implicating genome-wide nuclear programming as the cause. To determine whether these results could be reproduced, a different micro-array database (obtained from two types of muscle tissue, derived from 81 human donors aged between 16 to 89 years) was studied. Results This new database also revealed the existence of age, gender and tissue-specific features in a small group of functionally related genes. In order to further analyze this phenomenon, a method was developed for quantifying the contribution of different factors to the variability in gene expression, and for generating a database limited to residual values reflecting constitutional differences between individuals. These constitutional differences, presumably epigenetic in origin, contribute to about 50% of the observed residual variance which is connected with a network of interrelated changes in gene expression with some genes displaying a decrease or increase in residual variation with age. Conclusion Epigenetic variation in gene expression without a clear concomitant relation to gene function appears to be a widespread phenomenon. This variation is connected with interactions between genes, is gender and tissue specific and is related to cellular aging. This finding, together with the method developed for analysis, might contribute to the elucidation of the role of nuclear programming in differentiation, aging and carcinogenesis Reviewers This article was reviewed by Thiago M. Venancio (nominated by Aravind Iyer), Hua Li (nominated by Arcady Mushegian) and Arcady Mushegian and J.P.de Magelhaes (nominated by G. Church). PMID:19796384

Clinal variation or validation of a subspecies? A case study of the Graptemys nigrinoda complex (Testudines: Emydidae)

USGS Publications Warehouse

Ennen, Joshua R.; Kalis, Marley E.; Patterson, Adam L.; Kreiser, Brian R.; Lovich, Jeffrey E.; Godwin, James; Qualls, Carl P.

2014-01-01

Widely distributed species often display intraspecific morphological variation due to the abiotic and biotic gradients experienced across their ranges. Historically, in many vertebrate taxa, such as birds and reptiles, these morphological differences within a species were used to delimit subspecies. Graptemys nigrinoda is an aquatic turtle species endemic to the Mobile Bay Basin. Colour pattern and morphological variability were used to describe a subspecies (G. n. delticola) from the lower reaches of the system, although it and the nominate subspecies also reportedly intergrade over a large portion of the range. Other researchers have suggested that these morphological differences merely reflect clinal variation. Our molecular data (mtDNA) did not support the existence of the subspecies, as the haplotypes were differentiated by only a few base pairs and one haplotype was shared between the putative subspecies. While there were significant morphological and pattern differences among putative specimens of G. n. nigrinoda, G. n. delticola and G. n. nigrinoda × delticola, these differences probably represent clinal variation as they were also related to environmental variables [i.e. cumulative drainage area and drainage (categorical)]. Specimens occupying slow-current, high-turbidity river reaches (e.g. the Tensaw River) exhibited greater relative carapace heights and more dark pigmentation, while specimens occupying fast-current, clearer rivers (e.g. the upper Alabama, Cahaba and Tallapoosa rivers) exhibited lower carapace heights and more yellow pigmentation. Given the absence of clear molecular and morphological differences that are related to drainage characteristics, we suggest that there is not sufficient evidence for the recognition of G. n. delticola as a distinct subspecies.

Differential response of continental stock complexes of Atlantic salmon (Salmo salar) to the Atlantic Multidecadal Oscillation

NASA Astrophysics Data System (ADS)

Friedland, Kevin D.; Shank, Burton V.; Todd, Christopher D.; McGinnity, Philip; Nye, Janet A.

2014-05-01

Atlantic salmon, Salmo salar, in the North Atlantic are managed as a set of population complexes distributed in North America and Europe. In recent years, these complexes have experienced reduced marine survival and many populations within the complexes are at risk, especially those at the southern ends of the species amphi-Atlantic range. Atlantic salmon is an anadromous fish dividing its life history between residence in freshwater and the marine environment. The freshwater portion of the life history includes spawning and the rearing of juveniles where in-river production has tended to be relatively stable, whereas the first year at sea, termed the post-smolt year, is characterized by more variable rates of mortality. Although their habitats are widely separated geographically along the North Atlantic seaboards, strong recruitment coherence exists between North American and European stock complexes. This recruitment coherence is correlated with ocean temperature variation associated with the Atlantic Multidecadal Oscillation (AMO). The North Atlantic Oscillation (NAO) appears to be relatively unimportant as a driver of salmon abundance. The mechanism determining the link between AMO-related thermal variation and abundance appears to differ fundamentally for the two continental stock groupings. Whereas ocean climate variability during the first springtime months of juvenile salmon migration to sea appears to be important to the survival of North American stocks, summer climate variation appears to be central to adult recruitment variation for European stocks. This contrast in seasonal effects appears to be related to the varying roles of predation pressure and size-related mortality on the continental stock complexes. The anticipated warming due to global climate change will impose thermal conditions on salmon populations outside historical context and challenge the ability of many populations to persist.

Hospital Variation in Perioperative Complications for Laparoscopic Sleeve Gastrectomy in Michigan

PubMed Central

Pradarelli, Jason C.; Varban, Oliver A.; Ghaferi, Amir A.; Weiner, Matthew; Carlin, Arthur M.; Dimick, Justin B.

2015-01-01

Structured Abstract Background Laparoscopic sleeve gastrectomy has recently surpassed gastric bypass and laparoscopic adjustable gastric banding as the most common weight-loss procedure. Previously, substantial concerns existed regarding variation in perioperative safety with bariatric surgery. This study aimed to assess rates of perioperative complications for laparoscopic sleeve gastrectomy across hospitals and in relation to procedure volume. Study Design We analyzed 8,693 patients who underwent laparoscopic sleeve gastrectomy from 2013 through 2014 across 40 hospitals in the Michigan Bariatric Surgery Collaborative. Mixed-effects logistic regression was used to assess hospital variation in risk- and reliability-adjusted rates of overall and serious 30-day complications and their relationship with hospital annual stapling procedure volume (gastric bypass and sleeve gastrectomy). Results Overall, 5.4% of patients experienced perioperative complications. Adjusted rates of overall complications varied three-fold across hospitals, ranging from 3.6% (95% CI, 1.9–6.8%) to 11.0% (95% CI, 7.7–15.5%). Serious complications occurred in just 1.2% of patients and varied minimally. In this analysis, hospital volume was not associated with overall or serious complications. The 1 hospital with significantly lower overall complication rates was high-volume (≥125 procedures/year); however, of the 4 hospitals with significantly higher complication rates, 3 were medium-volume (50–124 procedures/year) and 1 was high-volume. The remaining hospitals were not significantly different than the cohort mean. Conclusions Serious complications among patients undergoing laparoscopic sleeve gastrectomy were relatively infrequent. Rates of overall complications varied widely across Michigan hospitals enrolled in a quality collaborative, although this variation was unrelated to volume standards required for accreditation as a comprehensive bariatric surgery center. PMID:26506567

Comparing regional infant death rates: the influence of preterm births <24 weeks of gestation.

PubMed

Smith, Lucy; Draper, Elizabeth S; Manktelow, Bradley N; Pritchard, Catherine; Field, David John

2013-03-01

To investigate regional variation in the registration of preterm births <24 weeks of gestation and the impact on infant death rates for English Primary Care Trusts (PCTs). Cohort study. England. All registered births (1 January 2005-31 December 2008) by gestational age and PCT (147 trusts) linked to infant deaths (up to 1 year of life). Late-fetal deaths at 22 and 23 weeks gestation (1 January 2005-31 December 2006). Extremely preterm (<24 weeks) birth rate per 1000 live births and percentage of births registered as live born by PCT. Infant death rate and rank of mortality for (1) all live births and (2) live births over 24 weeks gestation by PCT. Wide between-PCT variation existed in extremely preterm birth (<24 weeks) rates (per 1000 births) (90% central range (0.31, 1.91)) and percentages of births <24 weeks of gestation registered as live born (median 52.6%, 90% central range (26.3%, 79.5%)). Consequently, the percentage of infant deaths arising from these births varied (90% central range (6.7%, 31.9%)). Excluding births <24 weeks, led to significant changes in infant mortality rankings of PCTs, with a median worsening of 12 places for PCTs with low rates of live born preterm births <24 weeks of gestation compared with a median improvement of four ranks for those with higher live birth registration rates. Infant death rates in PCTs in England are influenced by variation in the registration of births where viability is uncertain. It is vital that this variation is minimised before infant mortality is used as indicator for monitoring health and performance and targeting interventions.

In vitro and ex vivo analysis of CHRNA3 and CHRNA5 haplotype expression.

PubMed

Doyle, Glenn A; Wang, Min-Jung; Chou, Andrew D; Oleynick, John U; Arnold, Steven E; Buono, Russell J; Ferraro, Thomas N; Berrettini, Wade H

2011-01-01

Genome-wide association studies implicate variations in CHRNA5 and CHRNA3 as being associated with nicotine addiction (NA). Multiple common haplotypes ("risk", "mixed" and "protective") exist in Europeans; however, high linkage disequilibrium between variations in CHRNA5 and CHRNA3 makes assigning causative allele(s) for NA difficult through genotyping experiments alone. We investigated whether CHRNA5 or CHRNA3 promoter haplotypes, associated previously with NA, might influence allelic expression levels. For in vitro analyses, promoter haplotypes were sub-cloned into a luciferase reporter vector. When assessed in BE(2)-C cells, luciferase expression was equivalent among CHRNA3 haplotypes, but the combination of deletion at rs3841324 and variation at rs503464 decreased CHRNA5 promoter-derived luciferase activity, possibly due to loss of an SP-1 and other site(s). Variation within the CHRNA5 5'UTR at rs55853698 and rs55781567 also altered luciferase expression in BE(2)-C cells. Allelic expression imbalance (AEI) from the "risk" or "protective" haplotypes was assessed in post-mortem brain tissue from individuals heterozygous at coding polymorphisms in CHRNA3 (rs1051730) or CHRNA5 (rs16969968). In most cases, equivalent allelic expression was observed; however, one individual showed CHRNA5 AEI that favored the "protective" allele and that was concordant with heterozygosity at polymorphisms ∼13.5 kb upstream of the CHRNA5 transcription start site. Putative enhancer activity from these distal promoter elements was assessed using heterologous promoter constructs. We observed no differences in promoter activity from the two distal promoter haplotypes examined, but found that the distal promoter region strongly repressed transcription. We conclude that CHRNA5 promoter variants may affect relative risk for NA in some heterozygous individuals.

Mapping the natural variation in whole bone stiffness and strength across skeletal sites

PubMed Central

Schlecht, Stephen H.; Bigelow, Erin M.R.; Jepsen, Karl J.

2016-01-01

Traits of the skeletal system are coordinately adjusted to establish mechanical homeostasis in response to genetic and environmental factors. Prior work demonstrated that this `complex adaptive' process is not perfect, revealing a two-fold difference in whole bone stiffness of the tibia across a population. Robustness (specifically, total cross-sectional area relative to length) varies widely across skeletal sites and between sexes. However, it is unknown whether the natural variation in whole bone stiffness and strength also varies across skeletal sites and between men and women. We tested the hypotheses that: 1) all major long bones of the appendicular skeleton demonstrate inherent, systemic constraints in the degree to which morphological and compositional traits can be adjusted for a given robustness; and 2) these traits covary in a predictable manner independent of body size and robustness. We assessed the functional relationships among robustness, cortical area (Ct.Ar), cortical tissue mineral density (Ct.TMD), and bone strength index (BSI) across the long bones of the upper and lower limbs of 115 adult men and women. All bones showed a significant (p < 0.001) positive regression between BSI and robustness after adjusting for body size, with slender bones being 1.7–2.3 times less stiff and strong in men and 1.3–2.8 times less stiff and strong in women compared to robust bones. Our findings are the first to document the natural inter-individual variation in whole bone stiffness and strength that exist within populations and that is predictable based on skeletal robustness for all major long bones. Documenting and further understanding this natural variation in strength may be critical for differentially diagnosing and treating skeletal fragility. PMID:24999223

Modeling Host Genetic Regulation of Influenza Pathogenesis in the Collaborative Cross

PubMed Central

Ferris, Martin T.; Aylor, David L.; Bottomly, Daniel; Whitmore, Alan C.; Aicher, Lauri D.; Bell, Timothy A.; Bradel-Tretheway, Birgit; Bryan, Janine T.; Buus, Ryan J.; Gralinski, Lisa E.; Haagmans, Bart L.; McMillan, Leonard; Miller, Darla R.; Rosenzweig, Elizabeth; Valdar, William; Wang, Jeremy; Churchill, Gary A.; Threadgill, David W.; McWeeney, Shannon K.; Katze, Michael G.; Pardo-Manuel de Villena, Fernando; Baric, Ralph S.; Heise, Mark T.

2013-01-01

Genetic variation contributes to host responses and outcomes following infection by influenza A virus or other viral infections. Yet narrow windows of disease symptoms and confounding environmental factors have made it difficult to identify polymorphic genes that contribute to differential disease outcomes in human populations. Therefore, to control for these confounding environmental variables in a system that models the levels of genetic diversity found in outbred populations such as humans, we used incipient lines of the highly genetically diverse Collaborative Cross (CC) recombinant inbred (RI) panel (the pre-CC population) to study how genetic variation impacts influenza associated disease across a genetically diverse population. A wide range of variation in influenza disease related phenotypes including virus replication, virus-induced inflammation, and weight loss was observed. Many of the disease associated phenotypes were correlated, with viral replication and virus-induced inflammation being predictors of virus-induced weight loss. Despite these correlations, pre-CC mice with unique and novel disease phenotype combinations were observed. We also identified sets of transcripts (modules) that were correlated with aspects of disease. In order to identify how host genetic polymorphisms contribute to the observed variation in disease, we conducted quantitative trait loci (QTL) mapping. We identified several QTL contributing to specific aspects of the host response including virus-induced weight loss, titer, pulmonary edema, neutrophil recruitment to the airways, and transcriptional expression. Existing whole-genome sequence data was applied to identify high priority candidate genes within QTL regions. A key host response QTL was located at the site of the known anti-influenza Mx1 gene. We sequenced the coding regions of Mx1 in the eight CC founder strains, and identified a novel Mx1 allele that showed reduced ability to inhibit viral replication, while maintaining protection from weight loss. PMID:23468633

Analyses of amplified fragment length polymorphisms (AFLP) indicate rapid radiation of Diospyros species (Ebenaceae) endemic to New Caledonia

PubMed Central

2013-01-01

Background Radiation in some plant groups has occurred on islands and due to the characteristic rapid pace of phenotypic evolution, standard molecular markers often provide insufficient variation for phylogenetic reconstruction. To resolve relationships within a clade of 21 closely related New Caledonian Diospyros species and evaluate species boundaries we analysed genome-wide DNA variation via amplified fragment length polymorphisms (AFLP). Results A neighbour-joining (NJ) dendrogram based on Dice distances shows all species except D. minimifolia, D. parviflora and D. vieillardii to form unique clusters of genetically similar accessions. However, there was little variation between these species clusters, resulting in unresolved species relationships and a star-like general NJ topology. Correspondingly, analyses of molecular variance showed more variation within species than between them. A Bayesian analysis with BEAST produced a similar result. Another Bayesian method, this time a clustering method, Structure, demonstrated the presence of two groups, highly congruent with those observed in a principal coordinate analysis (PCO). Molecular divergence between the two groups is low and does not correspond to any hypothesised taxonomic, ecological or geographical patterns. Conclusions We hypothesise that such a pattern could have been produced by rapid and complex evolution involving a widespread progenitor for which an initial split into two groups was followed by subsequent fragmentation into many diverging populations, which was followed by range expansion of then divergent entities. Overall, this process resulted in an opportunistic pattern of phenotypic diversification. The time since divergence was probably insufficient for some species to become genetically well-differentiated, resulting in progenitor/derivative relationships being exhibited in a few cases. In other cases, our analyses may have revealed evidence for the existence of cryptic species, for which more study of morphology and ecology are now required. PMID:24330478

CLASSIFYING COASTAL ENVIRONMENTS: HISTORICAL PESPECTIVE AND CURRENT NECESSITY

EPA Science Inventory

Coastal environments are particularly complex due to variations in geology and upstream watersheds, and are subject to dynamic spatial and temporal changes. Their diverse characteristics result in wide variations in response to environmental stressors such as nutrient over-enrich...

Gravel road paving guidelines, technical summary.

DOT National Transportation Integrated Search

2016-11-01

The percentage of gravel roads in rural areas in Kansas is higher than most states. A wide variation of traffic volumes across different regions and variations of local conditions and scenarios present a great challenge for local agencies to determin...

The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine.

PubMed

Elhaik, Eran; Yusuf, Leeban; Anderson, Ainan I J; Pirooznia, Mehdi; Arnellos, Dimitrios; Vilshansky, Gregory; Ercal, Gunes; Lu, Yontao; Webster, Teresa; Baird, Michael L; Esposito, Umberto

2017-12-01

The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation, drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity. We thereby aimed to design the Diversity of REcent and Ancient huMan (DREAM)-an all-inclusive microarray that would allow both identification of known associations and exploration of standing questions in genetic anthropology, forensics, and personalized medicine. DREAM includes probes to interrogate ancestry informative markers obtained from over 450 human populations, over 200 ancient genomes, and 10 archaic hominins. DREAM can identify 94% and 61% of all known Y and mitochondrial haplogroups, respectively, and was vetted to avoid interrogation of clinically relevant markers. To demonstrate its capabilities, we compared its FST distributions with those of the 1000 Genomes Project and commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, DREAM's autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. DREAM performances are further illustrated in biogeographical, identical by descent, and copy number variation analyses. In summary, with approximately 800,000 markers spanning nearly 2,000 genes, DREAM is a useful tool for genetic anthropology, forensic, and personalized medicine studies. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Oral anticoagulant re-initiation following intracerebral hemorrhage in non-valvular atrial fibrillation: Global survey of the practices of neurologists, neurosurgeons and thrombosis experts.

PubMed

Xu, Yan; Shoamanesh, Ashkan; Schulman, Sam; Dowlatshahi, Dar; Al-Shahi Salman, Rustam; Moldovan, Ioana Doina; Wells, Philip Stephen; AlKherayf, Fahad

2018-01-01

While oral anticoagulants (OACs) are highly effective for ischemic stroke prevention in atrial fibrillation, intracerebral hemorrhage (ICH) remains the most feared complication of OAC. Clinical controversy remains regarding OAC resumption and its timing for ICH survivors with atrial fibrillation because the balance between risks and benefits has not been investigated in randomized trials. To survey the practice of stroke neurologists, thrombosis experts and neurosurgeons on OAC re-initiation following OAC-associated ICH. An online survey was distributed to members of the International Society for Thrombosis and Haemostasis, Canadian Stroke Consortium, NAVIGATE-ESUS trial investigators (Clinicatrials.gov identifier NCT02313909) and American Association of Neurological Surgeons. Demographic factors and 11 clinical scenarios were included. Two hundred twenty-eight participants from 38 countries completed the survey. Majority of participants were affiliated with academic centers, and >20% managed more than 15 OAC-associated ICH patients/year. Proportion of respondents suggesting OAC anticoagulant resumption varied from 30% (for cerebral amyloid angiopathy) to 98% (for traumatic ICH). Within this group, there was wide distribution in response for timing of resumption: 21.4% preferred to re-start OACs after 1-3 weeks of incident ICH, while 25.3% opted to start after 1-3 months. Neurosurgery respondents preferred earlier OAC resumption compared to stroke neurologists or thrombosis experts in 5 scenarios (p<0.05 by Kendall's tau). Wide variations in current practice exist among management of OAC-associated ICH, with decisions influenced by patient- and provider-related factors. As these variations likely reflect the lack of high quality evidence, randomized trials are direly needed in this population.

Local adaptations in bryophytes revisited: the genetic structure of the calcium-tolerant peatmoss Sphagnum warnstorfii along geographic and pH gradients

PubMed Central

Mikulášková, Eva; Hájek, Michal; Veleba, Adam; Johnson, Matthew G; Hájek, Tomáš; Shaw, Jonathan A

2015-01-01

Bryophytes dominate some ecosystems despite their extraordinary sensitivity to habitat quality. Nevertheless, some species behave differently across various regions. The existence of local adaptations is questioned by a high dispersal ability, which is thought to redistribute genetic variability among populations. Although Sphagnum warnstorfii is an important ecosystem engineer in fen peatlands, the causes of its rather wide niche along the pH/calcium gradient are poorly understood. Here, we studied the genetic variability of its global populations, with a detailed focus on the wide pH/calcium gradient in Central Europe. Principal coordinates analysis of 12 polymorphic microsatellite loci revealed a significant gradient coinciding with water pH, but independent of geography; even samples from the same fens were clearly separated along this gradient. However, most of the genetic variations remained unexplained, possibly because of the introgression from phylogenetically allied species. This explanation is supported by the small heterogeneous cluster of samples that appeared when populations morphologically transitional to S. subnites, S. rubellum, or S. russowii were included into the analysis. Alternatively, this unexplained variation might be attributed to a legacy of glacial refugia with recently dissolved ecological and biogeographic consequences. Isolation by distance appeared at the smallest scale only (up to 43 km). Negative spatial correlations occurred more frequently, mainly at long distances (up to 950 km), implying a genetic similarity among samples which are very distant geographically. Our results confirm the high dispersal ability of peatmosses, but simultaneously suggested that their ability to cope with a high pH/calcium level is at least partially determined genetically, perhaps via specific physiological mechanisms or a hummock-forming ability. PMID:25628880

Using a Learning Collaborative Strategy With Office-based Practices to Increase Access and Improve Quality of Care for Patients With Opioid Use Disorders

PubMed Central

Nordstrom, Benjamin R.; Saunders, Elizabeth C.; McLeman, Bethany; Meier, Andrea; Xie, Haiyi; Lambert-Harris, Chantal; Tanzman, Beth; Brooklyn, John; King, Gregory; Kloster, Nels; Lord, Clifton Frederick; Roberts, William; McGovern, Mark P.

