Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora

PubMed Central

Steige, Kim A.; Laenen, Benjamin; Reimegård, Johan; Slotte, Tanja

2017-01-01

Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora. We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are under weaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species. PMID:28096395

[Ethnic origin of patients remains important].

PubMed

Stronks, Karien

2013-01-01

The ethnic diversity in medical practices is increasing rapidly. In the Netherlands, ethnic groups are predominantly defined on the basis of their geographical origin, e.g. inhabitants of Turkish, Moroccan or Surinamese origin. The prevalence of health problems and the utilisation of health care differ between ethnic groups. This ethnic variation arises, firstly, from characteristics that are inherent to these groups such as genetic profile and culture, and, secondly, from characteristics that reflect their position in Dutch society such as socio-economic position and discrimination on the other. If we could fully understand which of these specific characteristics leads to a specific pattern of health problems or health care use, the classification of patient into ethnic groups would then become redundant. As long as we do not completely understand this variation, however, ethnic origin is a good entry-point for targeting health care to groups of patients.

PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities.

PubMed

Malekpour, Seyed Amir; Pezeshk, Hamid; Sadeghi, Mehdi

2016-11-03

Copy Number Variation (CNV) is envisaged to be a major source of large structural variations in the human genome. In recent years, many studies apply Next Generation Sequencing (NGS) data for the CNV detection. However, still there is a necessity to invent more accurate computational tools. In this study, mate pair NGS data are used for the CNV detection in a Hidden Markov Model (HMM). The proposed HMM has position specific emission probabilities, i.e. a Gaussian mixture distribution. Each component in the Gaussian mixture distribution captures a different type of aberration that is observed in the mate pairs, after being mapped to the reference genome. These aberrations may include any increase (decrease) in the insertion size or change in the direction of mate pairs that are mapped to the reference genome. This HMM with Position-Specific Emission probabilities (PSE-HMM) is utilized for the genome-wide detection of deletions and tandem duplications. The performance of PSE-HMM is evaluated on a simulated dataset and also on a real data of a Yoruban HapMap individual, NA18507. PSE-HMM is effective in taking observation dependencies into account and reaches a high accuracy in detecting genome-wide CNVs. MATLAB programs are available at http://bs.ipm.ir/softwares/PSE-HMM/ .

Racial/ethnic variation in EBV-positive classical Hodgkin lymphoma in California populations

PubMed Central

Glaser, Sally L.; Gulley, Margaret L.; Clarke, Christina A.; Keegan, Theresa H.; Chang, Ellen T.; Shema, Sarah J.; Craig, Fiona E.; DiGiuseppe, Joseph A.; Dorfman, Ronald F.; Mann, Risa B.; Anton-Culver, Hoda; Ambinder, Richard F.

2009-01-01

Epstein-Barr virus (EBV) is detected in the tumor cells of some but not all Hodgkin lymphoma (HL) patients, and evidence indicates that EBV-positive and –negative HL are distinct entities. Racial/ethnic variation in EBV-positive HL in international comparisons suggests etiologic roles for environmental and genetic factors, but these studies used clinical series and evaluated EBV presence by differing protocols. Therefore, we evaluated EBV presence in the tumors of a large (n=1,032), racially and sociodemographically diverse series of California incident classical HL cases with uniform pathology re-review and EBV detection methods. Tumor EBV-positivity was associated with Hispanic and Asian/Pacific Islander (API) but not black race/ethnicity, irrespective of demographic and clinical factors. Complex race-specific associations were observed between EBV-positive HL and age, sex, histology, stage, neighborhood socioeconomic status (SES), and birth place. In Hispanics, EBV-positive HL was associated not only with young and older age, male sex, and mixed cellularity histology, but also with foreign birth and lower SES in females, suggesting immune function responses to correlates of early childhood experience and later environmental exposures, respectively, as well as of pregnancy. For APIs, a lack of association with birth place may reflect the higher SES of API than Hispanic immigrants. In blacks, EBV-positive HL was associated with later-stage disease, consistent with racial/ethnic variation in certain cytokine polymorphisms. The racial/ethnic variation in our findings suggests that EBV-positive HL results from an intricate interplay of early- and later-life environmental, hormonal, and genetic factors leading to depressed immune function and poorly controlled EBV infection. PMID:18646185

Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans

PubMed Central

Jagoda, Evelyn; Lawson, Daniel J; Wall, Jeffrey D; Lambert, David; Muller, Craig; Westaway, Michael; Leavesley, Matthew; Capellini, Terence D; Mirazón Lahr, Marta; Gerbault, Pascale; Thomas, Mark G; Migliano, Andrea Bamberg; Willerslev, Eske; Metspalu, Mait; Pagani, Luca

2018-01-01

Abstract Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the postintrogression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI) in which archaic haplotypes rose to high frequencies in humans as a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse data set, we report novel cases of selection on introgressed variation in living humans and shortlist among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans. PMID:29220488

Widespread Transient Hoogsteen Base-Pairs in Canonical Duplex DNA with Variable Energetics

PubMed Central

Alvey, Heidi S.; Gottardo, Federico L.; Nikolova, Evgenia N.; Al-Hashimi, Hashim M.

2015-01-01

Hoogsteen base-pairing involves a 180 degree rotation of the purine base relative to Watson-Crick base-pairing within DNA duplexes, creating alternative DNA conformations that can play roles in recognition, damage induction, and replication. Here, using Nuclear Magnetic Resonance R1ρ relaxation dispersion, we show that transient Hoogsteen base-pairs occur across more diverse sequence and positional contexts than previously anticipated. We observe sequence-specific variations in Hoogsteen base-pair energetic stabilities that are comparable to variations in Watson-Crick base-pair stability, with Hoogsteen base-pairs being more abundant for energetically less favorable Watson-Crick base-pairs. Our results suggest that the variations in Hoogsteen stabilities and rates of formation are dominated by variations in Watson-Crick base pair stability, suggesting a late transition state for the Watson-Crick to Hoogsteen conformational switch. The occurrence of sequence and position-dependent Hoogsteen base-pairs provide a new potential mechanism for achieving sequence-dependent DNA transactions. PMID:25185517

Effect of genomic drift of influenza PCR tests.

PubMed

Stellrecht, Kathleen A; Nattanmai, Seela M; Butt, Jumshan; Maceira, Vincente P; Espino, Alvin A; Castro, Allan J; Landes, Allen; Dresser, Nicolas; Butt, Shafiq A

2017-08-01

Nucleic acid amplification assays have become the method of choice for influenza (Flu) testing due to superior accuracy and faster turnaround time. Although assays are designed to detect highly conserved genomic targets, mutations can influence test sensitivity. Most of the circulating viruses in the United States during the 2014-2015 season were associated with significant genetic drift; however, the effect on testing was unknown. We compared the performance of Prodesse ProFlu+/ProFAST+ (PFlu/PFAST), FilmArray Respiratory Panel (RP), cobas ® Influenza A/B test (cIAB), and Xpert ® Flu (Xpt) in a retrospective analysis of consecutive nasopharyngeal specimens received for a two-week period during the winter of 2015. Furthermore, limits of detection (LOD) were determined with six isolates of Flu. Of the 275 specimens, 63 were positive for FluA by PFAST, 60 were positive by RP, 58 were positive by cIAB and 52 were positive by Xpt. Only a subset of 135 specimens was tested by PFlu, of which 32 were positive. The sensitivity/specificity for PFAST, RP, cIAB, Xpt and PFlu was 100/99.1%, 96.7/99.5%, 91.8/99.1%, 85.2%/100%, and 75.6%/98.9%, respectively. LOD analyses demonstrated assay performance variations were strain associated. Specifically, PFlu's and cIAB's LODs were higher with A/Texas/50/2012-like and A/Switzerland/9715293/2013-like strains, while Xpt's highest LOD was with the Swiss strain. Strain-associated assay performance variation is known to occur with other Flu test methods; hence, it is not surprising that such variation would be observed with molecular tests. Careful monitoring and reporting for strain-associated variances are warranted for all test methods. Copyright © 2017 Elsevier B.V. All rights reserved.

Distinctiveness of the Roma population within CYP2B6 worldwide variation.

PubMed

Tomas, Željka; Kuhanec, Antonija; Škarić-Jurić, Tatjana; Petranović, Matea Zajc; Narančić, Nina Smolej; Janićijević, Branka; Salihović, Marijana Peričić

2017-11-01

To determine variation of CYP2B6 gene within the genetically specific Croatian Roma (Gypsy) population originating from India and to examine it in the worldwide perspective. Seven SNP loci (rs12721655, rs2279343, rs28399499, rs34097093, rs3745274, rs7260329 and rs8192709) were genotyped in 439 subjects using Kompetitive Allele Specific PCR (KASP) method. The Croatian Roma took an outlying position in CYP2B6 variation from the worldwide perspective mainly due to their exceptionally high minor allele frequency (MAF) for rs8192709 (12.8%), and lower for rs2279343 (21.1%) compared with south Asian populations. This study provides the first data of several CYP2B6 polymorphisms in Roma population and indicates the need for systematic investigation of the most important pharmacogenes' variants in this large, transnationally isolated population worldwide.

Plant Fertilization Interacts with Life History: Variation in Stoichiometry and Performance in Nettle-Feeding Butterflies

PubMed Central

Audusseau, Hélène; Kolb, Gundula; Janz, Niklas

2015-01-01

Variation in food stoichiometry affects individual performance and population dynamics, but it is also likely that species with different life histories should differ in their sensitivity to food stoichiometry. To address this question, we investigated the ability of the three nettle-feeding butterflies (Aglais urticae, Polygonia c-album, and Aglais io) to respond adaptively to induced variation in plant stoichiometry in terms of larval performance. We hypothesized that variation in larval performance between plant fertilization treatments should be functionally linked to species differences in host plant specificity. We found species-specific differences in larval performance between plant fertilization treatments that could not be explained by nutrient limitation. We showed a clear evidence of a positive correlation between food stoichiometry and development time to pupal stage and pupal mass in A. urticae. The other two species showed a more complex response. Our results partly supported our prediction that host plant specificity affects larval sensitivity to food stoichiometry. However, we suggest that most of the differences observed may instead be explained by differences in voltinism (number of generations per year). We believe that the potential of some species to respond adaptively to variation in plant nutrient content needs further attention in the face of increased eutrophication due to nutrient leakage from human activities. PMID:25932628

Plant fertilization interacts with life history: variation in stoichiometry and performance in nettle-feeding butterflies.

PubMed

Audusseau, Hélène; Kolb, Gundula; Janz, Niklas

2015-01-01

Variation in food stoichiometry affects individual performance and population dynamics, but it is also likely that species with different life histories should differ in their sensitivity to food stoichiometry. To address this question, we investigated the ability of the three nettle-feeding butterflies (Aglais urticae, Polygonia c-album, and Aglais io) to respond adaptively to induced variation in plant stoichiometry in terms of larval performance. We hypothesized that variation in larval performance between plant fertilization treatments should be functionally linked to species differences in host plant specificity. We found species-specific differences in larval performance between plant fertilization treatments that could not be explained by nutrient limitation. We showed a clear evidence of a positive correlation between food stoichiometry and development time to pupal stage and pupal mass in A. urticae. The other two species showed a more complex response. Our results partly supported our prediction that host plant specificity affects larval sensitivity to food stoichiometry. However, we suggest that most of the differences observed may instead be explained by differences in voltinism (number of generations per year). We believe that the potential of some species to respond adaptively to variation in plant nutrient content needs further attention in the face of increased eutrophication due to nutrient leakage from human activities.

Diversity of human copy number variation and multicopy genes.

PubMed

Sudmant, Peter H; Kitzman, Jacob O; Antonacci, Francesca; Alkan, Can; Malig, Maika; Tsalenko, Anya; Sampas, Nick; Bruhn, Laurakay; Shendure, Jay; Eichler, Evan E

2010-10-29

Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.

Dietary Variation and Evolution of Gene Copy Number among Dog Breeds

PubMed Central

Reiter, Taylor; Jagoda, Evelyn; Capellini, Terence D.

2016-01-01

Prolonged human interactions and artificial selection have influenced the genotypic and phenotypic diversity among dog breeds. Because humans and dogs occupy diverse habitats, ecological contexts have likely contributed to breed-specific positive selection. Prior to the advent of modern dog-feeding practices, there was likely substantial variation in dietary landscapes among disparate dog breeds. As such, we investigated one type of genetic variant, copy number variation, in three metabolic genes: glucokinase regulatory protein (GCKR), phytanol-CoA 2-hydroxylase (PHYH), and pancreatic α-amylase 2B (AMY2B). These genes code for proteins that are responsible for metabolizing dietary products that originate from distinctly different food types: sugar, meat, and starch, respectively. After surveying copy number variation among dogs with diverse dietary histories, we found no correlation between diet and positive selection in either GCKR or PHYH. Although it has been previously demonstrated that dogs experienced a copy number increase in AMY2B relative to wolves during or after the dog domestication process, we demonstrate that positive selection continued to act on amylase copy number in dog breeds that consumed starch-rich diets in time periods after domestication. Furthermore, we found that introgression with wolves is not responsible for deterioration of positive selection on AMY2B among diverse dog breeds. Together, this supports the hypothesis that the amylase copy number expansion is found universally in dogs. PMID:26863414

Dietary Variation and Evolution of Gene Copy Number among Dog Breeds.

PubMed

Reiter, Taylor; Jagoda, Evelyn; Capellini, Terence D

2016-01-01

Prolonged human interactions and artificial selection have influenced the genotypic and phenotypic diversity among dog breeds. Because humans and dogs occupy diverse habitats, ecological contexts have likely contributed to breed-specific positive selection. Prior to the advent of modern dog-feeding practices, there was likely substantial variation in dietary landscapes among disparate dog breeds. As such, we investigated one type of genetic variant, copy number variation, in three metabolic genes: glucokinase regulatory protein (GCKR), phytanol-CoA 2-hydroxylase (PHYH), and pancreatic α-amylase 2B (AMY2B). These genes code for proteins that are responsible for metabolizing dietary products that originate from distinctly different food types: sugar, meat, and starch, respectively. After surveying copy number variation among dogs with diverse dietary histories, we found no correlation between diet and positive selection in either GCKR or PHYH. Although it has been previously demonstrated that dogs experienced a copy number increase in AMY2B relative to wolves during or after the dog domestication process, we demonstrate that positive selection continued to act on amylase copy number in dog breeds that consumed starch-rich diets in time periods after domestication. Furthermore, we found that introgression with wolves is not responsible for deterioration of positive selection on AMY2B among diverse dog breeds. Together, this supports the hypothesis that the amylase copy number expansion is found universally in dogs.

Sensitive detection of KIT D816V in patients with mastocytosis.

PubMed

Tan, Angela; Westerman, David; McArthur, Grant A; Lynch, Kevin; Waring, Paul; Dobrovic, Alexander

2006-12-01

The 2447 A > T pathogenic variation at codon 816 of exon 17 (D816V) in the KIT gene, occurring in systemic mastocytosis (SM), leads to constitutive activation of tyrosine kinase activity and confers resistance to the tyrosine kinase inhibitor imatinib mesylate. Thus detection of this variation in SM patients is important for determining treatment strategy, but because the population of malignant cells carrying this variation is often small relative to the normal cell population, standard molecular detection methods can be unsuccessful. We developed 2 methods for detection of KIT D816V in SM patients. The first uses enriched sequencing of mutant alleles (ESMA) after BsmAI restriction enzyme digestion, and the second uses an allele-specific competitive blocker PCR (ACB-PCR) assay. We used these methods to assess 26 patients undergoing evaluation for SM, 13 of whom had SM meeting WHO classification criteria (before variation testing), and we compared the results with those obtained by direct sequencing. The sensitivities of the ESMA and the ACB-PCR assays were 1% and 0.1%, respectively. According to the ACB-PCR assay results, 65% (17/26) of patients were positive for D816V. Of the 17 positive cases, only 23.5% (4/17) were detected by direct sequencing. ESMA detected 2 additional exon 17 pathogenic variations, D816Y and D816N, but detected only 12 (70.5%) of the 17 D816V-positive cases. Overall, 100% (15/15) of the WHO-classified SM cases were codon 816 pathogenic variation positive. These findings demonstrate that the ACB-PCR assay combined with ESMA is a rapid and highly sensitive approach for detection of KIT D816V in SM patients.

TU-F-CAMPUS-T-04: Variations in Nominally Identical Small Fields From Photon Jaw Reproducibility and Associated Effects On Small Field Dosimetric Parameters

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

Muir, B R; McEwen, M R

2015-06-15

Purpose: To investigate uncertainties in small field output factors and detector specific correction factors from variations in field size for nominally identical fields using measurements and Monte Carlo simulations. Methods: Repeated measurements of small field output factors are made with the Exradin W1 (plastic scintillation detector) and the PTW microDiamond (synthetic diamond detector) in beams from the Elekta Precise linear accelerator. We investigate corrections for a 0.6x0.6 cm{sup 2} nominal field size shaped with secondary photon jaws at 100 cm source to surface distance (SSD). Measurements of small field profiles are made in a water phantom at 10 cm depthmore » using both detectors and are subsequently used for accurate detector positioning. Supplementary Monte Carlo simulations with EGSnrc are used to calculate the absorbed dose to the detector and absorbed dose to water under the same conditions when varying field size. The jaws in the BEAMnrc model of the accelerator are varied by a reasonable amount to investigate the same situation without the influence of measurements uncertainties (such as detector positioning or variation in beam output). Results: For both detectors, small field output factor measurements differ by up to 11 % when repeated measurements are made in nominally identical 0.6x0.6 cm{sup 2} fields. Variations in the FWHM of measured profiles are consistent with field size variations reported by the accelerator. Monte Carlo simulations of the dose to detector vary by up to 16 % under worst case variations in field size. These variations are also present in calculations of absorbed dose to water. However, calculated detector specific correction factors are within 1 % when varying field size because of cancellation of effects. Conclusion: Clinical physicists should be aware of potentially significant uncertainties in measured output factors required for dosimetry of small fields due to field size variations for nominally identical fields.« less

The spatial architecture of protein function and adaptation

PubMed Central

McLaughlin, Richard N.; Poelwijk, Frank J.; Raman, Arjun; Gosal, Walraj S.; Ranganathan, Rama

2014-01-01

Statistical analysis of protein evolution suggests a design for natural proteins in which sparse networks of coevolving amino acids (termed sectors) comprise the essence of three-dimensional structure and function1, 2, 3, 4, 5. However, proteins are also subject to pressures deriving from the dynamics of the evolutionary process itself—the ability to tolerate mutation and to be adaptive to changing selection pressures6, 7, 8, 9, 10. To understand the relationship of the sector architecture to these properties, we developed a high-throughput quantitative method for a comprehensive single-mutation study in which every position is substituted individually to every other amino acid. Using a PDZ domain (PSD95pdz3) model system, we show that sector positions are functionally sensitive to mutation, whereas non-sector positions are more tolerant to substitution. In addition, we find that adaptation to a new binding specificity initiates exclusively through variation within sector residues. A combination of just two sector mutations located near and away from the ligand-binding site suffices to switch the binding specificity of PSD95pdz3 quantitatively towards a class-switching ligand. The localization of functional constraint and adaptive variation within the sector has important implications for understanding and engineering proteins. PMID:23041932

Latitudinal variation of leaf stomatal traits from species to community level in forests: linkage with ecosystem productivity

PubMed Central

Wang, Ruili; Yu, Guirui; He, Nianpeng; Wang, Qiufeng; Zhao, Ning; Xu, Zhiwei; Ge, Jianping

2015-01-01

To explore the latitudinal variation of stomatal traits from species to community level and their linkage with net primary productivity (NPP), we investigated leaf stomatal density (SDL) and stomatal length (SLL) across 760 species from nine forest ecosystems in eastern China, and calculated the community-level SD (SDC) and SL (SLC) through species-specific leaf area index (LAI). Our results showed that latitudinal variation in species-level SDL and SLL was minimal, but community-level SDC and SLC decreased clearly with increasing latitude. The relationship between SD and SL was negative across species and different plant functional types (PFTs), but positive at the community level. Furthermore, community-level SDC correlated positively with forest NPP, and explained 51% of the variation in NPP. These findings indicate that the trade-off by regulating SDL and SLL may be an important strategy for plant individuals to adapt to environmental changes, and temperature acts as the main factor influencing community-level stomatal traits through alteration of species composition. Importantly, our findings provide new insight into the relationship between plant traits and ecosystem function. PMID:26403303

An Indoor Pedestrian Positioning Method Using HMM with a Fuzzy Pattern Recognition Algorithm in a WLAN Fingerprint System

PubMed Central

Ni, Yepeng; Liu, Jianbo; Liu, Shan; Bai, Yaxin

2016-01-01

With the rapid development of smartphones and wireless networks, indoor location-based services have become more and more prevalent. Due to the sophisticated propagation of radio signals, the Received Signal Strength Indicator (RSSI) shows a significant variation during pedestrian walking, which introduces critical errors in deterministic indoor positioning. To solve this problem, we present a novel method to improve the indoor pedestrian positioning accuracy by embedding a fuzzy pattern recognition algorithm into a Hidden Markov Model. The fuzzy pattern recognition algorithm follows the rule that the RSSI fading has a positive correlation to the distance between the measuring point and the AP location even during a dynamic positioning measurement. Through this algorithm, we use the RSSI variation trend to replace the specific RSSI value to achieve a fuzzy positioning. The transition probability of the Hidden Markov Model is trained by the fuzzy pattern recognition algorithm with pedestrian trajectories. Using the Viterbi algorithm with the trained model, we can obtain a set of hidden location states. In our experiments, we demonstrate that, compared with the deterministic pattern matching algorithm, our method can greatly improve the positioning accuracy and shows robust environmental adaptability. PMID:27618053

Y-Chromosome Variation in Hominids: Intraspecific Variation Is Limited to the Polygamous Chimpanzee

PubMed Central

Greve, Gabriele; Alechine, Evguenia; Pasantes, Juan J.; Hodler, Christine; Rietschel, Wolfram; Robinson, Terence J.; Schempp, Werner

2011-01-01

Background We have previously demonstrated that the Y-specific ampliconic fertility genes DAZ (deleted in azoospermia) and CDY (chromodomain protein Y) varied with respect to copy number and position among chimpanzees (Pan troglodytes). In comparison, seven Y-chromosomal lineages of the bonobo (Pan paniscus), the chimpanzee's closest living relative, showed no variation. We extend our earlier comparative investigation to include an analysis of the intraspecific variation of these genes in gorillas (Gorilla gorilla) and orangutans (Pongo pygmaeus), and examine the resulting patterns in the light of the species' markedly different social and mating behaviors. Methodology/Principal Findings Fluorescence in situ hybridization analysis (FISH) of DAZ and CDY in 12 Y-chromosomal lineages of western lowland gorilla (G. gorilla gorilla) and a single lineage of the eastern lowland gorilla (G. beringei graueri) showed no variation among lineages. Similar findings were noted for the 10 Y-chromosomal lineages examined in the Bornean orangutan (Pongo pygmaeus), and 11 Y-chromosomal lineages of the Sumatran orangutan (P. abelii). We validated the contrasting DAZ and CDY patterns using quantitative real-time polymerase chain reaction (qPCR) in chimpanzee and bonobo. Conclusion/Significance High intraspecific variation in copy number and position of the DAZ and CDY genes is seen only in the chimpanzee. We hypothesize that this is best explained by sperm competition that results in the variant DAZ and CDY haplotypes detected in this species. In contrast, bonobos, gorillas and orangutans—species that are not subject to sperm competition—showed no intraspecific variation in DAZ and CDY suggesting that monoandry in gorillas, and preferential female mate choice in bonobos and orangutans, probably permitted the fixation of a single Y variant in each taxon. These data support the notion that the evolutionary history of a primate Y chromosome is not simply encrypted in its DNA sequences, but is also shaped by the social and behavioral circumstances under which the specific species has evolved. PMID:22216243

Group delay variations of GPS transmitting and receiving antennas

NASA Astrophysics Data System (ADS)

Wanninger, Lambert; Sumaya, Hael; Beer, Susanne

2017-09-01

GPS code pseudorange measurements exhibit group delay variations at the transmitting and the receiving antenna. We calibrated C1 and P2 delay variations with respect to dual-frequency carrier phase observations and obtained nadir-dependent corrections for 32 satellites of the GPS constellation in early 2015 as well as elevation-dependent corrections for 13 receiving antenna models. The combined delay variations reach up to 1.0 m (3.3 ns) in the ionosphere-free linear combination for specific pairs of satellite and receiving antennas. Applying these corrections to the code measurements improves code/carrier single-frequency precise point positioning, ambiguity fixing based on the Melbourne-Wübbena linear combination, and determination of ionospheric total electron content. It also affects fractional cycle biases and differential code biases.

Short communication: Early modification of the circadian organization of cow activity in relation to disease or estrus.

PubMed

Veissier, Isabelle; Mialon, Marie-Madeleine; Sloth, Karen Helle

2017-05-01

Biological rhythms are an essential regulator of life. There is evidence that circadian rhythm of activity is disrupted under chronic stress in animals and humans, and it may also be less marked during diseases. Here we investigated whether a detectable circadian rhythm of activity exists in dairy cows in commercial settings using a real-time positioning system. We used CowView (GEA Farm Technologies) to regularly record the individual positions of 350 cows in a Danish dairy farm over 5 mo and to infer the cows' activity (resting, feeding, in alley). We ran a factorial correspondence analysis on the cows' activities and used the first component of this analysis to express the variations in activity. On this axis, the activities obtained the following weights: resting = -0.15; in alleys = +0.12; feeding = +0.34. By applying these weights to the proportions of time each cow spent on each of the 3 activities, we were able to chart a circadian rhythm of activity. We found that average level of activity of a cow on a given day and its variations during that day varied with specific states (i.e., estrus, lameness, mastitis). More specifically, circadian variations in activity appeared to be particularly sensitive and to vary 1 to 2 d before the farmer detected a disorder. These findings offer promising avenues for further research to design models to predict physiological or pathological states of cows from real-time positioning data. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Reproduction reduces photosynthetic capacity in females of the subdioecious Honckenya peploides

NASA Astrophysics Data System (ADS)

Sánchez-Vilas, Julia; Retuerto, Rubén

2011-03-01

As a consequence of the different reproductive functions performed by the sexes, sexually dimorphic/polymorphic plants may exhibit gender-related variations in the energy and resources allocated to reproduction, and in the physiological processes that underlie these differences. This study investigated whether the sexes of the subdioecious plant Honckenya peploides differ in ecophysiological traits related to photosynthetic capacity and whether possible differences depend on reproductive status and on the plant's position (edge or centre) in the population. We registered in three sites in NW Spain, the sex and density of shoots of two segregated clumps of plants. These clumps represent an extreme case of sex-ratio variation across space, with separated single-sex clumps of plants. In two of these sites we measured photosynthetic efficiencies, chlorophyll content, and specific leaf areas. In females, reproduction reduced photochemical efficiency, chlorophyll content and increased the specific leaf area, which is a key leaf trait related to photosynthetic capacity. In males, no differences due to reproduction were detected. The position within the clump affected the specific leaf area of the shoots, with shoots growing at the edge having the lowest values, regardless of the sex. Finally, the effects of position in photosynthetic efficiency and chlorophyll content where highly variable among clumps. We conclude that the differential effects of reproduction on sexes may entail different costs that could be crucial in the outcome of interactions between them, contributing to their spatial segregation.

Preliminary Investigations of an Optical Assembly Tracking Mechanism for LISA

NASA Technical Reports Server (NTRS)

Thorpe, James Ira; Stebbins, Robin

2010-01-01

After injection into their specific orbits, the position of the LISA spacecraft are not actively controlled. Rather the spacecraft are allowed to passively follow their trajectories and the roughly equilateral triangular constellation is preserved. Slight variations in the orbits cause the constellation to experience both periodic and secular variations, one consequence of which is a variation in the interior angles of the constellation on the order of one degree. This variation is larger than the field of view of the LISA telescope, requiring a mechanism for each spacecraft to maintain pointing to its two companions. This Optical Assembly Tracking Mechanism (OATM) will be used to accommodate these variations while maintaining pointing at the ten nanoradian level to the far spacecraft. Here we report on a possible design for the OATM as well as initial results from a test campaign of a piezo-inchworm actuator used to drive the mechanism.

Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes.

PubMed

Kachhap, Sangita; Singh, Balvinder

2015-01-01

In most of homeodomain-DNA complexes, glutamine or lysine is present at 50th position and interacts with 5th and 6th nucleotide of core recognition region. Molecular dynamics simulations of Msx-1-DNA complex (Q50-TG) and its variant complexes, that is specific (Q50K-CC), nonspecific (Q50-CC) having mutation in DNA and (Q50K-TG) in protein, have been carried out. Analysis of protein-DNA interactions and structure of DNA in specific and nonspecific complexes show that amino acid residues use sequence-dependent shape of DNA to interact. The binding free energies of all four complexes were analysed to define role of amino acid residue at 50th position in terms of binding strength considering the variation in DNA on stability of protein-DNA complexes. The order of stability of protein-DNA complexes shows that specific complexes are more stable than nonspecific ones. Decomposition analysis shows that N-terminal amino acid residues have been found to contribute maximally in binding free energy of protein-DNA complexes. Among specific protein-DNA complexes, K50 contributes more as compared to Q50 towards binding free energy in respective complexes. The sequence dependence of local conformation of DNA enables Q50/Q50K to make hydrogen bond with nucleotide(s) of DNA. The changes in amino acid sequence of protein are accommodated and stabilized around TAAT core region of DNA having variation in nucleotides.

A Validation of Parafoveal Semantic Information Extraction in Reading Chinese

ERIC Educational Resources Information Center

Zhou, Wei; Kliegl, Reinhold; Yan, Ming

2013-01-01

Parafoveal semantic processing has recently been well documented in reading Chinese sentences, presumably because of language-specific features. However, because of a large variation of fixation landing positions on pretarget words, some preview words actually were located in foveal vision when readers' eyes landed close to the end of the…

Identification of Vibrio parahaemolyticus Strains at the Species Level by PCR Targeted to the toxR Gene

PubMed Central

Kim, Yung Bu; Okuda, Jun; Matsumoto, Chiho; Takahashi, Naoki; Hashimoto, Satoru; Nishibuchi, Mitsuaki

1999-01-01

The DNA colony hybridization test with the polynucleotide probe for Vibrio parahaemolyticus toxR gene was performed. All 373 strains of V. parahaemolyticus gave positive results, and the strains belonging to four other Vibrio species including Vibrio alginolyticus gave weakly positive results, suggesting that toxR sequence variation may reflect the phylogenetic relationships of Vibrio species. We then established a toxR-targeted PCR protocol for the specific detection of V. parahaemolyticus. PMID:10074546

Functional heterogeneity and heritability in CHO cell populations.

PubMed

Davies, Sarah L; Lovelady, Clare S; Grainger, Rhian K; Racher, Andrew J; Young, Robert J; James, David C

2013-01-01

In this study, we address the hypothesis that it is possible to exploit genetic/functional variation in parental Chinese hamster ovary (CHO) cell populations to isolate clonal derivatives that exhibit superior, heritable attributes for biomanufacturing--new parental cell lines which are inherently more "fit for purpose." One-hundred and ninety-nine CHOK1SV clones were isolated from a donor CHOK1SV parental population by limiting dilution cloning and microplate image analysis, followed by primary analysis of variation in cell-specific proliferation rate during extended deep-well microplate suspension culture of individual clones to accelerate genetic drift in isolated cultures. A subset of 100 clones were comparatively evaluated for transient production of a recombinant monoclonal antibody (Mab) and green fluorescent protein following transfection of a plasmid vector encoding both genes. The heritability of both cell-specific proliferation rate and Mab production was further assessed using a subset of 23 clones varying in functional capability that were subjected to cell culture regimes involving both cryopreservation and extended sub-culture. These data showed that whilst differences in transient Mab production capability were not heritable per se, clones exhibiting heritable variation in specific proliferation rate, endocytotic transfectability and N-glycan processing were identified. Finally, for clonal populations most "evolved" by extended sub-culture in vitro we investigated the relationship between cellular protein biomass content, specific proliferation rate and cell surface N-glycosylation. Rapid-specific proliferation rate was inversely correlated to CHO cell size and protein content, and positively correlated to cell surface glycan content, although substantial clone-specific variation in ability to accumulate cell biomass was evident. Taken together, our data reveal the dynamic nature of the CHO cell functional genome and the potential to evolve and isolate CHO cell variants with improved functional properties in vitro. Copyright © 2012 Wiley Periodicals, Inc.

Explaining biomass growth of tropical canopy trees: the importance of sapwood.

PubMed

van der Sande, Masha T; Zuidema, Pieter A; Sterck, Frank

2015-04-01

Tropical forests are important in worldwide carbon (C) storage and sequestration. C sequestration of these forests may especially be determined by the growth of canopy trees. However, the factors driving variation in growth among such large individuals remain largely unclear. We evaluate how crown traits [total leaf area, specific leaf area and leaf nitrogen (N) concentration] and stem traits [sapwood area (SA) and sapwood N concentration] measured for individual trees affect absolute biomass growth for 43 tropical canopy trees belonging to four species, in a moist forest in Bolivia. Biomass growth varied strongly among trees, between 17.3 and 367.3 kg year(-1), with an average of 105.4 kg year(-1). We found that variation in biomass growth was chiefly explained by a positive effect of SA, and not by tree size or other traits examined. SA itself was positively associated with sapwood growth, sapwood lifespan and basal area. We speculate that SA positively affects the growth of individual trees mainly by increasing water storage, thus securing water supply to the crown. These positive roles of sapwood on growth apparently offset the increased respiration costs incurred by more sapwood. This is one of the first individual-based studies to show that variation in sapwood traits-and not crown traits-explains variation in growth among tropical canopy trees. Accurate predictions of C dynamics in tropical forests require similar studies on biomass growth of individual trees as well as studies evaluating the dual effect of sapwood (water provision vs. respiratory costs) on tropical tree growth.

Catch me if you can--the use of image guidance in the radiotherapy of an unusual case of esophageal cancer.

PubMed

Jensen, Alexandra D; Grehn, Christian; Nikoghosyan, Anna; Thieke, Christian; Krempien, Robert; Huber, Peter E; Debus, Jürgen; Münter, Marc W

2009-07-01

Despite maximum therapy the prognosis of esophageal carcinoma still remains extremely poor. New treatment strategies including improved radiation therapy techniques promise better outcome by improving local control through precise dose delivery due to higher conformality. A 62-year-old patient with locally advanced carcinoma of the gastroesophageal junction underwent definitive radiochemotherapy with intensity-modulated radiation therapy (IMRT). On positioning control with the in-room CT, the distal esophagus, and hence the tumor, was found to be highly mobile exhibiting changes in position of up to 4 cm from fraction to fraction. IMRT plans were created for various positions establishing a plan library to choose from as appropriate. CT scans were performed prior to each treatment fraction to clarify esophagus position in order to choose the adequate treatment plan. Image guidance was crucial in this unusual case of esophageal carcinoma. Without the information from position control CTs, the tumor would have received only about half the prescribed dose due to variations in position. For this specific case, in-room CT scans are probably superior to kilo- or megavoltage CTs due to the higher soft-tissue contrast enabling detection of positioning variation of the organ and offering the possibility to use the CT for treatment planning.

Community-weighted mean of leaf traits and divergence of wood traits predict aboveground biomass in secondary subtropical forests.

PubMed

Ali, Arshad; Yan, En-Rong; Chang, Scott X; Cheng, Jun-Yang; Liu, Xiang-Yu

2017-01-01

Subtropical forests are globally important in providing ecological goods and services, but it is not clear whether functional diversity and composition can predict aboveground biomass in such forests. We hypothesized that high aboveground biomass is associated with high functional divergence (FDvar, i.e., niche complementarity) and community-weighted mean (CWM, i.e., mass ratio; communities dominated by a single plant strategy) of trait values. Structural equation modeling was employed to determine the direct and indirect effects of stand age and the residual effects of CWM and FDvar on aboveground biomass across 31 plots in secondary forests in subtropical China. The CWM model accounted for 78, 20, 6 and 2% of the variation in aboveground biomass, nitrogen concentration in young leaf, plant height and specific leaf area of young leaf, respectively. The FDvar model explained 74, 13, 7 and 0% of the variation in aboveground biomass, plant height, twig wood density and nitrogen concentration in young leaf, respectively. The variation in aboveground biomass, CWM of leaf nitrogen concentration and specific leaf area, and FDvar of plant height, twig wood density and nitrogen concentration in young leaf explained by the joint model was 86, 20, 13, 7, 2 and 0%, respectively. Stand age had a strong positive direct effect but low indirect positive effects on aboveground biomass. Aboveground biomass was negatively related to CWM of nitrogen concentration in young leaf, but positively related to CWM of specific leaf area of young leaf and plant height, and FDvar of plant height, twig wood density and nitrogen concentration in young leaf. Leaf and wood economics spectra are decoupled in regulating the functionality of forests, communities with diverse species but high nitrogen conservative and light acquisitive strategies result in high aboveground biomass, and hence, supporting both the mass ratio and niche complementarity hypotheses in secondary subtropical forests. Copyright © 2016 Elsevier B.V. All rights reserved.

Capturing Physiology of Emotion along Facial Muscles: A Method of Distinguishing Feigned from Involuntary Expressions

NASA Astrophysics Data System (ADS)

Khan, Masood Mehmood; Ward, Robert D.; Ingleby, Michael

The ability to distinguish feigned from involuntary expressions of emotions could help in the investigation and treatment of neuropsychiatric and affective disorders and in the detection of malingering. This work investigates differences in emotion-specific patterns of thermal variations along the major facial muscles. Using experimental data extracted from 156 images, we attempted to classify patterns of emotion-specific thermal variations into neutral, and voluntary and involuntary expressions of positive and negative emotive states. Initial results suggest (i) each facial muscle exhibits a unique thermal response to various emotive states; (ii) the pattern of thermal variances along the facial muscles may assist in classifying voluntary and involuntary facial expressions; and (iii) facial skin temperature measurements along the major facial muscles may be used in automated emotion assessment.

Design of experiments on 135 cloned poplar trees to map environmental influence in greenhouse.

PubMed

Pinto, Rui Climaco; Stenlund, Hans; Hertzberg, Magnus; Lundstedt, Torbjörn; Johansson, Erik; Trygg, Johan

2011-01-31

To find and ascertain phenotypic differences, minimal variation between biological replicates is always desired. Variation between the replicates can originate from genetic transformation but also from environmental effects in the greenhouse. Design of experiments (DoE) has been used in field trials for many years and proven its value but is underused within functional genomics including greenhouse experiments. We propose a strategy to estimate the effect of environmental factors with the ultimate goal of minimizing variation between biological replicates, based on DoE. DoE can be analyzed in many ways. We present a graphical solution together with solutions based on classical statistics as well as the newly developed OPLS methodology. In this study, we used DoE to evaluate the influence of plant specific factors (plant size, shoot type, plant quality, and amount of fertilizer) and rotation of plant positions on height and section area of 135 cloned wild type poplar trees grown in the greenhouse. Statistical analysis revealed that plant position was the main contributor to variability among biological replicates and applying a plant rotation scheme could reduce this variation. Copyright © 2010 Elsevier B.V. All rights reserved.

Variations in the axis of motion during head repositioning--a comparison of subjects with whiplash-associated disorders or non-specific neck pain and healthy controls.

PubMed

Grip, Helena; Sundelin, Gunnevi; Gerdle, Björn; Karlsson, J Stefan

2007-10-01

The ability to reproduce head position can be affected in patients after a neck injury. The repositioning error is commonly used as a measure of proprioception, but variations in the movement might provide additional information. The axis of motion and target performance were analyzed during a head repositioning task (flexion, extension and side rotations) for 24 control subjects, 22 subjects with whiplash-associated disorders and 21 with non-specific neck pain. Questionnaires regarding pain intensity and fear avoidance were collected. Head position and axis of motion parameters were calculated using a helical axis model with a moving window of 4 degrees . During flexion the whiplash group had a larger constant repositioning error than the control group (-1.8(2.9) degrees vs. 0.1(2.4) degrees , P=0.04). The axis was more inferior in both neck pain groups (12.0(1.6)cm vs. 14.5(2.0)cm, P<0.05) indicating movement at a lower level in the spine. Including pain intensity from shoulder and neck region as covariates showed an effect on the axis position (P=0.03 and 0.04). During axial rotation to the left there was more variation in axis direction for neckpain groups as compared with controls (4.0(1.7) degrees and 3.7(2.4) degrees vs. 2.3(1.9) degrees , P=0.01 and 0.05). No significant difference in fear avoidance was found between the two neck pain groups. Measuring variation in the axis of motion together with target performance gives objective measures on proprioceptive ability that are difficult to quantify by visual inspection. Repositioning errors were in general small, suggesting it is not sufficient as a single measurement variable in a clinical situation, but should be measured in combination with other tests, such as range of motion.

Characterization of Prdm9 in equids and sterility in mules.

PubMed

Steiner, Cynthia C; Ryder, Oliver A

2013-01-01

Prdm9 (Meisetz) is the first speciation gene discovered in vertebrates conferring reproductive isolation. This locus encodes a meiosis-specific histone H3 methyltransferase that specifies meiotic recombination hotspots during gametogenesis. Allelic differences in Prdm9, characterized for a variable number of zinc finger (ZF) domains, have been associated with hybrid sterility in male house mice via spermatogenic failure at the pachytene stage. The mule, a classic example of hybrid sterility in mammals also exhibits a similar spermatogenesis breakdown, making Prdm9 an interesting candidate to evaluate in equine hybrids. In this study, we characterized the Prdm9 gene in all species of equids by analyzing sequence variation of the ZF domains and estimating positive selection. We also evaluated the role of Prdm9 in hybrid sterility by assessing allelic differences of ZF domains in equine hybrids. We found remarkable variation in the sequence and number of ZF domains among equid species, ranging from five domains in the Tibetan kiang and Asiatic wild ass, to 14 in the Grevy's zebra. Positive selection was detected in all species at amino acid sites known to be associated with DNA-binding specificity of ZF domains in mice and humans. Equine hybrids, in particular a quartet pedigree composed of a fertile mule showed a mosaic of sequences and number of ZF domains suggesting that Prdm9 variation does not seem by itself to contribute to equine hybrid sterility.

Characterization of Prdm9 in Equids and Sterility in Mules

PubMed Central

Steiner, Cynthia C.; Ryder, Oliver A.

2013-01-01

Prdm9 (Meisetz) is the first speciation gene discovered in vertebrates conferring reproductive isolation. This locus encodes a meiosis-specific histone H3 methyltransferase that specifies meiotic recombination hotspots during gametogenesis. Allelic differences in Prdm9, characterized for a variable number of zinc finger (ZF) domains, have been associated with hybrid sterility in male house mice via spermatogenic failure at the pachytene stage. The mule, a classic example of hybrid sterility in mammals also exhibits a similar spermatogenesis breakdown, making Prdm9 an interesting candidate to evaluate in equine hybrids. In this study, we characterized the Prdm9 gene in all species of equids by analyzing sequence variation of the ZF domains and estimating positive selection. We also evaluated the role of Prdm9 in hybrid sterility by assessing allelic differences of ZF domains in equine hybrids. We found remarkable variation in the sequence and number of ZF domains among equid species, ranging from five domains in the Tibetan kiang and Asiatic wild ass, to 14 in the Grevy’s zebra. Positive selection was detected in all species at amino acid sites known to be associated with DNA-binding specificity of ZF domains in mice and humans. Equine hybrids, in particular a quartet pedigree composed of a fertile mule showed a mosaic of sequences and number of ZF domains suggesting that Prdm9 variation does not seem by itself to contribute to equine hybrid sterility. PMID:23613924

Comparative analyses across cattle genders and breeds reveal the pitfalls caused by false positive and lineage-differential copy number variations.

PubMed

Zhou, Yang; Utsunomiya, Yuri T; Xu, Lingyang; Hay, El Hamidi Abdel; Bickhart, Derek M; Sonstegard, Tad S; Van Tassell, Curtis P; Garcia, Jose Fernando; Liu, George E

2016-07-06

We compared CNV region (CNVR) results derived from 1,682 Nellore cattle with equivalent results derived from our previous analysis of Bovine HapMap samples. By comparing CNV segment frequencies between different genders and groups, we identified 9 frequent, false positive CNVRs with a total length of 0.8 Mbp that were likely caused by assembly errors. Although there was a paucity of lineage specific events, we did find one 54 kb deletion on chr5 significantly enriched in Nellore cattle. A few highly frequent CNVRs present in both datasets were detected within genomic regions containing olfactory receptor, ATP-binding cassette, and major histocompatibility complex genes. We further evaluated their impacts on downstream bioinformatics and CNV association analyses. Our results revealed pitfalls caused by false positive and lineage-differential copy number variations and will increase the accuracy of future CNV studies in both taurine and indicine cattle.

International variation in the prevalence of preclinical colorectal cancer: Implications for predictive values of noninvasive screening tests and potential target populations for screening

PubMed Central

Stock, Christian; Brenner, Hermann

2017-01-01

Screening for colorectal cancer (CRC) is implemented in an increasing number of countries. We aimed to assess international variation in the prevalence of preclinical CRC and the resulting variation in positive and negative predictive values (PPVs, NPVs) of existing and potential CRC screening tests in various countries. Using age‐ and sex‐specific CRC incidence data and transition rates from preclinical to clinical CRC we estimated overall and age‐ and sex‐specific prevalence of preclinical CRC in the target population aged 50–74 years in different parts of the world. These prevalence estimates were used to derive PPVs and NPVs for existing and potential noninvasive screening tests with varying levels of sensitivity and specificity. Within all regions and countries, prevalence strongly increases with age and is higher in men than in women. In addition, major variation was seen between regions and countries, with overall prevalence varying between 1 and 0.1%. As a result, PPVs are expected to strongly vary between ∼10% for men in high incidence countries, such as Australia and Germany, and 1% for women in low incidence countries, whereas NPVs are expected to be consistently well above 99%. Variation in CRC prevalence profoundly affects expected PPVs of screening tests, and PPVs should be carefully considered when decisions on screening tests and strategies are made for specific populations and health care systems. Here, we provide estimates of preclinical CRC and expected PPVs and NPVs of noninvasive screening tests, which may enhance the empirical basis for planning of population‐based CRC screening strategies. PMID:28670788

Characterization of natural polymorphic sites of the HIV-1 integrase before the introduction of HIV-1 integrase inhibitors in Germany

PubMed Central

Meixenberger, Karolin; Pouran Yousef, Kaveh; Somogyi, Sybille; Fiedler, Stefan; Bartmeyer, Barbara; von Kleist, Max; Kücherer, Claudia

2014-01-01

Introduction The aim of our study was to analyze the occurrence and evolution of HIV-1 integrase polymorphisms during the HIV-1 epidemic in Germany prior to the introduction of the first integrase inhibitor raltegravir in 2007. Materials and Methods Plasma samples from drug-naïve HIV-1 infected individuals newly diagnosed between 1986 and 2006 were used to determine PCR-based population sequences of the HIV-1 integrase (amino acids 1–278). The HIV-1 subtype was determined using the REGA HIV-1 subtyping tool. We calculated the frequency of amino acids at each position of the HIV-1 integrase in 337 subtype B strains for the time periods 1986–1989, 1991–1994, 1995–1998, 1999–2002, and 2003–2006. Positions were defined as polymorphic if amino acid variation was >1% in any period. Logistic regression was used to identify trends in amino acid variation over time. Resistance-associated mutations were identified according to the IAS 2013 list and the HIVdb, ANRS and GRADE algorithms. Results Overall, 56.8% (158/278) amino acid positions were polymorphic and 15.8% (25/158) of these positions exhibited a significant trend in amino acid variation over time. Proportionately, most polymorphic positions (63.3%, 31/49) were detected in the N-terminal zinc finger domain of the HIV-1 integrase. Motifs and residues essential for HIV-1 integrase activity were little polymorphic, but within the minimal non-specific DNA binding region I220-D270 up to 18.1% amino acid variation was noticed, including four positions with significant amino acid variation over time (S230, D232, D256, A265). No major resistance mutations were identified, and minor resistance mutations were rarely observed without trend over time. E157Q considered by HIVdb, ANRS, and GRADE algorithms was the most frequent resistance-associated polymorphism with an overall prevalence of 2.4%. Conclusions Detailed knowledge of the evolutionary variation of HIV-1 integrase polymorphisms is important to understand the development of resistance in the presence of the drug. Our results will contribute to define the relevance of integrase polymorphisms in HIV-strains resistant to integrase inhibitors and to improve resistance interpretation algorithms. PMID:25397491

Assessment of genetic variation for pathogen-specific mastitis resistance in Valle del Belice dairy sheep.

PubMed

Tolone, Marco; Larrondo, Cristian; Yáñez, José M; Newman, Scott; Sardina, Maria Teresa; Portolano, Baldassare

2016-07-28

Mastitis resistance is a complex and multifactorial trait, and its expression depends on both genetic and environmental factors, including infection pressure. The objective of this research was to determine the genetic basis of mastitis resistance to specific pathogens using a repeatability threshold probit animal model. The most prevalent isolated pathogens were coagulase-negative staphylococci (CNS); 39 % of records and 77 % of the animals infected at least one time in the whole period of study. There was significant genetic variation only for Streptococci (STR). In addition, there was a positive genetic correlation between STR and all pathogens together (ALL) (0.36 ± 0.22), and CNS and ALL (0.92 ± 0.04). The results of our study support the presence of significant genetic variation for mastitis caused by Streptococci and suggest the importance of discriminating between different pathogens causing mastitis due to the fact that they most likely influence different genetic traits. Low heritabilities for pathogen specific-mastitis resistance may be considered when including bacteriological status as a measure of mastitis presence to implement breeding strategies for improving udder health in dairy ewes.

Effects of Gene Duplication, Positive Selection, and Shifts in Gene Expression on the Evolution of the Venom Gland Transcriptome in Widow Spiders

PubMed Central

Haney, Robert A.; Clarke, Thomas H.; Gadgil, Rujuta; Fitzpatrick, Ryan; Hayashi, Cheryl Y.; Ayoub, Nadia A.; Garb, Jessica E.

2016-01-01

Gene duplication and positive selection can be important determinants of the evolution of venom, a protein-rich secretion used in prey capture and defense. In a typical model of venom evolution, gene duplicates switch to venom gland expression and change function under the action of positive selection, which together with further duplication produces large gene families encoding diverse toxins. Although these processes have been demonstrated for individual toxin families, high-throughput multitissue sequencing of closely related venomous species can provide insights into evolutionary dynamics at the scale of the entire venom gland transcriptome. By assembling and analyzing multitissue transcriptomes from the Western black widow spider and two closely related species with distinct venom toxicity phenotypes, we do not find that gene duplication and duplicate retention is greater in gene families with venom gland biased expression in comparison with broadly expressed families. Positive selection has acted on some venom toxin families, but does not appear to be in excess for families with venom gland biased expression. Moreover, we find 309 distinct gene families that have single transcripts with venom gland biased expression, suggesting that the switching of genes to venom gland expression in numerous unrelated gene families has been a dominant mode of evolution. We also find ample variation in protein sequences of venom gland–specific transcripts, lineage-specific family sizes, and ortholog expression among species. This variation might contribute to the variable venom toxicity of these species. PMID:26733576

Individuals in food webs: the relationships between trophic position, omnivory and among-individual diet variation.

PubMed

Svanbäck, Richard; Quevedo, Mario; Olsson, Jens; Eklöv, Peter

2015-05-01

Among-individual diet variation is common in natural populations and may occur at any trophic level within a food web. Yet, little is known about its variation among trophic levels and how such variation could affect phenotypic divergence within populations. In this study we investigate the relationships between trophic position (the population's range and average) and among-individual diet variation. We test for diet variation among individuals and across size classes of Eurasian perch (Perca fluviatilis), a widespread predatory freshwater fish that undergoes ontogenetic niche shifts. Second, we investigate among-individual diet variation within fish and invertebrate populations in two different lake communities using stable isotopes. Third, we test potential evolutionary implications of population trophic position by assessing the relationship between the proportion of piscivorous perch (populations of higher trophic position) and the degree of phenotypic divergence between littoral and pelagic perch sub-populations. We show that among-individual diet variation is highest at intermediate trophic positions, and that this high degree of among-individual variation likely causes an increase in the range of trophic positions among individuals. We also found that phenotypic divergence was negatively related to trophic position in a population. This study thus shows that trophic position is related to and may be important for among-individual diet variation as well as to phenotypic divergence within populations.

New mutations and an updated database for the patched-1 (PTCH1) gene.

PubMed

Reinders, Marie G; van Hout, Antonius F; Cosgun, Betûl; Paulussen, Aimée D; Leter, Edward M; Steijlen, Peter M; Mosterd, Klara; van Geel, Michel; Gille, Johan J

2018-05-01

Basal cell nevus syndrome (BCNS) is an autosomal dominant disorder characterized by multiple basal cell carcinomas (BCCs), maxillary keratocysts, and cerebral calcifications. BCNS most commonly is caused by a germline mutation in the patched-1 (PTCH1) gene. PTCH1 mutations are also described in patients with holoprosencephaly. We have established a locus-specific database for the PTCH1 gene using the Leiden Open Variation Database (LOVD). We included 117 new PTCH1 variations, in addition to 331 previously published unique PTCH1 mutations. These new mutations were found in 141 patients who had a positive PTCH1 mutation analysis in either the VU University Medical Centre (VUMC) or Maastricht University Medical Centre (MUMC) between 1995 and 2015. The database contains 331 previously published unique PTCH1 mutations and 117 new PTCH1 variations. We have established a locus-specific database for the PTCH1 gene using the Leiden Open Variation Database (LOVD). The database provides an open collection for both clinicians and researchers and is accessible online at http://www.lovd.nl/PTCH1. © 2018 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc.