2016-01-01

Objectives Rapidly escalating rates of heroin and prescription opioid use have been widely observed in rural areas across the United States. Although US Food and Drug Administration-approved medications for opioid use disorders exist, they are not routinely accessible to patients. One medication, buprenorphine, can be prescribed by waivered physicians in office-based practice settings, but practice patterns vary widely. This study explored the use of a learning collaborative method to improve the provision of buprenorphine in the state of Vermont. Methods We initiated a learning collaborative with 4 cohorts of physician practices (28 total practices). The learning collaborative consisted of a series of 4 face-to-face and 5 teleconference sessions over 9 months. Practices collected and reported on 8 quality-improvement data measures, which included the number of patients prescribed buprenorphine, and the percent of unstable patients seen weekly. Changes from baseline to 8 months were examined using a p-chart and logistic regression methodology. Results Physician engagement in the learning collaborative was favorable across all 4 cohorts (85.7%). On 6 of the 7 quality-improvement measures, there were improvements from baseline to 8 months. On 4 measures, these improvements were statistically significant (P < 0.001). Importantly, practice variation decreased over time on all measures. The number of patients receiving medication increased only slightly (3.4%). Conclusions Results support the effectiveness of a learning collaborative approach to engage physicians, modestly improve patient access, and significantly reduce practice variation. The strategy is potentially generalizable to other systems and regions struggling with this important public health problem. PMID:26900669

Isomorphic semantic mapping of variant call format (VCF2RDF).

PubMed

Penha, Emanuel Diego S; Iriabho, Egiebade; Dussaq, Alex; de Oliveira, Diana Magalhães; Almeida, Jonas S

2017-02-15

The move of computational genomics workflows to Cloud Computing platforms is associated with a new level of integration and interoperability that challenges existing data representation formats. The Variant Calling Format (VCF) is in a particularly sensitive position in that regard, with both clinical and consumer-facing analysis tools relying on this self-contained description of genomic variation in Next Generation Sequencing (NGS) results. In this report we identify an isomorphic map between VCF and the reference Resource Description Framework. RDF is advanced by the World Wide Web Consortium (W3C) to enable representations of linked data that are both distributed and discoverable. The resulting ability to decompose VCF reports of genomic variation without loss of context addresses the need to modularize and govern NGS pipelines for Precision Medicine. Specifically, it provides the flexibility (i.e. the indexing) needed to support the wide variety of clinical scenarios and patient-facing governance where only part of the VCF data is fitting. Software libraries with a claim to be both domain-facing and consumer-facing have to pass the test of portability across the variety of devices that those consumers in fact adopt. That is, ideally the implementation should itself take place within the space defined by web technologies. Consequently, the isomorphic mapping function was implemented in JavaScript, and was tested in a variety of environments and devices, client and server side alike. These range from web browsers in mobile phones to the most popular micro service platform, NodeJS. The code is publicly available at https://github.com/ibl/VCFr , with a live deployment at: http://ibl.github.io/VCFr/ . jonas.almeida@stonybrookmedicine.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Health System Resource Gaps and Associated Mortality from Pandemic Influenza across Six Asian Territories

PubMed Central

Rudge, James W.; Hanvoravongchai, Piya; Krumkamp, Ralf; Chavez, Irwin; Adisasmito, Wiku; Ngoc Chau, Pham; Phommasak, Bounlay; Putthasri, Weerasak; Shih, Chin-Shui; Stein, Mart; Timen, Aura; Touch, Sok; Reintjes, Ralf; Coker, Richard

2012-01-01

Background Southeast Asia has been the focus of considerable investment in pandemic influenza preparedness. Given the wide variation in socio-economic conditions, health system capacity across the region is likely to impact to varying degrees on pandemic mitigation operations. We aimed to estimate and compare the resource gaps, and potential mortalities associated with those gaps, for responding to pandemic influenza within and between six territories in Asia. Methods and Findings We collected health system resource data from Cambodia, Indonesia (Jakarta and Bali), Lao PDR, Taiwan, Thailand and Vietnam. We applied a mathematical transmission model to simulate a “mild-to-moderate” pandemic influenza scenario to estimate resource needs, gaps, and attributable mortalities at province level within each territory. The results show that wide variations exist in resource capacities between and within the six territories, with substantial mortalities predicted as a result of resource gaps (referred to here as “avoidable” mortalities), particularly in poorer areas. Severe nationwide shortages of mechanical ventilators were estimated to be a major cause of avoidable mortalities in all territories except Taiwan. Other resources (oseltamivir, hospital beds and human resources) are inequitably distributed within countries. Estimates of resource gaps and avoidable mortalities were highly sensitive to model parameters defining the transmissibility and clinical severity of the pandemic scenario. However, geographic patterns observed within and across territories remained similar for the range of parameter values explored. Conclusions The findings have important implications for where (both geographically and in terms of which resource types) investment is most needed, and the potential impact of resource mobilization for mitigating the disease burden of an influenza pandemic. Effective mobilization of resources across administrative boundaries could go some way towards minimizing avoidable deaths. PMID:22363739

Health system resource gaps and associated mortality from pandemic influenza across six Asian territories.

PubMed

Rudge, James W; Hanvoravongchai, Piya; Krumkamp, Ralf; Chavez, Irwin; Adisasmito, Wiku; Chau, Pham Ngoc; Phommasak, Bounlay; Putthasri, Weerasak; Shih, Chin-Shui; Stein, Mart; Timen, Aura; Touch, Sok; Reintjes, Ralf; Coker, Richard

2012-01-01

Southeast Asia has been the focus of considerable investment in pandemic influenza preparedness. Given the wide variation in socio-economic conditions, health system capacity across the region is likely to impact to varying degrees on pandemic mitigation operations. We aimed to estimate and compare the resource gaps, and potential mortalities associated with those gaps, for responding to pandemic influenza within and between six territories in Asia. We collected health system resource data from Cambodia, Indonesia (Jakarta and Bali), Lao PDR, Taiwan, Thailand and Vietnam. We applied a mathematical transmission model to simulate a "mild-to-moderate" pandemic influenza scenario to estimate resource needs, gaps, and attributable mortalities at province level within each territory. The results show that wide variations exist in resource capacities between and within the six territories, with substantial mortalities predicted as a result of resource gaps (referred to here as "avoidable" mortalities), particularly in poorer areas. Severe nationwide shortages of mechanical ventilators were estimated to be a major cause of avoidable mortalities in all territories except Taiwan. Other resources (oseltamivir, hospital beds and human resources) are inequitably distributed within countries. Estimates of resource gaps and avoidable mortalities were highly sensitive to model parameters defining the transmissibility and clinical severity of the pandemic scenario. However, geographic patterns observed within and across territories remained similar for the range of parameter values explored. The findings have important implications for where (both geographically and in terms of which resource types) investment is most needed, and the potential impact of resource mobilization for mitigating the disease burden of an influenza pandemic. Effective mobilization of resources across administrative boundaries could go some way towards minimizing avoidable deaths.

Efficient genotype compression and analysis of large genetic variation datasets

PubMed Central

Layer, Ryan M.; Kindlon, Neil; Karczewski, Konrad J.; Quinlan, Aaron R.

2015-01-01

Genotype Query Tools (GQT) is a new indexing strategy that expedites analyses of genome variation datasets in VCF format based on sample genotypes, phenotypes and relationships. GQT’s compressed genotype index minimizes decompression for analysis, and performance relative to existing methods improves with cohort size. We show substantial (up to 443 fold) performance gains over existing methods and demonstrate GQT’s utility for exploring massive datasets involving thousands to millions of genomes. PMID:26550772

Study of weak solutions for parabolic variational inequalities with nonstandard growth conditions.

PubMed

Dong, Yan

2018-01-01

In this paper, we study the degenerate parabolic variational inequality problem in a bounded domain. First, the weak solutions of the variational inequality are defined. Second, the existence and uniqueness of the solutions in the weak sense are proved by using the penalty method and the reduction method.

Variational formulation for Black-Scholes equations in stochastic volatility models

NASA Astrophysics Data System (ADS)

Gyulov, Tihomir B.; Valkov, Radoslav L.

2012-11-01

In this note we prove existence and uniqueness of weak solutions to a boundary value problem arising from stochastic volatility models in financial mathematics. Our settings are variational in weighted Sobolev spaces. Nevertheless, as it will become apparent our variational formulation agrees well with the stochastic part of the problem.

Parents or predators: Examining intraseasonal variation in nest survival for migratory passerine

Treesearch

Robin Hirsch-Jacobson; W. Andrew Cox; Emily E. Tewes; Frank R., III Thompson; John Faaborg

2012-01-01

For birds, risk of nest predation can vary within a breeding season, but few data exist that explain why such variation occurs. We investigated intraseasonal variation of nest survival of the Acadian Flycatcher (Empidonax virescens) in Midwestern forests and tested whether four of the adults' reproductive strategies (clutch size, nest...

Identification and ranking of environmental threats with ecosystem vulnerability distributions.

PubMed

Zijp, Michiel C; Huijbregts, Mark A J; Schipper, Aafke M; Mulder, Christian; Posthuma, Leo

2017-08-24

Responses of ecosystems to human-induced stress vary in space and time, because both stressors and ecosystem vulnerabilities vary in space and time. Presently, ecosystem impact assessments mainly take into account variation in stressors, without considering variation in ecosystem vulnerability. We developed a method to address ecosystem vulnerability variation by quantifying ecosystem vulnerability distributions (EVDs) based on monitoring data of local species compositions and environmental conditions. The method incorporates spatial variation of both abiotic and biotic variables to quantify variation in responses among species and ecosystems. We show that EVDs can be derived based on a selection of locations, existing monitoring data and a selected impact boundary, and can be used in stressor identification and ranking for a region. A case study on Ohio's freshwater ecosystems, with freshwater fish as target species group, showed that physical habitat impairment and nutrient loads ranked highest as current stressors, with species losses higher than 5% for at least 6% of the locations. EVDs complement existing approaches of stressor assessment and management, which typically account only for variability in stressors, by accounting for variation in the vulnerability of the responding ecosystems.

Quantifying Geographic Variation in Health Care Outcomes in the United States before and after Risk-Adjustment.

PubMed

Rosenberg, Barry L; Kellar, Joshua A; Labno, Anna; Matheson, David H M; Ringel, Michael; VonAchen, Paige; Lesser, Richard I; Li, Yue; Dimick, Justin B; Gawande, Atul A; Larsson, Stefan H; Moses, Hamilton

2016-01-01

Despite numerous studies of geographic variation in healthcare cost and utilization at the local, regional, and state levels across the U.S., a comprehensive characterization of geographic variation in outcomes has not been published. Our objective was to quantify variation in US health outcomes in an all-payer population before and after risk-adjustment. We used information from 16 independent data sources, including 22 million all-payer inpatient admissions from the Healthcare Cost and Utilization Project (which covers regions where 50% of the U.S. population lives) to analyze 24 inpatient mortality, inpatient safety, and prevention outcomes. We compared outcome variation at state, hospital referral region, hospital service area, county, and hospital levels. Risk-adjusted outcomes were calculated after adjusting for population factors, co-morbidities, and health system factors. Even after risk-adjustment, there exists large geographical variation in outcomes. The variation in healthcare outcomes exceeds the well publicized variation in US healthcare costs. On average, we observed a 2.1-fold difference in risk-adjusted mortality outcomes between top- and bottom-decile hospitals. For example, we observed a 2.3-fold difference for risk-adjusted acute myocardial infarction inpatient mortality. On average a 10.2-fold difference in risk-adjusted patient safety outcomes exists between top and bottom-decile hospitals, including an 18.3-fold difference for risk-adjusted Central Venous Catheter Bloodstream Infection rates. A 3.0-fold difference in prevention outcomes exists between top- and bottom-decile counties on average; including a 2.2-fold difference for risk-adjusted congestive heart failure admission rates. The population, co-morbidity, and health system factors accounted for a range of R2 between 18-64% of variability in mortality outcomes, 3-39% of variability in patient safety outcomes, and 22-70% of variability in prevention outcomes. The amount of variability in health outcomes in the U.S. is large even after accounting for differences in population, co-morbidities, and health system factors. These findings suggest that: 1) additional examination of regional and local variation in risk-adjusted outcomes should be a priority; 2) assumptions of uniform hospital quality that underpin rationale for policy choices (such as narrow insurance networks or antitrust enforcement) should be challenged; and 3) there exists substantial opportunity for outcomes improvement in the US healthcare system.

10 CFR 1021.330 - Programmatic (including site-wide) NEPA documents.

Code of Federal Regulations, 2010 CFR

2010-01-01

... prepare a programmatic EIS or EA (40 CFR 1502.4). DOE may also prepare a programmatic EIS or EA at any... Analysis, DOE shall determine whether the existing EIS remains adequate or whether to prepare a new site-wide EIS or supplement the existing EIS, as appropriate. The determination and supporting analysis...

Short-focus and ultra-wide-angle lens design in wavefront coding

NASA Astrophysics Data System (ADS)

Zhang, Jiyan; Huang, Yuanqing; Xiong, Feibing

2016-10-01

Wavefront coding (WFC) is a hybrid technology designed to increase depth of field of conventional optics. The goal of our research is to apply this technology to the short-focus and ultra-wide-angle lens which suffers from the aberration related with large field of view (FOV) such as coma and astigmatism. WFC can also be used to compensate for other aberration which is sensitive to the FOV. Ultra-wide-angle lens has a little depth of focus because it has small F number and short-focus. We design a hybrid lens combing WFC with the ultra-wide-angle lens. The full FOV and relative aperture of the final design are up to170° and 1/1.8 respectively. The focal length is 2 mm. We adopt the cubic phase mask (CPM) in the design. The conventional design will have a wide variation of the point spread function (PSF) across the FOV and it is very sensitive with the variation of the FOV. The new design we obtain the PSF is nearly invariant over the whole FOV. But the result of the design also shows the little difference between the horizontal and vertical length of the PSF. We analyze that the CPM is non-symmetric phase mask and the FOV is so large, which will generate variation in the final image quality. For that reason, we apply a new method to avoid that happened. We try to make the rays incident on the CPM with small angle and decrease the deformation of the PSF. The experimental result shows the new method to optimize the CPM is fit for the ultra-wide-angle lens. The research above will be a helpful instruction to design the ultra-wide-angle lens with WFC.

Variation in Educational Outcomes and Policies across Countries and of Schools within Countries. NBER Working Paper No. 16293

ERIC Educational Resources Information Center

Freeman, Richard B.; Machin, Stephen; Viarengo, Martina

2010-01-01

This study examines the variation in educational outcomes across and within countries using the TIMSS mathematics tests. It documents the wide cross-country variation in the level and dispersion of test scores. Countries with the highest test scores are those with the least inequality in scores, which suggests a "virtuous" equity-efficiency…

Cerebral perfusion computed tomography deconvolution via structure tensor total variation regularization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeng, Dong; Zhang, Xinyu; Bian, Zhaoying, E-mail: zybian@smu.edu.cn, E-mail: jhma@smu.edu.cn

Purpose: Cerebral perfusion computed tomography (PCT) imaging as an accurate and fast acute ischemic stroke examination has been widely used in clinic. Meanwhile, a major drawback of PCT imaging is the high radiation dose due to its dynamic scan protocol. The purpose of this work is to develop a robust perfusion deconvolution approach via structure tensor total variation (STV) regularization (PD-STV) for estimating an accurate residue function in PCT imaging with the low-milliampere-seconds (low-mAs) data acquisition. Methods: Besides modeling the spatio-temporal structure information of PCT data, the STV regularization of the present PD-STV approach can utilize the higher order derivativesmore » of the residue function to enhance denoising performance. To minimize the objective function, the authors propose an effective iterative algorithm with a shrinkage/thresholding scheme. A simulation study on a digital brain perfusion phantom and a clinical study on an old infarction patient were conducted to validate and evaluate the performance of the present PD-STV approach. Results: In the digital phantom study, visual inspection and quantitative metrics (i.e., the normalized mean square error, the peak signal-to-noise ratio, and the universal quality index) assessments demonstrated that the PD-STV approach outperformed other existing approaches in terms of the performance of noise-induced artifacts reduction and accurate perfusion hemodynamic maps (PHM) estimation. In the patient data study, the present PD-STV approach could yield accurate PHM estimation with several noticeable gains over other existing approaches in terms of visual inspection and correlation analysis. Conclusions: This study demonstrated the feasibility and efficacy of the present PD-STV approach in utilizing STV regularization to improve the accuracy of residue function estimation of cerebral PCT imaging in the case of low-mAs.« less

Climate warming, marine protected areas and the ocean-scale integrity of coral reef ecosystems.

PubMed

Graham, Nicholas A J; McClanahan, Tim R; MacNeil, M Aaron; Wilson, Shaun K; Polunin, Nicholas V C; Jennings, Simon; Chabanet, Pascale; Clark, Susan; Spalding, Mark D; Letourneur, Yves; Bigot, Lionel; Galzin, René; Ohman, Marcus C; Garpe, Kajsa C; Edwards, Alasdair J; Sheppard, Charles R C

2008-08-27

Coral reefs have emerged as one of the ecosystems most vulnerable to climate variation and change. While the contribution of a warming climate to the loss of live coral cover has been well documented across large spatial and temporal scales, the associated effects on fish have not. Here, we respond to recent and repeated calls to assess the importance of local management in conserving coral reefs in the context of global climate change. Such information is important, as coral reef fish assemblages are the most species dense vertebrate communities on earth, contributing critical ecosystem functions and providing crucial ecosystem services to human societies in tropical countries. Our assessment of the impacts of the 1998 mass bleaching event on coral cover, reef structural complexity, and reef associated fishes spans 7 countries, 66 sites and 26 degrees of latitude in the Indian Ocean. Using Bayesian meta-analysis we show that changes in the size structure, diversity and trophic composition of the reef fish community have followed coral declines. Although the ocean scale integrity of these coral reef ecosystems has been lost, it is positive to see the effects are spatially variable at multiple scales, with impacts and vulnerability affected by geography but not management regime. Existing no-take marine protected areas still support high biomass of fish, however they had no positive affect on the ecosystem response to large-scale disturbance. This suggests a need for future conservation and management efforts to identify and protect regional refugia, which should be integrated into existing management frameworks and combined with policies to improve system-wide resilience to climate variation and change.

[Study on the variation of arsenic concentration in groundwater and chemical characteristics of arsenic in sediment cores at the areas with endemic arsenic poison disease in Jianghan Plain].

PubMed

Zhou, Suhua; Ye, Hengpeng; Li, Mingjian; Xiong, Peisheng; Du, Dongyun; Wang, Jingwen

2015-06-01

To understand the variation of arsenic concentration in underground water at the endemic arsenic poison disease area of Jianghan Plain so as to better understand the spatial distribution of high arsenic groundwater, hydro-chemical evolution and source of arsenic in this region. Thirty underground water samples were collected respectively around 3 km radius of the two houses where arsenic poisoning patients lived, in Xiantao and Honghu. Sediment cores of three drillings were collected as well. Both paired t-test or paired Wilcoxon Signed Ranking Test were used to compare the arsenic concentration of water. The arsenic concentration in 2011-2012 appeared lower than that in 2006-2007 at the Nanhong village of Xiantao (t = 4.645 3, P < 0.000 1), but was higher (S = -150, P < 0.000 1) in the Yaohe village of Honghu. The pH value showed weak acidity with Eh as weak oxidated. Positive correlations were observed between arsenic concentration and Cl, HCO3(-), Fe, Mn. However, negative correlations were found between As and SO4(2-), NO3(-). The range of arsenic content in the sediment was 1.500 mg/kg to 17.289 mg/kg. The maximum arsenic content existed in the soil layer, while the minimum arsenic content existed in the sand layer. The concentration of arsenic varied widely with time and space at endemic arsenic poison disease area of Jianghan Plain. Characteristics of these water chemicals showed significant differences, when compared to the groundwater from Datong Basin, Shanxi Shanyin and Hetao Plain of Inner Mongolia, which presented a typical environment with high arsenic contents in the groundwater. The arsenic content in the sediment samples seemed related to the lithologic structure.

The multiple meanings of global health governance: a call for conceptual clarity.

PubMed

Lee, Kelley; Kamradt-Scott, Adam

2014-04-28

The term global health governance (GHG) is now widely used, with over one thousand works published in the scholarly literature, almost all since 2002. Amid this rapid growth there is considerable variation in how the term is defined and applied, generating confusion as to the boundaries of the subject, the perceived problems in practice, and the goals to be achieved through institutional reform. This paper is based on the results of a separate scoping study of peer reviewed GHG research from 1990 onwards which undertook keyword searches of public health and social science databases. Additional works, notably books, book chapters and scholarly articles, not currently indexed, were identified through Web of Science citation searches. After removing duplicates, book reviews, commentaries and editorials, we reviewed the remaining 250 scholarly works in terms of how the concept of GHG is applied. More specifically, we identify what is claimed as constituting GHG, how it is problematised, the institutional features of GHG, and what forms and functions are deemed ideal. After examining the broader notion of global governance and increasingly ubiquitous term "global health", the paper identifies three ontological variations in GHG scholarship - the scope of institutional arrangements, strengths and weaknesses of existing institutions, and the ideal form and function of GHG. This has produced three common, yet distinct, meanings of GHG that have emerged - globalisation and health governance, global governance and health, and governance for global health. There is a need to clarify ontological and definitional distinctions in GHG scholarship and practice, and be critically reflexive of their normative underpinnings. This will enable greater precision in describing existing institutional arrangements, as well as serve as a prerequisite for a fuller debate about the desired nature of GHG.

Along-axis segmentation and isostasy in the Western rift, East Africa

NASA Astrophysics Data System (ADS)

Upcott, N. M.; Mukasa, R. K.; Ebinger, C. J.; Karner, G. D.