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism

PubMed Central

Kutyavin, Tanya; Stamatoyannopoulos, John A.

2012-01-01

The average individual is expected to harbor thousands of variants within non-coding genomic regions involved in gene regulation. However, it is currently not possible to interpret reliably the functional consequences of genetic variation within any given transcription factor recognition sequence. To address this, we comprehensively analyzed heritable genome-wide binding patterns of a major sequence-specific regulator (CTCF) in relation to genetic variability in binding site sequences across a multi-generational pedigree. We localized and quantified CTCF occupancy by ChIP-seq in 12 related and unrelated individuals spanning three generations, followed by comprehensive targeted resequencing of the entire CTCF–binding landscape across all individuals. We identified hundreds of variants with reproducible quantitative effects on CTCF occupancy (both positive and negative). While these effects paralleled protein–DNA recognition energetics when averaged, they were extensively buffered by striking local context dependencies. In the significant majority of cases buffering was complete, resulting in silent variants spanning every position within the DNA recognition interface irrespective of level of binding energy or evolutionary constraint. The prevalence of complex partial or complete buffering effects severely constrained the ability to predict reliably the impact of variation within any given binding site instance. Surprisingly, 40% of variants that increased CTCF occupancy occurred at positions of human–chimp divergence, challenging the expectation that the vast majority of functional regulatory variants should be deleterious. Our results suggest that, even in the presence of “perfect” genetic information afforded by resequencing and parallel studies in multiple related individuals, genomic site-specific prediction of the consequences of individual variation in regulatory DNA will require systematic coupling with empirical functional genomic measurements. PMID:22457641

A numerical investigation on the effect of RF coil feed variability on global and local electromagnetic field exposure in human body models at 64 MHz.

PubMed

Lucano, Elena; Liberti, Micaela; Lloyd, Tom; Apollonio, Francesca; Wedan, Steve; Kainz, Wolfgang; Angelone, Leonardo M

2018-02-01

This study aims to investigate how the positions of the feeding sources of the transmit radiofrequency (RF) coil, field orientation direction with respect to the patient, and patient dimensions affect the global and local electromagnetic exposure in human body models. Three RF coil models were implemented, namely a specific two-source (S2) feed and two multisource feed configurations: generic 32-source (G32) and hybrid 16-source (H16). Thirty-two feeding conditions were studied for the S2, whereas two were studied for the G32 and H16. The study was performed using five human body models. Additionally, for two of the body models, the case of a partially implanted lead was evaluated. The results showed an overall variation due to coil feeding conditions of the whole-body specific absorption rate (SAR) of less than 20%, but deviations up to 98% of the magnitude of the electric field tangential to a possible lead path. For the analysis with the partially implanted lead, a variation of local SAR at the tip of the lead of up to 60% was observed with respect to feed position and field orientation direction. The results of this study suggest that specific information about feed position and field orientation direction must be considered for an accurate evaluation of patient exposure. Magn Reson Med 79:1135-1144, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Deep sequencing in library selection projects: what insight does it bring?

PubMed

Glanville, J; D'Angelo, S; Khan, T A; Reddy, S T; Naranjo, L; Ferrara, F; Bradbury, A R M

2015-08-01

High throughput sequencing is poised to change all aspects of the way antibodies and other binders are discovered and engineered. Millions of available sequence reads provide an unprecedented sampling depth able to guide the design and construction of effective, high quality naïve libraries containing tens of billions of unique molecules. Furthermore, during selections, high throughput sequencing enables quantitative tracing of enriched clones and position-specific guidance to amino acid variation under positive selection during antibody engineering. Successful application of the technologies relies on specific PCR reagent design, correct sequencing platform selection, and effective use of computational tools and statistical measures to remove error, identify antibodies, estimate diversity, and extract signatures of selection from the clone down to individual structural positions. Here we review these considerations and discuss some of the remaining challenges to the widespread adoption of the technology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Deep sequencing in library selection projects: what insight does it bring?

PubMed Central

Glanville, J; D’Angelo, S; Khan, T.A.; Reddy, S. T.; Naranjo, L.; Ferrara, F.; Bradbury, A.R.M.

2015-01-01

High throughput sequencing is poised to change all aspects of the way antibodies and other binders are discovered and engineered. Millions of available sequence reads provide an unprecedented sampling depth able to guide the design and construction of effective, high quality naïve libraries containing tens of billions of unique molecules. Furthermore, during selections, high throughput sequencing enables quantitative tracing of enriched clones and position-specific guidance to amino acid variation under positive selection during antibody engineering. Successful application of the technologies relies on specific PCR reagent design, correct sequencing platform selection, and effective use of computational tools and statistical measures to remove error, identify antibodies, estimate diversity, and extract signatures of selection from the clone down to individual structural positions. Here we review these considerations and discuss some of the remaining challenges to the widespread adoption of the technology. PMID:26451649

Mapping From an Instrumented Glove to a Robot Hand

NASA Technical Reports Server (NTRS)

Goza, Michael

2005-01-01

An algorithm has been developed to solve the problem of mapping from (1) a glove instrumented with joint-angle sensors to (2) an anthropomorphic robot hand. Such a mapping is needed to generate control signals to make the robot hand mimic the configuration of the hand of a human attempting to control the robot. The mapping problem is complicated by uncertainties in sensor locations caused by variations in sizes and shapes of hands and variations in the fit of the glove. The present mapping algorithm is robust in the face of these uncertainties, largely because it includes a calibration sub-algorithm that inherently adapts the mapping to the specific hand and glove, without need for measuring the hand and without regard for goodness of fit. The algorithm utilizes a forward-kinematics model of the glove derived from documentation provided by the manufacturer of the glove. In this case, forward-kinematics model signifies a mathematical model of the glove fingertip positions as functions of the sensor readings. More specifically, given the sensor readings, the forward-kinematics model calculates the glove fingertip positions in a Cartesian reference frame nominally attached to the palm. The algorithm also utilizes an inverse-kinematics model of the robot hand. In this case, inverse-kinematics model signifies a mathematical model of the robot finger-joint angles as functions of the robot fingertip positions. Again, more specifically, the inverse-kinematics model calculates the finger-joint commands needed to place the fingertips at specified positions in a Cartesian reference frame that is attached to the palm of the robot hand and that nominally corresponds to the Cartesian reference frame attached to the palm of the glove. Initially, because of the aforementioned uncertainties, the glove fingertip positions calculated by the forwardkinematics model in the glove Cartesian reference frame cannot be expected to match the robot fingertip positions in the robot-hand Cartesian reference frame. A calibration must be performed to make the glove and robot-hand fingertip positions correspond more precisely. The calibration procedure involves a few simple hand poses designed to provide well-defined fingertip positions. One of the poses is a fist. In each of the other poses, a finger touches the thumb. The calibration subalgorithm uses the sensor readings from these poses to modify the kinematical models to make the two sets of fingertip positions agree more closely.

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

Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm

PubMed Central

Öhrmalm, Christina; Jobs, Magnus; Eriksson, Ronnie; Golbob, Sultan; Elfaitouri, Amal; Benachenhou, Farid; Strømme, Maria; Blomberg, Jonas

2010-01-01

One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts and distributions of mismatching bases, e.g. synonymous mutations, in target DNA. Microsphere-linked 70-mer probes were hybridized in 3M TMAC buffer to biotinylated single-stranded (ss) DNA for subsequent analysis in a Luminex® system. When mismatches interrupted contiguous matching stretches of 6 nt or longer, it had a strong impact on hybridization. Contiguous matching stretches are more important than the same number of matching nucleotides separated by mismatches into several regions. dInosine, but not 5-nitroindole, substitutions at mismatching positions stabilized hybridization remarkably well, comparable to N (4-fold) wobbles in the same positions. In contrast to shorter probes, 70-nt probes with judiciously placed dInosine substitutions and/or wobble positions were remarkably mismatch tolerant, with preserved specificity. An algorithm, NucZip, was constructed to model the nucleation and zipping phases of hybridization, integrating both local and distant binding contributions. It predicted hybridization more exactly than previous algorithms, and has the potential to guide the design of variation-tolerant yet specific probes. PMID:20864443

Relationships between beliefs about medications and nonadherence to prescribed chronic medications.

PubMed

Phatak, Hemant M; Thomas, Joseph

2006-10-01

Medication beliefs of patients with a specific medical condition have been associated with nonadherence to drugs used to treat that condition. However, associations between medication beliefs and nonadherence of individuals on chronic, multiple medications have not been studied. To investigate associations between patients' medication beliefs and nonadherence to chronic drug therapy. A cross-sectional, self-administered survey of patients waiting to see pharmacists at an outpatient pharmacy in a primary care clinic was conducted. Participants' medication beliefs were assessed using the Beliefs about Medicines Questionnaire, and nonadherence was assessed using the Morisky Medication Adherence Scale. Pearson correlation analysis was used to assess bivariate associations between medication beliefs and nonadherence. Regression was used to assess relative strength of associations between various medication beliefs and nonadherence and also to assess the significance of the interactions between those beliefs and nonadherence. There were positive bivariate associations between specific concerns about medications (p < 0.001), perceived general harmful effects of medications (p < 0.001), and perceived overprescribing of medications by physicians (p < 0.001) and medication nonadherence. When relative strength of associations between each medication belief and nonadherence was assessed, while controlling for other medication beliefs, specific-necessity (p = 0.02) and specific-concerns (p = 0.01) exhibited significant negative and positive associations with nonadherence, respectively. All two-way interactions between variables in the model were insignificant. A model consisting of age, total number of drugs used, and medication beliefs, that is, specific-necessity, specific-concerns, general-overuse, and general-harm, accounted for 26.5% of variance. Medication beliefs alone explained 22.4% of variation in nonadherence to chronic drug therapy. Patients' medication beliefs explained a significant portion of variation in medication nonadherence.

Position specific morphological characteristics of top-level male handball players.

PubMed

Srhoj, V; Marinović, M; Rogulj, N

2002-06-01

With the aim of determining the common morphological features of senior male handball players and of analyzing their specificities i.e. the probable variation between the four playing positions (back court players, wings, pivots, goalkeepers), 25 anthropometric measures were applied to the sample of 49 players, members of three top-quality handball teams. The basic descriptive parameters were calculated and then an analysis of variance and a cluster analysis were performed. A mesomorphic, athletic body- type was obtained with a marked longitudinal skeleton dimensionality, but also with a balanced ratio between the skeletal system and muscle mass and with low values of subcutaneous fat tissue. Back court players and goalkeepers are superior in terms of outstanding skeletal dimensions and circumferences. Line players, i.e. wings and pivots, have somewhat lower longitudinal measures, whereas pronounced voluminosity and a slightly higher fat tissue value differentiate pivots from players in other positions. Cluster analysis revealed a greater homogeneity in the morphological profiles of the samples of line players (wings and pivots) than in the profiles of backs or goalkeepers. The obtained position-related differences in morphological characteristics of players suggest that the experienced players from the sample were earlier successfully subjected to the selection process and oriented to a particular playing position because of the observed correspondence between their body-type and specific kinesiological demands of the position in question. Therefore, in top-quality team-handball it would be recommendable to select players whose morphological profiles are as compatible as possible with positional specificities in the demand for the game.

Positive serum specific IgE has a short half-life in patients with penicillin allergy and reversal does not always indicate tolerance.

PubMed

Hjortlund, Janni; Mortz, Charlotte Gotthard; Stage, Tore Bjerregaard; Skov, Per Stahl; Dahl, Ronald; Bindslev-Jensen, Carsten

2014-01-01

The positive and negative predictive values of specific IgE to penicillins are not well established for penicillin hypersensitivity. One reason may be that serum IgE levels to penicillin diminish over time. The objective in this study was to investigate variations in serum half-life (T½) for specific IgE to penicillins (s-IgE) and to evaluate the outcome of penicillin challenges in patients with previous but not present specific IgE to penicillins. Two subgroups were investigated. All included patients had a history of penicillin allergy with reported symptoms such as urticaria/angioedema or unclassified cutaneous rash. T½ of specific IgE to penicillins was calculated based on sera from 29 patients with repeated measurements of s-IgE. Twenty-two patients with a previous positive s-IgE was followed and challenged with penicillin when IgE had become negative. The T½ for s-IgE varied between the 26 patients with decreasing s-IgE from 1.6 months to 76.4 months and 52% had a T½ of less than a year. The three patients with stable and increasing IgE-values showed T½ approaching infinity A total of 29 challenges with β-lactams were performed. Four different patterns were seen when evaluating the clinical reaction to challenge (positive/negative) and post-challenge boost of s-IgE (yes/no). Eight (36.4%) had negative challenge and negative post-challenge s-IgE, eight (36.4%) negative challenge, but positive post-challenge s-IgE levels. 3 (13.6%) had positive challenge and positive post-challenge s-IgE whereas 3 (13.6%) were challenge positive, but had negative post-challenge s-IgE. Specific IgE to penicillins declines over time stressing the importance of a close time relation between diagnostic work-up and clinical reaction. Reversal of previously positive s-IgE may still be associated with positive penicillin challenges and/or re-boostering of s-IgE to positivity.

Impact of user fees on day use attendance at New Hampshire state parks

Treesearch

Allison A. Rechisky; Bradford N. Williamson

1992-01-01

This paper examines state park day use attendance data over a ten year period, 1980 - 1990, for variations in attendance effected by increases in user fees. A non-controllable variable the weather has been taken into account. The results of this paper suggest that user fees can be successfully collected at specific locations and provide positive income without...

PAH Emission in the Orion Bar

NASA Technical Reports Server (NTRS)

Bregman, Jesse; Sloan, G. C.

1996-01-01

The emission from polycyclic aromatic hydrocarbons (PAH's) in the Orion Bar region is investigated using a combination of narrow-band imaging and long-slit spectroscopy. The goal was to study how the strength of the PAH bands vary with spatial position in this edge-on photo-dissociation region. The specific focus here is how these variations constrain the carrier of the 3.4 micron band.

Neighborhood diversity of potentially pathogenic bacteria in drinking water from the city of Maroua, Cameroon.

PubMed

Healy-Profitós, Jessica; Lee, Seungjun; Mouhaman, Arabi; Garabed, Rebecca; Moritz, Mark; Piperata, Barbara; Lee, Jiyoung

2016-06-01

This study examined the spatial variation of potential gastrointestinal pathogens within drinking water sources and home storage containers in four neighborhoods in Maroua, Cameroon. Samples were collected from source (n = 28) and home containers (n = 60) in each study neighborhood. Pathogen contamination was assessed using quantitative polymerase chain reaction, targeting Campylobacter spp., Shiga toxin producing Escherichia coli (virulence genes, stx1 and stx2), and Salmonella spp. Microbial source tracking (MST) targeted three different host-specific markers: HF183 (human), Rum2Bac (ruminant) and GFD (poultry) to identify contamination sources. Staphylococcus aureus and the tetracycline-resistance gene (tetQ) were assessed to measure human hand contact and presence of antibiotic-resistant bacteria. Pathogen/MST levels were compared statistically and spatially, and neighborhood variation was compared with previously collected demographic information. All the test fecal markers and pathogens (except Arcobacter) were detected in home and source samples. Two neighborhoods tested positive for most pathogens/MST while the others only tested positive for one or two. Spatial variation of pathogens/MST existed between sources, storage containers, and neighborhoods. Differing population density and ethno-economic characteristics could potentially explain variation. Future research should explore the influence of demographic and ethno-economic factors on water quality during microbial risk assessments in urban Africa.

Soil Aggregate Stability and Grassland Productivity Associations in a Northern Mixed-Grass Prairie

PubMed Central

Reinhart, Kurt O.; Vermeire, Lance T.

2016-01-01

Soil aggregate stability data are often predicted to be positively associated with measures of plant productivity, rangeland health, and ecosystem functioning. Here we revisit the hypothesis that soil aggregate stability is positively associated with plant productivity. We measured local (plot-to-plot) variation in grassland community composition, plant (aboveground) biomass, root biomass, % water-stable soil aggregates, and topography. After accounting for spatial autocorrelation, we observed a negative association between % water-stable soil aggregates (0.25–1 and 1–2 mm size classes of macroaggregates) and dominant graminoid biomass, and negative associations between the % water-stable aggregates and the root biomass of a dominant sedge (Carex filifolia). However, variation in total root biomass (0–10 or 0–30 cm depths) was either negatively or not appreciably associated with soil aggregate stabilities. Overall, regression slope coefficients were consistently negative thereby indicating the general absence of a positive association between measures of plant productivity and soil aggregate stability for the study area. The predicted positive association between factors was likely confounded by variation in plant species composition. Specifically, sampling spanned a local gradient in plant community composition which was likely driven by niche partitioning along a subtle gradient in elevation. Our results suggest an apparent trade-off between some measures of plant biomass production and soil aggregate stability, both known to affect the land’s capacity to resist erosion. These findings further highlight the uncertainty of plant biomass-soil stability associations. PMID:27467598

Soil Aggregate Stability and Grassland Productivity Associations in a Northern Mixed-Grass Prairie.

PubMed

Reinhart, Kurt O; Vermeire, Lance T

2016-01-01

Soil aggregate stability data are often predicted to be positively associated with measures of plant productivity, rangeland health, and ecosystem functioning. Here we revisit the hypothesis that soil aggregate stability is positively associated with plant productivity. We measured local (plot-to-plot) variation in grassland community composition, plant (aboveground) biomass, root biomass, % water-stable soil aggregates, and topography. After accounting for spatial autocorrelation, we observed a negative association between % water-stable soil aggregates (0.25-1 and 1-2 mm size classes of macroaggregates) and dominant graminoid biomass, and negative associations between the % water-stable aggregates and the root biomass of a dominant sedge (Carex filifolia). However, variation in total root biomass (0-10 or 0-30 cm depths) was either negatively or not appreciably associated with soil aggregate stabilities. Overall, regression slope coefficients were consistently negative thereby indicating the general absence of a positive association between measures of plant productivity and soil aggregate stability for the study area. The predicted positive association between factors was likely confounded by variation in plant species composition. Specifically, sampling spanned a local gradient in plant community composition which was likely driven by niche partitioning along a subtle gradient in elevation. Our results suggest an apparent trade-off between some measures of plant biomass production and soil aggregate stability, both known to affect the land's capacity to resist erosion. These findings further highlight the uncertainty of plant biomass-soil stability associations.

Use of high-frequency peak in spectral analysis of heart rate increment to improve screening of obstructive sleep apnoea.

PubMed

Poupard, Laurent; Court-Fortune, Isabelle; Pichot, Vincent; Chouchou, Florian; Barthélémy, Jean-Claude; Roche, Frédéric

2011-12-01

Several studies have correlated the ratio of the very low frequency power spectral density of heart rate increment (%VLFI) with obstructive sleep apnoea syndrome (OSAS). However, patients with impaired heart rate variability may exhibit large variations of heart rate increment (HRI) spectral pattern and alter the screening accuracy of the method. To overcome this limitation, the present study uses the high-frequency increment (HFI) peak in the HRI spectrum, which corresponds to the respiratory influence on RR variations over the frequency range 0.2 to 0.4 Hz. We evaluated 288 consecutive patients referred for snoring, observed nocturnal breathing cessation and/or daytime sleepiness. Patients were classified as OSAS if their apnoea plus hypopnoea index (AHI) during polysomnography exceeded 15 events per hour. Synchronized electrocardiogram Holter monitoring allowed HRI analysis. Using a %VLFI threshold >2.4% for identifying the presence of OSAS, sensitivity for OSAS was 74.9%, specificity 51%, positive predictive value 54.9% and negative predictive value 71.7% (33 false negative subjects). Using threshold for %VLFI >2.4% and HFI peak position >0.4 Hz, negative predictive value increased to 78.2% while maintaining specificity at 50.6%. Among 11 subjects with %VLFI <2.4% and HFI peak >0.4 Hz, nine demonstrated moderate to severe OSAS (AHI >30). HFI represents a minimal physiological criterion for applying %VLFI by ensuring that heart rate variations are band frequency limited.

A simple cosmology with a varying fine structure constant.

PubMed

Sandvik, Håvard Bunes; Barrow, John D; Magueijo, João

2002-01-21

We investigate the cosmological consequences of a theory in which the electric charge e can vary. In this theory the fine structure "constant," alpha, remains almost constant in the radiation era, undergoes a small increase in the matter era, but approaches a constant value when the universe starts accelerating because of a positive cosmological constant. This model satisfies geonuclear, nucleosynthesis, and cosmic microwave background constraints on time variation in alpha, while fitting the observed accelerating Universe and evidence for small alpha variations in quasar spectra. It also places specific restrictions on the nature of the dark matter. Further tests, involving stellar spectra and Eötvös experiments, are proposed.

Enumeration of antigen-specific CD8+ T lymphocytes by single-platform, HLA tetramer-based flow cytometry: a European multicenter evaluation.

PubMed

Heijnen, Ingmar A F M; Barnett, David; Arroz, Maria J; Barry, Simon M; Bonneville, Marc; Brando, Bruno; D'hautcourt, Jean-Luc; Kern, Florian; Tötterman, Thomas H; Marijt, Erik W A; Bossy, David; Preijers, Frank W M B; Rothe, Gregor; Gratama, Jan W

2004-11-01

HLA class I peptide tetramers represent powerful diagnostic tools for detection and monitoring of antigen-specific CD8(+) T cells. The impetus for the current multicenter study is the critical need to standardize tetramer flow cytometry if it is to be implemented as a routine diagnostic assay. Hence, the European Working Group on Clinical Cell Analysis set out to develop and evaluate a single-platform tetramer-based method that used cytomegalovirus (CMV) as the antigenic model. Absolute numbers of CMV-specific CD8(+) T cells were obtained by combining the percentage of tetramer-binding cells with the absolute CD8(+) T-cell count. Six send-outs of stabilized blood from healthy individuals or CMV-carrying donors with CMV-specific CD8(+) T-cell counts of 3 to 10 cells/microl were distributed to 7 to 16 clinical sites. These sites were requested to enumerate CD8(+) T cells and, in the case of CMV-positive donors, CMV-specific subsets on three separate occasions using the standard method. Between-site coefficients of variation of less than 10% (absolute CD8(+) T-cell counts) and approximately 30% (percentage and absolute numbers of CMV-specific CD8(+) T cells) were achieved. Within-site coefficients of variation were approximately 5% (absolute CD8(+) T-cell counts), approximately 9% (percentage CMV-specific CD8(+) T cells), and approximately 17% (absolute CMV-specific CD8(+) T-cell counts). The degree of variation tended to correlate inversely with the proportion of CMV-specific CD8(+) T-cell subsets. The single-platform MHC tetramer-based method for antigen-specific CD8(+) T-cell counting has been evaluated by a European group of laboratories and can be considered a reproducible assay for routine enumeration of antigen-specific CD8(+) T cells. (c) 2004 Wiley-Liss, Inc.

Cross-linguistic variation in the neurophysiological response to semantic processing: Evidence from anomalies at the borderline of awareness

PubMed Central

Tune, Sarah; Schlesewsky, Matthias; Small, Steven L.; Sanford, Anthony J.; Bohan, Jason; Sassenhagen, Jona; Bornkessel-Schlesewsky, Ina

2014-01-01

The N400 event-related brain potential (ERP) has played a major role in the examination of how the human brain processes meaning. For current theories of the N400, classes of semantic inconsistencies which do not elicit N400 effects have proven particularly influential. Semantic anomalies that are difficult to detect are a case in point (“borderline anomalies”, e.g. “After an air crash, where should the survivors be buried?”), engendering a late positive ERP response but no N400 effect in English (Sanford, Leuthold, Bohan, & Sanford, 2011). In three auditory ERP experiments, we demonstrate that this result is subject to cross-linguistic variation. In a German version of Sanford and colleagues' experiment (Experiment 1), detected borderline anomalies elicited both N400 and late positivity effects compared to control stimuli or to missed borderline anomalies. Classic easy-to-detect semantic (non-borderline) anomalies showed the same pattern as in English (N400 plus late positivity). The cross-linguistic difference in the response to borderline anomalies was replicated in two additional studies with a slightly modified task (Experiment 2a: German; Experiment 2b: English), with a reliable LANGUAGE × ANOMALY interaction for the borderline anomalies confirming that the N400 effect is subject to systematic cross-linguistic variation. We argue that this variation results from differences in the language-specific default weighting of top-down and bottom-up information, concluding that N400 amplitude reflects the interaction between the two information sources in the form-to-meaning mapping. PMID:24447768

The lateral variation of P n velocity gradient under Eurasia

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

Yang, Xiaoning

We report that mantle lid P wave velocity gradient, or P n velocity gradient, reflects the depth and lateral variations of thermal and rheological state of the uppermost mantle. Mapping the P n velocity gradient and its lateral variation helps us gain insight into the temperature, composition, and dynamics of the uppermost mantle. In addition, because P n velocity gradient has profound influence on P n propagation behavior, an accurate mapping of P n velocity gradient also improves the modeling and prediction of P n travel times and amplitudes. In this study, I used measured P n travel times tomore » derive path-specific P n velocity gradients. I then inverted these velocity gradients for two-dimensional (2-D) P n velocity-gradient models for Eurasia based on the assumption that a path-specific Pn velocity gradient is the mean of laterally varying P n velocity gradients along the P n path. Result from a Monte Carlo simulation indicates that the assumption is appropriate. The 2-D velocity-gradient models show that most of Eurasia has positive velocity gradients. High velocity gradients exist mainly in tectonically active regions. Most tectonically stable regions show low and more uniform velocity gradients. In conclusion, strong velocity-gradient variations occur largely along convergent plate boundaries, particularly under overriding plates.« less

The lateral variation of P n velocity gradient under Eurasia

DOE PAGES

Yang, Xiaoning

2017-05-03

We report that mantle lid P wave velocity gradient, or P n velocity gradient, reflects the depth and lateral variations of thermal and rheological state of the uppermost mantle. Mapping the P n velocity gradient and its lateral variation helps us gain insight into the temperature, composition, and dynamics of the uppermost mantle. In addition, because P n velocity gradient has profound influence on P n propagation behavior, an accurate mapping of P n velocity gradient also improves the modeling and prediction of P n travel times and amplitudes. In this study, I used measured P n travel times tomore » derive path-specific P n velocity gradients. I then inverted these velocity gradients for two-dimensional (2-D) P n velocity-gradient models for Eurasia based on the assumption that a path-specific Pn velocity gradient is the mean of laterally varying P n velocity gradients along the P n path. Result from a Monte Carlo simulation indicates that the assumption is appropriate. The 2-D velocity-gradient models show that most of Eurasia has positive velocity gradients. High velocity gradients exist mainly in tectonically active regions. Most tectonically stable regions show low and more uniform velocity gradients. In conclusion, strong velocity-gradient variations occur largely along convergent plate boundaries, particularly under overriding plates.« less

Local connected fractal dimension analysis in gill of fish experimentally exposed to toxicants.