1996-02-01

Structural variations along the southern sectors of the Western rift, East Africa, have previously been described, but subsurface structures in the northern sector (Uganda, Zaire) are virtually unknown. Our aims are to investigate the along-axis segmentation of the northern sector, thereby adding to the structural picture of the Western rift, and to study the isostatic compensation of the varying rift morphology along the sector's length. This study describes the first gravity survey to be carried out on the shallow Lake Albert, forward models of these and existing gravity data, and the results from inverse modeling of existing aeromagnetic data designed to delimit border and transfer fault systems. Our tectonic model shows that the northern rift sector is segmented along-axis into five 25 to 65-km-wide, 80 to 100-km-long rift segments, characterized by closed-contour Bouguer anomaly lows, and bounded by steep gravity, aeromagnetic, and topographic/bathymetric gradients. Werner and Euler deconvolution results and gravity anomaly data reveal that some faulted basins are separated by structural highs and cross-rift ramps or faults and suggest sedimentary basin depths of 4-6 km. Forward modeling of structural and free-air gravity profiles across individual basins and flanks using a model that assumes flexural compensation also suggests sediment thicknesses of up to 5.5 km, similar to the estimates from magnetic data. The basin and flank morphology can be explained by 6-9 km of extension of a lithosphere with an effective elastic thickness (Te) of 25 km (equivalent to a flexural rigidity of 1.4 × 1023 N m), similar to results in other Western rift basins. Potential field data and lithospheric strength estimates in the Western rift system show small along-axis variations in lithospheric structure, regardless of the presence or absence of Cenozoic magmatism.

The multiple meanings of global health governance: a call for conceptual clarity

PubMed Central

2014-01-01

Background The term global health governance (GHG) is now widely used, with over one thousand works published in the scholarly literature, almost all since 2002. Amid this rapid growth there is considerable variation in how the term is defined and applied, generating confusion as to the boundaries of the subject, the perceived problems in practice, and the goals to be achieved through institutional reform. Methodology This paper is based on the results of a separate scoping study of peer reviewed GHG research from 1990 onwards which undertook keyword searches of public health and social science databases. Additional works, notably books, book chapters and scholarly articles, not currently indexed, were identified through Web of Science citation searches. After removing duplicates, book reviews, commentaries and editorials, we reviewed the remaining 250 scholarly works in terms of how the concept of GHG is applied. More specifically, we identify what is claimed as constituting GHG, how it is problematised, the institutional features of GHG, and what forms and functions are deemed ideal. Results After examining the broader notion of global governance and increasingly ubiquitous term “global health”, the paper identifies three ontological variations in GHG scholarship - the scope of institutional arrangements, strengths and weaknesses of existing institutions, and the ideal form and function of GHG. This has produced three common, yet distinct, meanings of GHG that have emerged – globalisation and health governance, global governance and health, and governance for global health. Conclusions There is a need to clarify ontological and definitional distinctions in GHG scholarship and practice, and be critically reflexive of their normative underpinnings. This will enable greater precision in describing existing institutional arrangements, as well as serve as a prerequisite for a fuller debate about the desired nature of GHG. PMID:24775919

Solutions to variational inequalities of parabolic type

NASA Astrophysics Data System (ADS)

Zhu, Yuanguo

2006-09-01

The existence of strong solutions to a kind of variational inequality of parabolic type is investigated by the theory of semigroups of linear operators. As an application, an abstract semi permeable media problem is studied.

Characterization of Relatively Large Track Geometry Variations

DOT National Transportation Integrated Search

1982-03-01

An analysis of existing track geometry data is described from which the signatures of key track geometry variations related to severe track-train dynamic interaction are identified and quantified. Mathematical representations of these signatures are ...

Rail transit fare collection: Policy and technology assessment

NASA Technical Reports Server (NTRS)

Deshpande, G. K.; Cucchissi, J.; Heft, R. C.

1982-01-01

The impact of fare policies and fare structure on the selection of equipment was investigated, fare collection systems are described, hardware and technology related problems are documented, and the requirements of a fare collection simulation model are outlined. Major findings include: (1) a wide variation in the fare collection systems and equipment, caused primarily by historical precedence; (2) the reliability of AFC equipment used at BART and WMATA discouraged other properties from considering use of similar equipment; (3) existing equipment may not meet the fare collection needs of properties in the near future; (4) the cost of fare collection operation and maintenance is high; and (5) the relatively small market in fare collection equipment discourages new product development by suppliers. Recommendations for fare collection R&D programs include development of new hardware to meet rail transit needs, study of impacts of alternate fare policies increased communication among policymakers, and consensus on fare policy issues.

Are community-level financial data adequate to assess population health investments?

PubMed

Casper, Tim; Kindig, David A

2012-01-01

The variation in health outcomes among communities results largely from different levels of financial and nonfinancial policy investments over time; these natural experiments should offer investment and policy guidance for a business model on population health. However, little such guidance exists. We examined the availability of data in a sample of Wisconsin counties for expenditures in selected categories of health care, public health, human services, income support, job development, and education. We found, as predicted by the National Committee on Vital and Health Statistics in 2002, that availability is often limited by the challenges of difficulty in locating useable data, a lack of resources among public agencies to upgrade information technology systems for making data more usable and accessible to the public, and a lack of enterprise-wide coordination and geographic detail in data collection efforts. These challenges must be overcome to provide policy-relevant information for optimal population health resource allocation.

HOMER: The hybrid optimization model for electric renewable

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lilienthal, P.; Flowers, L.; Rossmann, C.

1995-12-31

Hybrid renewable systems are often more cost-effective than grid extensions or isolated diesel generators for providing power to remote villages. There are a wide variety of hybrid systems being developed for village applications that have differing combinations of wind, photovoltaics, batteries, and diesel generators. Due to variations in loads and resources determining the most appropriate combination of these components for a particular village is a difficult modelling task. To address this design problem the National Renewable Energy Laboratory has developed the Hybrid Optimization Model for Electric Renewables (HOMER). Existing models are either too detailed for screening analysis or too simplemore » for reliable estimation of performance. HOMER is a design optimization model that determines the configuration, dispatch, and load management strategy that minimizes life-cycle costs for a particular site and application. This paper describes the HOMER methodology and presents representative results.« less

Documenting different domains of promotion of autonomy in families.

PubMed

Manzi, Claudia; Regalia, Camillo; Pelucchi, Sara; Fincham, Frank D

2012-04-01

Parental promotion of autonomy for offspring well-being has been widely recognized in developmental psychology. Recent studies, however, show that this association varies across cultures. Such variation may reflect inappropriate measurement of this dimension of parenting. Therefore, three existing measures of promotion of autonomy were used to derive different dimensions related to the promotion of autonomy in three different domains - promotion of autonomous thought, promotion of autonomous decision-making, and promotion of physical separation. The cross-cultural significance of this three-component model was tested in samples of late adolescents (n = 1361) from four nations- the US, Belgium, Italy and China. Data from all four countries best fit a three dimensional model but the covariance between the three dimensions was moderated by culture. Culture also moderated the impact of promotion of autonomy on offspring well-being. Copyright © 2011 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Geomagnetic spikes on the core-mantle boundary

NASA Astrophysics Data System (ADS)

Davies, Christopher; Constable, Catherine

2017-05-01

Extreme variations of Earth's magnetic field occurred in the Levant region around 1000 BC, when the field intensity rapidly rose and fell by a factor of 2. No coherent link currently exists between this intensity spike and the global field produced by the core geodynamo. Here we show that the Levantine spike must span >60° longitude at Earth's surface if it originates from the core-mantle boundary (CMB). Several low intensity data are incompatible with this geometric bound, though age uncertainties suggest these data could have sampled the field before the spike emerged. Models that best satisfy energetic and geometric constraints produce CMB spikes 8-22° wide, peaking at O(100) mT. We suggest that the Levantine spike reflects an intense CMB flux patch that grew in place before migrating northwest, contributing to growth of the dipole field. Estimates of Ohmic heating suggest that diffusive processes likely govern the ultimate decay of geomagnetic spikes.

Changes in population and agricultural land in conterminous United States counties, 1790 to 1997

USGS Publications Warehouse

Waisanen, Pamela J.; Bliss, Norman B.

2002-01-01

We have developed a data set of changes in population and agricultural land for the conterminous United States at the county level, resulting in more spatial detail than in previously available compilations. The purpose was to provide data on the timing of land conversion as an input to dynamic models of the carbon cycle, although a wide variety of applications exist for the physical, biological, and social sciences. The spatial data represent the appropriate county boundaries for each census year between 1790 and 1997, and the census attributes are attached to the appropriate spatial region. The resulting time series and maps show the history of population (1790-1990) and the history of agricultural development (1850-1997). The patterns of agricultural development reflect the influences of climate, soil productivity, increases in population size, variations in the general economy, and technological changes in the energy, transportation, and agricultural sectors.

Organochlorine pesticides residue in lakes of Khorezm, Uzbekistan

USGS Publications Warehouse

Rosen, Michael R.; Nishonov, Bakhriddin; Fayzieva, Dilorom; Saito, L.; Lamers, J.

2009-01-01

The Khorezm province in northwest Uzbekistan is a productive agricultural area within the Aral Sea Basin that produces cotton, rice and wheat. Various organochlorine pesticides were widely used for cotton production before Uzbekistan's independence in 1991. In Khorezm, small lakes have formed in natural depressions that receive inputs mostly from agricultural runoff. Samples from lake waters and sediments, as well as water from the Amu Darya River (which is the source of most of the lake water) have been analyzed to study variations in the concentrations of organochlorine pesticides residues during the year. Low concentrations of DDT, DDD, DDE, a-HCH and y-HCH compounds were found in water and sediment samples. The concentration of persistent organochlorine pesticides (DDT and HCH) in water and sediment is much lower than the maximum permissible concentrations that exist for water and soil. According to these preliminary results, the investigated lakes in Khorezm appear to be suitable for recreation or for aquaculture.

Observational data needs for plasma phenomena

NASA Technical Reports Server (NTRS)

Niedner, M. B., Jr.

1981-01-01

Bright comets display a rich variety of interesting plasma phenomena which occur over an enormous range of spatial scales, and which require different observational techniques to be studied effectively. Wide-angle photography of high time resolution is probably the best method of studying the phenomenon of largest known scale: the plasma tail disconnection event (DE), which has been attributed to magnetic reconnection at interplanetary sector boundary crossings. These structures usually accelerate as they recede from the head region and observed velocities are typically in the range 50 V km/s. They are often visible for several days following the time of disconnection, and are sometimes seen out past 0.2 AU from the cometary head. The following areas pertaining to plasma phenomena in the ionoshere are addressed: the existence, size, and heliocentric distance variations of the contact surface, and the observational signatures of magnetic reconnection at sector boundary crossings.

Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor

PubMed Central

Decker, Brennan; Davis, Brian W.; Rimbault, Maud; Long, Adrienne H.; Karlins, Eric; Jagannathan, Vidhya; Reiman, Rebecca; Parker, Heidi G.; Drögemüller, Cord; Corneveaux, Jason J.; Chapman, Erica S.; Trent, Jeffery M.; Leeb, Tosso; Huentelman, Matthew J.; Wayne, Robert K.; Karyadi, Danielle M.; Ostrander, Elaine A.

2015-01-01

Canine transmissible venereal tumor (CTVT) is a parasitic cancer clone that has propagated for thousands of years via sexual transfer of malignant cells. Little is understood about the mechanisms that converted an ancient tumor into the world's oldest known continuously propagating somatic cell lineage. We created the largest existing catalog of canine genome-wide variation and compared it against two CTVT genome sequences, thereby separating alleles derived from the founder's genome from somatic mutations that must drive clonal transmissibility. We show that CTVT has undergone continuous adaptation to its transmissible allograft niche, with overlapping mutations at every step of immunosurveillance, particularly self-antigen presentation and apoptosis. We also identified chronologically early somatic mutations in oncogenesis- and immune-related genes that may represent key initiators of clonal transmissibility. Thus, we provide the first insights into the specific genomic aberrations that underlie CTVT's dogged perseverance in canids around the world. PMID:26232412

Performance Optimization of Marine Science and Numerical Modeling on HPC Cluster

PubMed Central

Yang, Dongdong; Yang, Hailong; Wang, Luming; Zhou, Yucong; Zhang, Zhiyuan; Wang, Rui; Liu, Yi

2017-01-01

Marine science and numerical modeling (MASNUM) is widely used in forecasting ocean wave movement, through simulating the variation tendency of the ocean wave. Although efforts have been devoted to improve the performance of MASNUM from various aspects by existing work, there is still large space unexplored for further performance improvement. In this paper, we aim at improving the performance of propagation solver and data access during the simulation, in addition to the efficiency of output I/O and load balance. Our optimizations include several effective techniques such as the algorithm redesign, load distribution optimization, parallel I/O and data access optimization. The experimental results demonstrate that our approach achieves higher performance compared to the state-of-the-art work, about 3.5x speedup without degrading the prediction accuracy. In addition, the parameter sensitivity analysis shows our optimizations are effective under various topography resolutions and output frequencies. PMID:28045972

Mixing characterization of highly underexpanded fluid jets with real gas expansion

NASA Astrophysics Data System (ADS)

Förster, Felix J.; Baab, Steffen; Steinhausen, Christoph; Lamanna, Grazia; Ewart, Paul; Weigand, Bernhard

2018-03-01

We report a comprehensive speed of sound database for multi-component mixing of underexpanded fuel jets with real gas expansion. The paper presents several reference test cases with well-defined experimental conditions providing quantitative data for validation of computational simulations. Two injectant fluids, fundamentally different with respect to their critical properties, are brought to supercritical state and discharged into cold nitrogen at different pressures. The database features a wide range of nozzle pressure ratios covering the regimes that are generally classified as highly and extremely highly underexpanded jets. Further variation is introduced by investigating different injection temperatures. Measurements are obtained along the centerline at different axial positions. In addition, an adiabatic mixing model based on non-ideal thermodynamic mixture properties is used to extract mixture compositions from the experimental speed of sound data. The concentration data obtained are complemented by existing experimental data and represented by an empirical fit.

Play therapy: a case-based example of a nondirective approach.

PubMed

Lawver, Timothy; Blankenship, Kelly

2008-10-01

Play therapy is a treatment modality in which the therapist engages in play with the child. Its use has been documented in a variety of settings and with a variety of diagnoses. Treating within the context of play brings the therapist and the therapy to the level of the child. By way of an introduction to this approach, a case is presented of a six-year-old boy with oppositional defiant disorder. The presentation focuses on the events and interactions of a typical session with an established patient. The primary issues of the session are aggression, self worth, and self efficacy. These themes manifest themselves through the content of the child's play and narration of his actions. The therapist then reflects these back to the child while gently encouraging the child toward more positive play. Though the example is one of nondirective play therapy, a wide range of variation exists under the heading of play therapy.

Play Therapy

PubMed Central

Lawver, Timothy; Blankenship, Kelly

2008-01-01

Play therapy is a treatment modality in which the therapist engages in play with the child. Its use has been documented in a variety of settings and with a variety of diagnoses. Treating within the context of play brings the therapist and the therapy to the level of the child. By way of an introduction to this approach, a case is presented of a six-year-old boy with oppositional defiant disorder. The presentation focuses on the events and interactions of a typical session with an established patient. The primary issues of the session are aggression, self worth, and self efficacy. These themes manifest themselves through the content of the child’s play and narration of his actions. The therapist then reflects these back to the child while gently encouraging the child toward more positive play. Though the example is one of nondirective play therapy, a wide range of variation exists under the heading of play therapy. PMID:19724720

Model-based object classification using unification grammars and abstract representations

NASA Astrophysics Data System (ADS)

Liburdy, Kathleen A.; Schalkoff, Robert J.

1993-04-01

The design and implementation of a high level computer vision system which performs object classification is described. General object labelling and functional analysis require models of classes which display a wide range of geometric variations. A large representational gap exists between abstract criteria such as `graspable' and current geometric image descriptions. The vision system developed and described in this work addresses this problem and implements solutions based on a fusion of semantics, unification, and formal language theory. Object models are represented using unification grammars, which provide a framework for the integration of structure and semantics. A methodology for the derivation of symbolic image descriptions capable of interacting with the grammar-based models is described and implemented. A unification-based parser developed for this system achieves object classification by determining if the symbolic image description can be unified with the abstract criteria of an object model. Future research directions are indicated.

Factors that influence producer decisions to implement management strategies.

PubMed

Field, Thomas G

2014-12-01

Cow-calf enterprises in the USA are widely divergent in size, locale, resource availability, management skill, and market focus. Furthermore, variation exists in dependence on the cow-calf enterprise as a primary source of income, perception about the utility of a particular management practice or technology, and assessment of cost: benefit resulting from implementation impact decisions. Enterprises with larger cow inventories, greater dependence on income from the cattle enterprise, and that retain ownership further into the supply chain beyond the cow-calf operation are more likely to institute management protocols such as vaccination programs, defined calving seasons, and reproductive technologies. Successful cow-calf managers place the highest priority on herd nutrition, pasture and range management, herd health, financial management marketing, production management, and genetics. Management practices are more likely to be adopted when they align with a manager's perception of the utility, labor availability, favorable cost: benefit outcomes and profit motivation.

A rare variant of internal anatomy of a third mandibular molar: a case report.

PubMed

Nimigean, V; Nimigean, Vanda Roxana; Sălăvăstru, D I

2011-01-01

The several anatomical variations existing in the root canal system may contribute to failure of the root canal therapy. Knowledge of the internal dental morphology is a complex and extremely important point for planning and performing endodontic therapy. This paper reports the case of a left mandibular third molar that presented only one dental conical root and only one aberrant radicular canal with an initial annular portion situated in the coronar third of the root and a linear portion at the level of the other two thirds of the dental root, which opened through an apical foramen. Root canal therapy and case management are described. Features like wide crown access, adequate illumination and use of exploring files where important for successful completion of the endodontic treatment. The treatment was performed through conventional methods. This clinical case constitutes a rare anatomical variant of internal radicular morphology.

Customization in Prescribing for Bipolar Disorder

PubMed Central

Hodgkin, Dominic; Volpe-Vartanian, Joanna; Merrick, Elizabeth L.; Horgan, Constance M.; Nierenberg, Andrew A.; Frank, Richard G.; Lee, Sue

2011-01-01

For many disorders, patient heterogeneity requires physicians to customize their treatment to each patient’s needs. We test for the existence of customization in physicians’ prescribing for bipolar disorder, using data from a naturalistic clinical effectiveness trial of bipolar disorder treatment (STEP-BD), which did not constrain physician prescribing. Multinomial logit is used to model the physician’s choice among five combinations of drug classes. We find that our observed measure of the patient’s clinical status played only a limited role in the choice among drug class combinations, even for conditions such as mania that are expected to affect class choice. However, treatment of a patient with given characteristics differed widely depending on which physician was seen. The explanatory power of the model was low. There was variation within each physician’s prescribing, but the results do not suggest a high degree of customization in physicians’ prescribing, based on our measure of clinical status. PMID:21506194

Customization in prescribing for bipolar disorder.

PubMed

Hodgkin, Dominic; Volpe-Vartanian, Joanna; Merrick, Elizabeth L; Horgan, Constance M; Nierenberg, Andrew A; Frank, Richard G; Lee, Sue

2012-06-01

For many disorders, patient heterogeneity requires physicians to customize their treatment to each patient's needs. We test for the existence of customization in physicians' prescribing for bipolar disorder, using data from a naturalistic clinical effectiveness trial of bipolar disorder treatment (STEP-BD), which did not constrain physician prescribing. Multinomial logit is used to model the physician's choice among five combinations of drug classes. We find that our observed measure of the patient's clinical status played only a limited role in the choice among drug class combinations, even for conditions such as mania that are expected to affect class choice. However, treatment of a patient with given characteristics differed widely depending on which physician was seen. The explanatory power of the model was low. There was variation within each physician's prescribing, but the results do not suggest a high degree of customization in physicians' prescribing, based on our measure of clinical status. Copyright © 2011 John Wiley & Sons, Ltd.

Proper expression of metabolizable energy in avian energetics

USGS Publications Warehouse

Miller, M.R.; Reinecke, K.J.

1984-01-01

We review metabolizable energy (ME) concepts and present evidence suggesting that the form of ME used for analyses of avian energetics can affect interpretation of results. Apparent ME (AME) is the most widely used measure of food energy available to birds. True ME(TME) differs from AME in recognizing fecal and urinary energy of nonfood origin as metabolized energy. Only AME values obtained from test birds fed at maintenance levels should be used for energy analyses. A practical assay for TME has shown that TME estimates are less sensitive than AME to variation in food intake. The TME assay may be particularly useful in studies of natural foods that are difficult to obtain in quantities large enough to supply test birds with maintenance requirements. Energy budgets calculated from existence metabolism should be expressed as kJ of AME and converted to food requirements with estimates of metabolizability given in kJ AME/g.

A global analysis of the 1991 geomagnetic jerk

NASA Astrophysics Data System (ADS)

De Michelis, Paola; Cafarella, Lili; Meloni, Antonio

2000-12-01

A recent examination of the geomagnetic annual mean values for the European magnetic observatories has shown the existence of a sudden change in the secular acceleration in about 1991 (Cafarella & Meloni 1995; Macmillan 1996). Using first differences of the Y (east geomagnetic field component) mean values from 74 observatories, the worldwide character of the 1991 impulse has been determined (De Michelis et al. 1998). Using data from 109 observatories widely distributed all over the world, the structure of the secular variation for the X (north) and Z (vertical) magnetic field intensities around 1990 was investigated, and evidence of this most recent jerk was found. External effects were removed from the annual mean data by comparing the long-term variations of the geomagnetic field components at individual observatories with the long-term variations of two geomagnetic indices, aa and Dst, and of a solar index, the Wolf number R. A careful analysis has been carried out on the amplitude of the external disturbance, on its dependence on latitude, and on the weights of the geomagnetic indices in the evaluation of the resulting external field. The secular variation has been evaluated from the corrected annual means. Around 1990, the secular variation can be fitted at many observatories by two straight lines with a sudden and marked change in slope. In this manner the jerk occurrence time and the intensity of the step in the second time derivative (ΔX'', ΔY'' and ΔZ'') were computed. Maps of ΔX'', ΔY'' and ΔZ'' provide information on the worldwide intensity distribution of the examined event. Maps of the jerk occurrence-time distributions are also given. The mean jerk occurrence time is 1990.1+/-0.6. Finally, a spherical harmonic analysis was used to complete the quantitative description of this phenomenon in order to study the trend of the energy density spectrum as a function of the harmonic degree n.