PubMed

Manera, Maurizio; Giari, Luisa; De Pasquale, Joseph A; Sayyaf Dezfuli, Bahram

2016-06-01

An operator-neutral method was implemented to objectively assess European seabass, Dicentrarchus labrax (Linnaeus, 1758) gill pathology after experimental exposure to cadmium (Cd) and terbuthylazine (TBA) for 24 and 48h. An algorithm-derived local connected fractal dimension (LCFD) frequency measure was used in this comparative analysis. Canonical variates (CVA) and linear discriminant analysis (LDA) were used to evaluate the discrimination power of the method among exposure classes (unexposed, Cd exposed, TBA exposed). Misclassification, sensitivity and specificity, both with original and cross-validated cases, were determined. LCFDs frequencies enhanced the differences among classes which were visually selected after their means, respective variances and the differences between Cd and TBA exposed means, with respect to unexposed mean, were analyzed by scatter plots. Selected frequencies were then scanned by means of LDA, stepwise analysis, and Mahalanobis distance to detect the most discriminative frequencies out of ten originally selected. Discrimination resulted in 91.7% of cross-validated cases correctly classified (22 out of 24 total cases), with sensitivity and specificity, respectively, of 95.5% (1 false negative with respect to 21 really positive cases) and 75% (1 false positive with respect to 3 really negative cases). CVA with convex hull polygons ensured prompt, visually intuitive discrimination among exposure classes and graphically supported the false positive case. The combined use of semithin sections, which enhanced the visual evaluation of the overall lamellar structure; of LCFD analysis, which objectively detected local variation in complexity, without the possible bias connected to human personnel; and of CVA/LDA, could be an objective, sensitive and specific approach to study fish gill lamellar pathology. Furthermore this approach enabled discrimination with sufficient confidence between exposure classes or pathological states and avoided misdiagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

Fully Scalable Porous Metal Electrospray Propulsion

DTIC Science & Technology

2012-03-20

particular emphasis on the variation of specific impulse for multi-modal propulsion is currently carried out by MIT and the Busek Company under an...Beam profile distributions in the negative (left) and positive (center) modes as visualized directly thorough a multi-channel plate and phosphor...screen. These profiles are parabolic (right) indicating the non-thermal character of these type of ion beams. Microscopic Image of pattern imprinted on Si

Inter-institutional Variation in Use of Caesarean Delivery for Labour Dystocia.

PubMed

Riddell, Corinne A; Hutcheon, Jennifer A; Strumpf, Erin C; Abenhaim, Haim A; Kaufman, Jay S

2017-11-01

To establish the degree of variation across hospitals in the use of Caesarean delivery for the indication of labour dystocia before and after accounting for maternal, fetal, and hospital characteristics. This study was a retrospective, population-based cohort study of nulliparous women delivering term singletons in cephalic position following labour. Delivery visits were extracted from three provincial perinatal registries in the Canadian provinces of Ontario, Alberta, and British Columbia, from 2008-2012. Crude hospital-specific rates of Caesarean delivery for labour dystocia were reported, and these rates were then stabilized to account for hospitals with low delivery volumes. Rates were then adjusted for maternal, fetal, and hospital characteristics using hierarchical logistic regression. Among 403 205 women delivering at 170 hospitals, the overall Caesarean delivery rate was 21.0%, and the rate of Caesarean delivery for labour dystocia was 12.7%, indicating that 60% of all Caesarean deliveries were performed in part for this indication. The middle 95% of hospitals had Caesarean delivery rates for labour dystocia ranging from 4.5% to 24.7%. Differences in maternal case mix and hospital characteristics explained only a small proportion of this variation (95% central range 6.3%-21.7%). Considerable inter-hospital variation in rates of Caesarean delivery for labour dystocia remained after accounting for differences in maternal and hospital factors. Reporting systems that monitor variation in inter-institutional rates should incorporate stabilization and adjustment for case-mix differences and consider indication-specific rates of Caesarean delivery to more fairly compare hospital performance and better target interventions to reduce Caesarean delivery for specific indications. Copyright © 2017 The Society of Obstetricians and Gynaecologists of Canada/La Société des obstétriciens et gynécologues du Canada. Published by Elsevier Inc. All rights reserved.

Sequence variation identified in the 18S rRNA gene of Theileria mutans and Theileria velifera from the African buffalo (Syncerus caffer).

PubMed

Chaisi, Mamohale E; Collins, Nicola E; Potgieter, Fred T; Oosthuizen, Marinda C

2013-01-16

The African buffalo (Syncerus caffer) is a natural reservoir host for both pathogenic and non-pathogenic Theileria species. These often occur naturally as mixed infections in buffalo. Although the benign and mildly pathogenic forms do not have any significant economic importance, their presence could complicate the interpretation of diagnostic test results aimed at the specific diagnosis of the pathogenic Theileria parva in cattle and buffalo in South Africa. The 18S rRNA gene has been used as the target in a quantitative real-time PCR (qPCR) assay for the detection of T. parva infections. However, the extent of sequence variation within this gene in the non-pathogenic Theileria spp. of the Africa buffalo is not well known. The aim of this study was, therefore, to characterise the full-length 18S rRNA genes of Theileria mutans, Theileria sp. (strain MSD) and T. velifera and to determine the possible influence of any sequence variation on the specific detection of T. parva using the 18S rRNA qPCR. The reverse line blot (RLB) hybridization assay was used to select samples which either tested positive for several different Theileria spp., or which hybridised only with the Babesia/Theileria genus-specific probe and not with any of the Babesia or Theileria species-specific probes. The full-length 18S rRNA genes from 14 samples, originating from 13 buffalo and one bovine from different localities in South Africa, were amplified, cloned and the resulting recombinants sequenced. Variations in the 18S rRNA gene sequences were identified in T. mutans, Theileria sp. (strain MSD) and T. velifera, with the greatest diversity observed amongst the T. mutans variants. This variation possibly explained why the RLB hybridization assay failed to detect T. mutans and T. velifera in some of the analysed samples. Copyright © 2012 Elsevier B.V. All rights reserved.

Comparison of CpG island methylator phenotype (CIMP) frequency in colon cancer using different probe- and gene-specific scoring alternatives on recommended multi-gene panels.

PubMed

Berg, Marianne; Hagland, Hanne R; Søreide, Kjetil

2014-01-01

In colorectal cancer a distinct subgroup of tumours demonstrate the CpG island methylator phenotype (CIMP). However, a consensus of how to score CIMP is not reached, and variation in definition may influence the reported CIMP prevalence in tumours. Thus, we sought to compare currently suggested definitions and cut-offs for methylation markers and how they influence CIMP classification in colon cancer. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), with subsequent fragment analysis, was used to investigate methylation of tumour samples. In total, 31 CpG sites, located in 8 different genes (RUNX3, MLH1, NEUROG1, CDKN2A, IGF2, CRABP1, SOCS1 and CACNA1G) were investigated in 64 distinct colon cancers and 2 colon cancer cell lines. The Ogino gene panel includes all 8 genes, in addition to the Weisenberger panel of which only 5 of the 8 genes included were investigated. In total, 18 alternative combinations of scoring of CIMP positivity on probe-, gene-, and panel-level were analysed and compared. For 47 samples (71%), the CIMP status was constant and independent of criteria used for scoring; 34 samples were constantly scored as CIMP negative, and 13 (20%) consistently scored as CIMP positive. Only four of 31 probes (13%) investigated showed no difference in the numbers of positive samples using the different cut-offs. Within the panels a trend was observed that increasing the gene-level stringency resulted in a larger difference in CIMP positive samples than increasing the probe-level stringency. A significant difference between positive samples using 'the most stringent' as compared to 'the least stringent' criteria (20% vs 46%, respectively; p<0.005) was demonstrated. A statistical significant variation in the frequency of CIMP depending on the cut-offs and genes included in a panel was found, with twice as many positives samples by least compared to most stringent definition used.

Potential environmental influences on variation in body size and sexual size dimorphism among Arizona populations of the western diamond-backed rattlesnake (Crotalus atrox)

USGS Publications Warehouse

Amarello, Melissa; Nowak, Erica M.; Taylor, Emily N.; Schuett, Gordon W.; Repp, Roger A.; Rosen, Philip C.; Hardy, David L.

2010-01-01

Differences in resource availability and quality along environmental gradients are important influences contributing to intraspecific variation in body size, which influences numerous life-history traits. Here, we examined variation in body size and sexual size dimorphism (SSD) in relation to temperature, seasonality, and precipitation among 10 populations located throughout Arizona of the western diamond-backed rattlesnake (Crotalus atrox). Specifically, in our analyses we addressed the following questions: (i) Are adult males larger in cooler, wetter areas? (ii) Does female body size respond differently to environmental variation? (iii) Is seasonality a better predictor of body size variation? (iv) Is SSD positively correlated with increased resources? We demonstrate that male and female C. atrox are larger in body size in cooler (i.e., lower average annual maximum, minimum, and mean temperature) and wetter areas (i.e., higher average annual precipitation, more variable precipitation, and available surface water). Although SSD in C. atrox appeared to be more pronounced in cooler, wetter areas, this relationship did not achieve statistical significance.

Black-White variations in the lagged reciprocal relationship between religiosity and perceived control.

PubMed

Oates, Gary

2013-06-01

This national longitudinal data-based multi-population LISREL study, the most comprehensive assessment to date of racial variations in the (in)congruity between religiosity and perceived control, gauges variation among Black and White Americans in the lagged reciprocal relationship between religiosity dimensions and mastery. Racial variation in the reciprocal religiosity-perceived control relationship has hitherto gone un-addressed. Prior investigations have also typically utilised cross-sectional samples - often from regional or age-specific populations. The observed public religiosity-mastery relationship over time exhibits signs of mutual reinforcement among Blacks: public religiosity enhances Blacks' subsequent mastery, while prior mastery borderline-significantly enhances their public religiosity. The subjective religiosity-mastery relationship among Whites evinces a marginally countervailing pattern: Subjective religiosity diminishes Whites' mastery, while mastery borderline-significantly enhances their subjective religiosity. The inordinately positive public religiosity-effect on Blacks' mastery notably constitutes solid support for the " resource compensation " perspective on the impact of religiosity on mastery across dominant and subordinate groups.

Genomics of a Metamorphic Timing QTL: met1 Maps to a Unique Genomic Position and Regulates Morph and Species-Specific Patterns of Brain Transcription

PubMed Central

Page, Robert B.; Boley, Meredith A.; Kump, David K.; Voss, Stephen R.

2013-01-01

Very little is known about genetic factors that regulate life history transitions during ontogeny. Closely related tiger salamanders (Ambystoma species complex) show extreme variation in metamorphic timing, with some species foregoing metamorphosis altogether, an adaptive trait called paedomorphosis. Previous studies identified a major effect quantitative trait locus (met1) for metamorphic timing and expression of paedomorphosis in hybrid crosses between the biphasic Eastern tiger salamander (Ambystoma tigrinum tigrinum) and the paedomorphic Mexican axolotl (Ambystoma mexicanum). We used existing hybrid mapping panels and a newly created hybrid cross to map the met1 genomic region and determine the effect of met1 on larval growth, metamorphic timing, and gene expression in the brain. We show that met1 maps to the position of a urodele-specific chromosome rearrangement on linkage group 2 that uniquely brought functionally associated genes into linkage. Furthermore, we found that more than 200 genes were differentially expressed during larval development as a function of met1 genotype. This list of differentially expressed genes is enriched for proteins that function in the mitochondria, providing evidence of a link between met1, thyroid hormone signaling, and mitochondrial energetics associated with metamorphosis. Finally, we found that met1 significantly affected metamorphic timing in hybrids, but not early larval growth rate. Collectively, our results show that met1 regulates species and morph-specific patterns of brain transcription and life history variation. PMID:23946331

Intraspecific variation in fine root respiration and morphology in response to in situ soil nitrogen fertility in a 100-year-old Chamaecyparis obtusa forest.

PubMed

Makita, Naoki; Hirano, Yasuhiro; Sugimoto, Takanobu; Tanikawa, Toko; Ishii, Hiroaki

2015-12-01

Soil N fertility has an effect on belowground C allocation, but the physiological and morphological responses of individual fine root segments to variations in N availability under field conditions are still unclear. In this study, the direction and magnitude of the physiological and morphological function of fine roots in response to variable in situ soil N fertility in a forest site were determined. We measured the specific root respiration (Rr) rate, N concentration and morphology of fine root segments with 1-3 branching orders in a 100-year-old coniferous forest of Chamaecyparis obtusa. Higher soil N fertility induced higher Rr rates, root N concentration, and specific root length (SRL), and lower root tissue density (RTD). In all fertility levels, the Rr rates were significantly correlated positively with root N and SRL and negatively with RTD. The regression slopes of respiration with root N and RTD were significantly higher along the soil N fertility gradient. Although no differences in the slopes of Rr and SRL relationship were found across the levels, there were significant shifts in the intercept along the common slope. These results suggest that a contrasting pattern in intraspecific relationships between specific Rr and N, RTD, and SRL exists among soils with different N fertility. Consequently, substantial increases in soil N fertility would exert positive effects on organ-scale root performance by covarying the Rr, root N, and morphology for their potential nutrient and water uptake.

Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates.

PubMed

Edelson, Benjamin S; Best, Timothy P; Olenyuk, Bogdan; Nickols, Nicholas G; Doss, Raymond M; Foister, Shane; Heckel, Alexander; Dervan, Peter B

2004-01-01

A pivotal step forward in chemical approaches to controlling gene expression is the development of sequence-specific DNA-binding molecules that can enter live cells and traffic to nuclei unaided. DNA-binding polyamides are a class of programmable, sequence-specific small molecules that have been shown to influence a wide variety of protein-DNA interactions. We have synthesized over 100 polyamide-fluorophore conjugates and assayed their nuclear uptake profiles in 13 mammalian cell lines. The compiled dataset, comprising 1300 entries, establishes a benchmark for the nuclear localization of polyamide-dye conjugates. Compounds in this series were chosen to provide systematic variation in several structural variables, including dye composition and placement, molecular weight, charge, ordering of the aromatic and aliphatic amino-acid building blocks and overall shape. Nuclear uptake does not appear to be correlated with polyamide molecular weight or with the number of imidazole residues, although the positions of imidazole residues affect nuclear access properties significantly. Generally negative determinants for nuclear access include the presence of a beta-Ala-tail residue and the lack of a cationic alkyl amine moiety, whereas the presence of an acetylated 2,4-diaminobutyric acid-turn is a positive factor for nuclear localization. We discuss implications of these data on the design of polyamide-dye conjugates for use in biological systems.

Sexual selection explains sex-specific growth plasticity and positive allometry for sexual size dimorphism in a reef fish

PubMed Central

Walker, Stefan P. W.; McCormick, Mark I.

2009-01-01

In 1950, Rensch noted that in clades where males are the larger sex, sexual size dimorphism (SSD) tends to be more pronounced in larger species. This fundamental allometric relationship is now known as ‘Rensch's rule’. While most researchers attribute Rensch's rule to sexual selection for male size, experimental evidence is lacking. Here, we suggest that ultimate hypotheses for Rensch's rule should also apply to groups of individuals and that individual trait plasticity can be used to test those hypotheses experimentally. Specifically, we show that in the sex-changing fish Parapercis cylindrica, larger males have larger harems with larger females, and that SSD increases with harem size. Thus, sexual selection for male body size is the ultimate cause of sexual size allometry. In addition, we experimentally illustrate a positive relationship between polygyny potential and individual growth rate during sex change from female to male. Thus, sexual selection is the ultimate cause of variation in growth rate, and variation in growth rate is the proximate cause of sexual size allometry. Taken together, our results provide compelling evidence in support of the sexual selection hypothesis for Rensch's rule and highlight the potential importance of individual growth modification in the shaping of morphological patterns in Nature. PMID:19553253

Direct and indirect genetic and fine-scale location effects on breeding date in song sparrows.

PubMed

Germain, Ryan R; Wolak, Matthew E; Arcese, Peter; Losdat, Sylvain; Reid, Jane M

2016-11-01

Quantifying direct and indirect genetic effects of interacting females and males on variation in jointly expressed life-history traits is central to predicting microevolutionary dynamics. However, accurately estimating sex-specific additive genetic variances in such traits remains difficult in wild populations, especially if related individuals inhabit similar fine-scale environments. Breeding date is a key life-history trait that responds to environmental phenology and mediates individual and population responses to environmental change. However, no studies have estimated female (direct) and male (indirect) additive genetic and inbreeding effects on breeding date, and estimated the cross-sex genetic correlation, while simultaneously accounting for fine-scale environmental effects of breeding locations, impeding prediction of microevolutionary dynamics. We fitted animal models to 38 years of song sparrow (Melospiza melodia) phenology and pedigree data to estimate sex-specific additive genetic variances in breeding date, and the cross-sex genetic correlation, thereby estimating the total additive genetic variance while simultaneously estimating sex-specific inbreeding depression. We further fitted three forms of spatial animal model to explicitly estimate variance in breeding date attributable to breeding location, overlap among breeding locations and spatial autocorrelation. We thereby quantified fine-scale location variances in breeding date and quantified the degree to which estimating such variances affected the estimated additive genetic variances. The non-spatial animal model estimated nonzero female and male additive genetic variances in breeding date (sex-specific heritabilities: 0·07 and 0·02, respectively) and a strong, positive cross-sex genetic correlation (0·99), creating substantial total additive genetic variance (0·18). Breeding date varied with female, but not male inbreeding coefficient, revealing direct, but not indirect, inbreeding depression. All three spatial animal models estimated small location variance in breeding date, but because relatedness and breeding location were virtually uncorrelated, modelling location variance did not alter the estimated additive genetic variances. Our results show that sex-specific additive genetic effects on breeding date can be strongly positively correlated, which would affect any predicted rates of microevolutionary change in response to sexually antagonistic or congruent selection. Further, we show that inbreeding effects on breeding date can also be sex specific and that genetic effects can exceed phenotypic variation stemming from fine-scale location-based variation within a wild population. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics*

PubMed Central

Li, Jing; Su, Zengliu; Ma, Ze-Qiang; Slebos, Robbert J. C.; Halvey, Patrick; Tabb, David L.; Liebler, Daniel C.; Pao, William; Zhang, Bing

2011-01-01

Shotgun proteomics data analysis usually relies on database search. However, commonly used protein sequence databases do not contain information on protein variants and thus prevent variant peptides and proteins from been identified. Including known coding variations into protein sequence databases could help alleviate this problem. Based on our recently published human Cancer Proteome Variation Database, we have created a protein sequence database that comprehensively annotates thousands of cancer-related coding variants collected in the Cancer Proteome Variation Database as well as noncancer-specific ones from the Single Nucleotide Polymorphism Database (dbSNP). Using this database, we then developed a data analysis workflow for variant peptide identification in shotgun proteomics. The high risk of false positive variant identifications was addressed by a modified false discovery rate estimation method. Analysis of colorectal cancer cell lines SW480, RKO, and HCT-116 revealed a total of 81 peptides that contain either noncancer-specific or cancer-related variations. Twenty-three out of 26 variants randomly selected from the 81 were confirmed by genomic sequencing. We further applied the workflow on data sets from three individual colorectal tumor specimens. A total of 204 distinct variant peptides were detected, and five carried known cancer-related mutations. Each individual showed a specific pattern of cancer-related mutations, suggesting potential use of this type of information for personalized medicine. Compatibility of the workflow has been tested with four popular database search engines including Sequest, Mascot, X!Tandem, and MyriMatch. In summary, we have developed a workflow that effectively uses existing genomic data to enable variant peptide detection in proteomics. PMID:21389108

New MYC IHC Classifier Integrating Quantitative Architecture Parameters to Predict MYC Gene Translocation in Diffuse Large B-Cell Lymphoma

PubMed Central

Dong, Wei-Feng; Canil, Sarah; Lai, Raymond; Morel, Didier; Swanson, Paul E.; Izevbaye, Iyare

2018-01-01

A new automated MYC IHC classifier based on bivariate logistic regression is presented. The predictor relies on image analysis developed with the open-source ImageJ platform. From a histologic section immunostained for MYC protein, 2 dimensionless quantitative variables are extracted: (a) relative distance between nuclei positive for MYC IHC based on euclidean minimum spanning tree graph and (b) coefficient of variation of the MYC IHC stain intensity among MYC IHC-positive nuclei. Distance between positive nuclei is suggested to inversely correlate MYC gene rearrangement status, whereas coefficient of variation is suggested to inversely correlate physiological regulation of MYC protein expression. The bivariate classifier was compared with 2 other MYC IHC classifiers (based on percentage of MYC IHC positive nuclei), all tested on 113 lymphomas including mostly diffuse large B-cell lymphomas with known MYC fluorescent in situ hybridization (FISH) status. The bivariate classifier strongly outperformed the “percentage of MYC IHC-positive nuclei” methods to predict MYC+ FISH status with 100% sensitivity (95% confidence interval, 94-100) associated with 80% specificity. The test is rapidly performed and might at a minimum provide primary IHC screening for MYC gene rearrangement status in diffuse large B-cell lymphomas. Furthermore, as this bivariate classifier actually predicts “permanent overexpressed MYC protein status,” it might identify nontranslocation-related chromosomal anomalies missed by FISH. PMID:27093450

Malaria surveys using rapid diagnostic tests and validation of results using post hoc quantification of Plasmodium falciparum histidine-rich protein 2.

PubMed

Plucinski, Mateusz; Dimbu, Rafael; Candrinho, Baltazar; Colborn, James; Badiane, Aida; Ndiaye, Daouda; Mace, Kimberly; Chang, Michelle; Lemoine, Jean F; Halsey, Eric S; Barnwell, John W; Udhayakumar, Venkatachalam; Aidoo, Michael; Rogier, Eric

2017-11-07

Rapid diagnostic test (RDT) positivity is supplanting microscopy as the standard measure of malaria burden at the population level. However, there is currently no standard for externally validating RDT results from field surveys. Individuals' blood concentration of the Plasmodium falciparum histidine rich protein 2 (HRP2) protein were compared to results of HRP2-detecting RDTs in participants from field surveys in Angola, Mozambique, Haiti, and Senegal. A logistic regression model was used to estimate the HRP2 concentrations corresponding to the 50 and 90% level of detection (LOD) specific for each survey. There was a sigmoidal dose-response relationship between HRP2 concentration and RDT positivity for all surveys. Variation was noted in estimates for field RDT sensitivity, with the 50% LOD ranging between 0.076 and 6.1 ng/mL and the 90% LOD ranging between 1.1 and 53 ng/mL. Surveys conducted in two different provinces of Angola using the same brand of RDT and same study methodology showed a threefold difference in LOD. Measures of malaria prevalence estimated using population RDT positivity should be interpreted in the context of potentially large variation in RDT LODs between, and even within, surveys. Surveys based on RDT positivity would benefit from external validation of field RDT results by comparing RDT positivity and antigen concentration.

Directional and balancing selection in human beta-defensins.

PubMed

Hollox, Edward J; Armour, John A L

2008-04-16

In primates, infection is an important force driving gene evolution, and this is reflected in the importance of infectious disease in human morbidity today. The beta-defensins are key components of the innate immune system, with antimicrobial and cell signalling roles, but also reproductive functions. Here we examine evolution of beta-defensins in catarrhine primates and variation within different human populations. We show that five beta-defensin genes that do not show copy number variation in humans show evidence of positive selection in catarrhine primates, and identify specific codons that have been under selective pressure. Direct haplotyping of DEFB127 in humans suggests long-term balancing selection: there are two highly diverged haplotype clades carrying different variants of a codon that, in primates, is positively selected. For DEFB132, we show that extensive diversity, including a four-state amino acid polymorphism (valine, isoleucine, alanine and threonine at position 93), is present in hunter-gatherer populations, both African and non-African, but not found in samples from agricultural populations. Some, but not all, beta-defensin genes show positive selection in catarrhine primates. There is suggestive evidence of different selective pressures on these genes in humans, but the nature of the selective pressure remains unclear and is likely to differ between populations.

Loss of specificity: native but not invasive populations of Triadica sebifera vary in tolerance to different herbivores.

PubMed

Carrillo, Juli; McDermott, Daniel; Siemann, Evan

2014-03-01

During introduction, invasive plants can be released from specialist herbivores, but may retain generalist herbivores and encounter novel enemies. For fast-growing invasive plants, tolerance of herbivory via compensatory regrowth may be an important defense against generalist herbivory, but it is unclear whether tolerance responses are specifically induced by different herbivores and whether specificity differs among native and invasive plant populations. We conducted a greenhouse experiment to examine the variation among native and invasive populations of Chinese tallow tree, Triadica sebifera, in their specificity of tolerance responses to herbivores by exposing plants to herbivory from either one of two generalist caterpillars occurring in the introduced range of Triadica. Simultaneously, we measured the specificity of another defensive trait, extrafloral nectar (EFN) production, to detect potential tradeoffs between resistance and tolerance of herbivores. Invasive populations had higher aboveground biomass tolerance than native populations, and responded non-specifically to either herbivore, while native populations had significantly different and specific aboveground biomass responses to the two herbivores. Both caterpillar species similarly induced EFN in native and invasive populations. Plant tolerance and EFN were positively correlated or had no relationship and biomass in control and herbivore-damaged plants was positively correlated, suggesting little costs of tolerance. Relationships among these vegetative traits depended on herbivore type, suggesting that some defense traits may have positive associations with growth-related processes that are differently induced by herbivores. Importantly, loss of specificity in invasive populations indicates subtle evolutionary changes in defenses in invasive plants that may relate to and enhance their invasive success.

Gender-specific activity demands experienced during semiprofessional basketball game play.

PubMed

Scanlan, Aaron T; Dascombe, Ben J; Kidcaff, Andrew P; Peucker, Jessica L; Dalbo, Vincent J

2015-07-01

To compare game activity demands between female and male semiprofessional basketball players. Female (n=12) and male (n=12) semiprofessional basketball players were monitored across 3 competitive games. Time-motion-analysis procedures quantified player activity into predefined movement categories across backcourt (BC) and frontcourt (FC) positions. Activity frequencies, durations, and distances were calculated relative to live playing time (min). Work:rest ratios were also calculated using the video data. Game activity was compared between genders for each playing position and all players. Female players performed at greater running work-rates than male players (45.7±1.4 vs. 42.1±1.7 m/min, P=.05), while male players performed more dribbling than female players (2.5±0.3 vs. 3.0±0.2 s/min; 8.4±0.3 vs. 9.7±0.7 m/min, P=.05). Positional analyses revealed that female BC players performed more low-intensity shuffling (P=.04) and jumping (P=.05), as well as longer (P=.04) jogging durations, than male BC players. Female FC players executed more upper-body activity (P=.03) and larger work:rest ratios (P<.001) than male FC players. No significant gender differences were observed in the overall intermittent demands, distance traveled, high-intensity shuffling activity, and sprinting requirements during game play. These findings indicate that gender-specific running and dribbling differences might exist in semiprofessional basketball. Furthermore, position-specific variations between female and male basketball players should be considered. These data may prove useful in the development of gender-specific conditioning plans relative to playing position in basketball.

An in vitro simulation model to assess the severity of edge loading and wear, due to variations in component positioning in hip joint replacements.