Variations in outcomes by residential location for women with breast cancer: a systematic review

PubMed Central

Dasgupta, Paramita; Youlden, Danny R; Garvey, Gail; Aitken, Joanne F; Wallington, Isabella; Chynoweth, Jennifer; Zorbas, Helen; Youl, Philippa H

2018-01-01

Objectives To systematically assess the evidence for variations in outcomes at each step along the breast cancer continuum of care for Australian women by residential location. Design Systematic review. Methods Systematic searches of peer-reviewed articles in English published from 1 January 1990 to 24 November 2017 using PubMed, EMBASE, CINAHL and Informit databases. Inclusion criteria were: population was adult female patients with breast cancer; Australian setting; outcome measure was survival, patient or tumour characteristics, screening rates or frequencies, clinical management, patterns of initial care or post-treatment follow-up with analysis by residential location or studies involving non-metropolitan women only. Included studies were critically appraised using a modified Newcastle–Ottawa Scale. Results Seventy-four quantitative studies met the inclusion criteria. Around 59% were considered high quality, 34% moderate and 7% low. No eligible studies examining treatment choices or post-treatment follow-up were identified. Non-metropolitan women consistently had poorer survival, with most of this differential being attributed to more advanced disease at diagnosis, treatment-related factors and socioeconomic disadvantage. Compared with metropolitan women, non-metropolitan women were more likely to live in disadvantaged areas and had differing clinical management and patterns of care. However, findings regarding geographical variations in tumour characteristics or diagnostic outcomes were inconsistent. Conclusions A general pattern of poorer survival and variations in clinical management for Australian female patients with breast cancer from non-metropolitan areas was evident. However, the wide variability in data sources, measures, study quality, time periods and geographical classification made direct comparisons across studies challenging. The review highlighted the need to promote standardisation of geographical classifications and increased comparability of data systems. It also identified key gaps in the existing literature including a lack of studies on advanced breast cancer, geographical variations in treatment choices from the perspective of patients and post-treatment follow-up. PMID:29706597

Geographic Variation and Disparity in Stimulant Treatment of Adults and Children in the United States in 2008

PubMed Central

McDonald, Douglas C.; Jalbert, Sarah Kuck

2016-01-01

Objective This study estimated the prevalence of stimulant treatment among both adults and children at national, state, and county levels during 2008 and explored explanations for wide variations in treatment prevalence. Methods Records of 24.1 million stimulant prescriptions dispensed to insured and uninsured patients were obtained from approximately 76% of U.S. retail pharmacies. Data were weighted to estimate treatment prevalence on March 15, 2008, for all U.S. states and counties. Regression models were used to estimate the associations among the counties’ treatment rates and the characteristics of the counties and their resident populations. Results An estimated 2.5% of children ≤17 years of age (3.5% of males and 1.5% of females) and .6% of persons >17 years of age were being treated with stimulants in March 2008. Treatment prevalence among states varied widely, and variation among counties was even wider. Two-thirds of the variation among counties in treatment prevalence was associated with supply of physicians, socioeconomic composition of the population, and, among children, funding for special education. Rates of children and adults in treatment were highly correlated. Conclusions Wide variations in treatment prevalence signal disparities between established clinical practice guidelines and actual practice, especially for primary care, where most patients prescribed stimulants are managed. Better education and training for physicians may improve identification and treatment, thereby reducing disparities in care for attention-deficit hyperactivity disorder and other disabling conditions. PMID:23912601

Yellowstone bison genetics: let us move forward

USGS Publications Warehouse

Halbert, Natalie D.; Gogan, Peter J.P.; Hedrick, Philip W.; Wahl, Jacquelyn M.; Derr, James N.

2012-01-01

White and Wallen (2012) disagree with the conclusions and suggestions made in our recent assessment of population structure among Yellowstone National Park (YNP) bison based on 46 autosomal microsatellite loci in 661 animals (Halbert et al. 2012). First, they suggest that "the existing genetic substructure (that we observed) was artificially created." Specifically, they suggest that the substructure observed between the northern and central populations is the result of human activities, both historical and recent. In fact, the genetic composition of all known existing bison herds was created by, or has been influenced by, anthropogenic activities, although this obviously does not reduce the value of these herds for genetic conservation (Dratch and Gogan 2010). As perspective, many, if not most, species of conservation concern have been influenced by human actions and as a result currently exist as isolated populations. However, it is quite difficult to distinguish between genetic differences caused by human actions and important ancestral variation contained in separate populations without data from early time periods. Therefore, to not lose genetic variation that may be significant or indicative of important genetic variation, the generally acceptable management approach is to attempt to retain this variation based on the observed population genetic subdivision (Hedrick et al. 1986).

SEASONAL AND LONGITUDINAL HOMOGENEITY OF SUSPENDED PARTICLES IN SAN FRANCISCO BAY, CA

EPA Science Inventory

Coastal environments are particularly complex due to variations in geology and upstream watersheds, and are subject to dynamic spatial and temporal changes. Their diverse characteristics result in wide variations in response to environmental stressors such as nutrient over-enrich...

Genome-wide association study of rice grain width variation.

PubMed

Zheng, Xiao-Ming; Gong, Tingting; Ou, Hong-Ling; Xue, Dayuan; Qiao, Weihua; Wang, Junrui; Liu, Sha; Yang, Qingwen; Olsen, Kenneth M

2018-04-01

Seed size is variable within many plant species, and understanding the underlying genetic factors can provide insights into mechanisms of local environmental adaptation. Here we make use of the abundant genomic and germplasm resources available for rice (Oryza sativa) to perform a large-scale genome-wide association study (GWAS) of grain width. Grain width varies widely within the crop and is also known to show climate-associated variation across populations of its wild progenitor. Using a filtered dataset of >1.9 million genome-wide SNPs in a sample of 570 cultivated and wild rice accessions, we performed GWAS with two complementary models, GLM and MLM. The models yielded 10 and 33 significant associations, respectively, and jointly yielded seven candidate locus regions, two of which have been previously identified. Analyses of nucleotide diversity and haplotype distributions at these loci revealed signatures of selection and patterns consistent with adaptive introgression of grain width alleles across rice variety groups. The results provide a 50% increase in the total number of rice grain width loci mapped to date and support a polygenic model whereby grain width is shaped by gene-by-environment interactions. These loci can potentially serve as candidates for studies of adaptive seed size variation in wild grass species.

Strongly nonlinear parabolic variational inequalities.

PubMed

Browder, F E; Brézis, H

1980-02-01

An existence and uniqueness result is established for a general class of variational inequalities for parabolic partial differential equations of the form partial differentialu/ partial differentialt + A(u) + g(u) = f with g nondecreasing but satisfying no growth condition. The proof is based upon a type of compactness result for solutions of variational inequalities that should find a variety of other applications.

Test Format and the Variation of Gender Achievement Gaps within the United States

ERIC Educational Resources Information Center

Reardon, Sean; Fahle, Erin; Kalogrides, Demetra; Podolsky, Anne; Zarate, Rosalia

2016-01-01

Prior research demonstrates the existence of gender achievement gaps and the variation in the magnitude of these gaps across states. This paper characterizes the extent to which the variation of gender achievement gaps on standardized tests across the United States can be explained by differing state accountability test formats. A comprehensive…

Algal-bacterial co-variation in streams: a cross-stream comparison

Treesearch

Xueqing Gao; Ola A. Olapade; Mark W. Kershner; Laura G. Leff

2004-01-01

Algal-bacterial co-variation has been frequently observed in lentic and marine environments, but the existence of such relationships in lotic ecosystems is not well established. To examine possible co-variation, bacterial number and chlorophyll-a concentration in water and sediments of nine streams from different regions in the USA were examined. In the water, a strong...

Altitude and latitude variations in avionics SEU and atmospheric neutron flux

DOE Office of Scientific and Technical Information (OSTI.GOV)

Normand, E.; Baker, T.J.

1993-12-01

The direct cause of single event upsets in SRAMs at aircraft altitudes by the atmospheric neutrons has previously been documented. The variation of the in-flight SEU rate with latitude is demonstrated by new data over a wide range of geographical locations. New measurements and models of the atmospheric neutron flux are also evaluated to characterize its variation with altitude, latitude and solar activity.

Dental Caries Progression Among U.S. Marine Corps Personnel Following Operational Deployment

DTIC Science & Technology

2012-06-01

86 dental faculty members at 16 French universities, Tubert- Jeannin and colleagues37 found wide variation in restorative treatment thresholds...lesions, assessment of restorations, and treatment decisions, which ultimately led to variation in their 27     students’ treatment modalities...almost one-third of all teeth. This substantial variation among practitioners is most likely due to differences in individual practitioners’ criteria

An analysis of beak shape variation in two ages of domestic turkeys (Meleagris gallopavo) using landmark-based geometric morphometrics.

PubMed

Dalton, Hillary A; Wood, Benjamin J; Widowski, Tina M; Guerin, Michele T; Torrey, Stephanie

2017-01-01

The objective of this study was to assess beak shape variation in domestic turkeys (Meleagris gallopavo) and determine the effects of age, sex, and beak size on beak shape variation using geometric morphometrics. Dorsal and right lateral images were taken of 2442 turkeys at 6 and 18.5 weeks of age. Landmarks were digitized in tpsDig in three analyses of the dorsal upper mandible, lateral upper mandible, and lateral lower mandible shape of each turkey at both ages. The coordinate data were then subjected to a principal components analysis (PCA), multivariate regression, and a canonical variates analysis (CVA) with a Procrustes ANOVA in MorphoJ. For the dorsal images, three principal components (PCs) showed beak shape variation ranged from long, narrow, and pointed to short, wide, and blunt upper mandibles at both ages (6 weeks: 95.36%, 18.5 weeks: 92.21%). Three PCs showed the lateral upper mandible shape variation ranged from long, wide beaks with long, curved beak tips to short, narrow beaks with short, pointed beak tips at both ages (6 weeks: 94.91%, 18.5 weeks: 94.33%). Three PCs also explained 97.80% (6 weeks) and 97.11% (18.5 weeks) of the lateral lower mandible shape variation ranging from wide and round to narrow and thin lower mandibles with superior/inferior beak tip shifts. Beak size accounted for varying proportions of the beak shape variation (0.96-54.76%; P < 0.0001) in the three analyses of each age group. For all the analyses, the CVA showed sexual dimorphism in beak shape (P < 0.0001) with female upper mandibles appearing wider and blunter dorsally with long, curved beak tips laterally. Whereas male turkey upper mandibles had a narrow, pointed dorsal appearance and short, pointed beak tips laterally. Future applications of beak shape variability could have a genetic and welfare value by incorporating beak shape variation to select for specific turkey beak phenotypes as an alternative to beak treatment.

An analysis of beak shape variation in two ages of domestic turkeys (Meleagris gallopavo) using landmark-based geometric morphometrics

PubMed Central

Widowski, Tina M.; Guerin, Michele T.

2017-01-01

The objective of this study was to assess beak shape variation in domestic turkeys (Meleagris gallopavo) and determine the effects of age, sex, and beak size on beak shape variation using geometric morphometrics. Dorsal and right lateral images were taken of 2442 turkeys at 6 and 18.5 weeks of age. Landmarks were digitized in tpsDig in three analyses of the dorsal upper mandible, lateral upper mandible, and lateral lower mandible shape of each turkey at both ages. The coordinate data were then subjected to a principal components analysis (PCA), multivariate regression, and a canonical variates analysis (CVA) with a Procrustes ANOVA in MorphoJ. For the dorsal images, three principal components (PCs) showed beak shape variation ranged from long, narrow, and pointed to short, wide, and blunt upper mandibles at both ages (6 weeks: 95.36%, 18.5 weeks: 92.21%). Three PCs showed the lateral upper mandible shape variation ranged from long, wide beaks with long, curved beak tips to short, narrow beaks with short, pointed beak tips at both ages (6 weeks: 94.91%, 18.5 weeks: 94.33%). Three PCs also explained 97.80% (6 weeks) and 97.11% (18.5 weeks) of the lateral lower mandible shape variation ranging from wide and round to narrow and thin lower mandibles with superior/inferior beak tip shifts. Beak size accounted for varying proportions of the beak shape variation (0.96–54.76%; P < 0.0001) in the three analyses of each age group. For all the analyses, the CVA showed sexual dimorphism in beak shape (P < 0.0001) with female upper mandibles appearing wider and blunter dorsally with long, curved beak tips laterally. Whereas male turkey upper mandibles had a narrow, pointed dorsal appearance and short, pointed beak tips laterally. Future applications of beak shape variability could have a genetic and welfare value by incorporating beak shape variation to select for specific turkey beak phenotypes as an alternative to beak treatment. PMID:28934330

Sinonasal anatomical variations: their relationship with chronic rhinosinusitis and effect on the severity of disease-a computerized tomography assisted anatomical and clinical study.

PubMed

Kaygusuz, Ahmet; Haksever, Mehmet; Akduman, Davut; Aslan, Sündüs; Sayar, Zeynep

2014-09-01

The anatomy of the sinonasal area has a very wide rage of anatomical variations. The significance of these anatomical variations in pathogenesis of rhinosinusitis, which is the commonest disease in the region, is still unclear. The aims of the study were to compare the rate of sinonasal anatomical variations with development and severity of chronic rhinosinusitis patients. CT scan of paranasal sinuses images of 99 individuals were retrospectively reviewed. 65 cases of chronic rhinosinusitis (study group) who had undergone endoscopic sinus surgery were compared with 34 cases without chronic rhinosinusitis (control group). Also in study group Lund-Mackay score of the sinus disease were calculated and compared to the rate of related anatomical variations. There were 74 (74.7 %) males and 25 (25.2 %) females with ages ranging from 13 to 70 years (mean 32.2 years). The anatomical variations recorded were: Septal deviation 47 (72.3) in study and 25 (73.5 %) in control group, concha bullosa 27 (41.5 %) in study and 18 (52.9 %) in control group, overpneumatized ethmoid bulla 17 (26.1 %) in study and 14 (41.1 %) in control group, pneumatized uncinate 3 (4.6 %) in study and 3 (8.8 %) in control group, agger nasi 42 (64.6 %) in study and 19 (55.8 %) in control group, paradoxical middle turbinates 9 (13.8 %) in study and 4 (11.7 %) in control group, Onodi cell 6 (9.2 %) in study and 2 (5.8 %) in control group, Haller's cells (infraorbital ethmoid cell) 9 (13.8 %) in study and 7 (20.5 %) in control group. None of these results were statistically significant between study and control group (p > 0.05). Lund-Mackay score (which was assumed to show the severity of the disease) of the maxillary, ethmoid and frontal sinus were calculated and compared to rate of septal deviation, concha bullosa, agger nasi cells. No significant correlation was conducted (p > 0.05). The results of study showed no statistically significant correlation between sinonasal anatomical variations and pathologies of the paranasal sinus. Also these anatomical variations did not increase the severity of pre-existing sinusitis significantly. This is a retrospective cohort study (2b).

Animal breeding strategies can improve meat quality attributes within entire populations.

PubMed

Berry, D P; Conroy, S; Pabiou, T; Cromie, A R

2017-10-01

The contribution of animal breeding to changes in animal performance is well documented across a range of species. Once genetic variation in a trait exists, then breeding to improve the characteristics of that trait is possible, if so desired. Considerable genetic variation exists in a range of meat quality attributes across a range of species. The genetic variation that exists for meat quality is as large as observed for most performance traits; thus, within a well-structured breeding program, rapid genetic gain for meat quality could be possible. The rate of genetic gain can be augmented through the integration of DNA-based technologies into the breeding program; such DNA-based technologies should, however, be based on thousands of DNA markers dispersed across the entire genome. Genetic and genomic technologies can also have beneficial impact outside the farm gate as a tool to segregate carcasses or meat cuts based on expected meat quality features. Copyright © 2017 Elsevier Ltd. All rights reserved.

Poster exhibitions at conferences: are we doing it properly?

PubMed

Beamish, Andrew J; Ansell, James; Foster, Jessica J; Foster, Kathryn A; Egan, Richard J

2015-01-01

Literature exploring the educational value and quality of conference poster presentation is scarce. The aim of this study was to identify and describe the variation in poster exhibitions across a spectrum of conferences attended by trainees. Prospective observational assessment of conference posters was carried out across 7 variables at 4 conferences attended by surgical trainees in 2012. Posters were compared by individual variables and according to overall poster score combining all 7 variables examined. The number of authors listed was also compared. Random samples of consecutively numbered posters were examined at the exhibitions of 4 conferences, which included a UK national medical education conference (Association for the Study of Medical Education), a UK international surgical conference (Association of Surgeons of Great Britain and Ireland), a European oncology conference (European Society of Surgical Oncology), and a North American joint medical and surgical conference (Digestive Diseases Week). Significant variation existed between conferences in posters and their presentation. The proportion of presenters failing to display their posters ranged from 3% to 26% (p < 0.0001). Adherence to size guidelines varied from 89% to 100% (p = 0.002). The inclusion of references ranged from 19% to 82% (p < 0.0001). The presence of a presenting author during the allocated session varied widely from 21% to 86% (p < 0.0001). No significant variation was observed in the proportion of posters that were formatted using aims, methods, results, and conclusion sections (81%-93%; p = 0.513) or in the proportion of posters that were identified as difficult to read (24%-28%; p = 0.919). Association for the Study of Medical Education outperformed each of the other exhibitions overall (p < 0.0001). Posters with greater than the median of 4 authors performed significantly better across all areas (p < 0.0001-0.042) except presenter attendance (p = 0.480). Poster exhibitions varied widely, with room for improvement at all 4 conferences. Lessons can be learned by all conferences from each other to improve presenter engagement with and the educational value of poster exhibitions. Copyright © 2014 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

PubMed Central

Urrestarazu, Jorge; Muranty, Hélène; Denancé, Caroline; Leforestier, Diane; Ravon, Elisa; Guyader, Arnaud; Guisnel, Rémi; Feugey, Laurence; Aubourg, Sébastien; Celton, Jean-Marc; Daccord, Nicolas; Dondini, Luca; Gregori, Roberto; Lateur, Marc; Houben, Patrick; Ordidge, Matthew; Paprstein, Frantisek; Sedlak, Jiri; Nybom, Hilde; Garkava-Gustavsson, Larisa; Troggio, Michela; Bianco, Luca; Velasco, Riccardo; Poncet, Charles; Théron, Anthony; Moriya, Shigeki; Bink, Marco C. A. M.; Laurens, François; Tartarini, Stefano; Durel, Charles-Eric

2017-01-01

Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs. PMID:29176988

A three-dimensional meso-macroscopic model for Li-Ion intercalation batteries

DOE PAGES

Allu, S.; Kalnaus, S.; Simunovic, S.; ...

2016-06-09

Through this study, we present a three-dimensional computational formulation for electrode-electrolyte-electrode system of Li-Ion batteries. The physical consistency between electrical, thermal and chemical equations is enforced at each time increment by driving the residual of the resulting coupled system of nonlinear equations to zero. The formulation utilizes a rigorous volume averaging approach typical of multiphase formulations used in other fields and recently extended to modeling of supercapacitors [1]. Unlike existing battery modeling methods which use segregated solution of conservation equations and idealized geometries, our unified approach can model arbitrary battery and electrode configurations. The consistency of multi-physics solution also allowsmore » for consideration of a wide array of initial conditions and load cases. The formulation accounts for spatio-temporal variations of material and state properties such as electrode/void volume fractions and anisotropic conductivities. The governing differential equations are discretized using the finite element method and solved using a nonlinearly consistent approach that provides robust stability and convergence. The new formulation was validated for standard Li-ion cells and compared against experiments. Finally, its scope and ability to capture spatio-temporal variations of potential and lithium distribution is demonstrated on a prototypical three-dimensional electrode problem.« less

Cloud Macroscopic Organization: Order Emerging from Randomness

NASA Technical Reports Server (NTRS)

Yuan, Tianle

2011-01-01

Clouds play a central role in many aspects of the climate system and their forms and shapes are remarkably diverse. Appropriate representation of clouds in climate models is a major challenge because cloud processes span at least eight orders of magnitude in spatial scales. Here we show that there exists order in cloud size distribution of low-level clouds, and that it follows a power-law distribution with exponent gamma close to 2. gamma is insensitive to yearly variations in environmental conditions, but has regional variations and land-ocean contrasts. More importantly, we demonstrate this self-organizing behavior of clouds emerges naturally from a complex network model with simple, physical organizing principles: random clumping and merging. We also demonstrate symmetry between clear and cloudy skies in terms of macroscopic organization because of similar fundamental underlying organizing principles. The order in the apparently complex cloud-clear field thus has its root in random local interactions. Studying cloud organization with complex network models is an attractive new approach that has wide applications in climate science. We also propose a concept of cloud statistic mechanics approach. This approach is fully complementary to deterministic models, and the two approaches provide a powerful framework to meet the challenge of representing clouds in our climate models when working in tandem.

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing

NASA Astrophysics Data System (ADS)

Ferreira, Pedro G.; Oti, Martin; Barann, Matthias; Wieland, Thomas; Ezquina, Suzana; Friedländer, Marc R.; Rivas, Manuel A.; Esteve-Codina, Anna; Estivill, Xavier; Guigó, Roderic; Dermitzakis, Emmanouil; Antonarakis, Stylianos; Meitinger, Thomas; Strom, Tim M.; Palotie, Aarno; François Deleuze, Jean; Sudbrak, Ralf; Lerach, Hans; Gut, Ivo; Syvänen, Ann-Christine; Gyllensten, Ulf; Schreiber, Stefan; Rosenstiel, Philip; Brunner, Han; Veltman, Joris; Hoen, Peter A. C. T.; Jan van Ommen, Gert; Carracedo, Angel; Brazma, Alvis; Flicek, Paul; Cambon-Thomsen, Anne; Mangion, Jonathan; Bentley, David; Hamosh, Ada; Rosenstiel, Philip; Strom, Tim M.; Lappalainen, Tuuli; Guigó, Roderic; Sammeth, Michael

2016-09-01

Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA- and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-individual genetic impact on gene expression viable. Employing mRNA-sequencing data from the Geuvadis Project and genome sequencing data from the 1000 Genomes Project we show that the computational analysis of DNA sequences around splice sites and poly-A signals is able to explain several observations in the phenotype data. In contrast to widespread assessments of statistically significant associations between DNA polymorphisms and quantitative traits, we developed a computational tool to pinpoint the molecular mechanisms by which genetic markers drive variation in RNA-processing, cataloguing and classifying alleles that change the affinity of core RNA elements to their recognizing factors. The in silico models we employ further suggest RNA editing can moonlight as a splicing-modulator, albeit less frequently than genomic sequence diversity. Beyond existing annotations, we demonstrate that the ultra-high resolution of RNA-Seq combined from 462 individuals also provides evidence for thousands of bona fide novel elements of RNA processing—alternative splice sites, introns, and cleavage sites—which are often rare and lowly expressed but in other characteristics similar to their annotated counterparts.

Agricultural Management Practices Explain Variation in Global Yield Gaps of Major Crops

NASA Astrophysics Data System (ADS)

Mueller, N. D.; Gerber, J. S.; Ray, D. K.; Ramankutty, N.; Foley, J. A.

2010-12-01

The continued expansion and intensification of agriculture are key drivers of global environmental change. Meeting a doubling of food demand in the next half-century will further induce environmental change, requiring either large cropland expansion into carbon- and biodiversity-rich tropical forests or increasing yields on existing croplands. Closing the “yield gaps” between the most and least productive farmers on current agricultural lands is a necessary and major step towards preserving natural ecosystems and meeting future food demand. Here we use global climate, soils, and cropland datasets to quantify yield gaps for major crops using equal-area climate analogs. Consistent with previous studies, we find large yield gaps for many crops in Eastern Europe, tropical Africa, and parts of Mexico. To analyze the drivers of yield gaps, we collected sub-national agricultural management data and built a global dataset of fertilizer application rates for over 160 crops. We constructed empirical crop yield models for each climate analog using the global management information for 17 major crops. We find that our climate-specific models explain a substantial amount of the global variation in yields. These models could be widely applied to identify management changes needed to close yield gaps, analyze the environmental impacts of agricultural intensification, and identify climate change adaptation techniques.

Intraspecific variation in exploratory behavior and elevational affinity in a widely distributed songbird.

PubMed

Poblete, Yanina; Gutiérrez, Víctor; Cid, Valeska; Newsome, Seth D; Sabat, Pablo; Vasquez, Rodrigo A

2018-04-01

Populations of the same species can vary substantially in their behavioral and morphometric traits when they are subject to different environmental pressures, which may lead to the development of different adaptive strategies. We quantified variation in exploratory behavior and morphometric traits among two rufous-collared sparrow populations that occur at low and high elevations in central Chile. Moreover, we used census and δ 2 H values of feather and blood to evaluate migration. We found that individual sparrows inhabiting high elevations were larger and showed more intense exploratory behavior in comparison with those that were captured at lower elevation. Moreover, we observed a steady decline in sparrow abundance during the winter and similar δ 2 H values for blood collected in the winter and summer at this site, which were significantly lower than blood δ 2 H values observed at low elevation. This pattern suggests that individuals do not move long distances during winter, and likely they remain at similar elevations in refuge habitats. As predicted, our results support the existent of different adaptive strategies among populations of the same species, and suggest that the combination of behavioral, morphometric, and stable isotope data is a novel and robust integrative approach to assess differences in adaptation across environmental gradients.

Mutation intolerant genes and targets of FMRP are enriched for nonsynonymous alleles in schizophrenia.

PubMed

Leonenko, Ganna; Richards, Alexander L; Walters, James T; Pocklington, Andrew; Chambert, Kimberly; Al Eissa, Mariam M; Sharp, Sally I; O'Brien, Niamh L; Curtis, David; Bass, Nicholas J; McQuillin, Andrew; Hultman, Christina; Moran, Jennifer L; McCarroll, Steven A; Sklar, Pamela; Neale, Benjamin M; Holmans, Peter A; Owen, Michael J; Sullivan, Patrick F; O'Donovan, Michael C

2017-10-01

Risk of schizophrenia is conferred by alleles occurring across the full spectrum of frequencies from common SNPs of weak effect through to ultra rare alleles, some of which may be moderately to highly penetrant. Previous studies have suggested that some of the risk of schizophrenia is attributable to uncommon alleles represented on Illumina exome arrays. Here, we present the largest study of exomic variation in schizophrenia to date, using samples from the United Kingdom and Sweden (10,011 schizophrenia cases and 13,791 controls). Single variants, genes, and gene sets were analyzed for association with schizophrenia. No single variant or gene reached genome-wide significance. Among candidate gene sets, we found significant enrichment for rare alleles (minor allele frequency [MAF] < 0.001) in genes intolerant of loss-of-function (LoF) variation and in genes whose messenger RNAs bind to fragile X mental retardation protein (FMRP). We further delineate the genetic architecture of schizophrenia by excluding a role for uncommon exomic variants (0.01 ≤ MAF ≥ 0.001) that confer a relatively large effect (odds ratio [OR] > 4). We also show risk alleles within this frequency range exist, but confer smaller effects and should be identified by larger studies. © 2017 Wiley Periodicals, Inc.

Three-Dimensional Piecewise-Continuous Class-Shape Transformation of Wings

NASA Technical Reports Server (NTRS)

Olson, Erik D.

2015-01-01

Class-Shape Transformation (CST) is a popular method for creating analytical representations of the surface coordinates of various components of aerospace vehicles. A wide variety of two- and three-dimensional shapes can be represented analytically using only a modest number of parameters, and the surface representation is smooth and continuous to as fine a degree as desired. This paper expands upon the original two-dimensional representation of airfoils to develop a generalized three-dimensional CST parametrization scheme that is suitable for a wider range of aircraft wings than previous formulations, including wings with significant non-planar shapes such as blended winglets and box wings. The method uses individual functions for the spanwise variation of airfoil shape, chord, thickness, twist, and reference axis coordinates to build up the complete wing shape. An alternative formulation parameterizes the slopes of the reference axis coordinates in order to relate the spanwise variation to the tangents of the sweep and dihedral angles. Also discussed are methods for fitting existing wing surface coordinates, including the use of piecewise equations to handle discontinuities, and mathematical formulations of geometric continuity constraints. A subsonic transport wing model is used as an example problem to illustrate the application of the methodology and to quantify the effects of piecewise representation and curvature constraints.

Medicare part D and the nursing home setting.

PubMed

Stevenson, David G; Huskamp, Haiden A; Newhouse, Joseph P

2008-08-01

The purpose of this article is to explore how the introduction of Medicare Part D is changing the operations of long-term-care pharmacies (LTCPs) and nursing homes, as well as implications of those changes for nursing home residents. We reviewed existing sources of information and interviewed stakeholders across various perspectives. We conducted 31 semistructured telephone interviews with key stakeholders between November 2006 and January 2007. Part D represents a substantial departure from how prescription drugs were previously financed and administered in nursing homes, and nursing home providers and LTCPs have struggled in adapting to some of these changes. Part D increased the variation around formularies and drug management processes for residents at the facility level, creating additional burden on clinical and pharmacy staff and introducing a tension between facilities' need to dispense medications quickly and assuring of coverage for those drugs. Nursing home and LTCP stakeholders perceive wide variation across Part D plans in their ability to meet the needs of nursing home residents. Although LTCPs, nursing homes and their clinicians, and Part D plans will gain experience with the benefit in the nursing home setting over time, stakeholders we interviewed identified a range of longer term issues and questions that merit attention as the benefit proceeds.

Medicare Part D and the Nursing Home Setting

PubMed Central

Stevenson, David G.; Huskamp, Haiden A.; Newhouse, Joseph P.

2008-01-01

Purpose To explore how Medicare Part D's introduction is changing the operations of long-term care pharmacies (LTCPs) and nursing homes, as well as implications of those changes for nursing home residents. Design and Methods We reviewed existing sources of information and interviewed stakeholders across various perspectives. Thirty-one semi-structured, telephone interviews were conducted with key stakeholders between November 2006 and January 2007. Results Part D represents a substantial departure from how prescription drugs were previously financed and administered in nursing homes, and nursing home providers and LTCPs have struggled in adapting to some of these changes. Part D increased the variation around formularies and drug management processes for residents at the facility level, creating additional burden on clinical and pharmacy staff and introducing a tension between facilities' need to dispense medications quickly and assuring coverage for those drugs. Nursing home and LTCP stakeholders perceive wide variation across Part D plans in their ability to meet the needs of nursing home residents. Implications Although LTCPs, nursing homes and their clinicians, and Part D plans will gain experience with the benefit in the nursing home setting over time, stakeholders we interviewed identified a range of longer-term issues and questions that merit attention as the benefit proceeds. PMID:18728293

A critical analysis of the current state of neurosurgery training in Pakistan

PubMed Central

Shamim, M. Shahzad; Tahir, M. Zubair; Godil, Saniya Siraj; Kumar, Rajesh; Siddiqui, Arshad Ali

2011-01-01

Objective: To observe interdepartmental variation in the availability of resources and academic activities within the various neurosurgery programs of Pakistan. Methods: This was a proforma-based survey of neurosurgery trainees and young neurosurgeons of Pakistan, looking at the academic infrastructure and output of their programs. The proforma was filled by 36 respondents from 11 neurosurgery centers of the country. All these centers were accredited for neurosurgery training in Pakistan. Results: Out of the 36 respondents, 30 were completing a Fellowship training (FCPS) and six were enrolled for a Master in Surgery (MS) program. About 80% of the participants used the Youman's Textbook of Neurosurgery as a reference book. Only 40% of the candidates had access to more than one indexed neurosurgery journal. Structured academic sessions (e.g., journal clubs and neuropathology meetings) were lacking in a majority of the training institutes, 95% of the trainees had no microsurgical laboratory experience, and modern neurosurgical tools (frameless neuronavigation system, neuroendoscopy) were in use at a few centers only. Conclusion: Neurosurgery training in Pakistan is not uniform and wide variations exist between the programs at the centers evaluated. We recommend exchange programs between centers at national and international levels, to allow trainees to gain first-hand exposure to training components not available in their own center. PMID:22276237

Anthropometric Measurements Usage in Medical Sciences

PubMed Central

Utkualp, Nevin; Ercan, Ilker

2015-01-01

Morphometry is introduced as quantitative approach to seek information concerning variations and changes in the forms of organisms that described the relationship between the human body and disease. Scientists of all civilization, who existed until today, examined the human body using anthropometric methods. For these reasons, anthropometric data are used in many contexts to screen for or monitor disease. Anthropometry, a branch of morphometry, is the study of the size and shape of the components of biological forms and their variations in populations. Morphometrics can also be defined as the quantitative analysis of biological forms. The field has developed rapidly over the last two decades to the extent that we now distinguish between traditional morphometrics and the more recent geometric morphometrics. Advances in imaging technology have resulted in the protection of a greater amount of morphological information and have permitted the analysis of this information. The oldest and most commonly used of these methods is radiography. With developments in this area, CT and MRI have also been started to be used in screening of the internal organs. Morphometric measurements that are used in medicine, are widely used in the diagnosis and the follow-up and the treatment of the disease, today. In addition, in cosmetology use of these new measurements is increasing every day. PMID:26413519

Cannibals in space: the coevolution of cannibalism and dispersal in spatially structured populations.

PubMed

Rudolf, Volker H W; Kamo, Masashi; Boots, Mike

2010-05-01

The propensity for cannibalism varies considerably both within and between species. Currently we have little understanding of both the causes of this variation and its evolutionary consequences for other life-history traits. We examine how different levels of spatial structure affect the evolution of cannibalism and how cannibalism in turn drives the evolution of dispersal. Using pair approximations and simulations, we show that cannibalism can easily evolve in spatially structured populations as long as some dispersal exists. Furthermore, for a wide range of intermediate levels of spatial structure, we find the possibility of evolutionary branching leading to polymorphism in cannibalism. We also show that cannibalism itself can have important evolutionary consequences and select for increased dispersal rates, thus helping to determine the spatial structure of populations. The coevolution of cannibalism and dispersal results in the evolution of various alternative life-history strategies with different dispersal and cannibalism regimes. Which strategy evolves depends on the environmental conditions that determine initial cannibalism rates. Our results therefore suggest that differences in spatial structure could explain variation in the propensity for cannibalism and cannibalistic polyphenism. Furthermore, results emphasize that cannibalism can drive the evolution of other life-history traits and determine the spatial structure of natural populations.

The American Quarter Horse: Population Structure and Relationship to the Thoroughbred

PubMed Central

2014-01-01

A breed known for its versatility, the American Quarter Horse (QH), is increasingly bred for performance in specific disciplines. The impact of selective breeding on the diversity and structure of the QH breed was evaluated using pedigree analysis and genome-wide SNP data from horses representing 6 performance groups (halter, western pleasure, reining, working cow, cutting, and racing). Genotype data (36 037 single nucleotide polymorphisms [SNPs]) from 36 Thoroughbreds were also evaluated with those from the 132 performing QHs to evaluate the Thoroughbred’s influence on QH diversity. Results showed significant population structure among all QH performance groups excepting the comparison between the cutting and working cow horses; divergence was greatest between the cutting and racing QHs, the latter of which had a large contribution of Thoroughbred ancestry. Significant coancestry and the potential for inbreeding exist within performance groups, especially when considering the elite performers. Relatedness within performance groups is increasing with popular sires contributing disproportionate levels of variation to each discipline. Expected heterozygosity, inbreeding, F ST, cluster, and haplotype analyses suggest these QHs can be broadly classified into 3 categories: stock, racing, and pleasure/halter. Although the QH breed as a whole contains substantial genetic diversity, current breeding practices have resulted in this variation being sequestered into subpopulations. PMID:24293614

Evidence for weak genetic recombination at the PTP2 locus of Nosema ceranae.

PubMed

Gómez-Moracho, Tamara; Bartolomé, Carolina; Martín-Hernández, Raquel; Higes, Mariano; Maside, Xulio

2015-04-01

The microsporidian Nosema ceranae is an emergent pathogen that threatens the health of honeybees and other pollinators all over the world. Its recent rapid spread across a wide variety of host species and environments demonstrated an enhanced ability of adaptation, which seems to contradict the lack of evidence for genetic recombination and the absence of a sexual stage in its life cycle. Here we retrieved fresh data of the patterns of genetic variation at the PTP2 locus in naturally infected Apis mellifera colonies, by means of single genome amplification. This technique, designed to prevent the formation of chimeric haplotypes during polymerase chain reaction (PCR), provides more reliable estimates of the diversity levels and haplotype structure than standard PCR-cloning methods. Our results are consistent with low but significant rates of recombination in the history of the haplotypes detected: estimates of the population recombination rate are of the order of 30 and support recent evidence for unexpectedly high levels of variation of the parasites within honeybee colonies. These observations suggest the existence of a diploid stage at some point in the life cycle of this parasite and are relevant for our understanding of the dynamics of its expanding population. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparative assessment of bioanalytical method validation guidelines for pharmaceutical industry.

PubMed

Kadian, Naveen; Raju, Kanumuri Siva Rama; Rashid, Mamunur; Malik, Mohd Yaseen; Taneja, Isha; Wahajuddin, Muhammad

2016-07-15

The concepts, importance, and application of bioanalytical method validation have been discussed for a long time and validation of bioanalytical methods is widely accepted as pivotal before they are taken into routine use. United States Food and Drug Administration (USFDA) guidelines issued in 2001 have been referred for every guideline released ever since; may it be European Medical Agency (EMA) Europe, National Health Surveillance Agency (ANVISA) Brazil, Ministry of Health and Labour Welfare (MHLW) Japan or any other guideline in reference to bioanalytical method validation. After 12 years, USFDA released its new draft guideline for comments in 2013, which covers the latest parameters or topics encountered in bioanalytical method validation and approached towards the harmonization of bioanalytical method validation across the globe. Even though the regulatory agencies have general agreement, significant variations exist in acceptance criteria and methodology. The present review highlights the variations, similarities and comparison between bioanalytical method validation guidelines issued by major regulatory authorities worldwide. Additionally, other evaluation parameters such as matrix effect, incurred sample reanalysis including other stability aspects have been discussed to provide an ease of access for designing a bioanalytical method and its validation complying with the majority of drug authority guidelines. Copyright © 2016. Published by Elsevier B.V.

Copy Number Variations in Tilapia Genomes.

PubMed

Li, Bi Jun; Li, Hong Lian; Meng, Zining; Zhang, Yong; Lin, Haoran; Yue, Gen Hua; Xia, Jun Hong

2017-02-01

Discovering the nature and pattern of genome variation is fundamental in understanding phenotypic diversity among populations. Although several millions of single nucleotide polymorphisms (SNPs) have been discovered in tilapia, the genome-wide characterization of larger structural variants, such as copy number variation (CNV) regions has not been carried out yet. We conducted a genome-wide scan for CNVs in 47 individuals from three tilapia populations. Based on 254 Gb of high-quality paired-end sequencing reads, we identified 4642 distinct high-confidence CNVs. These CNVs account for 1.9% (12.411 Mb) of the used Nile tilapia reference genome. A total of 1100 predicted CNVs were found overlapping with exon regions of protein genes. Further association analysis based on linear model regression found 85 CNVs ranging between 300 and 27,000 base pairs significantly associated to population types (R 2  > 0.9 and P > 0.001). Our study sheds first insights on genome-wide CNVs in tilapia. These CNVs among and within tilapia populations may have functional effects on phenotypes and specific adaptation to particular environments.

A Sequential Shifting Algorithm for Variable Rotor Speed Control

NASA Technical Reports Server (NTRS)

Litt, Jonathan S.; Edwards, Jason M.; DeCastro, Jonathan A.

2007-01-01

A proof of concept of a continuously variable rotor speed control methodology for rotorcraft is described. Variable rotor speed is desirable for several reasons including improved maneuverability, agility, and noise reduction. However, it has been difficult to implement because turboshaft engines are designed to operate within a narrow speed band, and a reliable drive train that can provide continuous power over a wide speed range does not exist. The new methodology proposed here is a sequential shifting control for twin-engine rotorcraft that coordinates the disengagement and engagement of the two turboshaft engines in such a way that the rotor speed may vary over a wide range, but the engines remain within their prescribed speed bands and provide continuous torque to the rotor; two multi-speed gearboxes facilitate the wide rotor speed variation. The shifting process begins when one engine slows down and disengages from the transmission by way of a standard freewheeling clutch mechanism; the other engine continues to apply torque to the rotor. Once one engine disengages, its gear shifts, the multi-speed gearbox output shaft speed resynchronizes and it re-engages. This process is then repeated with the other engine. By tailoring the sequential shifting, the rotor may perform large, rapid speed changes smoothly, as demonstrated in several examples. The emphasis of this effort is on the coordination and control aspects for proof of concept. The engines, rotor, and transmission are all simplified linear models, integrated to capture the basic dynamics of the problem.

Shared genetic basis for migraine and ischemic stroke: A genome-wide analysis of common variants.

PubMed

Malik, Rainer; Freilinger, Tobias; Winsvold, Bendik S; Anttila, Verneri; Vander Heiden, Jason; Traylor, Matthew; de Vries, Boukje; Holliday, Elizabeth G; Terwindt, Gisela M; Sturm, Jonathan; Bis, Joshua C; Hopewell, Jemma C; Ferrari, Michel D; Rannikmae, Kristiina; Wessman, Maija; Kallela, Mikko; Kubisch, Christian; Fornage, Myriam; Meschia, James F; Lehtimäki, Terho; Sudlow, Cathie; Clarke, Robert; Chasman, Daniel I; Mitchell, Braxton D; Maguire, Jane; Kaprio, Jaakko; Farrall, Martin; Raitakari, Olli T; Kurth, Tobias; Ikram, M Arfan; Reiner, Alex P; Longstreth, W T; Rothwell, Peter M; Strachan, David P; Sharma, Pankaj; Seshadri, Sudha; Quaye, Lydia; Cherkas, Lynn; Schürks, Markus; Rosand, Jonathan; Ligthart, Lannie; Boncoraglio, Giorgio B; Davey Smith, George; van Duijn, Cornelia M; Stefansson, Kari; Worrall, Bradford B; Nyholt, Dale R; Markus, Hugh S; van den Maagdenberg, Arn M J M; Cotsapas, Chris; Zwart, John A; Palotie, Aarno; Dichgans, Martin

2015-05-26

To quantify genetic overlap between migraine and ischemic stroke (IS) with respect to common genetic variation. We applied 4 different approaches to large-scale meta-analyses of genome-wide data on migraine (23,285 cases and 95,425 controls) and IS (12,389 cases and 62,004 controls). First, we queried known genome-wide significant loci for both disorders, looking for potential overlap of signals. We then analyzed the overall shared genetic load using polygenic scores and estimated the genetic correlation between disease subtypes using data derived from these models. We further interrogated genomic regions of shared risk using analysis of covariance patterns between the 2 phenotypes using cross-phenotype spatial mapping. We found substantial genetic overlap between migraine and IS using all 4 approaches. Migraine without aura (MO) showed much stronger overlap with IS and its subtypes than migraine with aura (MA). The strongest overlap existed between MO and large artery stroke (LAS; p = 6.4 × 10(-28) for the LAS polygenic score in MO) and between MO and cardioembolic stroke (CE; p = 2.7 × 10(-20) for the CE score in MO). Our findings indicate shared genetic susceptibility to migraine and IS, with a particularly strong overlap between MO and both LAS and CE pointing towards shared mechanisms. Our observations on MA are consistent with a limited role of common genetic variants in this subtype. © 2015 American Academy of Neurology.