PubMed

O'Dwyer Lancaster-Jones, O; Williams, S; Jennings, L M; Thompson, J; Isaac, G H; Fisher, J; Al-Hajjar, M

2017-09-23

The aim of this study was to develop a preclinical in vitro method to predict the occurrence and severity of edge loading condition associated with the dynamic separation of the centres of the head and cup (in the absence of impingement) for variations in surgical positioning of the cup. Specifically, this study investigated the effect of both the variations in the medial-lateral translational mismatch between the centres of the femoral head and acetabular cup and the variations in the cup inclination angles on the occurrence and magnitude of the dynamic separation, the severity of edge loading, and the wear rate of ceramic-on-ceramic hip replacement bearings in a multi-station hip joint simulator during a walking gait cycle. An increased mismatch between the centres of rotation of the femoral head and acetabular cup resulted in an increased level of dynamic separation and an increase in the severity of edge loading condition which led to increased wear rate in ceramic-on-ceramic bearings. Additionally for a given translational mismatch, an increase in the cup inclination angle gave rise to increased dynamic separation, worst edge loading conditions, and increased wear. To reduce the occurrence and severity of edge loading, the relative positions (the mismatch) of the centres of rotation of the head and the cup should be considered alongside the rotational position of the acetabular cup. This study has considered the combination of mechanical and tribological factors for the first time in the medial-lateral axis only, involving one rotational angle (inclination) and one translational mismatch. © 2017 The Authors Journal of Biomedical Materials Research Part B: Applied Biomaterials Published by Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2017. © 2017 The Authors Journal of Biomedical Materials Research Part B: Applied Biomaterials Published by Wiley Periodicals, Inc.

Identifying selectively important amino acid positions associated with alternative habitat environments in fish mitochondrial genomes.

PubMed

Xia, Jun Hong; Li, Hong Lian; Zhang, Yong; Meng, Zi Ning; Lin, Hao Ran

2018-05-01

Fish species inhabitating seawater (SW) or freshwater (FW) habitats have to develop genetic adaptations to alternative environment factors, especially salinity. Functional consequences of the protein variations associated with habitat environments in fish mitochondrial genomes have not yet received much attention. We analyzed 829 complete fish mitochondrial genomes and compared the amino acid differences of 13 mitochondrial protein families between FW and SW fish groups. We identified 47 specificity determining sites (SDS) that associated with FW or SW environments from 12 mitochondrial protein families. Thirty-two (68%) of the SDS sites are hydrophobic, 13 (28%) are neutral, and the remaining sites are acidic or basic. Seven of those SDS from ND1, ND2 and ND5 were scored as probably damaging to the protein structures. Furthermore, phylogenetic tree based Bayes Empirical Bayes analysis also detected 63 positive sites associated with alternative habitat environments across ten mtDNA proteins. These signatures could be important for studying mitochondrial genetic variation relevant to fish physiology and ecology.

Daily associations between anxiety and alcohol use: variation by sustained attention, set shifting, and gender.

PubMed

Dvorak, Robert D; Simons, Jeffrey S

2014-12-01

Many theories of emotion regulation and alcohol use posit that alcohol is consumed as a way to regulate negative mood. However, the literature has conflicting evidence on mood-alcohol use associations. Understanding how individual differences affect mood-alcohol use associations remains an important area of study. Previous research has suggested that cognitive abilities may affect the relationship between mood and alcohol. The current ecological momentary study examined associations between daytime anxious and positive mood and both (a) the likelihood of alcohol use and (b) the intensity of use on drinking nights as a function of sustained attention, set shifting, and gender. Participants (n = 100) completed assessments of sustained attention and set shifting, then carried palmtop computers for 21 days, reporting mood and alcohol use up to 8 times per day. Results showed that positive mood was consistently associated with both likelihood and intensity of alcohol use, but the association between positive mood and alcohol outcomes was not affected by cognitive abilities. Anxious mood was positively associated with the likelihood of drinking for men with high cognitive abilities. Anxious mood was positively associated with intoxication on drinking nights for men with high sustained attention, but inversely associated with intoxication on drinking nights for women with high sustained attention. Results suggest that variation in mood, executive functioning, and gender interact to contribute to observed differences in drinking behavior. These differences may be the result of gender-specific coping strategies in response to negative emotion.

Unique LCR variations among lineages of HPV16, 18 and 45 isolates from women with normal cervical cytology in Ghana.

PubMed

Awua, Adolf K; Adanu, Richard M K; Wiredu, Edwin K; Afari, Edwin A; Zubuch, Vanessa A; Asmah, Richard H; Severini, Alberto

2017-04-21

In addition to being useful for classification, sequence variations of human Papillomavirus (HPV) genotypes have been implicated in differential oncogenic potential and a differential association with the different histological forms of invasive cervical cancer. These associations have also been indicated for HPV genotype lineages and sub-lineages. In order to better understand the potential implications of lineage variation in the occurrence of cervical cancers in Ghana, we studied the lineages of the three most prevalent HPV genotypes among women with normal cytology as baseline to further studies. Of previously collected self- and health personnel-collected cervical specimen, 54, which were positive for HPV16, 18 and 45, were selected and the long control region (LCR) of each HPV genotype was separately amplified by a nested PCR. DNA sequences of 41 isolates obtained with the forward and reverse primers by Sanger sequencing were analysed. Nucleotide sequence variations of the HPV16 genotypes were observed at 30 positions within the LCR (7460 - 7840). Of these, 19 were the known variations for the lineages B and C (African lineages), while the other 11 positions had variations unique to the HPV16 isolates of this study. For the HPV18 isolates, the variations were at 35 positions, 22 of which were known variations of Africa lineages and the other 13 were unique variations observed for the isolates obtained in this study (at positions 7799 and 7813). HPV45 isolates had variations at 35 positions and 2 (positions 7114 and 97) were unique to the isolates of this study. This study provides the first data on the lineages of HPV 16, 18 and 45 isolates from Ghana. Although the study did not obtain full genome sequence data for a comprehensive comparison with known lineages, these genotypes were predominately of the Africa lineages and had some unique sequence variations at positions that suggest potential oncogenic implications. These data will be useful for comparison with lineages of these genotypes from women with cervical lesion and all the forms of invasive cervical cancers.

Stochastic and compensatory effects limit persistence of variation in body mass of young caribou

USGS Publications Warehouse

Dale, Bruce W.; Adams, Layne G.; Collins, William B.; Joly, Kyle; Valkenburg, Patrick; Tobey, Robert

2008-01-01

Nutritional restriction during growth can have short- and long-term effects on fitness; however, animals inhabiting uncertain environments may exhibit adaptations to cope with variation in food availability. We examined changes in body mass in free-ranging female caribou (Rangifer tarandus) by measuring mass at birth and at 4, 11, and 16 months of age to evaluate the relative importance of seasonal nutrition to growth, the persistence of cohort-specific variation in body mass through time, and compensatory growth of individuals. Relative mean body mass of cohorts did not persist through time. Compensatory growth of smaller individuals was not observed in summer; however, small calves exhibited more positive change in body mass than did large calves. Compensation occurred during periods of nutritional restriction (winter) rather than during periods of rapid growth (summer) thus differing from the conventional view of compensatory growth.

Development of Species-Specific Primers for Agronomical Thrips and Multiplex Assay for Quarantine Identification of Western Flower Thrips.

PubMed

Yeh, W B; Tseng, M J; Chang, N T; Wu, S Y; Tsai, Y S

2014-10-01

While morphological identification of thrips species has been difficult because of their minute size and a lack of easily recognizable characteristics, molecular identification based on the development of specific molecular markers can be easily and reliably carried out. Among the known molecular markers, the nuclear internal transcribed spacer (ITS) exhibits distinguishable variations among thrips species. In this study, sequences of ITS2 region of 10 agriculturally important thrips were established to design species-specific primers for polymerase chain reaction (PCR). ITS2 sequence variations within these species were far less than those among species, indicating the suitability of this marker for species-specific primers design. These primers, though with one or two sporadically variable positions, showed a good efficacy within species. The specificity of these primers, examined on thrips species belonging to 15 genera, proved satisfactory. Furthermore, a multiplex PCR was used successfully for identifying Frankliniella occidentalis (Pergande), an insect pest monitored for quarantine purpose, and three additional thrips also commonly found in imported agricultural products and field samples, i.e., Thrips tabaci Lindeman, Thrips hawaiiensis (Morgan), and Frankliniella intonsa (Trybom). This study has demonstrated that specific primers and multiplex PCR based on ITS2 are reliable, convenient, and diagnostic tool to discriminate thrips species of quarantine and agricultural importance. © 2014 Entomological Society of America.

Tip clearance effects on loads and performances of semi-open impeller centrifugal pumps at different specific speeds

NASA Astrophysics Data System (ADS)

Boitel, G.; Fedala, D.; Myon, N.

2016-11-01

Relevant industrial standards or customer's specifications could strictly forbid any device adjusting the axial rotor/stator position, so that tip clearance between semi-open impeller and casing might become a result of the pump machining tolerances and assembling process, leading to big tip clearance variations compared to its nominal value. Consequently, large disparities of global performances (head, power, efficiency) and axial loads are observed with high risk of both specifications noncompliance and bearing damages. This work aims at quantifying these variations by taking into account tip clearance value and pump specific speed. Computational Fluid Dynamics is used to investigate this phenomenon by means of steady simulations led on a semi-open centrifugal pump numerical model including secondary flows, based on a k-omega SST turbulence model. Four different specific speed pump sizes are simulated (from 8 to 50, SI units), with three tip clearances for each size on a wide flow range (from 40% to 120% of the best efficiency point). The numerical results clearly show that head, power and efficiency increase as the tip clearance decreases for the whole flow range. This effect is more significant when the specific speed is low. Meanwhile, the resulting axial thrust on the impeller is very sensitive to the tip clearance and can even lead to direction inversion.

COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples

PubMed Central

Krishnan, Neeraja M.; Gaur, Prakhar; Chaudhary, Rakshit; Rao, Arjun A.; Panda, Binay

2012-01-01

Copy Number Alterations (CNAs) such as deletions and duplications; compose a larger percentage of genetic variations than single nucleotide polymorphisms or other structural variations in cancer genomes that undergo major chromosomal re-arrangements. It is, therefore, imperative to identify cancer-specific somatic copy number alterations (SCNAs), with respect to matched normal tissue, in order to understand their association with the disease. We have devised an accurate, sensitive, and easy-to-use tool, COPS, COpy number using Paired Samples, for detecting SCNAs. We rigorously tested the performance of COPS using short sequence simulated reads at various sizes and coverage of SCNAs, read depths, read lengths and also with real tumor:normal paired samples. We found COPS to perform better in comparison to other known SCNA detection tools for all evaluated parameters, namely, sensitivity (detection of true positives), specificity (detection of false positives) and size accuracy. COPS performed well for sequencing reads of all lengths when used with most upstream read alignment tools. Additionally, by incorporating a downstream boundary segmentation detection tool, the accuracy of SCNA boundaries was further improved. Here, we report an accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs using short-read sequence data. In addition to cancer, COPS can be used for any disease as long as sequence reads from both disease and normal samples from the same individual are available. An added boundary segmentation detection module makes COPS detected SCNA boundaries more specific for the samples studied. COPS is available at ftp://115.119.160.213 with username “cops” and password “cops”. PMID:23110103

Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1.

PubMed

Martin, Maureen P; Naranbhai, Vivek; Shea, Patrick R; Qi, Ying; Ramsuran, Veron; Vince, Nicolas; Gao, Xiaojiang; Thomas, Rasmi; Brumme, Zabrina L; Carlson, Jonathan M; Wolinsky, Steven M; Goedert, James J; Walker, Bruce D; Segal, Florencia P; Deeks, Steven G; Haas, David W; Migueles, Stephen A; Connors, Mark; Michael, Nelson; Fellay, Jacques; Gostick, Emma; Llewellyn-Lacey, Sian; Price, David A; Lafont, Bernard A; Pymm, Phillip; Saunders, Philippa M; Widjaja, Jacqueline; Wong, Shu Cheng; Vivian, Julian P; Rossjohn, Jamie; Brooks, Andrew G; Carrington, Mary

2018-05-01

HLA-B*57 control of HIV involves enhanced CD8+ T cell responses against infected cells, but extensive heterogeneity exists in the level of HIV control among B*57+ individuals. Using whole-genome sequencing of untreated B*57+ HIV-1-infected controllers and noncontrollers, we identified a single variant (rs643347A/G) encoding an isoleucine-to-valine substitution at position 47 (I47V) of the inhibitory killer cell immunoglobulin-like receptor KIR3DL1 as the only significant modifier of B*57 protection. The association was replicated in an independent cohort and across multiple outcomes. The modifying effect of I47V was confined to B*57:01 and was not observed for the closely related B*57:03. Positions 2, 47, and 54 tracked one another nearly perfectly, and 2 KIR3DL1 allotypes differing only at these 3 positions showed significant differences in binding B*57:01 tetramers, whereas the protective allotype showed lower binding. Thus, variation in an immune NK cell receptor that binds B*57:01 modifies its protection. These data highlight the exquisite specificity of KIR-HLA interactions in human health and disease.

Analysis of simian immunodeficiency virus sequence variation in tissues of rhesus macaques with simian AIDS.

PubMed Central

Kodama, T; Mori, K; Kawahara, T; Ringler, D J; Desrosiers, R C

1993-01-01

One rhesus macaque displayed severe encephalomyelitis and another displayed severe enterocolitis following infection with molecularly cloned simian immunodeficiency virus (SIV) strain SIVmac239. Little or no free anti-SIV antibody developed in these two macaques, and they died relatively quickly (4 to 6 months) after infection. Manifestation of the tissue-specific disease in these macaques was associated with the emergence of variants with high replicative capacity for macrophages and primary infection of tissue macrophages. The nature of sequence variation in the central region (vif, vpr, and vpx), the env gene, and the nef long terminal repeat (LTR) region in brain, colon, and other tissues was examined to see whether specific genetic changes were associated with SIV replication in brain or gut. Sequence analysis revealed strong conservation of the intergenic central region, nef, and the LTR. However, analysis of env sequences in these two macaques and one other revealed significant, interesting patterns of sequence variation. (i) Changes in env that were found previously to contribute to the replicative ability of SIVmac for macrophages in culture were present in the tissues of these animals. (ii) The greatest variability was located in the regions between V1 and V2 and from "V3" through C3 in gp120, which are different in location from the variable regions observed previously in animals with strong antibody responses and long-term persistent infection. (iii) The predominant sequence change of D-->N at position 385 in C3 is most surprising, since this change in both SIV and human immunodeficiency virus type 1 has been associated with dramatically diminished affinity for CD4 and replication in vitro. (iv) The nature of sequence changes at some positions (146, 178, 345, 385, and "V3") suggests that viral replication in brain and gut may be facilitated by specific sequence changes in env in addition to those that impart a general ability to replicate well in macrophages. These results demonstrate that complex selective pressures, including immune responses and varying cell and tissue specificity, can influence the nature of sequence changes in env. Images PMID:8411355

Response of Demographic Rates of Tropical Trees to Light Availability: Can Position-Based Competition Indices Replace Information from Canopy Census Data?

PubMed Central

Grote, Steffi; Condit, Richard; Hubbell, Stephen; Wirth, Christian; Rüger, Nadja

2013-01-01

For trees in tropical forests, competition for light is thought to be a central process that offers opportunities for niche differentiation through light gradient partitioning. In previous studies, a canopy index based on three-dimensional canopy census data has been shown to be a good predictor of species-specific demographic rates across the entire tree community on Barro Colorado Island, Panama, and has allowed quantifying between-species variation in light response. However, almost all other forest census plots lack data on the canopy structure. Hence, this study aims at assessing whether position-based neighborhood competition indices can replace information from canopy census data and produce similar estimates of the interspecific variation of light responses. We used inventory data from the census plot at Barro Colorado Island and calculated neighborhood competition indices with varying relative effects of the size and distance of neighboring trees. Among these indices, we selected the one that was most strongly correlated with the canopy index. We then compared outcomes of hierarchical Bayesian models for species-specific recruitment and growth rates including either the canopy index or the selected neighborhood competition index as predictor. Mean posterior estimates of light response parameters were highly correlated between models (r>0.85) and indicated that most species regenerate and grow better in higher light. Both light estimation approaches consistently found that the interspecific variation of light response was larger for recruitment than for growth rates. However, the classification of species into different groups of light response, e.g. weaker than linear (decelerating) vs. stronger than linear (accelerating) differed between approaches. These results imply that while the classification into light response groups might be biased when using neighborhood competition indices, they may be useful for determining species rankings and between-species variation of light response and therefore enable large comparative studies between different forest census plots. PMID:24324723

Effects of body condition on buoyancy in endangered North Atlantic right whales.

PubMed

Nousek-McGregor, Anna E; Miller, Carolyn A; Moore, Michael J; Nowacek, Douglas P

2014-01-01

Buoyancy is an important consideration for diving marine animals, resulting in specific ecologically relevant adaptations. Marine mammals use blubber as an energy reserve, but because this tissue is also positively buoyant, nutritional demands have the potential to cause considerable variation in buoyancy. North Atlantic right whales Eubalaena glacialis are known to be positively buoyant as a result of their blubber, and the thickness of this layer varies considerably, but the effect of this variation on buoyancy has not been explored. This study compared the duration and rate of ascending and descending glides, recorded with an archival tag, with blubber thickness, measured with an ultrasound device, in free-swimming right whales. Ascending whales with thicker blubber had shorter portions of active propulsion and longer passive glides than whales with thinner blubber, suggesting that blubber thickness influences buoyancy because the buoyant force is acting in the same direction as the animal's movement during this phase. Whales with thinner layers also used similar body angles and velocities when traveling to and from depth, while those with thicker layers used shallower ascent angles but achieved higher ascent velocities. Such alterations in body angle may help to reduce the cost of transport when swimming against the force of buoyancy in a state of augmented positive buoyancy, which represents a dynamic response to reduce the energetic consequences of physiological changes. These results have considerable implications for any diving marine animal during periods of nutritional stress, such as during seasonal migrations and annual variations in prey availability.

Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives.

PubMed

Meinhardt, Sarah; Swint-Kruse, Liskin

2008-12-01

In protein families, conserved residues often contribute to a common general function, such as DNA-binding. However, unique attributes for each homolog (e.g. recognition of alternative DNA sequences) must arise from variation in other functionally-important positions. The locations of these "specificity determinant" positions are obscured amongst the background of varied residues that do not make significant contributions to either structure or function. To isolate specificity determinants, a number of bioinformatics algorithms have been developed. When applied to the LacI/GalR family of transcription regulators, several specificity determinants are predicted in the 18 amino acids that link the DNA-binding and regulatory domains. However, results from alternative algorithms are only in partial agreement with each other. Here, we experimentally evaluate these predictions using an engineered repressor comprising the LacI DNA-binding domain, the LacI linker, and the GalR regulatory domain (LLhG). "Wild-type" LLhG has altered DNA specificity and weaker lacO(1) repression compared to LacI or a similar LacI:PurR chimera. Next, predictions of linker specificity determinants were tested, using amino acid substitution and in vivo repression assays to assess functional change. In LLhG, all predicted sites are specificity determinants, as well as three sites not predicted by any algorithm. Strategies are suggested for diminishing the number of false negative predictions. Finally, individual substitutions at LLhG specificity determinants exhibited a broad range of functional changes that are not predicted by bioinformatics algorithms. Results suggest that some variants have altered affinity for DNA, some have altered allosteric response, and some appear to have changed specificity for alternative DNA ligands.

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

PubMed Central

McDaniell, Ryan; Lee, Bum-Kyu; Song, Lingyun; Liu, Zheng; Boyle, Alan P.; Erdos, Michael R.; Scott, Laura J.; Morken, Mario A.; Kucera, Katerina S.; Battenhouse, Anna; Keefe, Damian; Collins, Francis S.; Willard, Huntington F.; Lieb, Jason D.; Furey, Terrence S.; Crawford, Gregory E.; Iyer, Vishwanath R.; Birney, Ewan

2010-01-01

The extent to which variation in chromatin structure and transcription factor binding may influence gene expression, and thus underlie or contribute to variation in phenotype, is unknown. To address this question, we cataloged both individual-to-individual variation and differences between homologous chromosomes within the same individual (allele-specific variation) in chromatin structure and transcription factor binding in lymphoblastoid cells derived from individuals of geographically diverse ancestry. Ten percent of active chromatin sites were individual-specific; a similar proportion were allele-specific. Both individual-specific and allele-specific sites were commonly transmitted from parent to child, which suggests that they are heritable features of the human genome. Our study shows that heritable chromatin status and transcription factor binding differ as a result of genetic variation and may underlie phenotypic variation in humans. PMID:20299549

Vertical jumping tests in volleyball: reliability, validity, and playing-position specifics.

PubMed

Sattler, Tine; Sekulic, Damir; Hadzic, Vedran; Uljevic, Ognjen; Dervisevic, Edvin

2012-06-01

Vertical jumping is known to be important in volleyball, and jumping performance tests are frequently studied for their reliability and validity. However, most studies concerning jumping in volleyball have dealt with standard rather than sport-specific jumping procedures and tests. The aims of this study, therefore, were (a) to determine the reliability and factorial validity of 2 volleyball-specific jumping tests, the block jump (BJ) test and the attack jump (AJ) test, relative to 2 frequently used and systematically validated jumping tests, the countermovement jump test and the squat jump test and (b) to establish volleyball position-specific differences in the jumping tests and simple anthropometric indices (body height [BH], body weight, and body mass index [BMI]). The BJ was performed from a defensive volleyball position, with the hands positioned in front of the chest. During an AJ, the players used a 2- to 3-step approach and performed a drop jump with an arm swing followed by a quick vertical jump. A total of 95 high-level volleyball players (all men) participated in this study. The reliability of the jumping tests ranged from 0.97 to 0.99 for Cronbach's alpha coefficients, from 0.93 to 0.97 for interitem correlation coefficients and from 2.1 to 2.8 for coefficients of variation. The highest reliability was found for the specific jumping tests. The factor analysis extracted one significant component, and all of the tests were highly intercorrelated. The analysis of variance with post hoc analysis showed significant differences between 5 playing positions in some of the jumping tests. In general, receivers had a greater jumping capacity, followed by libero players. The differences in jumping capacities should be emphasized vis-a-vis differences in the anthropometric measures of players, where middle hitters had higher BH and body weight, followed by opposite hitters and receivers, with no differences in the BMI between positions.

Numerical Investigations of Slip Phenomena in Centrifugal Compressor Impellers

NASA Astrophysics Data System (ADS)

Huang, Jeng-Min; Luo, Kai-Wei; Chen, Ching-Fu; Chiang, Chung-Ping; Wu, Teng-Yuan; Chen, Chun-Han

2013-03-01

This study systematically investigates the slip phenomena in the centrifugal air compressor impellers by CFD. Eight impeller blades for different specific speeds, wrap angles and exit blade angles are designed by compressor design software to analyze their flow fields. Except for the above three variables, flow rate and number of blades are the other two. Results show that the deviation angle decreases as the flow rate increases. The specific speed is not an important parameter regarding deviation angle or slip factor for general centrifugal compressor impellers. The slip onset position is closely related to the position of the peak value in the blade loading factor distribution. When no recirculation flow is present at the shroud, the variations of slip factor under various flow rates are mainly determined by difference between maximum blade angle and exit blade angle, Δβmax-2. The solidity should be of little importance to slip factor correlations in centrifugal compressor impellers.

Disability impact and coping in mothers of children with intellectual disabilities and multiple disabilities.

PubMed

Kishore, M Thomas

2011-12-01

Understanding the disability impact on parenting and caregiving is important for intervention. The present study was designed to understand the differences in perceived disability impact and related coping in mothers having children with intellectual disabilities alone compared to those having children with intellectual disabilities and additional disabilities. Accordingly, 30 mothers of children with intellectual disabilities and 30 mothers of children with intellectual and additional disabilities were assessed for disability impact and coping. Group differences for disability impact were present in specific domains but not overall. Despite variations in coping pattern, both positive and negative coping strategies were observed in both groups. The results may imply that the impact of intellectual disability is so pervasive that except in certain domains mothers may not perceive the further impact of additional disabilities. Positive coping does not rule out negative coping strategies. These findings have specific relevance to service delivery in a cultural context.

Spatial and temporal variability of microgeographic genetic structure in white-tailed deer

USGS Publications Warehouse

Scribner, Kim T.; Smith, Michael H.; Chesser, Ronald K.

1997-01-01

Techniques are described that define contiguous genetic subpopulations of white-tailed deer (Odocoileus virginianus) based on the spatial dispersion of 4,749 individuals that possessed discrete character values (alleles or genotypes) during each of 6 years (1974-1979). White-tailed deer were not uniformly distributed in space, but exhibited considerable spatial genetic structuring. Significant non-random clusters of individuals were documented during each year based on specific alleles and genotypes at the Sdh locus. Considerable temporal variation was observed in the position and genetic composition of specific clusters, which reflected changes in allele frequency in small geographic areas. The position of clusters did not consistently correspond with traditional management boundaries based on major discontinuities in habitat (swamp versus upland) and hunt compartments that were defined by roads and streams. Spatio-temporal stability of observed genetic contiguous clusters was interpreted relative to method and intensity of harvest, movements, and breeding ecology.

Cross-dialectal variation in formant dynamics of American English vowels

PubMed Central

Fox, Robert Allen; Jacewicz, Ewa

2009-01-01

This study aims to characterize the nature of the dynamic spectral change in vowels in three distinct regional varieties of American English spoken in the Western North Carolina, in Central Ohio, and in Southern Wisconsin. The vowels ∕ɪ, ε, e, æ, aɪ∕ were produced by 48 women for a total of 1920 utterances and were contained in words of the structure ∕bVts∕ and ∕bVdz∕ in sentences which elicited nonemphatic and emphatic vowels. Measurements made at the vowel target (i.e., the central 60% of the vowel) produced a set of acoustic parameters which included position and movement in the F1 by F2 space, vowel duration, amount of spectral change [measured as vector length (VL) and trajectory length (TL)], and spectral rate of change. Results revealed expected variation in formant dynamics as a function of phonetic factors (vowel emphasis and consonantal context). However, for each vowel and for each measure employed, dialect was a strong source of variation in vowel-inherent spectral change. In general, the dialect-specific nature and amount of spectral change can be characterized quite effectively by position and movement in the F1 by F2 space, vowel duration, TL (but not VL which underestimates formant movement), and spectral rate of change. PMID:19894839

Vowel change across three age groups of speakers in three regional varieties of American English

PubMed Central

Jacewicz, Ewa; Fox, Robert A.; Salmons, Joseph

2011-01-01

This acoustic study examines sound (vowel) change in apparent time across three successive generations of 123 adult female speakers ranging in age from 20 to 65 years old, representing three regional varieties of American English, typical of western North Carolina, central Ohio and southeastern Wisconsin. A set of acoustic measures characterized the dynamic nature of formant trajectories, the amount of spectral change over the course of vowel duration and the position of the spectral centroid. The study found a set of systematic changes to /I, ε, æ/ including positional changes in the acoustic space (mostly lowering of the vowels) and significant variation in formant dynamics (increased monophthongization). This common sound change is evident in both emphatic (articulated clearly) and nonemphatic (casual) productions and occurs regardless of dialect-specific vowel dispersions in the vowel space. The cross-generational and cross-dialectal patterns of variation found here support an earlier report by Jacewicz, Fox, and Salmons (2011) which found this recent development in these three dialect regions in isolated citation-form words. While confirming the new North American Shift in different styles of production, the study underscores the importance of addressing the stress-related variation in vowel production in a careful and valid assessment of sound change. PMID:22125350

Evolution and inheritance of early embryonic patterning in D. simulans and D. sechellia

PubMed Central

Lott, Susan E.; Ludwig, Michael Z.; Kreitman, Martin

2010-01-01

Pattern formation in Drosophila is a widely studied example of a robust developmental system. Such robust systems pose a challenge to adaptive evolution, as they mask variation which selection may otherwise act upon. Yet we find variation in the localization of expression domains (henceforth ‘stripe allometry’) in the pattern formation pathway. Specifically, we characterize differences in the gap genes giant and Kruppel, and the pair-rule gene even-skipped, which differ between the sibling species D. simulans and D. sechellia. In a double-backcross experiment, stripe allometry is consistent with maternal inheritance of stripe positioning and multiple genetic factors, with a distinct genetic basis from embryo length. Embryos produced by F1 and F2 backcross mothers exhibit novel spatial patterns of gene expression relative to the parental species, with no measurable increase in positional variance among individuals. Buffering of novel spatial patterns in the backcross genotypes suggests that robustness need not be disrupted in order for the trait to evolve, and perhaps the system is incapable of evolving to prevent the expression of all genetic variation. This limitation, and the ability of natural selection to act on minute genetic differences that are within the “margin of error” for the buffering mechanism, indicates that developmentally buffered traits can evolve without disruption of robustness PMID:21121913

Therapygenetics in mindfulness-based cognitive therapy: do genes have an impact on therapy-induced change in real-life positive affective experiences?

PubMed

Bakker, J M; Lieverse, R; Menne-Lothmann, C; Viechtbauer, W; Pishva, E; Kenis, G; Geschwind, N; Peeters, F; van Os, J; Wichers, M

2014-04-22

Positive affect (PA) has an important role in resilience against depression and has been shown to increase with mindfulness-based cognitive therapy (MBCT). To elucidate the underlying mechanisms of change in PA as well as develop insights that may benefit personalized medicine, the current study examined the contribution of genetic variation to individual differences in change in PA in response to MBCT. Individuals (n=126) with residual depressive symptoms were randomized to either an MBCT group or treatment as usual. PA was assessed using experience sampling methodology (ESM). Single-nucleotide polymorphisms (SNPs) in genes known to be involved in reward functioning were selected. SNPs in the genes for brain-derived neurotrophic factor (BDNF), the muscarinic acetylcholine receptor M2 (CHRM2), the dopamine receptor D4 (DRD4) and the μ1 opioid receptor (OPRM1) significantly moderated the impact of treatment condition over time on PA. Genetic variation in the genes for CHRM2 and OPRM1 specifically had an impact on the level of PA following MBCT. The current study shows that variation in response to MBCT may be contingent on genetic factors associated with the regulation of PA. These findings contribute to our understanding of the processes moderating response to treatment and prediction of treatment outcome.

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

Assessment of total and organic vanadium levels and their bioaccumulation in edible sea cucumbers: tissues distribution, inter-species-specific, locational differences and seasonal variations.

PubMed

Liu, Yanjun; Zhou, Qingxin; Xu, Jie; Xue, Yong; Liu, Xiaofang; Wang, Jingfeng; Xue, Changhu

2016-02-01

The objective of this study is to investigate the levels, inter-species-specific, locational differences and seasonal variations of vanadium in sea cucumbers and to validate further several potential factors controlling the distribution of metals in sea cucumbers. Vanadium levels were evaluated in samples of edible sea cucumbers and were demonstrated exhibit differences in different seasons, species and sampling sites. High vanadium concentrations were measured in the sea cucumbers, and all of the vanadium detected was in an organic form. Mean vanadium concentrations were considerably higher in the blood (sea cucumber) than in the other studied tissues. The highest concentration of vanadium (2.56 μg g(-1)), as well as a higher degree of organic vanadium (85.5 %), was observed in the Holothuria scabra samples compared with all other samples. Vanadium levels in Apostichopus japonicus from Bohai Bay and Yellow Sea have marked seasonal variations. Average values of 1.09 μg g(-1) of total vanadium and 0.79 μg g(-1) of organic vanadium were obtained in various species of sea cucumbers. Significant positive correlations between vanadium in the seawater and V org in the sea cucumber (r = 81.67 %, p = 0.00), as well as between vanadium in the sediment and V org in the sea cucumber (r = 77.98 %, p = 0.00), were observed. Vanadium concentrations depend on the seasons (salinity, temperature), species, sampling sites and seawater environment (seawater, sediment). Given the adverse toxicological effects of inorganic vanadium and positive roles in controlling the development of diabetes in humans, a regular monitoring programme of vanadium content in edible sea cucumbers can be recommended.

Hydraulic efficiency and coordination with xylem resistance to cavitation, leaf function, and growth performance among eight unrelated Populus deltoidesxPopulus nigra hybrids.

PubMed

Fichot, Régis; Chamaillard, Sylvain; Depardieu, Claire; Le Thiec, Didier; Cochard, Hervé; Barigah, Têtè S; Brignolas, Franck

2011-03-01

Tests were carried out to determine whether variations in the hydraulic architecture of eight Populus deltoides×Populus nigra genotypes could be related to variations in leaf function and growth performance. Measurements were performed in a coppice plantation on 1-year-old shoots under optimal irrigation. Hydraulic architecture was characterized through estimates of hydraulic efficiency (the ratio of conducting sapwood area to leaf area, A(X):A(L); leaf- and xylem-specific hydraulic conductance of defoliated shoots, k(SL) and k(SS), respectively; apparent whole-plant leaf-specific hydraulic conductance, k(plant)) and xylem safety (water potential inducing 50% loss in hydraulic conductance). The eight genotypes spanned a significant range of k(SL) from 2.63  kg s(-1) m(-2) MPa(-1) to 4.18  kg s(-1) m(-2) MPa(-1), variations being mostly driven by k(SS) rather than A(X):A(L). There was a strong trade-off between hydraulic efficiency and xylem safety. Values of k(SL) correlated positively with k(plant), indicating that high-pressure flowmeter (HPFM) measurements of stem hydraulic efficiency accurately reflected whole-plant water transport efficiency of field-grown plants at maximum transpiration rate. No clear relationship could be found between hydraulic efficiency and either net CO(2) assimilation rates, water-use efficiency estimates (intrinsic water-use efficiency and carbon isotope discrimination against (13)C), or stomatal characteristics (stomatal density and stomatal pore area index). Estimates of hydraulic efficiency were negatively associated with relative growth rate. This unusual pattern, combined with the trade-off observed between hydraulic efficiency and xylem safety, provides the rationale for the positive link already reported between relative growth rate and xylem safety among the same eight P. deltoides×P. nigra genotypes.

Identification of Novel Genetic Markers of Breast Cancer Survival

PubMed Central

Guo, Qi; Schmidt, Marjanka K.; Kraft, Peter; Canisius, Sander; Chen, Constance; Khan, Sofia; Tyrer, Jonathan; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Michailidou, Kyriaki; Lush, Michael; Kar, Siddhartha; Beesley, Jonathan; Dunning, Alison M.; Shah, Mitul; Czene, Kamila; Darabi, Hatef; Eriksson, Mikael; Lambrechts, Diether; Weltens, Caroline; Leunen, Karin; Bojesen, Stig E.; Nordestgaard, Børge G.; Nielsen, Sune F.; Flyger, Henrik; Chang-Claude, Jenny; Rudolph, Anja; Seibold, Petra; Flesch-Janys, Dieter; Blomqvist, Carl; Aittomäki, Kristiina; Fagerholm, Rainer; Muranen, Taru A.; Couch, Fergus J.; Olson, Janet E.; Vachon, Celine; Andrulis, Irene L.; Knight, Julia A.; Glendon, Gord; Mulligan, Anna Marie; Broeks, Annegien; Hogervorst, Frans B.; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick; Le Marchand, Loic; Hopper, John L.; Tsimiklis, Helen; Apicella, Carmel; Southey, Melissa C.; Cox, Angela; Cross, Simon S.; Reed, Malcolm W. R.; Giles, Graham G.; Milne, Roger L.; McLean, Catriona; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Hooning, Maartje J.; Hollestelle, Antoinette; Martens, John W. M.; van den Ouweland, Ans M. W.; Marme, Federik; Schneeweiss, Andreas; Yang, Rongxi; Burwinkel, Barbara; Figueroa, Jonine; Chanock, Stephen J.; Lissowska, Jolanta; Sawyer, Elinor J.; Tomlinson, Ian; Kerin, Michael J.; Miller, Nicola; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Holleczek, Bernd; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M.; Li, Jingmei; Brand, Judith S.; Humphreys, Keith; Devilee, Peter; Tollenaar, Rob A. E. M.; Seynaeve, Caroline; Radice, Paolo; Peterlongo, Paolo; Bonanni, Bernardo; Mariani, Paolo; Fasching, Peter A.; Beckmann, Matthias W.; Hein, Alexander; Ekici, Arif B.; Chenevix-Trench, Georgia; Balleine, Rosemary; Phillips, Kelly-Anne; Benitez, Javier; Zamora, M. Pilar; Arias Perez, Jose Ignacio; Menéndez, Primitiva; Jakubowska, Anna; Lubinski, Jan; Jaworska-Bieniek, Katarzyna; Durda, Katarzyna; Hamann, Ute; Kabisch, Maria; Ulmer, Hans Ulrich; Rüdiger, Thomas; Margolin, Sara; Kristensen, Vessela; Nord, Silje; Evans, D. Gareth; Abraham, Jean E.; Earl, Helena M.; Hiller, Louise; Dunn, Janet A.; Bowden, Sarah; Berg, Christine; Campa, Daniele; Diver, W. Ryan; Gapstur, Susan M.; Gaudet, Mia M.; Hankinson, Susan E.; Hoover, Robert N.; Hüsing, Anika; Kaaks, Rudolf; Machiela, Mitchell J.; Willett, Walter; Barrdahl, Myrto; Canzian, Federico; Chin, Suet-Feung; Caldas, Carlos; Hunter, David J.; Lindstrom, Sara; García-Closas, Montserrat; Hall, Per; Easton, Douglas F.; Eccles, Diana M.; Rahman, Nazneen; Nevanlinna, Heli; Pharoah, Paul D. P.

2015-01-01

Background: Survival after a diagnosis of breast cancer varies considerably between patients, and some of this variation may be because of germline genetic variation. We aimed to identify genetic markers associated with breast cancer–specific survival. Methods: We conducted a large meta-analysis of studies in populations of European ancestry, including 37954 patients with 2900 deaths from breast cancer. Each study had been genotyped for between 200000 and 900000 single nucleotide polymorphisms (SNPs) across the genome; genotypes for nine million common variants were imputed using a common reference panel from the 1000 Genomes Project. We also carried out subtype-specific analyses based on 6881 estrogen receptor (ER)–negative patients (920 events) and 23059 ER-positive patients (1333 events). All statistical tests were two-sided. Results: We identified one new locus (rs2059614 at 11q24.2) associated with survival in ER-negative breast cancer cases (hazard ratio [HR] = 1.95, 95% confidence interval [CI] = 1.55 to 2.47, P = 1.91 x 10–8). Genotyping a subset of 2113 case patients, of which 300 were ER negative, provided supporting evidence for the quality of the imputation. The association in this set of case patients was stronger for the observed genotypes than for the imputed genotypes. A second locus (rs148760487 at 2q24.2) was associated at genome-wide statistical significance in initial analyses; the association was similar in ER-positive and ER-negative case patients. Here the results of genotyping suggested that the finding was less robust. Conclusions: This is currently the largest study investigating genetic variation associated with breast cancer survival. Our results have potential clinical implications, as they confirm that germline genotype can provide prognostic information in addition to standard tumor prognostic factors. PMID:25890600

Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism

PubMed Central

Norman, Paul J.; Parham, Peter

2012-01-01

Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals’ classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores. PMID:23001684

Time dependent variation of carrying capacity of prestressed precast beam

NASA Astrophysics Data System (ADS)

Le, Tuan D.; Konečný, Petr; Matečková, Pavlína

2018-04-01

The article deals with the evaluation of the precast concrete element time dependent carrying capacity. The variation of the resistance is inherited property of laboratory as well as in-situ members. Thus the specification of highest, yet possible, laboratory sample resistance is important with respect to evaluation of laboratory experiments based on the test machine loading capabilities. The ultimate capacity is evaluated through the bending moment resistance of a simply supported prestressed concrete beam. The probabilistic assessment is applied. Scatter of random variables of compressive strength of concrete and effective height of the cross section is considered. Monte Carlo simulation technique is used to investigate the performance of the cross section of the beam with changes of tendons’ positions and compressive strength of concrete.

Low-income fathers' speech to toddlers during book reading versus toy play.

PubMed

Salo, Virginia C; Rowe, Meredith L; Leech, Kathryn A; Cabrera, Natasha J

2016-11-01

Fathers' child-directed speech across two contexts was examined. Father-child dyads from sixty-nine low-income families were videotaped interacting during book reading and toy play when children were 2;0. Fathers used more diverse vocabulary and asked more questions during book reading while their mean length of utterance was longer during toy play. Variation in these specific characteristics of fathers' speech that differed across contexts was also positively associated with child vocabulary skill measured on the MacArthur-Bates Communicative Development Inventory. Results are discussed in terms of how different contexts elicit specific qualities of child-directed speech that may promote language use and development.

Solitary pulmonary nodule evaluation in regions endemic for infectious diseases: Do regional variations impact the effectiveness of fluorodeoxyglucose positron emission tomography/computed tomography.

PubMed

Purandare, N C; Pramesh, C S; Agarwal, J P; Agrawal, A; Shah, S; Prabhash, K; Karimundackal, G; Jiwnani, S; Tandon, S; Rangarajan, V

2017-01-01

Fluorodeoxyglucose positron emission tomography/computed tomography (FDG-PET/CT) has become a preferred imaging modality for the evaluation of solitary pulmonary nodule (SPN), particularly in the developed world. Since FDG can concentrate in infective/inflammatory lesions, the diagnostic utility of FDG-PET can be questioned, particularly in regions endemic for infectious decisions. To evaluate the accuracy of FDG-PET/CT in evaluation of SPNs in a population endemic for infectious disease and to assess if regional variations have an impact on its effectiveness. All patients who underwent an FDG/PET-CT with a clinico-radiological diagnosis of SPN categorized as indeterminate were included. Based on a maximum standardized uptake values (SUVmax) cut-off of 2.5, lesions were classified as benign (<2.5) or malignant (>2.5) and compared with gold standard histopathology. The diagnostic accuracy of PET-CT to detect malignancy was calculated. On the basis of final histopathology, lesions were grouped as (a) malignant nodules (b) infective/granulomatous nodules with a specific diagnosis and (c) nonspecific inflammatory nodules. The SUVmaxbetween these groups was compared using nonparametric statistical tests. A total of 191 patients (129 males, 62 females) with a median age of 64 years (range: 36-83) were included. Totally, 144 nodules (75.3%) were malignant and 47 were benign (24.7%). Adenocarcinoma (n = 84) was the most common malignancy. Tuberculosis (n = 16) and nonspecific infections (n = 24) were the two most common benign pathologies. There was a significant overlap in the metabolic uptake of malignant (median SUVmax-11.2, range: 3.3-34.6) and tuberculous nodules (median SUVmax-10.3, range: 2.7-22.5) with no statistically difference between their SUVmaxvalues (P = 0.43). The false-positive rate was 65.2% and the false-negative rate was 5.5%. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of FDG-PET/CT for detecting malignancy were 94.4%, 34.7%, 81.9%, 66.6%, and 79.5%, respectively. Though FDG-PET scans show a very high sensitivity for malignant nodules, it has a high false-positive rate and reduced specificity when characterizing SPNs in an infectious endemic region. Physicians must be aware of this limitation in the workup of lung nodules, and regional variations must be considered before further management decisions are taken.

Median filtering detection using variation of neighboring line pairs for image forensics

NASA Astrophysics Data System (ADS)

Rhee, Kang Hyeon

2016-09-01

Attention to tampering by median filtering (MF) has recently increased in digital image forensics. For the MF detection (MFD), this paper presents a feature vector that is extracted from two kinds of variations between the neighboring line pairs: the row and column directions. Of these variations in the proposed method, one is defined by a gradient difference of the intensity values between the neighboring line pairs, and the other is defined by a coefficient difference of the Fourier transform (FT) between the neighboring line pairs. Subsequently, the constructed 19-dimensional feature vector is composed of these two parts. One is the extracted 9-dimensional from the space domain of an image and the other is the 10-dimensional from the frequency domain of an image. The feature vector is trained in a support vector machine classifier for MFD in the altered images. As a result, in the measured performances of the experimental items, the area under the receiver operating characteristic curve (AUC, ROC) by the sensitivity (PTP: the true positive rate) and 1-specificity (PFP: the false-positive rate) are above 0.985 and the classification ratios are also above 0.979. Pe (a minimal average decision error) ranges from 0 to 0.024, and PTP at PFP=0.01 ranges from 0.965 to 0.996. It is confirmed that the grade evaluation of the proposed variation-based MF detection method is rated as "Excellent (A)" by AUC is above 0.9.

Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisiae populations.

PubMed

Will, Jessica L; Kim, Hyun Seok; Clarke, Jessica; Painter, John C; Fay, Justin C; Gasch, Audrey P

2010-04-01

A major goal in evolutionary biology is to understand how adaptive evolution has influenced natural variation, but identifying loci subject to positive selection has been a challenge. Here we present the adaptive loss of a pair of paralogous genes in specific Saccharomyces cerevisiae subpopulations. We mapped natural variation in freeze-thaw tolerance to two water transporters, AQY1 and AQY2, previously implicated in freeze-thaw survival. However, whereas freeze-thaw-tolerant strains harbor functional aquaporin genes, the set of sensitive strains lost aquaporin function at least 6 independent times. Several genomic signatures at AQY1 and/or AQY2 reveal low variation surrounding these loci within strains of the same haplotype, but high variation between strain groups. This is consistent with recent adaptive loss of aquaporins in subgroups of strains, leading to incipient balancing selection. We show that, although aquaporins are critical for surviving freeze-thaw stress, loss of both genes provides a major fitness advantage on high-sugar substrates common to many strains' natural niche. Strikingly, strains with non-functional alleles have also lost the ancestral requirement for aquaporins during spore formation. Thus, the antagonistic effect of aquaporin function-providing an advantage in freeze-thaw tolerance but a fitness defect for growth in high-sugar environments-contributes to the maintenance of both functional and nonfunctional alleles in S. cerevisiae. This work also shows that gene loss through multiple missense and nonsense mutations, hallmarks of pseudogenization presumed to emerge after loss of constraint, can arise through positive selection.

CNV-TV: a robust method to discover copy number variation from short sequencing reads.

PubMed

Duan, Junbo; Zhang, Ji-Gang; Deng, Hong-Wen; Wang, Yu-Ping

2013-05-02

Copy number variation (CNV) is an important structural variation (SV) in human genome. Various studies have shown that CNVs are associated with complex diseases. Traditional CNV detection methods such as fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH) suffer from low resolution. The next generation sequencing (NGS) technique promises a higher resolution detection of CNVs and several methods were recently proposed for realizing such a promise. However, the performances of these methods are not robust under some conditions, e.g., some of them may fail to detect CNVs of short sizes. There has been a strong demand for reliable detection of CNVs from high resolution NGS data. A novel and robust method to detect CNV from short sequencing reads is proposed in this study. The detection of CNV is modeled as a change-point detection from the read depth (RD) signal derived from the NGS, which is fitted with a total variation (TV) penalized least squares model. The performance (e.g., sensitivity and specificity) of the proposed approach are evaluated by comparison with several recently published methods on both simulated and real data from the 1000 Genomes Project. The experimental results showed that both the true positive rate and false positive rate of the proposed detection method do not change significantly for CNVs with different copy numbers and lengthes, when compared with several existing methods. Therefore, our proposed approach results in a more reliable detection of CNVs than the existing methods.

Diel variation of the cellular carbon to nitrogen ratio of Chlorella autotrophica (Chlorophyta) growing in phosphorus- and nitrogen-limited continuous cultures.

PubMed

Ng, Wai Ho Albert; Liu, Hongbin

2015-02-01

We investigated the relationship between daily growth rates and diel variation of carbon (C) metabolism and C to nitrogen (N) ratio under P- and N-limitation in the green algae Chlorella autotrophica. To do this, continuous cultures of C. autotrophica were maintained in a cyclostat culture system under 14:10 light:dark cycle over a series of P- and N-limited growth rates. Cell abundance, together with cell size, as reflected by side scatter signal from flow cytometric analysis demonstrated a synchronized diel pattern with cell division occurring at night. Under either type of nutrient limitation, the cellular C:N ratio increased through the light period and decreased through the dark period over all growth rates, indicating a higher diel variation of C metabolism than that of N. Daily average cellular C:N ratios were higher at lower dilution rates under both types of nutrient limitation but cell enlargement was only observed at lower dilution rates under P-limitation. Carbon specific growth rates during the dark period positively correlated with cellular daily growth rates (dilution rates), with net loss of C during night at the lowest growth rates under N-limitation. Under P-limitation, dark C specific growth rates were close to zero at low dilution rates but also exhibited an increasing trend at high dilution rates. In general, diel variations of cellular C:N were low when dark C specific growth rates were high. This result indicated that the fast growing cells performed dark C assimilation at high rates, hence diminished the uncoupling of C and N metabolism at night. © 2014 Phycological Society of America.

Immunohistochemical study of temporal variations in cytochrome P-450 isozymes in rat testis and their modifications by the inductive effects of cadinenes

NASA Astrophysics Data System (ADS)

Kobayashi, Yasuhito; Motohashi, Yutaka; Miyazaki, Yoshifumi; Yatagai, Mitsuyoshi; Takano, Takehito

1991-12-01

Temporal variations in cytochrome P-450 isozymes of rat testis, PB-P-450 (forms of cytochrome P-450 strongly induced by phenobarbital) and MC-P-448 (forms of cytochrome P-450 strongly induced by 3-methylcholanthrene), were investigated immunohistochemically by the avidin-biotin-complex method using specific antibodies against PB-P-450 and MC-P-448 isozymes. Immunoreactivity to both PB-P-450 and MC-P-448 isozymes was observed in Leydig cells. The number of PB-P-450 positive Leydig cells was found to undergo significant time-of-day variation with a peak time of 0000 hours (light phase from 0800 to 2000 hours). Injection of cadinenes (300 mg/kg per day intraperitoneally at 48 and 96 h before sacrifice) induced PB-P-450 isozyme but did not induce MC-P-448 isozyme. The induction of PB-P-450 isozyme by cadinenes was time dependent, and the early dark phase (2000 and 0000 hours) was most sensitive. These results suggest that temporal variation of cytochrome P-450 isozymes is one of the important physiological variations in detoxification and activation of various xenobiotics and chemicals in the testis.

Variations in pore characteristics in high volatile bituminous coals: Implications for coal bed gas content

USGS Publications Warehouse

Mastalerz, Maria; Drobniak, A.; Strapoc, D.; Solano-Acosta, W.; Rupp, J.

2008-01-01

The Seelyville Coal Member of the Linton Formation (Pennsylvanian) in Indiana was studied to: 1) understand variations in pore characteristics within a coal seam at a single location and compare these variations with changes occurring between the same coal at different locations, 2) elaborate on the influence of mineral-matter and maceral composition on mesopore and micropore characteristics, and 3) discuss implications of these variations for coal bed gas content. The coal is high volatile bituminous rank with R0 ranging from 0.57% to 0.60%. BET specific surface areas (determined by nitrogen adsorption) of the coals samples studied range from 1.8 to 22.9??m2/g, BJH adsorption mesopore volumes from 0.0041 to 0.0339??cm3/g, and micropore volumes (determined by carbon dioxide adsorption) from 0.0315 to 0.0540??cm3/g. The coals that had the largest specific surface areas and largest mesopore volumes occur at the shallowest depths, whereas the smallest values for these two parameters occur in the deepest coals. Micropore volumes, in contrast, are not depth-dependent. In the coal samples examined for this study, mineral-matter content influenced both specific surface area as well as mesopore and micropore volumes. It is especially clear in the case of micropores, where an increase in mineral-matter content parallels the decrease of micropore volume of the coal. No obvious relationships were observed between the total vitrinite content and pore characteristics but, after splitting vitrinite into individual macerals, we see that collotelinite influences both meso- and micropore volume positively, whereas collodetrinite contributes to the reduction of mesopore and micropore volumes. There are large variations in gas content within a single coal at a single location. Because of this variability, the entire thickness of the coal must be desorbed in order to determine gas content reliably and to accurately calculate the level of gas saturation. ?? 2008 Elsevier B.V. All rights reserved.

Complexity of genetic mechanisms conferring nonuniformity of recombination in maize.

PubMed

Pan, Qingchun; Deng, Min; Yan, Jianbing; Li, Lin

2017-04-26

Recombinations occur nonuniformly across the maize genome. To dissect the genetic mechanisms underlying the nonuniformity of recombination, we performed quantitative trait locus (QTL) mapping using recombinant inbred line populations. Genome-wide QTL scan identified hundreds of QTLs with both cis-prone and trans- effects for recombination number variation. To provide detailed insights into cis- factors associated with recombination variation, we examined the genomic features around recombination hot regions, including density of genes, DNA transposons, retrotransposons, and some specific motifs. Compared to recombination variation in whole genome, more QTLs were mapped for variations in recombination hot regions. The majority QTLs for recombination hot regions are trans-QTLs and co-localized with genes from the recombination pathway. We also found that recombination variation was positively associated with the presence of genes and DNA transposons, but negatively related to the presence of long terminal repeat retrotransposons. Additionally, 41 recombination hot regions were fine-mapped. The high-resolution genotyping of five randomly selected regions in two F 2 populations verified that they indeed have ultra-high recombination frequency, which is even higher than that of the well-known recombination hot regions sh1-bz and a1-sh2. Taken together, our results further our understanding of recombination variation in plants.

Computational studies of transthoracic and transvenous defibrillation in a detailed 3-D human thorax model.