Challenges and Opportunities in Genome-Wide Environmental Interaction (GWEI) studies

PubMed Central

Aschard, Hugues; Lutz, Sharon; Maus, Bärbel; Duell, Eric J.; Fingerlin, Tasha; Chatterjee, Nilanjan; Kraft, Peter; Van Steen, Kristel

2012-01-01

The interest in performing gene-environment interaction studies has seen a significant increase with the increase of advanced molecular genetics techniques. Practically, it became possible to investigate the role of environmental factors in disease risk and hence to investigate their role as genetic effect modifiers. The understanding that genetics is important in the uptake and metabolism of toxic substances is an example of how genetic profiles can modify important environmental risk factors to disease. Several rationales exist to set up gene-environment interaction studies and the technical challenges related to these studies – when the number of environmental or genetic risk factors is relatively small – has been described before. In the post-genomic era, it is now possible to study thousands of genes and their interaction with the environment. This brings along a whole range of new challenges and opportunities. Despite a continuing effort in developing efficient methods and optimal bioinformatics infrastructures to deal with the available wealth of data, the challenge remains how to best present and analyze Genome-Wide Environmental Interaction (GWEI) studies involving multiple genetic and environmental factors. Since GWEIs are performed at the intersection of statistical genetics, bioinformatics and epidemiology, usually similar problems need to be dealt with as for Genome-Wide Association gene-gene Interaction (GWAI) studies. However, additional complexities need to be considered which are typical for large-scale epidemiological studies, but are also related to “joining” two heterogeneous types of data in explaining complex disease trait variation or for prediction purposes. PMID:22760307

Practical considerations to guide development of access controls and decision support for genetic information in electronic medical records.

PubMed

Darcy, Diana C; Lewis, Eleanor T; Ormond, Kelly E; Clark, David J; Trafton, Jodie A

2011-11-02

Genetic testing is increasingly used as a tool throughout the health care system. In 2011 the number of clinically available genetic tests is approaching 2,000, and wide variation exists between these tests in their sensitivity, specificity, and clinical implications, as well as the potential for discrimination based on the results. As health care systems increasingly implement electronic medical record systems (EMRs) they must carefully consider how to use information from this wide spectrum of genetic tests, with whom to share information, and how to provide decision support for clinicians to properly interpret the information. Although some characteristics of genetic tests overlap with other medical test results, there are reasons to make genetic test results widely available to health care providers and counterbalancing reasons to restrict access to these test results to honor patient preferences, and avoid distracting or confusing clinicians with irrelevant but complex information. Electronic medical records can facilitate and provide reasonable restrictions on access to genetic test results and deliver education and decision support tools to guide appropriate interpretation and use. This paper will serve to review some of the key characteristics of genetic tests as they relate to design of access control and decision support of genetic test information in the EMR, emphasizing the clear need for health information technology (HIT) to be part of optimal implementation of genetic medicine, and the importance of understanding key characteristics of genetic tests when designing HIT applications.

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

PubMed Central

2017-01-01

The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species. PMID:29181279

Charge Diffusion Variations in Pan-STARRS1 CCDs

NASA Astrophysics Data System (ADS)

Magnier, Eugene A.; Tonry, J. L.; Finkbeiner, D.; Schlafly, E.; Burgett, W. S.; Chambers, K. C.; Flewelling, H. A.; Hodapp, K. W.; Kaiser, N.; Kudritzki, R.-P.; Metcalfe, N.; Wainscoat, R. J.; Waters, C. Z.

2018-06-01

Thick back-illuminated deep-depletion CCDs have superior quantum efficiency over previous generations of thinned and traditional thick CCDs. As a result, they are being used for wide-field imaging cameras in several major projects. We use observations from the Pan-STARRS 3π survey to characterize the behavior of the deep-depletion devices used in the Pan-STARRS 1 Gigapixel Camera. We have identified systematic spatial variations in the photometric measurements and stellar profiles that are similar in pattern to the so-called “tree rings” identified in devices used by other wide-field cameras (e.g., DECam and Hypersuprime Camera). The tree-ring features identified in these other cameras result from lateral electric fields that displace the electrons as they are transported in the silicon to the pixel location. In contrast, we show that the photometric and morphological modifications observed in the GPC1 detectors are caused by variations in the vertical charge transportation rate and resulting charge diffusion variations.

Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors.

PubMed

Patin, Etienne; Hasan, Milena; Bergstedt, Jacob; Rouilly, Vincent; Libri, Valentina; Urrutia, Alejandra; Alanio, Cécile; Scepanovic, Petar; Hammer, Christian; Jönsson, Friederike; Beitz, Benoît; Quach, Hélène; Lim, Yoong Wearn; Hunkapiller, Julie; Zepeda, Magge; Green, Cherie; Piasecka, Barbara; Leloup, Claire; Rogge, Lars; Huetz, François; Peguillet, Isabelle; Lantz, Olivier; Fontes, Magnus; Di Santo, James P; Thomas, Stéphanie; Fellay, Jacques; Duffy, Darragh; Quintana-Murci, Lluís; Albert, Matthew L

2018-03-01

The quantification and characterization of circulating immune cells provide key indicators of human health and disease. To identify the relative effects of environmental and genetic factors on variation in the parameters of innate and adaptive immune cells in homeostatic conditions, we combined standardized flow cytometry of blood leukocytes and genome-wide DNA genotyping of 1,000 healthy, unrelated people of Western European ancestry. We found that smoking, together with age, sex and latent infection with cytomegalovirus, were the main non-genetic factors that affected variation in parameters of human immune cells. Genome-wide association studies of 166 immunophenotypes identified 15 loci that showed enrichment for disease-associated variants. Finally, we demonstrated that the parameters of innate cells were more strongly controlled by genetic variation than were those of adaptive cells, which were driven by mainly environmental exposure. Our data establish a resource that will generate new hypotheses in immunology and highlight the role of innate immunity in susceptibility to common autoimmune diseases.

Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster

PubMed Central

Dobson, Adam J.; Chaston, John M.; Newell, Peter D.; Donahue, Leanne; Hermann, Sara L.; Sannino, David R.; Westmiller, Stephanie; Wong, Adam C.-N.; Clark, Andrew G.; Lazzaro, Brian P.; Douglas, Angela E.

2015-01-01

Animals bear communities of gut microorganisms with substantial effects on animal nutrition, but the host genetic basis of these effects is unknown. Here, we use Drosophila to demonstrate substantial among-genotype variation in the effects of eliminating the gut microbiota on five host nutritional indices (weight, and protein, lipid, glucose and glycogen contents); this includes variation in both the magnitude and direction of microbiota-dependent effects. Genome-wide associations to identify the genetic basis of the microbiota-dependent variation reveal polymorphisms in largely non-overlapping sets of genes associated with variation in the nutritional traits, including strong representation of conserved genes functioning in signaling. Key genes identified by the GWA study are validated by loss-of-function mutations that altered microbiota-dependent nutritional effects. We conclude that the microbiota interacts with the animal at multiple points in the signaling and regulatory networks that determine animal nutrition. These interactions with the microbiota are likely conserved across animals, including humans. PMID:25692519

Stability of half-metallic behavior with lattice variation for Fe2MnZ (Z = Si, Ge, Sn) Heusler alloy

NASA Astrophysics Data System (ADS)

Jain, Vivek Kumar; Lakshmi, N.; Jain, Rakesh

2018-05-01

The electronic structure and magnetic properties with variation of lattice constant for Fe2MnZ (Z = Si, Ge, Sn) Heusler alloys have been studied. Optimized lattice constant are found to be 5.59, 5.69, 6.00 Å for Z= Si, Ge and Sn respectively. Total magnetic moments of the alloys are ˜3 µB as predicted by the Slater Pauling rule and is maintained over a wide range of lattice variation for all three alloys. Half metallic ferromagnetic nature with 100% spin polarization is observed for Fe2MnSi for a lattice range from 5.40-5.70 Å. Fe2MnGe and Fe2MnSn show ferromagnetic and metallic natures with more than 90% spin polarization over a wide range of lattice constant. Due to the stability of half metallic character of these alloys with respect to variation in the lattice parameters, they are promising robust materials suitable for spintronics device applications.

The Distribution of Basal Water Beneath the Greenland Ice Sheet from Radio-Echo Sounding

NASA Astrophysics Data System (ADS)

Jordan, T.; Williams, C.; Schroeder, D. M.; Martos, Y. M.; Cooper, M.; Siegert, M. J.; Paden, J. D.; Huybrechts, P.; Bamber, J. L.

2017-12-01

There is widespread, but often indirect, evidence that a significant fraction of the Greenland Ice Sheet is thawed at the bed. This includes major outlet glaciers and around the NorthGRIP ice-core in the interior. However, the ice-sheet-wide distribution of basal water is poorly constrained by existing observations, and the spatial relationship between basal water and other ice-sheet and subglacial properties is therefore largely unexplored. In principle, airborne radio-echo sounding (RES) surveys provide the necessary information and spatial coverage to infer the presence of basal water at the ice-sheet scale. However, due to uncertainty and spatial variation in radar signal attenuation, the commonly used water diagnostic, bed-echo reflectivity, is highly ambiguous and prone to spatial bias. Here we introduce a new RES diagnostic for the presence of basal water which incorporates both sharp step-transitions and rapid fluctuations in bed-echo reflectivity. This has the advantage of being (near) independent of attenuation model, and enables a decade of recent Operation Ice Bride RES survey data to be combined in a single map for basal water. The ice-sheet-wide water predictions are compared with: bed topography and drainage network structure, existing knowledge of the thermal state and geothermal heat flux, and ice velocity. In addition to the fast flowing ice-sheet margins, we also demonstrate widespread water routing and storage in parts of the slow-flowing northern interior. Notably, this includes a quasi-linear `corridor' of basal water, extending from NorthGRIP to Petermann glacier, which spatially correlates with a region of locally high (magnetic-derived) geothermal heat flux. The predicted water distribution places a new constraint upon the basal thermal state of the Greenland Ice Sheet, and could be used as an input for ice-sheet model simulations.

Patterns of trust in sources of health information.

PubMed

Lawson, Rob; Forbes, Sarah; Williams, John

2011-01-21

To understand the different patterns of trust that exist regarding different sources of information about health issues. Data from a large national health lifestyles survey of New Zealanders was examined using a factor analysis of trust toward 24 health information sources (HIS). Differences in trust are compared across a range of demographic variables. Factor analysis identified six different groupings of health information. Variations in trust in sources for health information are identified by age, employment status, level of education, income, sex and ethnic group. Systematic variations exist in the trust that people report with respect to different sources of health information. Understanding these variations may assist policymakers and other agencies which are responsible for planning the dissemination of health information.

HF-induced airglow structure as a proxy for ionospheric irregularity detection

NASA Astrophysics Data System (ADS)

Kendall, E. A.

2013-12-01

The High Frequency Active Auroral Research Program (HAARP) heating facility allows scientists to test current theories of plasma physics to gain a better understanding of the underlying mechanisms at work in the lower ionosphere. One powerful technique for diagnosing radio frequency interactions in the ionosphere is to use ground-based optical instrumentation. High-frequency (HF), heater-induced artificial airglow observations can be used to diagnose electron energies and distributions in the heated region, illuminate natural and/or artificially induced ionospheric irregularities, determine ExB plasma drifts, and measure quenching rates by neutral species. Artificial airglow is caused by HF-accelerated electrons colliding with various atmospheric constituents, which in turn emit a photon. The most common emissions are 630.0 nm O(1D), 557.7 nm O(1S), and 427.8 nm N2+(1NG). Because more photons will be emitted in regions of higher electron energization, it may be possible to use airglow imaging to map artificial field-aligned irregularities at a particular altitude range in the ionosphere. Since fairly wide field-of-view imagers are typically deployed in airglow campaigns, it is not well-known what meter-scale features exist in the artificial airglow emissions. Rocket data show that heater-induced electron density variations, or irregularities, consist of bundles of ~10-m-wide magnetic field-aligned filaments with a mean depletion depth of 6% [Kelley et al., 1995]. These bundles themselves constitute small-scale structures with widths of 1.5 to 6 km. Telescopic imaging provides high resolution spatial coverage of ionospheric irregularities and goes hand in hand with other observing techniques such as GPS scintillation, radar, and ionosonde. Since airglow observations can presumably image ionospheric irregularities (electron density variations), they can be used to determine the spatial scale variation, the fill factor, and the lifetime characteristics of irregularities. Telescopic imaging of airglow is a technique capable of simultaneously determining the properties of ionospheric irregularities at decameter resolution over a range of several kilometers. The HAARP telescopic imager consists of two cameras, a set of optics for each camera, and a robotic mount that supports and orients the system. The camera and optics systems are identical except for the camera lenses: one has a wide-angle lens (~19 degrees) and the other has a telescopic lens (~3 degrees). The telescopic imager has a resolution of ~20 m in the F layer and ~10 m in the E layer, which allows the observation of decameter- and kilometer-scale features. Analysis of telescopic data from HAARP campaigns over the last five years will be presented.

Genome-wide Association Studies from the Cancer Genetic Markers of Susceptibility (CGEMS) Initiative | Office of Cancer Genomics

Cancer.gov

CGEMS identifies common inherited genetic variations associated with a number of cancers, including breast and prostate. Data from these genome-wide association studies (GWAS) are available through the Division of Cancer Epidemiology & Genetics website.

Geographic Variation in Opioid Prescribing in the U.S.

PubMed Central

McDonald, Douglas C.; Carlson, Kenneth; Izrael, David

2012-01-01

Estimates of geographic variation among states and counties in the prevalence of opioid prescribing are developed using data from a large (135M) representative national sample of opioid prescriptions dispensed during 2008 by 37,000 retail pharmacies. Statistical analyses are used to estimate the extent to which county variation is explained by characteristics of resident populations, their healthcare utilization, proxy measures of morbidity, availability of healthcare resources, and prescription monitoring laws. Geographic variation in prevalence of prescribed opioids is large, greater than variation observed for other healthcare services. Counties having the highest prescribing rates for opioids were disproportionately located in Appalachia and in Southern and Western states. The number of available physicians was by far the strongest predictor of amounts prescribed, but only one-third of county variation is explained by the combination of all measured factors. Wide variation in prescribing opioids reflects weak consensus regarding the appropriate use of opioids for treating pain, especially chronic non-cancer pain. Patients’ demands for treatment have increased, more potent opioids have become available, an epidemic of abuse has emerged, and calls for increased government regulation are growing. Greater guidance, education and training in opioid prescribing are needed for clinicians to support appropriate prescribing practices. Perspective Wide geographic variation that does not reflect differences in the prevalence of injuries, surgeries, or conditions requiring analgesics raises questions about opioid prescribing practices. Low prescription rates may indicate under-treatment, while high rates may indicate overprescribing and insufficient attention to risks of misuse. PMID:23031398

Strongly nonlinear parabolic variational inequalities

PubMed Central

Browder, Felix E.; Brézis, Haim

1980-01-01

An existence and uniqueness result is established for a general class of variational inequalities for parabolic partial differential equations of the form ∂u/∂t + A(u) + g(u) = f with g nondecreasing but satisfying no growth condition. The proof is based upon a type of compactness result for solutions of variational inequalities that should find a variety of other applications. PMID:16592776

Evaluating the Policies that Lead to Substantial Tuition Variation at Public Land-Grant Universities

ERIC Educational Resources Information Center

Burgess, Brent

2011-01-01

The aim of this study is to evaluate the current state of, and the causes for, the substantial variation in the tuition rates of America's land-grant universities. This aim was pursued with the objective of trying to identify consistent and revealing policies and external characteristics related to the high level of variation that exists among…

Predictive models for radial sap flux variation in coniferous, diffuse-porous and ring-porous temperate trees

Treesearch

Aaron B. Berdanier; Chelcy F. Miniat; James S. Clark

2016-01-01

Accurately scaling sap flux observations to tree or stand levels requires accounting for variation in sap flux between wood types and by depth into the tree. However, existing models for radial variation in axial sap flux are rarely used because they are difficult to implement, there is uncertainty about their predictive ability and calibration measurements...

Mining and Querying Multimedia Data

DTIC Science & Technology

2011-09-29

able to capture more subtle spatial variations such as repetitiveness. Local feature descriptors such as SIFT [74] and SURF [12] have also been widely...empirically set to s = 90%, r = 50%, K = 20, where small variations lead to little perturbation of the output. The pseudo-code of the algorithm is...by constructing a three-layer graph based on clustering outputs, and executing a slight variation of random walk with restart algorithm. It provided

A plant-wide aqueous phase chemistry module describing pH variations and ion speciation/pairing in wastewater treatment process models.

PubMed

Flores-Alsina, Xavier; Kazadi Mbamba, Christian; Solon, Kimberly; Vrecko, Darko; Tait, Stephan; Batstone, Damien J; Jeppsson, Ulf; Gernaey, Krist V

2015-11-15

There is a growing interest within the Wastewater Treatment Plant (WWTP) modelling community to correctly describe physico-chemical processes after many years of mainly focusing on biokinetics. Indeed, future modelling needs, such as a plant-wide phosphorus (P) description, require a major, but unavoidable, additional degree of complexity when representing cationic/anionic behaviour in Activated Sludge (AS)/Anaerobic Digestion (AD) systems. In this paper, a plant-wide aqueous phase chemistry module describing pH variations plus ion speciation/pairing is presented and interfaced with industry standard models. The module accounts for extensive consideration of non-ideality, including ion activities instead of molar concentrations and complex ion pairing. The general equilibria are formulated as a set of Differential Algebraic Equations (DAEs) instead of Ordinary Differential Equations (ODEs) in order to reduce the overall stiffness of the system, thereby enhancing simulation speed. Additionally, a multi-dimensional version of the Newton-Raphson algorithm is applied to handle the existing multiple algebraic inter-dependencies. The latter is reinforced with the Simulated Annealing method to increase the robustness of the solver making the system not so dependent of the initial conditions. Simulation results show pH predictions when describing Biological Nutrient Removal (BNR) by the activated sludge models (ASM) 1, 2d and 3 comparing the performance of a nitrogen removal (WWTP1) and a combined nitrogen and phosphorus removal (WWTP2) treatment plant configuration under different anaerobic/anoxic/aerobic conditions. The same framework is implemented in the Benchmark Simulation Model No. 2 (BSM2) version of the Anaerobic Digestion Model No. 1 (ADM1) (WWTP3) as well, predicting pH values at different cationic/anionic loads. In this way, the general applicability/flexibility of the proposed approach is demonstrated, by implementing the aqueous phase chemistry module in some of the most frequently used WWTP process simulation models. Finally, it is shown how traditional wastewater modelling studies can be complemented with a rigorous description of aqueous phase and ion chemistry (pH, speciation, complexation). Copyright © 2015 Elsevier Ltd. All rights reserved.

Variational submanifolds of Euclidean spaces

NASA Astrophysics Data System (ADS)

Krupka, D.; Urban, Z.; Volná, J.

2018-03-01

Systems of ordinary differential equations (or dynamical forms in Lagrangian mechanics), induced by embeddings of smooth fibered manifolds over one-dimensional basis, are considered in the class of variational equations. For a given non-variational system, conditions assuring variationality (the Helmholtz conditions) of the induced system with respect to a submanifold of a Euclidean space are studied, and the problem of existence of these "variational submanifolds" is formulated in general and solved for second-order systems. The variational sequence theory on sheaves of differential forms is employed as a main tool for the analysis of local and global aspects (variationality and variational triviality). The theory is illustrated by examples of holonomic constraints (submanifolds of a configuration Euclidean space) which are variational submanifolds in geometry and mechanics.

Genome-wide association studies reveal a simple genetic basis of resistance to naturally coevolving viruses in Drosophila melanogaster.

PubMed

Magwire, Michael M; Fabian, Daniel K; Schweyen, Hannah; Cao, Chuan; Longdon, Ben; Bayer, Florian; Jiggins, Francis M

2012-01-01

Variation in susceptibility to infectious disease often has a substantial genetic component in animal and plant populations. We have used genome-wide association studies (GWAS) in Drosophila melanogaster to identify the genetic basis of variation in susceptibility to viral infection. We found that there is substantially more genetic variation in susceptibility to two viruses that naturally infect D. melanogaster (DCV and DMelSV) than to two viruses isolated from other insects (FHV and DAffSV). Furthermore, this increased variation is caused by a small number of common polymorphisms that have a major effect on resistance and can individually explain up to 47% of the heritability in disease susceptibility. For two of these polymorphisms, it has previously been shown that they have been driven to a high frequency by natural selection. An advantage of GWAS in Drosophila is that the results can be confirmed experimentally. We verified that a gene called pastrel--which was previously not known to have an antiviral function--is associated with DCV-resistance by knocking down its expression by RNAi. Our data suggest that selection for resistance to infectious disease can increase genetic variation by increasing the frequency of major-effect alleles, and this has resulted in a simple genetic basis to variation in virus resistance.

Intra- and Inter-Fractional Variation Prediction of Lung Tumors Using Fuzzy Deep Learning

PubMed Central

Park, Seonyeong; Lee, Suk Jin; Weiss, Elisabeth

2016-01-01

Tumor movements should be accurately predicted to improve delivery accuracy and reduce unnecessary radiation exposure to healthy tissue during radiotherapy. The tumor movements pertaining to respiration are divided into intra-fractional variation occurring in a single treatment session and inter-fractional variation arising between different sessions. Most studies of patients’ respiration movements deal with intra-fractional variation. Previous studies on inter-fractional variation are hardly mathematized and cannot predict movements well due to inconstant variation. Moreover, the computation time of the prediction should be reduced. To overcome these limitations, we propose a new predictor for intra- and inter-fractional data variation, called intra- and inter-fraction fuzzy deep learning (IIFDL), where FDL, equipped with breathing clustering, predicts the movement accurately and decreases the computation time. Through the experimental results, we validated that the IIFDL improved root-mean-square error (RMSE) by 29.98% and prediction overshoot by 70.93%, compared with existing methods. The results also showed that the IIFDL enhanced the average RMSE and overshoot by 59.73% and 83.27%, respectively. In addition, the average computation time of IIFDL was 1.54 ms for both intra- and inter-fractional variation, which was much smaller than the existing methods. Therefore, the proposed IIFDL might achieve real-time estimation as well as better tracking techniques in radiotherapy. PMID:27170914

Genetic variation in Dip5, an amino acid permease, and Pdr5, a multiple drug transporter, regulates glyphosate resistance in S. cerevisiae.