PubMed

Jorgenson, D B; Haynor, D R; Bardy, G H; Kim, Y

1995-02-01

A method for constructing and solving detailed patient-specific 3-D finite element models of the human thorax is presented for use in defibrillation studies. The method utilizes the patient's own X-ray CT scan and a simplified meshing scheme to quickly and efficiently generate a model typically composed of approximately 400,000 elements. A parameter sensitivity study on one human thorax model to examine the effects of variation in assigned tissue resistivity values, level of anatomical detail included in the model, and number of CT slices used to produce the model is presented. Of the seven tissue types examined, the average left ventricular (LV) myocardial voltage gradient was most sensitive to the values of myocardial and blood resistivity. Incorrectly simplifying the model, for example modeling the heart as a homogeneous structure by ignoring the blood in the chambers, caused the average LV myocardial voltage gradient to increase by 12%. The sensitivity of the model to variations in electrode size and position was also examined. Small changes (< 2.0 cm) in electrode position caused average LV myocardial voltage gradient values to increase by up to 12%. We conclude that patient-specific 3-D finite element modeling of human thoracic electric fields is feasible and may reduce the empiric approach to insertion of implantable defibrillators and improve transthoracic defibrillation techniques.

On the density of the corona in regions of type 3 activity

NASA Technical Reports Server (NTRS)

Kuiper, T. B. H.

1973-01-01

The east-west positions of 190 type 3 bursts were measured between 30 and 65 MHz with the log-periodic array at Clark Lake. A method is described to find the intrinsic variation of position with frequency of type 3 bursts based on the comparison of the positions of the bursts measured at any two arbitrary frequencies. It is found that the variation of position frequency agrees with the behaviour expected from coronal density models. This suggests that the measured positions were not seriously affected by scattering in the corona. Knowing the functional form of the variation of position with frequency for type 3 bursts, it is shown that the observed burst positions can be corrected for the effects of ionospheric refraction.

UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.

PubMed

Lua, Rhonald C; Wilson, Stephen J; Konecki, Daniel M; Wilkins, Angela D; Venner, Eric; Morgan, Daniel H; Lichtarge, Olivier

2016-01-04

The structure and function of proteins underlie most aspects of biology and their mutational perturbations often cause disease. To identify the molecular determinants of function as well as targets for drugs, it is central to characterize the important residues and how they cluster to form functional sites. The Evolutionary Trace (ET) achieves this by ranking the functional and structural importance of the protein sequence positions. ET uses evolutionary distances to estimate functional distances and correlates genotype variations with those in the fitness phenotype. Thus, ET ranks are worse for sequence positions that vary among evolutionarily closer homologs but better for positions that vary mostly among distant homologs. This approach identifies functional determinants, predicts function, guides the mutational redesign of functional and allosteric specificity, and interprets the action of coding sequence variations in proteins, people and populations. Now, the UET database offers pre-computed ET analyses for the protein structure databank, and on-the-fly analysis of any protein sequence. A web interface retrieves ET rankings of sequence positions and maps results to a structure to identify functionally important regions. This UET database integrates several ways of viewing the results on the protein sequence or structure and can be found at http://mammoth.bcm.tmc.edu/uet/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A common copy number variation polymorphism in the CNTNAP2 gene: sexual dimorphism in association with healthy aging and disease.

PubMed

Iakoubov, Leonid; Mossakowska, Malgorzata; Szwed, Malgorzata; Puzianowska-Kuznicka, Monika

2015-01-01

New therapeutic targets are needed to fight aging-related diseases and increase life span. A new female-specific association with diseases and limited survival past 80 years was recently reported for a copy number variation (CNV) in the CNTNAP4 gene from the neurexin superfamily. We asked whether there are CNVs that are associated with aging phenotypes within other genes from the neurexin superfamily and whether this association is sex specific. Select CNV polymorphisms were genotyped with proprietary TaqMan qPCR assays. A case/control study, in which a group of 81- to 90-year-old community-dwelling Caucasians with no chronic diseases (case) was compared to a similar control group of 65- to 75-year-olds, revealed a negative association with healthy aging for the ins allele of common esv11910 CNV in the CNTNAP2 gene (n = 388; OR = 0.29, 95% CI: 0.14-0.59, p = 0.0004 for males, and OR = 0.82, 95% CI: 0.42-1.57, p = 0.625 for females). This male-specific association was validated in a study of an independent group of 76- to 80-year-olds. To look for a corresponding positive association of the allele with aging-related diseases, two case subgroups of 81- to 90-year-olds, one composed of individuals with cognitive impairment and the other with various diseases not directly related to the nervous system, such as cardiovascular diseases, etc., were compared to a healthy control subgroup of the same age. A positive male-specific association was found for both cases (OR = 2.75, p = 0.008 for association with cognitive impairment, and OR = 3.18, p = 0.002 for other diseases combined). A new male-specific association with aging is reported for a CNV in the CNTNAP2 gene. The polymorphism might be useful for diagnosing individual genetic predispositions to healthy aging versus aging complicated by chronic diseases. © 2014 S. Karger AG, Basel.

Concentrations of oligomers and polymers of proanthocyanidins in red and purple rice bran and their relationships to total phenolics, flavonoids, antioxidant capacity and whole grain color.

PubMed

Chen, Ming-Hsuan; McClung, Anna M; Bergman, Christine J

2016-10-01

Proanthocyanidins, a flavonoids subgroup, are proposed to have chronic disease modulation properties. With the eventual goal of enhancing rice phytonutrient concentrations, we investigated the genotypic variation of the concentrations of individual oligomers and polymers of proanthocyanidins in red and purple rice brans. A 4.3-fold variation in total proanthocyanidins (sum of oligomers and polymers) in the extractable fraction was found and the concentration was highly correlated with total phenolics, total flavonoids and antiradical capacity. Variation in the proportion of oligomers and polymers existed, with monomers to trimers, 4-6mers, 7-10mers and polymers accounting for 7, 18, 26.5 and 48.7%, respectively, of the total. The redness value a(∗) of whole grain rice measured in CIE L(∗)a(∗)b(∗) color space was negatively and positively correlated with extractable and non-extractable proanthocyanidins, respectively. The variation found indicates it is possible to select rice with bran containing high levels of total proanthocyanidins and specific degree of polymerization profiles. Published by Elsevier Ltd.

Explaining health care expenditure variation: large-sample evidence using linked survey and health administrative data.

PubMed

Ellis, Randall P; Fiebig, Denzil G; Johar, Meliyanni; Jones, Glenn; Savage, Elizabeth

2013-09-01

Explaining individual, regional, and provider variation in health care spending is of enormous value to policymakers but is often hampered by the lack of individual level detail in universal public health systems because budgeted spending is often not attributable to specific individuals. Even rarer is self-reported survey information that helps explain this variation in large samples. In this paper, we link a cross-sectional survey of 267 188 Australians age 45 and over to a panel dataset of annual healthcare costs calculated from several years of hospital, medical and pharmaceutical records. We use this data to distinguish between cost variations due to health shocks and those that are intrinsic (fixed) to an individual over three years. We find that high fixed expenditures are positively associated with age, especially older males, poor health, obesity, smoking, cancer, stroke and heart conditions. Being foreign born, speaking a foreign language at home and low income are more strongly associated with higher time-varying expenditures, suggesting greater exposure to adverse health shocks. Copyright © 2013 John Wiley & Sons, Ltd.

Ancestry-Specific Methylation Patterns in Admixed Offspring from an Experimental Coyote and Gray Wolf Cross.

PubMed

vonHoldt, Bridgett; Heppenheimer, Elizabeth; Petrenko, Vladimir; Croonquist, Paula; Rutledge, Linda Y

2017-06-01

Reduced fitness of admixed individuals is typically attributed to genetic incompatibilities. Although mismatched genomes can lead to fitness changes, in some cases the reduction in hybrid fitness is subtle. The potential role of transcriptional regulation in admixed genomes could provide a mechanistic explanation for these discrepancies, but evidence is lacking for nonmodel organisms. Here, we explored the intersection of genetics and gene regulation in admixed genomes derived from an experimental cross between a western gray wolf and western coyote. We found a significant positive association between methylation and wolf ancestry, and identified outlier genes that have been previously implicated in inbreeding-related, or otherwise deleterious, phenotypes. We describe a pattern of site-specific, rather than genome-wide, methylation driven by inter-specific hybridization. Epigenetic variation is thus suggested to play a nontrivial role in both maintaining and combating mismatched genotypes through putative transcriptional mechanisms. We conclude that the regulation of gene expression is an underappreciated key component of hybrid genome functioning, but could also act as a potential source of novel and beneficial adaptive variation in hybrid offspring. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Age, period and cohort effects on suicide mortality in Russia, 1956-2005.

PubMed

Jukkala, Tanya; Stickley, Andrew; Mäkinen, Ilkka Henrik; Baburin, Aleksei; Sparén, Pär

2017-03-07

Russian suicide mortality rates changed rapidly over the second half of the twentieth century. This study attempts to differentiate between underlying period and cohort effects in relation to the changes in suicide mortality in Russia between 1956 and 2005. Sex- and age-specific suicide mortality data were analyzed using an age-period-cohort (APC) approach. Descriptive analyses and APC modeling with log-linear Poisson regression were performed. Strong period effects were observed for the years during and after Gorbachev's political reforms (including the anti-alcohol campaign) and for those following the break-up of the Soviet Union. After mutual adjustment, the cohort- and period-specific relative risk estimates for suicide revealed differing underlying processes. While the estimated period effects had an overall positive trend, cohort-specific developments indicated a positive trend for the male cohorts born between 1891 and 1931 and for the female cohorts born between 1891 and 1911, but a negative trend for subsequent cohorts. Our results indicate that the specific life experiences of cohorts may be important for variations in suicide mortality across time, in addition to more immediate effects of changes in the social environment.

Identifying personal microbiomes using metagenomic codes

PubMed Central

Franzosa, Eric A.; Huang, Katherine; Meadow, James F.; Gevers, Dirk; Lemon, Katherine P.; Bohannan, Brendan J. M.; Huttenhower, Curtis

2015-01-01

Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30–300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed >80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability—a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability. PMID:25964341

Little evidence of seasonal variation of natural infection by Leishmania infantum in dogs in Spain.

PubMed

Fernández-Bellon, H; Solano-Gallego, L; Rodríguez-Cortés, A; Ferrer, L; Gallego, M; Alberola, J; Ramis, A

2008-08-01

Leishmania infantum, the etiological agent of canine leishmaniosis in the Mediterranean region, is vectored by Phlebotomus spp sandflies, which are active during the warmer months of the year. In order to determine whether seasonality in transmission induces seasonal changes in the prevalence of infection by L. infantum and of parasite-specific immune response, two groups of dogs, one in February (n=37) and another in October (n=42), were studied. Clinical signs compatible with leishmaniosis, as well as presence of microscopic skin lesions in the muzzle were recorded for all dogs. Assays were also performed for detection of L. infantum parasites in muzzle skin samples (PCR, immunohistochemistry and culture), specific serum antibodies (ELISA), and specific lymphocyte proliferation and interferon-gamma production. Although prevalence of non-specific clinical signs increased significantly after the sandfly season, this was not the case for Leishmania-specific markers: positivity by PCR (24% vs. 21%) or immunohistochemistry (3% vs. 2%) of muzzle skin samples, as well as lymphocyte proliferation (59% vs. 50%) or interferon-gamma production (21% vs. 27%) were similar in February and in October. Only prevalence of positive specific antibody titers increased noticeably in October (8% vs. 20%), although this was not statistically significant. Overall, the sandfly season did not have a marked impact on the prevalence L. infantum infection or parasite-specific immune responses analyzed in this study.

[An analysis of skin prick test reactivity to dust mite in overweight and normal weight children with allergic asthma before and after specific immunotherapy].

PubMed

Wang, Jian; Huang, Ying; Zhang, Xue-Li; Huang, Xia; Xu, Xiao-Wen; Liang, Fan-Mei

2016-04-01

To study the skin prick test (SPT) reactivity to house dust mite allergens in overweight and normal weight children with allergic asthma before and after standard subcutaneous specific immunotherapy. Two hundred and fifteen children with allergic asthma who had positive SPT responses to Dermatophagoides pteronyssinus (DP) and Dermatophagoides farinae (DF) were enrolled. According to the weight index, they were classified into overweight (n=63) and normal weight groups (n=152). Skin indices (SI) to DP and DF were compared between the two groups at 6 months and 1 year after standard subcutaneous specific immunotherapy. The overweight group had a significantly larger histamine wheal diameter than the normal weight group after controlling the variation in testing time (P<0.05). After controlling the variation in weights, there were significant differences in the SIs to DP and DF before specific immunotherapy and at 6 months and 1 year after specific immunotherapy. At 6 months and 1 year after specific immunotherapy, the SIs to DP and DF were significantly reduced in both groups (P<0.05), and the overweight group had greater decreases in the SIs to DP and DF than the normal weight group. The overweight children with allergic asthma have stronger responses to histamine than the normal weight patients. Specific immunotherapy can reduce the reactivity to dust mite allergens in children with allergic asthma. Within one year after specific immunotherapy, the overweight children with allergic asthma have a significantly greater decrease in the reactivity to dust mite allergens than the normal weight patients.

Detecting measurement outliers: remeasure efficiently

NASA Astrophysics Data System (ADS)

Ullrich, Albrecht

2010-09-01

Shrinking structures, advanced optical proximity correction (OPC) and complex measurement strategies continually challenge critical dimension (CD) metrology tools and recipe creation processes. One important quality ensuring task is the control of measurement outlier behavior. Outliers could trigger false positive alarm for specification violations impacting cycle time or potentially yield. Constant high level of outliers not only deteriorates cycle time but also puts unnecessary stress on tool operators leading eventually to human errors. At tool level the sources of outliers are natural variations (e.g. beam current etc.), drifts, contrast conditions, focus determination or pattern recognition issues, etc. Some of these can result from suboptimal or even wrong recipe settings, like focus position or measurement box size. Such outliers, created by an automatic recipe creation process faced with more complicated structures, would manifest itself rather as systematic variation of measurements than the one caused by 'pure' tool variation. I analyzed several statistical methods to detect outliers. These range from classical outlier tests for extrema, robust metrics like interquartile range (IQR) to methods evaluating the distribution of different populations of measurement sites, like the Cochran test. The latter suits especially the detection of systematic effects. The next level of outlier detection entwines additional information about the mask and the manufacturing process with the measurement results. The methods were reviewed for measured variations assumed to be normally distributed with zero mean but also for the presence of a statistically significant spatial process signature. I arrive at the conclusion that intelligent outlier detection can influence the efficiency and cycle time of CD metrology greatly. In combination with process information like target, typical platform variation and signature, one can tailor the detection to the needs of the photomask at hand. By monitoring the outlier behavior carefully, weaknesses of the automatic recipe creation process can be spotted.

Variation at Extra-epitopic Amino Acid Residues Influences Suppression of Influenza Virus Replication by M158-66 Epitope-Specific CD8+ T Lymphocytes.

PubMed

van de Sandt, Carolien E; Pronk, Mark R; van Baalen, Carel A; Fouchier, Ron A M; Rimmelzwaan, Guus F

2018-06-01

Influenza virus-specific CD8 + T lymphocytes (CTLs) contribute to clearance of influenza virus infections and reduce disease severity. Variation at amino acid residues located in or outside CTL epitopes has been shown to affect viral recognition by virus-specific CTLs. In the present study, we investigated the effect of naturally occurring variation at residues outside the conserved immunodominant and HLA*0201-restricted M1 58-66 epitope, located in the influenza virus M1 protein, on the extent of virus replication in the presence of CTLs specific for the epitope. To this end, we used isogenic viruses with an M1 gene segment derived from either an avian or a human influenza virus, HLA-transgenic human epithelial cells, human T cell clones specific for the M1 58-66 epitope or a control epitope, and a novel, purposely developed in vitro system to coculture influenza virus-infected cells with T cells. We found that the M gene segment of a human influenza A/H3N2 virus afforded the virus the capacity to replicate better in the presence of M1 58-66 -specific CTLs than the M gene segment of avian viruses. These findings are in concordance with previously observed differential CTL activation, caused by variation at extra-epitopic residues, and may reflect an immune adaptation strategy of human influenza viruses that allows them to cope with potent CTL immunity to the M1 58-66 epitope in HLA-A*0201-positive individuals, resulting in increased virus replication and shedding and possibly increasing disease severity. IMPORTANCE Influenza viruses are among the leading causes of acute respiratory tract infections. CD8 + T lymphocytes display a high degree of cross-reactivity with influenza A viruses of various subtypes and are considered an important correlate of protection. Unraveling viral immune evasion strategies and identifying signs of immune adaptation are important for defining the role of CD8 + T lymphocytes in affording protection more accurately. Improving our insight into the interaction between influenza viruses and virus-specific CD8 + T lymphocyte immunity may help to advance our understanding of influenza virus epidemiology, aid in risk assessment of potentially pandemic influenza virus strains, and benefit the design of vaccines that induce more broadly protective immunity. Copyright © 2018 American Society for Microbiology.

There's More than Meets the Eye: Complex Associations of Daily Pain, Physical Symptoms, and Self-Efficacy with Activity in Middle and Older Adulthood.

PubMed

Curtis, Rachel G; Windsor, Tim D; Mogle, Jacqueline A; Bielak, Allison A M

2017-01-01

Participation in activities is associated with a range of positive outcomes in adulthood. Research has shown that pain and physical symptoms are associated with less activity in older adults, whereas higher self-efficacy is associated with more activity. Such research tends to examine cross-sectional or long-term between-person change, limiting the opportunity to explore dynamic within-person processes that unfold over shorter time periods. This study aimed to (1) replicate previous between-person associations of self-efficacy with engagement in activity and (2) examine whether daily variation in pain, physical symptoms, and self-efficacy corresponded with daily within-person variation in different types of activity. We predicted that participants would engage in less activity on days when they experienced more pain or physical symptoms than their average (a negative within-person association) and that participants would engage in more activity on days when self-efficacy was higher than average (a positive within-person association). This study used an online diary study to assess self- reported daily pain, physical symptoms, self-efficacy, and engagement in activity among 185 adults aged 51-84 years for up to 7 days. Multilevel modelling was used to examine whether between-person (average) and daily within-person variability in pain, physical symptoms, and self-efficacy were associated with social, physical, and mental activity. In line with previous research, between-person self-efficacy was positively associated with social and physical activity. Supporting the hypotheses, within-person self-efficacy was also positively associated with social and physical activity. The results for pain and physical symptoms were less consistent. Between-person pain was positively associated with social activity. Age interactions indicated that within-person pain was negatively associated with social activity and positively associated with physical activity among older adults. Within-person physical symptoms were positively related to social and mental activity. Stable individual differences as well as short-term within-person variation in physical and psychological functioning are associated with day-to-day variation in activity. Between-person associations did not always reflect within-person associations (e.g., for pain). These complex associations may be influenced by a range of factors including the type of activity and how it is defined (e.g., specific activities and their difficulty), the type of physical symptoms experienced, and age. © 2016 S. Karger AG, Basel.

Faster-X evolution of gene expression is driven by recessive adaptive cis-regulatory variation in Drosophila.

PubMed

Llopart, Ana

2018-05-01

The hemizygosity of the X (Z) chromosome fully exposes the fitness effects of mutations on that chromosome and has evolutionary consequences on the relative rates of evolution of X and autosomes. Specifically, several population genetics models predict increased rates of evolution in X-linked loci relative to autosomal loci. This prediction of faster-X evolution has been evaluated and confirmed for both protein coding sequences and gene expression. In the case of faster-X evolution for gene expression divergence, it is often assumed that variation in 5' noncoding sequences is associated with variation in transcript abundance between species but a formal, genomewide test of this hypothesis is still missing. Here, I use whole genome sequence data in Drosophila yakuba and D. santomea to evaluate this hypothesis and report positive correlations between sequence divergence at 5' noncoding sequences and gene expression divergence. I also examine polymorphism and divergence in 9,279 noncoding sequences located at the 5' end of annotated genes and detected multiple signals of positive selection. Notably, I used the traditional synonymous sites as neutral reference to test for adaptive evolution, but I also used bases 8-30 of introns <65 bp, which have been proposed to be a better neutral choice. X-linked genes with high degree of male-biased expression show the most extreme adaptive pattern at 5' noncoding regions, in agreement with faster-X evolution for gene expression divergence and a higher incidence of positively selected recessive mutations. © 2018 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Use of treatment log files in spot scanning proton therapy as part of patient-specific quality assurance

PubMed Central

Li, Heng; Sahoo, Narayan; Poenisch, Falk; Suzuki, Kazumichi; Li, Yupeng; Li, Xiaoqiang; Zhang, Xiaodong; Lee, Andrew K.; Gillin, Michael T.; Zhu, X. Ronald

2013-01-01

Purpose: The purpose of this work was to assess the monitor unit (MU) values and position accuracy of spot scanning proton beams as recorded by the daily treatment logs of the treatment control system, and furthermore establish the feasibility of using the delivered spot positions and MU values to calculate and evaluate delivered doses to patients. Methods: To validate the accuracy of the recorded spot positions, the authors generated and executed a test treatment plan containing nine spot positions, to which the authors delivered ten MU each. The spot positions were measured with radiographic films and Matrixx 2D ion-chambers array placed at the isocenter plane and compared for displacements from the planned and recorded positions. Treatment logs for 14 patients were then used to determine the spot MU values and position accuracy of the scanning proton beam delivery system. Univariate analysis was used to detect any systematic error or large variation between patients, treatment dates, proton energies, gantry angles, and planned spot positions. The recorded patient spot positions and MU values were then used to replace the spot positions and MU values in the plan, and the treatment planning system was used to calculate the delivered doses to patients. The results were compared with the treatment plan. Results: Within a treatment session, spot positions were reproducible within ±0.2 mm. The spot positions measured by film agreed with the planned positions within ±1 mm and with the recorded positions within ±0.5 mm. The maximum day-to-day variation for any given spot position was within ±1 mm. For all 14 patients, with ∼1 500 000 spots recorded, the total MU accuracy was within 0.1% of the planned MU values, the mean (x, y) spot displacement from the planned value was (−0.03 mm, −0.01 mm), the maximum (x, y) displacement was (1.68 mm, 2.27 mm), and the (x, y) standard deviation was (0.26 mm, 0.42 mm). The maximum dose difference between calculated dose to the patient based on the plan and recorded data was within 2%. Conclusions: The authors have shown that the treatment log file in a spot scanning proton beam delivery system is precise enough to serve as a quality assurance tool to monitor variation in spot position and MU value, as well as the delivered dose uncertainty from the treatment delivery system. The analysis tool developed here could be useful for assessing spot position uncertainty and thus dose uncertainty for any patient receiving spot scanning proton beam therapy. PMID:23387726

An embedded stress sensor for concrete SHM based on amorphous ferromagnetic microwires.

PubMed

Olivera, Jesús; González, Margarita; Fuente, José Vicente; Varga, Rastislav; Zhukov, Arkady; Anaya, José Javier

2014-10-24

A new smart concrete aggregate design as a candidate for applications in structural health monitoring (SHM) of critical elements in civil infrastructure is proposed. The cement-based stress/strain sensor was developed by utilizing the stress/strain sensing properties of a magnetic microwire embedded in cement-based composite (MMCC). This is a contact-less type sensor that measures variations of magnetic properties resulting from stress variations. Sensors made of these materials can be designed to satisfy the specific demand for an economic way to monitor concrete infrastructure health. For this purpose, we embedded a thin magnetic microwire in the core of a cement-based cylinder, which was inserted into the concrete specimen under study as an extra aggregate. The experimental results show that the embedded MMCC sensor is capable of measuring internal compressive stress around the range of 1-30 MPa. Two stress sensing properties of the embedded sensor under uniaxial compression were studied: the peak amplitude and peak position of magnetic switching field. The sensitivity values for the amplitude and position within the measured range were 5 mV/MPa and 2.5 µs/MPa, respectively.

Raman spectroscopy-based screening of hepatitis C and associated molecular changes

NASA Astrophysics Data System (ADS)

Bilal, Maria; Bilal, M.; Saleem, M.; Khan, Saranjam; Ullah, Rahat; Fatima, Kiran; Ahmed, M.; Hayat, Abbas; Shahzada, Shaista; Ullah Khan, Ehsan

2017-09-01

This study presents the optical screening of hepatitis C and its associated molecular changes in human blood sera using a partial least-squares regression model based on their Raman spectra. In total, 152 samples were tested through enzyme-linked immunosorbent assay for confirmation. This model utilizes minor spectral variations in the Raman spectra of the positive and control groups. Regression coefficients of this model were analyzed with reference to the variations in concentration of associated molecules in these two groups. It was found that trehalose, chitin, ammonia, and cytokines are positively correlated while lipids, beta structures of proteins, and carbohydrate-binding proteins are negatively correlated with hepatitis C. The regression vector yielded by this model is utilized to predict hepatitis C in unknown samples. This model has been evaluated by a cross-validation method, which yielded a correlation coefficient of 0.91. Moreover, 30 unknown samples were screened for hepatitis C infection using this model to test its performance. Sensitivity, specificity, accuracy, and area under the receiver operating characteristic curve from these predictions were found to be 93.3%, 100%, 96.7%, and 1, respectively.

The effect of different foot and hand set-up positions on backstroke start performance.

PubMed

de Jesus, Karla; de Jesus, Kelly; Abraldes, J Arturo; Mourão, Luis; Borgonovo-Santos, Márcio; Medeiros, Alexandre I A; Gonçalves, Pedro; Chainok, Phornpot; Fernandes, Ricardo J; Vaz, Mário A P; Vilas-Boas, João Paulo

2016-11-01

Foot and hand set-up position effects were analysed on backstroke start performance. Ten swimmers randomly completed 27 starts grouped in trials (n = 3) of each variation, changing foot (totally immersed, partially and totally emerged) and hand (lowest, highest horizontal and vertical) positioning. Fifteen cameras recorded kinematics, and four force plates collected hands and feet kinetics. Standardised mean difference and 95% confidence intervals were used. Variations with feet immersed have shown lower vertical centre of mass (CM) set-up position (0.16 m), vertical impulse exerted at the hands, horizontal and vertical impulse exerted at the feet (0.28, 0.41, 0.16 N/BW.s, respectively) than feet emerged with hands horizontal and vertically positioned. Most variations with feet partially emerged exhibited higher and lesser vertical impulse exerted at hands than feet immersed and emerged (e.g. vertical handgrip, 0.13, 0.15 N/BW.s, respectively). Variation with feet emerged and hands on the lowest horizontal handgrip depicted shorter horizontal (0.23, 0.26 m) and vertical CM positioning at flight (0.16, 0.15 m) than the highest horizontal and vertical handgrip, respectively. Start variations have not affected 15-m time. Variations with feet partially or totally emerged depicted advantages, but focusing on the entry and underwater biomechanics is relevant for a shorter start time.

The interplay between daily affect and sleep: a 2-week study of young women.

PubMed

Kalmbach, David A; Pillai, Vivek; Roth, Thomas; Drake, Christopher L

2014-12-01

Little attention has been paid to the relation between daily affect and sleep, as most prior studies have focused instead on the role of pathological mood in the context of sleep disturbance. However, understanding the transaction between normal variations in emotional experiences and sleep can shed light on the premorbid vulnerabilities that trigger the evolution of affect and sleep into more problematic states. The present study used a 2-week daily sampling approach to examine the impact of day-to-day variations in positive and negative affect on nightly self-reported sleep-onset latency, sleep duration and sleep quality in a sample of young women. Hierarchical linear modelling revealed temporal relations between positive and negative affect states and sleep parameters. Specifically, different aspects of both positive and negative affect were uniquely predictive of sleep indices, with sadness and serenity acting as the most consistent predictors. Additionally, better sleep quality was predictive of greater happiness the following day. These results highlight the importance of how our daily emotional experiences influence our nightly sleep and, in turn, how our sleep has an impact on our daily affect. Moreover, our findings may offer insight into the progression of normative levels of affect and sleep as they develop into comorbid depression, anxiety and insomnia. © 2014 European Sleep Research Society.