PubMed

Rong-Mullins, Xiaoqing; Ravishankar, Apoorva; McNeal, Kirsten A; Lonergan, Zachery R; Biega, Audrey C; Creamer, J Philip; Gallagher, Jennifer E G

2017-01-01

S. cerevisiae from different environments are subject to a wide range of selective pressures, whether intentional or by happenstance. Chemicals classified by their application, such as herbicides, fungicides and antibiotics, can affect non-target organisms. First marketed as RoundUp™, glyphosate is the most widely used herbicide. In plants, glyphosate inhibits EPSPS, of the shikimate pathway, which is present in many organisms but lacking in mammals. The shikimate pathway produces chorismate which is the precursor to all the aromatic amino acids, para-aminobenzoic acid, and Coenzyme Q10. Crops engineered to be resistant to glyphosate contain a homolog of EPSPS that is not bound by glyphosate. Here, we show that S. cerevisiae has a wide-range of glyphosate resistance. Sequence comparison between the target proteins, i.e., the plant EPSPS and the yeast orthologous protein Aro1, predicted that yeast would be resistant to glyphosate. However, the growth variation seen in the subset of yeast tested was not due to polymorphisms within Aro1, instead, it was caused by genetic variation in an ABC multiple drug transporter, Pdr5, and an amino acid permease, Dip5. Using genetic variation as a probe into glyphosate response, we uncovered mechanisms that contribute to the transportation of glyphosate in and out of the cell. Taking advantage of the natural genetic variation within yeast and measuring growth under different conditions that would change the use of the shikimate pathway, we uncovered a general transport mechanism of glyphosate into eukaryotic cells.

Genetic variation in Dip5, an amino acid permease, and Pdr5, a multiple drug transporter, regulates glyphosate resistance in S. cerevisiae

PubMed Central

McNeal, Kirsten A.; Lonergan, Zachery R.; Biega, Audrey C.; Creamer, J. Philip

2017-01-01

S. cerevisiae from different environments are subject to a wide range of selective pressures, whether intentional or by happenstance. Chemicals classified by their application, such as herbicides, fungicides and antibiotics, can affect non-target organisms. First marketed as RoundUp™, glyphosate is the most widely used herbicide. In plants, glyphosate inhibits EPSPS, of the shikimate pathway, which is present in many organisms but lacking in mammals. The shikimate pathway produces chorismate which is the precursor to all the aromatic amino acids, para-aminobenzoic acid, and Coenzyme Q10. Crops engineered to be resistant to glyphosate contain a homolog of EPSPS that is not bound by glyphosate. Here, we show that S. cerevisiae has a wide-range of glyphosate resistance. Sequence comparison between the target proteins, i.e., the plant EPSPS and the yeast orthologous protein Aro1, predicted that yeast would be resistant to glyphosate. However, the growth variation seen in the subset of yeast tested was not due to polymorphisms within Aro1, instead, it was caused by genetic variation in an ABC multiple drug transporter, Pdr5, and an amino acid permease, Dip5. Using genetic variation as a probe into glyphosate response, we uncovered mechanisms that contribute to the transportation of glyphosate in and out of the cell. Taking advantage of the natural genetic variation within yeast and measuring growth under different conditions that would change the use of the shikimate pathway, we uncovered a general transport mechanism of glyphosate into eukaryotic cells. PMID:29155836

Copy number variation signature to predict human ancestry

PubMed Central

2012-01-01

Background Copy number variations (CNVs) are genomic structural variants that are found in healthy populations and have been observed to be associated with disease susceptibility. Existing methods for CNV detection are often performed on a sample-by-sample basis, which is not ideal for large datasets where common CNVs must be estimated by comparing the frequency of CNVs in the individual samples. Here we describe a simple and novel approach to locate genome-wide CNVs common to a specific population, using human ancestry as the phenotype. Results We utilized our previously published Genome Alteration Detection Analysis (GADA) algorithm to identify common ancestry CNVs (caCNVs) and built a caCNV model to predict population structure. We identified a 73 caCNV signature using a training set of 225 healthy individuals from European, Asian, and African ancestry. The signature was validated on an independent test set of 300 individuals with similar ancestral background. The error rate in predicting ancestry in this test set was 2% using the 73 caCNV signature. Among the caCNVs identified, several were previously confirmed experimentally to vary by ancestry. Our signature also contains a caCNV region with a single microRNA (MIR270), which represents the first reported variation of microRNA by ancestry. Conclusions We developed a new methodology to identify common CNVs and demonstrated its performance by building a caCNV signature to predict human ancestry with high accuracy. The utility of our approach could be extended to large case–control studies to identify CNV signatures for other phenotypes such as disease susceptibility and drug response. PMID:23270563

Evidence that Magnetic Navigation and Geomagnetic Imprinting Shape Spatial Genetic Variation in Sea Turtles.

PubMed

Brothers, J Roger; Lohmann, Kenneth J

2018-04-23

The canonical drivers of population genetic structure, or spatial genetic variation, are isolation by distance and isolation by environment. Isolation by distance predicts that neighboring populations will be genetically similar and geographically distant populations will be genetically distinct [1]. Numerous examples also exist of isolation by environment, a phenomenon in which populations that inhabit similar environments (e.g., same elevation, temperature, or vegetation) are genetically similar even if they are distant, whereas populations that inhabit different environments are genetically distinct even when geographically close [2-4]. These dual models provide a widely accepted conceptual framework for understanding population structure [5-8]. Here, we present evidence for an additional, novel process that we call isolation by navigation, in which the navigational mechanism used by a long-distance migrant influences population structure independently of isolation by either distance or environment. Specifically, we investigated the population structure of loggerhead sea turtles (Caretta caretta) [9], which return to nest on their natal beaches by seeking out unique magnetic signatures along the coast-a behavior known as geomagnetic imprinting [10-12]. Results reveal that spatial variation in Earth's magnetic field strongly predicts genetic differentiation between nesting beaches, even when environmental similarities and geographic proximity are taken into account. The findings provide genetic corroboration of geomagnetic imprinting [10, 13]. Moreover, they provide strong evidence that geomagnetic imprinting and magnetic navigation help shape the population structure of sea turtles and perhaps numerous other long-distance migrants that return to their natal areas to reproduce [13-17]. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genetic Diversity of Candidatus Liberibacter asiaticus Based on Two Hypervariable Effector Genes in Thailand

PubMed Central

Puttamuk, Thamrongjet; Zhou, Lijuan; Thaveechai, Niphone; Zhang, Shouan; Armstrong, Cheryl M.; Duan, Yongping

2014-01-01

Huanglongbing (HLB), also known as citrus greening, is one of the most destructive diseases of citrus worldwide. HLB is associated with three species of ‘Candidatus Liberibacter’ with ‘Ca. L. asiaticus’ (Las) being the most widely distributed around the world, and the only species detected in Thailand. To understand the genetic diversity of Las bacteria in Thailand, we evaluated two closely-related effector genes, lasA I and lasA II, found within the Las prophages from 239 infected citrus and 55 infected psyllid samples collected from different provinces in Thailand. The results indicated that most of the Las-infected samples collected from Thailand contained at least one prophage sequence with 48.29% containing prophage 1 (FP1), 63.26% containing prophage 2 (FP2), and 19.38% containing both prophages. Interestingly, FP2 was found to be the predominant population in Las-infected citrus samples while Las-infected psyllids contained primarily FP1. The multiple banding patterns that resulted from amplification of lasA I imply extensive variation exists within the full and partial repeat sequence while the single band from lasA II indicates a low amount of variation within the repeat sequence. Phylogenetic analysis of Las-infected samples from 22 provinces in Thailand suggested that the bacterial pathogen may have been introduced to Thailand from China and the Philippines. This is the first report evaluating the genetic variation of a large population of Ca. L. asiaticus infected samples in Thailand using the two effector genes from Las prophage regions. PMID:25437428

Behavioral Variation in Gorillas: Evidence of Potential Cultural Traits

PubMed Central

Robbins, Martha M.; Ando, Chieko; Fawcett, Katherine A.; Grueter, Cyril C.; Hedwig, Daniela; Iwata, Yuji; Lodwick, Jessica L.; Masi, Shelly; Salmi, Roberta; Stoinski, Tara S.; Todd, Angelique; Vercellio, Veronica; Yamagiwa, Juichi

2016-01-01

The question of whether any species except humans exhibits culture has generated much debate, partially due to the difficulty of providing conclusive evidence from observational studies in the wild. A starting point for demonstrating the existence of culture that has been used for many species including chimpanzees and orangutans is to show that there is geographic variation in the occurrence of particular behavioral traits inferred to be a result of social learning and not ecological or genetic influences. Gorillas live in a wide variety of habitats across Africa and they exhibit flexibility in diet, behavior, and social structure. Here we apply the ‘method of exclusion’ to look for the presence/absence of behaviors that could be considered potential cultural traits in well-habituated groups from five study sites of the two species of gorillas. Of the 41 behaviors considered, 23 met the criteria of potential cultural traits, of which one was foraging related, nine were environment related, seven involved social interactions, five were gestures, and one was communication related. There was a strong positive correlation between behavioral dissimilarity and geographic distance among gorilla study sites. Roughly half of all variation in potential cultural traits was intraspecific differences (i.e. variability among sites within a species) and the other 50% of potential cultural traits were differences between western and eastern gorillas. Further research is needed to investigate if the occurrence of these traits is influenced by social learning. These findings emphasize the importance of investigating cultural traits in African apes and other species to shed light on the origin of human culture. PMID:27603668

Seasonal variation and trends in stroke hospitalizations and mortality in a South American community hospital.

PubMed

Díaz, Alejandro; Gerschcovich, Eliana Roldan; Díaz, Adriana A; Antía, Fabiana; Gonorazky, Sergio

2013-10-01

Numerous studies have reported the presence of temporal variations in biological processes. Seasonal variation (SV) in stroke has been widely studied, but little data have been published on this phenomenon in the Southern Hemisphere, and there have been no studies reported from Argentina. The goals of the present study were to describe the SV of admissions and deaths for stroke and examine trends in stroke morbidity and mortality over a 3-year period in a community hospital in Argentina. Hospital discharge reports from the electronic database of vital statistics between 1999 and 2001 were examined retrospectively. Patients who had a main discharge diagnosis of stroke (ischemic or hemorrhagic) or cerebrovascular accident (International Classification of Diseases, Ninth Revision codes 431, 432, 434, and 436) were selected. The study sample included 1382 hospitalizations by stroke (3.5% of all admissions). In-hospital mortality demonstrated a winter peak (25.5% vs 17% in summer; P = .001). The crude seasonal stroke attack rate (ischemic and hemorrhagic) was highest in winter (164 per 100,000 population; 95% CI, 159-169 per 100,000) and lowest in summer (124 per 100,000; 95% CI, 120-127 per 100,000; P = .008). Stroke admissions followed a seasonal pattern, with a winter-spring predominance (P = .008). Our data indicate a clear SV in stroke deaths and admissions in this region of Argentina. The existence of SV in stroke raises a different hypothesis about the rationale of HF admissions and provides information for the organization of care and resource allocation. Copyright © 2013 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Behavioral Variation in Gorillas: Evidence of Potential Cultural Traits.

PubMed

Robbins, Martha M; Ando, Chieko; Fawcett, Katherine A; Grueter, Cyril C; Hedwig, Daniela; Iwata, Yuji; Lodwick, Jessica L; Masi, Shelly; Salmi, Roberta; Stoinski, Tara S; Todd, Angelique; Vercellio, Veronica; Yamagiwa, Juichi

2016-01-01

The question of whether any species except humans exhibits culture has generated much debate, partially due to the difficulty of providing conclusive evidence from observational studies in the wild. A starting point for demonstrating the existence of culture that has been used for many species including chimpanzees and orangutans is to show that there is geographic variation in the occurrence of particular behavioral traits inferred to be a result of social learning and not ecological or genetic influences. Gorillas live in a wide variety of habitats across Africa and they exhibit flexibility in diet, behavior, and social structure. Here we apply the 'method of exclusion' to look for the presence/absence of behaviors that could be considered potential cultural traits in well-habituated groups from five study sites of the two species of gorillas. Of the 41 behaviors considered, 23 met the criteria of potential cultural traits, of which one was foraging related, nine were environment related, seven involved social interactions, five were gestures, and one was communication related. There was a strong positive correlation between behavioral dissimilarity and geographic distance among gorilla study sites. Roughly half of all variation in potential cultural traits was intraspecific differences (i.e. variability among sites within a species) and the other 50% of potential cultural traits were differences between western and eastern gorillas. Further research is needed to investigate if the occurrence of these traits is influenced by social learning. These findings emphasize the importance of investigating cultural traits in African apes and other species to shed light on the origin of human culture.

Spatial-temporal dynamics of NDVI and Chl-a concentration from 1998 to 2009 in the East coastal zone of China: integrating terrestrial and oceanic components.

PubMed

Hou, Xiyong; Li, Mingjie; Gao, Meng; Yu, Liangju; Bi, Xiaoli

2013-01-01

Annual normalized difference vegetation index (NDVI) and chlorophyll-a (Chl-a) concentration are the most important large-scale indicators of terrestrial and oceanic ecosystem net primary productivity. In this paper, the Sea-viewing Wide Field-of-view Sensor level 3 standard mapped image annual products from 1998 to 2009 are used to study the spatial-temporal characters of terrestrial NDVI and oceanic Chl-a concentration on two sides of the coastline of China by using the methods of mean value (M), coefficient of variation (CV), the slope of unary linear regression model (Slope), and the Hurst index (H). In detail, we researched and analyzed the spatial-temporal dynamics, the longitudinal zonality and latitudinal zonality, the direction, intensity, and persistency of historical changes. The results showed that: (1) spatial patterns of M and CV between NDVI and Chl-a concentration from 1998 to 2009 were very different. The dynamic variation of terrestrial NDVI was much mild, while the variation of oceanic Chl-a concentration was relatively much larger; (2) distinct longitudinal zonality was found for Chl-a concentration and NDVI due to their hypersensitivity to the distance to shoreline, and strong latitudinal zonality existed for Chl-a concentration while terrestrial NDVI had a very weak latitudinal zonality; (3) overall, the NDVI showed a slight decreasing trend while the Chl-a concentration showed a significant increasing trend in the past 12 years, and both of them exhibit strong self-similarity and long-range dependence which indicates opposite future trends between land and ocean.

Failure of evidence-based cancer care in the United States: the association between rectal cancer treatment, cancer center volume, and geography.

PubMed

Monson, John R T; Probst, Christian P; Wexner, Steven D; Remzi, Feza H; Fleshman, James W; Garcia-Aguilar, Julio; Chang, George J; Dietz, David W

2014-10-01

This study examines recent adherence to recommended neoadjuvant chemoradiotherapy guidelines for patients with rectal cancer across geographic regions and institution volume and assesses trends over time. A recent report by the Institute of Medicine described US cancer care as chaotic. Cited deficiencies included wide variation in adherence to evidence-based guidelines even where clear consensus exists. Patients operated on for clinical stage II and III rectal cancer were selected from the 2006-2011 National Cancer Data Base. Multivariable logistic regressions were used to assess variation in chemotherapy and radiation use by cancer center type, geographical location, and hospital volume. The analysis controlled for patient age at diagnosis, sex, race/ethnicity, primary payer, average household income, average education, urban/rural classification of patient residence, comorbidity, and oncologic stage. There were 30,994 patients who met the inclusion criteria. Use of neoadjuvant radiation therapy and chemotherapy varied significantly by type of cancer center. The highest rates of adherence were observed in high-volume centers compared with low-volume centers (78% vs 69%; adjusted odds ratio = 1.46; P < 0.001). This variation is mirrored by hospital geographic location. Primary payer and year of diagnosis were not predictive of rates of neoadjuvant chemoradiotherapy. Adherence to evidence-based treatment guidelines in rectal cancer is suboptimal in the United States, with significant differences based on hospital volume and geographic regions. Little improvement has occurred in the last 5 years. These results support the implementation of standardized care pathways and a Centers of Excellence program for US patients with rectal cancer.

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

USDA-ARS?s Scientific Manuscript database

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identi...

Genome-wide association as a means to understanding the mammary gland

USDA-ARS?s Scientific Manuscript database

Next-generation sequencing and related technologies have facilitated the creation of enormous public databases that catalogue genomic variation. These databases have facilitated a variety of approaches to discover new genes that regulate normal biology as well as disease. Genome wide association (...

Ensembl variation resources

PubMed Central

2010-01-01

Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org. PMID:20459805

Variation in radiographic protocols in paediatric interventional cardiology.

PubMed

McFadden, S L; Hughes, C M; Winder, R J

2013-06-01

The aim of this work is to determine current radiographic protocols in paediatric interventional cardiology (IC) in the UK and Ireland. To do this we investigated which imaging parameters/protocols are commonly used in IC in different hospitals, to identify if a standard technique is used and illustrate any variation in practice. A questionnaire was sent to all hospitals in the UK and Ireland which perform paediatric IC to obtain information on techniques used in each clinical department and on the range of clinical examinations performed. Ethical and research governance approval was sought from the Office for Research Ethics Committees Northern Ireland and the individual trusts. A response rate of 79% was achieved, and a wide variation in technique was found between hospitals. The main differences in technique involved variations in the use of an anti-scatter grid and the use of additional filtration to the radiation beam, frame rates for digital acquisition and pre-programmed projections/paediatric specific programming in the equipment. We conclude that there is no standard protocol for carrying out paediatric IC in the UK or Ireland. Each hospital carries out the IC procedure according to its own local protocols resulting in a wide variation in radiation dose.

A weighted U statistic for association analyses considering genetic heterogeneity.

PubMed

Wei, Changshuai; Elston, Robert C; Lu, Qing

2016-07-20

Converging evidence suggests that common complex diseases with the same or similar clinical manifestations could have different underlying genetic etiologies. While current research interests have shifted toward uncovering rare variants and structural variations predisposing to human diseases, the impact of heterogeneity in genetic studies of complex diseases has been largely overlooked. Most of the existing statistical methods assume the disease under investigation has a homogeneous genetic effect and could, therefore, have low power if the disease undergoes heterogeneous pathophysiological and etiological processes. In this paper, we propose a heterogeneity-weighted U (HWU) method for association analyses considering genetic heterogeneity. HWU can be applied to various types of phenotypes (e.g., binary and continuous) and is computationally efficient for high-dimensional genetic data. Through simulations, we showed the advantage of HWU when the underlying genetic etiology of a disease was heterogeneous, as well as the robustness of HWU against different model assumptions (e.g., phenotype distributions). Using HWU, we conducted a genome-wide analysis of nicotine dependence from the Study of Addiction: Genetics and Environments dataset. The genome-wide analysis of nearly one million genetic markers took 7h, identifying heterogeneous effects of two new genes (i.e., CYP3A5 and IKBKB) on nicotine dependence. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

The plastic surgery postcode lottery in England.

PubMed

Henderson, James

2009-12-01

The National Health Service (NHS) provides treatment free at the point of delivery to patients. Elective medical procedures in England are funded by 149 independent Primary Care Trusts (PCTs), which are each responsible for patients within a defined geographical area. There is wide variation of availability for many treatments, leading to a "postcode lottery" for healthcare provision in England. The aims were to review funding policies for cosmetic procedures, to evaluate the criteria used to decide eligibility against national guidelines, and to evaluate the extent of any postcode lottery for cosmetic surgery on the National Health Service. This study is the first comprehensive review of funding policies for cosmetic surgery in England. All PCTs in England were asked for their funding policies for cosmetic procedures including breast reduction & augmentation, removal of implants, mastopexy, abdominoplasty, facelift, blepharoplasty, rhinoplasty, pinnaplasty, body lifting, surgery for gynaecomastia and tattoo removal. Details of policies were received from 124/149 PCTs (83%). Guidelines varied widely; some refuse all procedures, whilst others allow a full range. Different and sometimes contradictory rules governing symptoms, body mass indices, breast sizes, weights, heights, and other criteria are used to assess patients for funding. Nationally produced guidelines were only followed by nine PCTs. A "postcode lottery" exists in the UK for plastic surgery procedures, despite national guidelines. Some of the more interesting findings are highlighted.

Patterns of public participation.

PubMed

Slutsky, Jean; Tumilty, Emma; Max, Catherine; Lu, Lanting; Tantivess, Sripen; Hauegen, Renata Curi; Whitty, Jennifer A; Weale, Albert; Pearson, Steven D; Tugendhaft, Aviva; Wang, Hufeng; Staniszewska, Sophie; Weerasuriya, Krisantha; Ahn, Jeonghoon; Cubillos, Leonardo

2016-08-15

Purpose - The paper summarizes data from 12 countries, chosen to exhibit wide variation, on the role and place of public participation in the setting of priorities. The purpose of this paper is to exhibit cross-national patterns in respect of public participation, linking those differences to institutional features of the countries concerned. Design/methodology/approach - The approach is an example of case-orientated qualitative assessment of participation practices. It derives its data from the presentation of country case studies by experts on each system. The country cases are located within the historical development of democracy in each country. Findings - Patterns of participation are widely variable. Participation that is effective through routinized institutional processes appears to be inversely related to contestatory participation that uses political mobilization to challenge the legitimacy of the priority setting process. No system has resolved the conceptual ambiguities that are implicit in the idea of public participation. Originality/value - The paper draws on a unique collection of country case studies in participatory practice in prioritization, supplementing existing published sources. In showing that contestatory participation plays an important role in a sub-set of these countries it makes an important contribution to the field because it broadens the debate about public participation in priority setting beyond the use of minipublics and the observation of public representatives on decision-making bodies.

Estimating the spin diffusion length and the spin Hall angle from spin pumping induced inverse spin Hall voltages

NASA Astrophysics Data System (ADS)

Roy, Kuntal

2017-11-01

There exists considerable confusion in estimating the spin diffusion length of materials with high spin-orbit coupling from spin pumping experiments. For designing functional devices, it is important to determine the spin diffusion length with sufficient accuracy from experimental results. An inaccurate estimation of spin diffusion length also affects the estimation of other parameters (e.g., spin mixing conductance, spin Hall angle) concomitantly. The spin diffusion length for platinum (Pt) has been reported in the literature in a wide range of 0.5-14 nm, and in particular it is a constant value independent of Pt's thickness. Here, the key reasonings behind such a wide range of reported values of spin diffusion length have been identified comprehensively. In particular, it is shown here that a thickness-dependent conductivity and spin diffusion length is necessary to simultaneously match the experimental results of effective spin mixing conductance and inverse spin Hall voltage due to spin pumping. Such a thickness-dependent spin diffusion length is tantamount to the Elliott-Yafet spin relaxation mechanism, which bodes well for transitional metals. This conclusion is not altered even when there is significant interfacial spin memory loss. Furthermore, the variations in the estimated parameters are also studied, which is important for technological applications.

Evaluation of simulation motion fidelity criteria in the vertical and directional axes

NASA Technical Reports Server (NTRS)

Schroeder, Jeffery A.

1993-01-01

An evaluation of existing motion fidelity criteria was conducted on the NASA Ames Vertical Motion Simulator. Experienced test pilots flew single-axis repositioning tasks in both the vertical and the directional axes. Using a first-order approximation of a hovering helicopter, tasks were flown with variations only in the filters that attenuate the commands to the simulator motion system. These filters had second-order high-pass characteristics, and the variations were made in the filter gain and natural frequency. The variations spanned motion response characteristics from nearly full math-model motion to fixed-base. Between configurations, pilots recalibrated their motion response perception by flying the task with full motion. Pilots subjectively rated the motion fidelity of subsequent configurations relative to this full motion case, which was considered the standard for comparison. The results suggested that the existing vertical-axis criterion was accurate for combinations of gain and natural frequency changes. However, if only the gain or the natural frequency was changed, the rated motion fidelity was better than the criterion predicted. In the vertical axis, the objective and subjective results indicated that a larger gain reduction was tolerated than the existing criterion allowed. The limited data collected in the yaw axis revealed that pilots had difficulty in distinguishing among the variations in the pure yaw motion cues.

What Matters in Education: A Decomposition of Educational Outcomes with Multiple Measures

ERIC Educational Resources Information Center

Li, Jinjing; Miranti, Riyana; Vidyattama, Yogi

2017-01-01

Significant variations in educational outcomes across both the spatial and socioeconomic spectra in Australia have been widely debated by policymakers in recent years. This paper examines these variations and decomposes educational outcomes into 3 major input factors: availability of school resources, socioeconomic background, and a latent factor…

Genome-wide association study of Arabidopsis thaliana identifies determinants of natural variation in seed oil composition

USDA-ARS?s Scientific Manuscript database

The renewable source of highly reduced carbon provided by plant triacylglycerols fills an ever increasing demand for food, biodiesel and industrial chemicals. Each of these uses requires different compositions of fatty acid proportions in seed oils. Identifying the genes responsible for variation in...

Influence of rock-soil spectral variation on the assessment of green biomass

NASA Technical Reports Server (NTRS)

Elvidge, C. D.; Lyon, R. J. P.

1985-01-01

A comparison of how n-spaced and ratio-based vegetation indices respond to rock and soil spectral variation is made, using a set of ground-based reflectance spectra and airborne Thematic Mapper imagery of the Virginia Range, NV. The influence of variations in rock-soil brightness on ratio-based vegetation indices is also discussed. It is shown that of all the vegetation indices tested, the perperdicular vegetation index is the most appropriate for use in multispectral imagery of arid and semiarid regions where there is a wide variation in substrate characteristics.

Analytical solutions for solute transport in groundwater and riverine flow using Green's Function Method and pertinent coordinate transformation method

NASA Astrophysics Data System (ADS)

Sanskrityayn, Abhishek; Suk, Heejun; Kumar, Naveen

2017-04-01

In this study, analytical solutions of one-dimensional pollutant transport originating from instantaneous and continuous point sources were developed in groundwater and riverine flow using both Green's Function Method (GFM) and pertinent coordinate transformation method. Dispersion coefficient and flow velocity are considered spatially and temporally dependent. The spatial dependence of the velocity is linear, non-homogeneous and that of dispersion coefficient is square of that of velocity, while the temporal dependence is considered linear, exponentially and asymptotically decelerating and accelerating. Our proposed analytical solutions are derived for three different situations depending on variations of dispersion coefficient and velocity, respectively which can represent real physical processes occurring in groundwater and riverine systems. First case refers to steady solute transport situation in steady flow in which dispersion coefficient and velocity are only spatially dependent. The second case represents transient solute transport in steady flow in which dispersion coefficient is spatially and temporally dependent while the velocity is spatially dependent. Finally, the third case indicates transient solute transport in unsteady flow in which both dispersion coefficient and velocity are spatially and temporally dependent. The present paper demonstrates the concentration distribution behavior from a point source in realistically occurring flow domains of hydrological systems including groundwater and riverine water in which the dispersivity of pollutant's mass is affected by heterogeneity of the medium as well as by other factors like velocity fluctuations, while velocity is influenced by water table slope and recharge rate. Such capabilities give the proposed method's superiority about application of various hydrological problems to be solved over other previously existing analytical solutions. Especially, to author's knowledge, any other solution doesn't exist for both spatially and temporally variations of dispersion coefficient and velocity. In this study, the existing analytical solutions from previous widely known studies are used for comparison as validation tools to verify the proposed analytical solution as well as the numerical code of the Two-Dimensional Subsurface Flow, Fate and Transport of Microbes and Chemicals (2DFATMIC) code and the developed 1D finite difference code (FDM). All such solutions show perfect match with the respective proposed solutions.

American lookback option with fixed strike price—2-D parabolic variational inequality

NASA Astrophysics Data System (ADS)

Chen, Xiaoshan; Yi, Fahuai; Wang, Lihe

In this paper we study a 2-dimensional parabolic variational inequality with financial background. We define a suitable weak formula and obtain existence and uniqueness of the problem. Moreover we analyze the behaviors of the free boundary surface.

Logarithmic circuit with wide dynamic range

NASA Technical Reports Server (NTRS)

Wiley, P. H.; Manus, E. A. (Inventor)

1978-01-01

A circuit deriving an output voltage that is proportional to the logarithm of a dc input voltage susceptible to wide variations in amplitude includes a constant current source which forward biases a diode so that the diode operates in the exponential portion of its voltage versus current characteristic, above its saturation current. The constant current source includes first and second, cascaded feedback, dc operational amplifiers connected in negative feedback circuit. An input terminal of the first amplifier is responsive to the input voltage. A circuit shunting the first amplifier output terminal includes a resistor in series with the diode. The voltage across the resistor is sensed at the input of the second dc operational feedback amplifier. The current flowing through the resistor is proportional to the input voltage over the wide range of variations in amplitude of the input voltage.

Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus

Treesearch

Daniel L. Lindner; Mark T. Banik

2011-01-01

Regions of rDNA are commonly used to infer phylogenetic relationships among fungal species and as DNA barcodes for identification. These regions occur in large tandem arrays, and concerted evolution is believed to reduce intragenomic variation among copies within these arrays, although some variation still might exist. Phylogenetic studies typically use consensus...

Towards a Global Unified Model of Europa's Tenuous Atmosphere

NASA Astrophysics Data System (ADS)

Plainaki, Christina; Cassidy, Tim A.; Shematovich, Valery I.; Milillo, Anna; Wurz, Peter; Vorburger, Audrey; Roth, Lorenz; Galli, André; Rubin, Martin; Blöcker, Aljona; Brandt, Pontus C.; Crary, Frank; Dandouras, Iannis; Jia, Xianzhe; Grassi, Davide; Hartogh, Paul; Lucchetti, Alice; McGrath, Melissa; Mangano, Valeria; Mura, Alessandro; Orsini, Stefano; Paranicas, Chris; Radioti, Aikaterini; Retherford, Kurt D.; Saur, Joachim; Teolis, Ben

2018-02-01

Despite the numerous modeling efforts of the past, our knowledge on the radiation-induced physical and chemical processes in Europa's tenuous atmosphere and on the exchange of material between the moon's surface and Jupiter's magnetosphere remains limited. In lack of an adequate number of in situ observations, the existence of a wide variety of models based on different scenarios and considerations has resulted in a fragmentary understanding of the interactions of the magnetospheric ion population with both the moon's icy surface and neutral gas envelope. Models show large discrepancy in the source and loss rates of the different constituents as well as in the determination of the spatial distribution of the atmosphere and its variation with time. The existence of several models based on very different approaches highlights the need of a detailed comparison among them with the final goal of developing a unified model of Europa's tenuous atmosphere. The availability to the science community of such a model could be of particular interest in view of the planning of the future mission observations (e.g., ESA's JUpiter ICy moons Explorer (JUICE) mission, and NASA's Europa Clipper mission). We review the existing models of Europa's tenuous atmosphere and discuss each of their derived characteristics of the neutral environment. We also discuss discrepancies among different models and the assumptions of the plasma environment in the vicinity of Europa. A summary of the existing observations of both the neutral and the plasma environments at Europa is also presented. The characteristics of a global unified model of the tenuous atmosphere are, then, discussed. Finally, we identify needed future experimental work in laboratories and propose some suitable observation strategies for upcoming missions.

Multiscale 3D Shape Analysis using Spherical Wavelets

PubMed Central

Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen

2013-01-01

Shape priors attempt to represent biological variations within a population. When variations are global, Principal Component Analysis (PCA) can be used to learn major modes of variation, even from a limited training set. However, when significant local variations exist, PCA typically cannot represent such variations from a small training set. To address this issue, we present a novel algorithm that learns shape variations from data at multiple scales and locations using spherical wavelets and spectral graph partitioning. Our results show that when the training set is small, our algorithm significantly improves the approximation of shapes in a testing set over PCA, which tends to oversmooth data. PMID:16685992

Multiscale 3D shape analysis using spherical wavelets.

PubMed

Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen R

2005-01-01

Shape priors attempt to represent biological variations within a population. When variations are global, Principal Component Analysis (PCA) can be used to learn major modes of variation, even from a limited training set. However, when significant local variations exist, PCA typically cannot represent such variations from a small training set. To address this issue, we present a novel algorithm that learns shape variations from data at multiple scales and locations using spherical wavelets and spectral graph partitioning. Our results show that when the training set is small, our algorithm significantly improves the approximation of shapes in a testing set over PCA, which tends to oversmooth data.

Primary Sjögren's syndrome with diffuse cystic lung changes developed systemic lupus erythematosus: a case report and literature review.

PubMed

Liu, Xiao; Li, Hao; Yin, Yunhong; Ma, Dedong; Qu, Yiqing

2017-05-23

Sjögren's syndrome (SS) is a chronic inflammatory autoimmune disease that can occur as a unique existence (primary Sjögren's syndrome) or merge with other systemic diseases like systemic lupus erythematosus (SLE), rheumatoid arthritis or systemic sclerosis (secondary Sjögren's syndrome). Data on the two diseases occurrence order are inadequate. Primary Sjögren's syndrome (pSS) may relatively uncommonly lead to diffuse cystic lung changes. We represent a female who was diagnosed pSS with diffuse cystic lung alterations developed SLE two years later. SS was diagnosed on account of the existence of dryness of eye and mouth, Schirmer's test, biopsy of the minor salivary glands of her lip, positive anti-SSA and anti-SSB antibody in the serum. Chest computed tomography image showed bilateral diffuse cystic changes with a wide variation in cyst size and distribution. SLE was finally diagnosed based on bilateral lower limb skin rash, gonarthritis and omarthritis, low level of complement, antinuclear antibody 1:640 and positive antibodies to double-stranded DNA. Improvement was achieved with therapy of corticosteroids, hydroxychloroquine and antibiotics. This report provides us clinical, diagnosis and treatment perception of SS-onset SLE as patient presenting diffuse cystic lung changes.

Hospital waste management in developing countries: A mini review.

PubMed

Ali, Mustafa; Wang, Wenping; Chaudhry, Nawaz; Geng, Yong

2017-06-01

Health care activities can generate different kinds of hazardous wastes. Mismanagement of these wastes can result in environmental and occupational health risks. Developing countries are resource-constrained when it comes to safe management of hospital wastes. This study summarizes the main issues faced in hospital waste management in developing countries. A review of the existing literature suggests that regulations and legislations focusing on hospital waste management are recent accomplishments in many of these countries. Implementation of these rules varies from one hospital to another. Moreover, wide variations exist in waste generation rates within as well as across these countries. This is mainly attributable to a lack of an agreement on the definitions and the methodology among the researchers to measure such wastes. Furthermore, hospitals in these countries suffer from poor waste segregation, collection, storage, transportation and disposal practices, which can lead to occupational and environmental risks. Knowledge and awareness regarding proper waste management remain low in the absence of training for hospital staff. Moreover, hospital sanitary workers, and scavengers, operate without the provision of safety equipment or immunization. Unsegregated waste is illegally recycled, leading to further safety risks. Overall, hospital waste management in developing countries faces several challenges. Sustainable waste management practices can go a long way in reducing the harmful effects of hospital wastes.

Development of analysis of volatile polyfluorinated alkyl substances in indoor air using thermal desorption-gas chromatography-mass spectrometry.

PubMed

Wu, Yaoxing; Chang, Victor W-C

2012-05-18

The study attempts to utilize thermal desorption (TD) coupled with gas chromatography-mass spectrometry (GC-MS) for determination of indoor airborne volatile polyfluorinated alkyl substances (PFASs), including four fluorinated alcohols (FTOHs), two fluorooctane sulfonamides (FOSAs), and two fluorooctane sulfonamidoethanols (FOSEs). Standard stainless steel tubes of Tenax/Carbograph 1 TD were employed for low-volume sampling and exhibited minimal breakthrough of target analytes in sample collection. The method recoveries were in the range of 88-119% for FTOHs, 86-138% for FOSAs, exhibiting significant improvement compared with other existing air sampling methods. However, the widely reported high method recoveries of FOSEs were also observed (139-210%), which was probably due to the structural differences between FOSEs and internal standards. Method detection limit, repeatability, linearity, and accuracy were reported as well. The approach has been successfully applied to routine quantification of targeted PFASs in indoor environment of Singapore. The significantly shorter sampling time enabled the observation of variations of concentrations of targeted PFASs within different periods of a day, with higher concentration levels at night while ventilation systems were shut off. This indicated the existence of indoor sources and the importance of building ventilation and air conditioning system. Copyright © 2012 Elsevier B.V. All rights reserved.

On the continuity of mean total normal stress in geometrical multiscale cardiovascular problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blanco, Pablo J., E-mail: pjblanco@lncc.br; INCT-MACC, Instituto Nacional de Ciência e Tecnologia em Medicina Assistida por Computação Científica, Petrópolis; Deparis, Simone, E-mail: simone.deparis@epfl.ch

2013-10-15

In this work an iterative strategy to implicitly couple dimensionally-heterogeneous blood flow models accounting for the continuity of mean total normal stress at interface boundaries is developed. Conservation of mean total normal stress in the coupling of heterogeneous models is mandatory to satisfy energetic consistency between them. Nevertheless, existing methodologies are based on modifications of the Navier–Stokes variational formulation, which are undesired when dealing with fluid–structure interaction or black box codes. The proposed methodology makes possible to couple one-dimensional and three-dimensional fluid–structure interaction models, enforcing the continuity of mean total normal stress while just imposing flow rate data or evenmore » the classical Neumann boundary data to the models. This is accomplished by modifying an existing iterative algorithm, which is also able to account for the continuity of the vessel area, when required. Comparisons are performed to assess differences in the convergence properties of the algorithms when considering the continuity of mean normal stress and the continuity of mean total normal stress for a wide range of flow regimes. Finally, examples in the physiological regime are shown to evaluate the importance, or not, of considering the continuity of mean total normal stress in hemodynamics simulations.« less

Confined aquifer head measurements and storage properties in the San Luis Valley, Colorado, from spaceborne InSAR observations

NASA Astrophysics Data System (ADS)

Chen, Jingyi; Knight, Rosemary; Zebker, Howard A.; Schreüder, Willem A.

2016-05-01

Interferometric Synthetic Aperture Radar (InSAR), a remote sensing technique for measuring centimeter-level surface deformation, is used to estimate hydraulic head in the confined aquifer of the San Luis Valley (SLV), Colorado. Reconstructing head measurements from InSAR in agricultural regions can be difficult, as InSAR phase data are often decorrelated due to vegetation growth. Analysis of 17 L-band ALOS PALSAR scenes, acquired between January 2007 and March 2011, demonstrates that comprehensive InSAR deformation measurements can be recovered over the vegetated groundwater basin with an improved processing strategy. Local skeletal storage coefficients and time delays between the head change and deformation are estimated through a joint InSAR-well data analysis. InSAR subsidence estimates are transformed to head changes with finer temporal and spatial resolution than is possible using existing well records alone. Both InSAR and well data suggest that little long-term water-storage loss occurred in the SLV over the study period and that inelastic compaction was negligible. The seasonal head variations derived from InSAR are consistent with the existing well data at most locations where confined aquifer pumping activity dominates. Our results demonstrate the advantages of InSAR measurements for basin-wide characterization of aquifer storage properties and groundwater levels over agricultural regions.

Transitional care for rheumatic conditions in Europe: current clinical practice and available resources.

PubMed

Clemente, Daniel; Leon, Leticia; Foster, Helen; Carmona, Loreto; Minden, Kirsten

2017-06-09

To assess European pediatric rheumatology providers' current clinical practices and resources used in the transition from child-centered to adult-oriented care. European pediatric rheumatologists were invited to complete a 17-item anonymized e-survey assessing current transition practices, transition policy awareness, and needs in advance of the publication of EULAR/PReS recommendations on transition. The response rate was 121/276 (44%), including responses from 115 centers in 22 European Union countries. Although 32/121 (26%) responded that their centers did not offer transition services, the majority (99%) agreed that a formalized process in transitioning patients to adult care is necessary. A minority (<30%) of respondents stated that they have a written transition policy although 46% have an informal transition process. Designated staff to support transitional care were available in a minority of centers: nurse (35%), physiotherapist (15%), psychologist (15%), social worker (8%), and occupational therapist (2%). The existence of a designated team member to coordinate transition was acknowledged in many centers (64% of respondents) although just 36% use a checklist for young people as part of individualized transitional care. This survey of European pediatric rheumatology providers regarding transitional care practices demonstrates agreement that transitional care is important, and wide variation in current provision of transition services exists.

Step-wise extinctions at the Cretaceous-Tertiary boundary and their climatic implications

NASA Technical Reports Server (NTRS)

Maurrasse, Florentin J-M. R.

1988-01-01

A comparative study of planktonic foraminifera and radiolarian assemblages from the Cretaceous-Tertiary (K-T) boundary section of the Beloc Formation in the southern Peninsula of Haiti, and the lowermost Danian sequence of the Micara Formation in southern Cuba reveals a remarkable pattern of step-wise extinctions. This pattern is consistent in both places despite the widely different lithologies of the two formations. Because of a step-wise extinction and the delayed disappearance of taxa known to be more representative of cooler water realms, it is inferred that a cooling trend which characterized the close of the Maastrichtian and the onset of the Tertiary had the major adverse effect on the existing biota. Although repetitive lithologic and faunal fluctuations throughout the Maastrichtian sediments found at Deep Sea Drilling Project (DSDP) site 146/149 in the Caribbean Sea indicate variations reminiscent of known climatically induced cycles in the Cenozoic, rapid biotic succession appears to have taken place during a crisis period of a duration greater than 2 mission years. Widespread and abundant volcanic activities recorded in the Caribbean area during the crisis period gives further credence to earlier contention that intense volcanism may have played a major role in exhacerbating pre-existing climatic conditions during that time.

Along Arc Structural Variation in the Izu-Bonin Arc and its Implications for Crustal Evolution Processes

NASA Astrophysics Data System (ADS)

Kodaira, S.; Sato, T.; Takahashi, N.; Ito, A.; Kaneda, Y.

2005-12-01

A continental-type middle crust having Vp = 6.1 - 6.3 km/s has been imaged at several oceanic island arcs (e.g. northern Izu, Mariana, Tonga, Kyushu-Palau ridge) since Suyehiro et al. (1996) has found a felsic middle crust in the northern Izu arc. A high velocity lower crust (Vp > 7.3 km/s) underlying the felsic middle crust has been also underlined as a characteristic structure in the northern Izu arc. A bulk composition of the crust in the Izu arc may indicate more mafic than that of a typical continental crust due to a large volume of the high velocity lower crust. Since a crust becomes more mature toward the north along the Izu-Bonin arc, investigating structural variation along the volcanic front has been believed to provide a fundamental knowledge for a crustal evolution process. In 2004 and 2005, Japan Agency for Marine-Earth Science and Technology has conducted two along arc wide-angle seismic surveys from the Sagami-bay to the Kita-Iwo jima, a total profile length of about 1000 km. Although data from the Bonin-part of the profile which were acquired this year has not been processed yet, a result from the Izu-part, from the Sagami-bay to Tori shima, shows significant structural variations along the volcanic front. The crustal thickness are varied with a wavelength of several tens of km, i.e., thickened up to 25-30 km around the volcanoes (the Miyake jama, Hachijo jima, Aoga sima, Sumisu jima), while thinned down to 20 km between them. The fine seismic velocity image obtained by refraction tomography as well as a wide-angle reflection migration shows that the variation of the crustal block having 6.0 - 6.7 km/s, which is a typical continental crustal velocity, is mainly responsible for the observed variation of the crustal thickness. The thickness of the high velocity lower crust is not significantly varied along the arc. Therefore, an average crustal seismic velocity (varied 6.6 to 7.0 km/s) represents a higher velocity that that of a typical continental crust (6. 4 km/s), and a negative correlation between the thickness of the 6.0 - 6.7 km/s block and the average crustal seismic velocity is recognized. In conclusion, the continental-type of the crust efficiently grow at the Quaternary volcanoes along Izu arc, but even at those areas the bulk composition of the entire crustal section shows more mafic than a continental crust due to the uniformly existing high velocity lower crust. A delamination process may be necessary to form a continental crust form the Izu island arc crust

Factors influencing variation in dentist service rates.

PubMed

Grembowski, D; Milgrom, P; Fiset, L

1990-01-01

In the previous article, we calculated dentist service rates for 200 general dentists based on a homogeneous, well-educated, upper-middle-class population of patients. Wide variations in the rates were detected. In this analysis, factors influencing variation in the rates were identified. Variation in rates for categories of dental services was explained by practice characteristics, patient exposure to fluoridated water supplies, and non-price competition in the dental market. Rates were greatest in large, busy practices in markets with high fees. Older practices consistently had lower rates across services. As a whole, these variables explained between 5 and 30 percent of the variation in the rates.