Site-Specific Carbon Isotopes in Organics

NASA Astrophysics Data System (ADS)

Piasecki, A.; Eiler, J. M.

2012-12-01

Natural organic molecules exhibit a wide range of internal site-specific isotope variation (i.e., molecules with same isotopic substitution type but different site). Such variations are generally unconstrained by bulk isotopic measurements. If known, site-specific variations might constrain temperatures of equilibrium, mechanisms of formation or consumption reactions, and possibly other details. For example, lipids can exhibit carbon isotope differences of up to 30‰ between adjacent carbon sites as a result of fractionations arising during decarboxylation of pyruvate and other steps in lipid biosynthesis(1). We present a method for site-specific carbon isotope analysis of propane, based on high-resolution, multi-collector gas source mass spectrometry, using a novel prototype instrument - the Thermo MAT 253 Ultra. This machine has an inlet system and electron bombardment ion source resembling those in conventional stable isotope gas source mass spectrometers, and the energy filter, magnet, and detector array resembling those in multi-collector ICPMS and TIMS. The detector array has 7 detector positions, 6 of which are movable, and each of which can collect ions with either a faraday cup (read through amplifiers ranging from 107-1012 ohms) or an SEM. High mass resolving power (up to 27,000, MRP = M/dM definition) is achieved through a narrow entrance slit, adjustable from 250 to 5 μm. Such resolution can cleanly separate isobaric interferences between isotopologues of organic molecules having the same cardinal mass (e.g., 13CH3 and 12CH2D). We use this technology to analyze the isotopologues and fragments of propane, and use such data to solve for the site-specific carbon isotope fractionation. By measuring isotopologues of both the one-carbon (13CH3) and the two-carbon (13C12CH4) fragment ion, we can solve for both bulk δ13C and the difference in δ13C between the terminal and central carbon position. We tested this method by analyzing mixtures between natural propane and labeled propane (13CH3-12CH2-12CH3). Results are consistent with the expected relative fractionations between the two fragments, indicating limited 'scrambling' of carbon positions of less than 2% in the source. The limits of precision of this method are currently ~0.5 ‰, sufficient to resolve known or suspected position-specific isotope effects in propane. We have explored the expected temperature-dependent equilibrium isotopic distributions of propane using density functional theory and quantum mechanical models of vibrational isotope effects. These models predict the homogeneous isotope exchange equilibria among the various isotopologues of propane, which include several of a wide range of effects that should be measurable by our methods. At 300 K we predict that the central carbon site is 15‰ higher in δ13C and 95 ‰ higher in δD than the terminal carbon site; similarly the molecule containing both a 13C and D in the central site is enriched by ~120 ‰ relative to a random isotopic distribution at 300 K. These predictions present targets for future experimental and empirical studies of the temperature dependence of isotopic ordering in propane. More generally, the methods we are developing for the study of intramolecular isotopic distributions in propane will serve as a model for future study of similar effects in other organic compounds. [1]DeNiro, Epstein (1977) Science Volume 197, 261-263.

Germline variants in the CYP19A1 gene are related to specific adverse events in aromatase inhibitor users: a substudy of Dutch patients in the TEAM trial.

PubMed

Fontein, Duveken B Y; Houtsma, Daniel; Nortier, Johan W R; Baak-Pablo, Renee F; Kranenbarg, Elma Meershoek-Klein; van der Straaten, Tahar R J H M; Putter, Hein; Seynaeve, Caroline; Gelderblom, Hans; van de Velde, Cornelis J H; Guchelaar, Henk-Jan

2014-04-01

Musculoskeletal adverse events (MSAEs) and vasomotor symptoms (VMSs) are known side-effects of aromatase inhibitors, and may be related to genetic variations of the aromatase gene (CYP19A1). We investigated the relationship between these specific AEs and single nucleotide polymorphisms (SNPs) in the CYP19A1 gene in postmenopausal, hormone receptor-positive early breast cancer (BC) patients treated with adjuvant exemestane for 5 years. Dutch patients who were randomized to receive 5 years of exemestane in the Tamoxifen Exemestane Adjuvant Multinational (TEAM) trial were included. A tagging-SNP approach was performed, covering 80 % of variations of the CYP19A1 gene with 30 SNPs. Logistic regression analyses were used to assess the risk of reporting VMSs or MSAEs in relation to genotypes within selected SNPs. Of 737 included patients, 281 patients reported at least one MSAE (n = 210) or VMS (n = 163). Homozygous AA genotype of rs934635 was associated with a significantly higher odds of MSAEs (multivariate odds ratio (OR) 4.66, p = 0.008) and VMSs (multivariate OR 2.78, p = 0.044). Regarding both rs1694189 and rs7176005, the homozygous variant genotypes (TT) were associated with a higher odds of VMSs, but not MSAEs (OR 1.758, p = 0.025 and OR 6.361, p = 0.021, respectively). Our exploratory analysis demonstrated that some CYP19A1 gene variations may be associated with MSAEs and/or VMSs. Specifically, patients with the homozygous variant rs934635 genotype reported more MSAEs and VMSs. Although further confirmatory studies are warranted, genomic profiling can help identify patients at an increased risk of reporting these specific AEs, potentiating further personalized BC treatment.

DNA Shape Dominates Sequence Affinity in Nucleosome Formation

NASA Astrophysics Data System (ADS)

Freeman, Gordon S.; Lequieu, Joshua P.; Hinckley, Daniel M.; Whitmer, Jonathan K.; de Pablo, Juan J.

2014-10-01

Nucleosomes provide the basic unit of compaction in eukaryotic genomes, and the mechanisms that dictate their position at specific locations along a DNA sequence are of central importance to genetics. In this Letter, we employ molecular models of DNA and proteins to elucidate various aspects of nucleosome positioning. In particular, we show how DNA's histone affinity is encoded in its sequence-dependent shape, including subtle deviations from the ideal straight B-DNA form and local variations of minor groove width. By relying on high-precision simulations of the free energy of nucleosome complexes, we also demonstrate that, depending on DNA's intrinsic curvature, histone binding can be dominated by bending interactions or electrostatic interactions. More generally, the results presented here explain how sequence, manifested as the shape of the DNA molecule, dominates molecular recognition in the problem of nucleosome positioning.

Genetic signatures coupled with lineage shift characterise endemic evolution of Dengue virus serotype 2 during 2015 outbreak in Delhi, India.

PubMed

Choudhary, Manish Chandra; Gupta, Ekta; Sharma, Shvetank; Hasnain, Nadeem; Agarwala, Pragya

2017-07-01

In 2015, New Delhi witnessed a massive outbreak of Dengue virus (DENV) resulting in high morbidity and mortality. We report the molecular characterisation of the dominant circulating DENV strain to understand its evolution and dispersal. DENV infections were diagnosed by detection of IgM/NS1 antigen, and serotyping was performed by C-PrM PCR. Envelope gene was amplified, and variation(s) in envelope gene were analysed. Phylogenetic tree construction, time-based phylogeny and origin of DENV were analysed. Site-specific selection pressure of envelope gene variants was analysed. Confirmed DENV infection was observed in 11.34% (32 of 282) cases, while PCR positivity for C-PrM region was observed in 54.16% (13 of 24) of NS1 antigen-positive cases. All samples belonged to serotype 2 and cosmopolitan genotype. Phylogenetic analysis using envelope gene revealed segregation of cosmopolitan genotype strains into specific lineages. The Indian strains clustered separately forming a distinct monophyletic lineage (lineage III) with a signature amino acid substitution viz., I162V and R288K. Selection pressure analysis revealed that 215D, 288R and 304K were positively selected sites. The rate of nucleotide substitution was 6.93 × 10 -4 substitutions site-1 year-1 with time to most common ancestor was around 10 years with JX475906 (Hyderabad strain) and JN030345 (Singapore strain) as its most probable ancestor. We observed evolution of a distinct lineage of DENV-2 strains on the Indian subcontinent with possible changes in endemic circulating dengue strains that might give rise to more pathogenic strains. © 2017 John Wiley & Sons Ltd.

Global mapping of transposon location.

PubMed

Gabriel, Abram; Dapprich, Johannes; Kunkel, Mark; Gresham, David; Pratt, Stephen C; Dunham, Maitreya J

2006-12-15

Transposable genetic elements are ubiquitous, yet their presence or absence at any given position within a genome can vary between individual cells, tissues, or strains. Transposable elements have profound impacts on host genomes by altering gene expression, assisting in genomic rearrangements, causing insertional mutations, and serving as sources of phenotypic variation. Characterizing a genome's full complement of transposons requires whole genome sequencing, precluding simple studies of the impact of transposition on interindividual variation. Here, we describe a global mapping approach for identifying transposon locations in any genome, using a combination of transposon-specific DNA extraction and microarray-based comparative hybridization analysis. We use this approach to map the repertoire of endogenous transposons in different laboratory strains of Saccharomyces cerevisiae and demonstrate that transposons are a source of extensive genomic variation. We also apply this method to mapping bacterial transposon insertion sites in a yeast genomic library. This unique whole genome view of transposon location will facilitate our exploration of transposon dynamics, as well as defining bases for individual differences and adaptive potential.

Modeling patterns of coral bleaching at a remote Central Pacific atoll.

PubMed

Williams, Gareth J; Knapp, Ingrid S; Maragos, James E; Davy, Simon K

2010-09-01

A mild bleaching event (9.2% prevalence) at Palmyra Atoll occurred in response to the 2009 ENSO, when mean water temperature reached 29.8-30.1 degrees C. Prevalence among both abundant and sparse taxa varied with no clear pattern in susceptibility relating to coral morphology. Seven taxon-specific models showed that turbidity exacerbated while prior exposure to higher background temperatures alleviated bleaching, with these predictors explaining an average 16.3% and 11.5% variation in prevalence patterns, respectively. Positive associations occurred between bleaching prevalence and both immediate temperature during the bleaching event (average 8.4% variation explained) and increased sand cover (average 3.7%). Despite these associations, mean unexplained variation in prevalence equalled 59%. Lower bleaching prevalence in areas experiencing higher background temperatures suggests acclimation to temperature stress among several coral genera, while WWII modifications may still be impacting the reefs via shoreline sediment re-distribution and increased turbidity, exacerbating coral bleaching susceptibility during periods of high temperature stress. Copyright 2010 Elsevier Ltd. All rights reserved.

Cloning of quantitative trait genes from rice reveals conservation and divergence of photoperiod flowering pathways in Arabidopsis and rice

PubMed Central

Matsubara, Kazuki; Hori, Kiyosumi; Ogiso-Tanaka, Eri; Yano, Masahiro

2014-01-01

Flowering time in rice (Oryza sativa L.) is determined primarily by daylength (photoperiod), and natural variation in flowering time is due to quantitative trait loci involved in photoperiodic flowering. To date, genetic analysis of natural variants in rice flowering time has resulted in the positional cloning of at least 12 quantitative trait genes (QTGs), including our recently cloned QTGs, Hd17, and Hd16. The QTGs have been assigned to specific photoperiodic flowering pathways. Among them, 9 have homologs in the Arabidopsis genome, whereas it was evident that there are differences in the pathways between rice and Arabidopsis, such that the rice Ghd7–Ehd1–Hd3a/RFT1 pathway modulated by Hd16 is not present in Arabidopsis. In this review, we describe QTGs underlying natural variation in rice flowering time. Additionally, we discuss the implications of the variation in adaptive divergence and its importance in rice breeding. PMID:24860584

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.

PubMed

Li, Ying-hui; Zhou, Guangyu; Ma, Jianxin; Jiang, Wenkai; Jin, Long-guo; Zhang, Zhouhao; Guo, Yong; Zhang, Jinbo; Sui, Yi; Zheng, Liangtao; Zhang, Shan-shan; Zuo, Qiyang; Shi, Xue-hui; Li, Yan-fei; Zhang, Wan-ke; Hu, Yiyao; Kong, Guanyi; Hong, Hui-long; Tan, Bing; Song, Jian; Liu, Zhang-xiong; Wang, Yaoshen; Ruan, Hang; Yeung, Carol K L; Liu, Jian; Wang, Hailong; Zhang, Li-juan; Guan, Rong-xia; Wang, Ke-jing; Li, Wen-bin; Chen, Shou-yi; Chang, Ru-zhen; Jiang, Zhi; Jackson, Scott A; Li, Ruiqiang; Qiu, Li-juan

2014-10-01

Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.

Anthropometrics of Italian Senior Male Rugby Union Players: From Elite to Second Division.

PubMed

Fontana, Federico Y; Colosio, Alessandro; De Roia, Gabriela F; Da Lozzo, Giorgio; Pogliaghi, Silvia

2015-09-01

Anthropometric evaluation of athletes is necessary to optimize talent identification and player development. To provide a specific anthropometric reference database of senior male rugby players competing at different levels in the southern European region. Cross-sectional. In 362 professional players (25 ± 4 y; 138 Italian national team, 97 first-division, and 127 second-division national championships) the authors measured mass, stature, and percentage body fat (plicometry). Mean, SD, and coefficient of variation were calculated for forwards and backs and for positional subgroups. Binomial logistic regression and receiver-operating-characteristic curve were performed to assess which variables best predicted level assignment (international vs national level). For all competitive levels forwards were significantly heavier and taller and had a larger percentage body fat and fat-free mass than backs. The lower the competitive level, the higher the within-role variability observed; furthermore, players in a specific positional subgroup were lighter, shorter, and fatter and had less fat-free mass. Fatfree mass is the variable that best predicts the likelihood of being classified as an international or national player (cutoff value 79.54 kg). The data confirm the specificity in the physical requirements of rugby in individual playing positions at all competitive levels and document significant differences among elite and 1st- and 2nd-division players in the same positional role. These differences may reflect the variable technical abilities, selection, training practices, and requirements of the game among these categories.

A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol

PubMed Central

Romek, Katarzyna M.; Nun, Pierrick; Remaud, Gérald S.; Silvestre, Virginie; Taïwe, Germain Sotoing; Lecerf-Schmidt, Florine; Boumendjel, Ahcène; De Waard, Michel; Robins, Richard J.

2015-01-01

Tramadol, previously only known as a synthetic analgesic, has now been found in the bark and wood of roots of the African medicinal tree Nauclea latifolia. At present, no direct evidence is available as to the biosynthetic pathway of its unusual skeleton. To provide guidance as to possible biosynthetic precursors, we have adopted a novel approach of retro-biosynthesis based on the position-specific distribution of isotopes in the extracted compound. Relatively recent developments in isotope ratio monitoring by 13C NMR spectrometry make possible the measurement of the nonstatistical position-specific natural abundance distribution of 13C (δ13Ci) within the molecule with better than 1‰ precision. Very substantial variation in the 13C positional distribution is found: between δ13Ci = −11 and −53‰. Distribution is not random and it is argued that the pattern observed can substantially be interpreted in relation to known causes of isotope fractionation in natural products. Thus, a plausible biosynthetic scheme based on sound biosynthetic principals of precursor–substrate relationships can be proposed. In addition, data obtained from the 18O/16O ratios in the oxygen atoms of the compound add support to the deductions made from the carbon isotope analysis. This paper shows how the use of 13C NMR at natural abundance can help with proposing a biosynthetic route to compounds newly found in nature or those difficult to tackle by conventional means. PMID:26106160

The interaction between nitrogen and phosphorous is a strong predictor of intra-plant variation in nitrogen isotope composition in a desert species

DOE PAGES

Zhang, Jinxin; Gu, Lianhong; Zhang, Jingbo; ...

2017-01-11

Understanding intra-plant variations in δ 15N is essential for fully utilizing the potential of δ 15N as an integrator of the terrestrial nitrogen (N) cycle and as an indicator of the relative limitation of N and phosphorous (P) on plant growth. Studying such variations can also yield insights into N metabolism by plant as a whole or by specific organs. However, few researchers have systematically evaluated intra-plant variations in δ 15N and their relationships with organ nutrient contents. We excavated whole plant architectures of Nitraria tangutorum Bobrov, a C 3 species of vital regional ecological importance, in two deserts inmore » northwestern China. We systematically and simultaneously measured N isotope ratios and N and P contents of different parts of the excavated plants. We found that intra-plant variations in δ 15N of N. tangutorum were positively correlated with corresponding organ N and P contents. However, it was the N × P interaction, not N and P individually or their linear combination, that was the strongest predictor of intra-plant δ 15N. Additionally, we showed that root δ 15N increased with depth into soil, a pattern similar to profiles of soil δ 15N reported by previous studies in different ecosystems. We hypothesized that the strong positive intra-plant δ 15N–N and P relationships are caused by three processes acting in conjunction: (1) N and P content-driven fractionating exchanges of ammonia between leaves and the atmosphere (volatilization) during photorespiration, (2) resorption and remobilization of N and P from senescing leaves, and (3) mixture of the re-translocated foliar N and P with existing pools in stems and roots. To test our hypothesis, future studies should investigate plant N volatilization and associated isotope fractionation and intra-plant variations in δ 15N in different species across ecosystems and climates.« less

The interaction between nitrogen and phosphorous is a strong predictor of intra-plant variation in nitrogen isotope composition in a desert species

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

Zhang, Jinxin; Gu, Lianhong; Zhang, Jingbo

Understanding intra-plant variations in δ 15N is essential for fully utilizing the potential of δ 15N as an integrator of the terrestrial nitrogen (N) cycle and as an indicator of the relative limitation of N and phosphorous (P) on plant growth. Studying such variations can also yield insights into N metabolism by plant as a whole or by specific organs. However, few researchers have systematically evaluated intra-plant variations in δ 15N and their relationships with organ nutrient contents. We excavated whole plant architectures of Nitraria tangutorum Bobrov, a C 3 species of vital regional ecological importance, in two deserts inmore » northwestern China. We systematically and simultaneously measured N isotope ratios and N and P contents of different parts of the excavated plants. We found that intra-plant variations in δ 15N of N. tangutorum were positively correlated with corresponding organ N and P contents. However, it was the N × P interaction, not N and P individually or their linear combination, that was the strongest predictor of intra-plant δ 15N. Additionally, we showed that root δ 15N increased with depth into soil, a pattern similar to profiles of soil δ 15N reported by previous studies in different ecosystems. We hypothesized that the strong positive intra-plant δ 15N–N and P relationships are caused by three processes acting in conjunction: (1) N and P content-driven fractionating exchanges of ammonia between leaves and the atmosphere (volatilization) during photorespiration, (2) resorption and remobilization of N and P from senescing leaves, and (3) mixture of the re-translocated foliar N and P with existing pools in stems and roots. To test our hypothesis, future studies should investigate plant N volatilization and associated isotope fractionation and intra-plant variations in δ 15N in different species across ecosystems and climates.« less

Specific features of the cathodoluminescence spectra of AlInGaN QWs, caused by the influence of phase separation and internal electric fields

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

Kuznetsova, Ya. V., E-mail: yana@mail.ioffe.ru; Jmerik, V. N.; Nechaev, D. V.

2016-07-15

The specific features of the cathodoluminescence (CL) spectra in AlInGaN heterostructures, caused by the influence of phase separation and internal electric fields, observed at varied CL excitation density, are studied. It is shown that the evolution of the CL spectrum and the variation in the spectral position of emission lines of nanoscale layers with current density in the primary electron beam makes it possible to identify the occurrence of phase separation in the layer and, in the absence of this separation, to estimate the electric-field strength in the active region of the structure.

Low-income fathers’ speech to toddlers during book reading versus toy play*

PubMed Central

Salo, Virginia C.; Rowe, Meredith L.; Leech, Kathryn A.; Cabrera, Natasha J.

2016-01-01

Fathers’ child-directed speech across two contexts was examined. Father–child dyads from sixty-nine low-income families were videotaped interacting during book reading and toy play when children were 2;0. Fathers used more diverse vocabulary and asked more questions during book reading while their mean length of utterance was longer during toy play. Variation in these specific characteristics of fathers’ speech that differed across contexts was also positively associated with child vocabulary skill measured on the MacArthur-Bates Communicative Development Inventory. Results are discussed in terms of how different contexts elicit specific qualities of child-directed speech that may promote language use and development. PMID:26541647

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…

Individual diet variation in a marine fish assemblage: Optimal Foraging Theory, Niche Variation Hypothesis and functional identity

NASA Astrophysics Data System (ADS)

Cachera, M.; Ernande, B.; Villanueva, M. C.; Lefebvre, S.

2017-02-01

Individual diet variation (i.e. diet variation among individuals) impacts intra- and inter-specific interactions. Investigating its sources and relationship with species trophic niche organization is important for understanding community structure and dynamics. Individual diet variation may increase with intra-specific phenotypic (or "individual state") variation and habitat variability, according to Optimal Foraging Theory (OFT), and with species trophic niche width, according to the Niche Variation Hypothesis (NVH). OFT proposes "proximate sources" of individual diet variation such as variations in habitat or size whereas NVH relies on "ultimate sources" related to the competitive balance between intra- and inter-specific competitions. The latter implies as a corollary that species trophic niche overlap, taken as inter-specific competition measure, decreases as species niche width and individual niche variation increase. We tested the complementary predictions of OFT and NVH in a marine fish assemblage using stomach content data and associated trophic niche metrics. The NVH predictions were tested between species of the assemblage and decomposed into a between- and a within-functional group component to assess the potential influence of species' ecological function. For most species, individual diet variation and niche overlap were consistently larger than expected. Individual diet variation increased with intra-specific variability in individual state and habitat, as expected from OFT. It also increased with species niche width but in compliance with the null expectation, thus not supporting the NVH. In contrast, species niche overlap increased significantly less than null expectation with both species niche width and individual diet variation, supporting NVH corollary. The between- and within-functional group components of the NVH relationships were consistent with those between species at the assemblage level. Changing the number of prey categories used to describe diet (from 16 to 41) did not change the results qualitatively. These results suggest that, besides proximate sources, intra-specific competition favors higher individual diet variation than expected while inter-specific competition limits the increase of individual diet variation and of species niche overlap with species niche expansion. This reveals partial trophic resource partitioning between species. Various niche metrics used in combination allow inferring competition effects on trophic niches' organization within communities.

Incipient Balancing Selection through Adaptive Loss of Aquaporins in Natural Saccharomyces cerevisiae Populations

PubMed Central

Will, Jessica L.; Kim, Hyun Seok; Clarke, Jessica; Painter, John C.; Fay, Justin C.; Gasch, Audrey P.

2010-01-01

A major goal in evolutionary biology is to understand how adaptive evolution has influenced natural variation, but identifying loci subject to positive selection has been a challenge. Here we present the adaptive loss of a pair of paralogous genes in specific Saccharomyces cerevisiae subpopulations. We mapped natural variation in freeze-thaw tolerance to two water transporters, AQY1 and AQY2, previously implicated in freeze-thaw survival. However, whereas freeze-thaw–tolerant strains harbor functional aquaporin genes, the set of sensitive strains lost aquaporin function at least 6 independent times. Several genomic signatures at AQY1 and/or AQY2 reveal low variation surrounding these loci within strains of the same haplotype, but high variation between strain groups. This is consistent with recent adaptive loss of aquaporins in subgroups of strains, leading to incipient balancing selection. We show that, although aquaporins are critical for surviving freeze-thaw stress, loss of both genes provides a major fitness advantage on high-sugar substrates common to many strains' natural niche. Strikingly, strains with non-functional alleles have also lost the ancestral requirement for aquaporins during spore formation. Thus, the antagonistic effect of aquaporin function—providing an advantage in freeze-thaw tolerance but a fitness defect for growth in high-sugar environments—contributes to the maintenance of both functional and nonfunctional alleles in S. cerevisiae. This work also shows that gene loss through multiple missense and nonsense mutations, hallmarks of pseudogenization presumed to emerge after loss of constraint, can arise through positive selection. PMID:20369021

Clinical factors and clinical variation influencing the reproducibility of interocclusal recording methods.

PubMed

Eriksson, A; Ockert-Eriksson, G; Lockowandt, P; Eriksson, O

2002-04-13

The reproducibility of clinical records of the occlusion was assessed in three dimensions using mounted casts. Three distinct areas were examined: 1) mandibular positions (intercuspal position (IP) or retruded contact position (RCP)), 2) materials used in recording the occlusion, 3) clinical variation. Interocclusal records were made in a random order of three patients: one fixed prosthodontics case, one removable partial denture case and one complete denture case, with two different types of waxes, record rims, two different brands of vinyl polysiloxanes and one irreversible hydrocolloid. Private practice and Karolinska Institute, Huddinge, Sweden. One general dental practitioner and three voluntary patients. Point estimation of variance components indicate that 70-93% of the variation of the positions of the mounted casts are caused by: 1) clinical variation for all three cases and in three directions, 2) the influence of recording materials 0-29%, and 3) mandibular positions (IP/RCP) 0-11%. The ranges of the positions of the mounted casts were lower for the dentate case (0.04-1.39 mm) than for the partially dentate case (0.17-2.65 mm), which in turn was lower than those for the edentulous case (1.42-5.59 mm). Clinical variation seems to dominate the variation in positions of mounting casts when making interocclusal records, rather than mandibular position or the recording materials used. Therefore a dentist who makes one single interocclusal record cannot presume that it will reproduce the interocclusal relationship intended, which in the present study was most obvious for the edentulous case. The results showed that impression materials stabilised by a tray did not differ significantly from waxes and record rims concerning the reproducibility. Therefore the stabilised impression materials are an alternative, which also give additional advantages like reduction of appointments as well as superior accuracy.

Optimal body size and energy expenditure during winter: why are voles smaller in declining populations?

PubMed

Ergon, Torbjørn; Speakman, John R; Scantlebury, Michael; Cavanagh, Rachel; Lambin, Xavier

2004-03-01

Winter is energetically challenging for small herbivores because of greater energy requirements for thermogenesis at a time when little energy is available. We formulated a model predicting optimal wintering body size, accounting for the scaling of both energy expenditure and assimilation to body size, and the trade-off between survival benefits of a large size and avoiding survival costs of foraging. The model predicts that if the energy cost of maintaining a given body mass differs between environments, animals should be smaller in the more demanding environments, and there should be a negative correlation between body mass and daily energy expenditure (DEE) across environments. In contrast, if animals adjust their energy intake according to variation in survival costs of foraging, there should be a positive correlation between body mass and DEE. Decreasing temperature always increases equilibrium DEE, but optimal body mass may either increase or decrease in colder climates depending on the exact effects of temperature on mass-specific survival and energy demands. Measuring DEE with doubly labeled water on wintering Microtus agrestis at four field sites, we found that DEE was highest at the sites where voles were smallest despite a positive correlation between DEE and body mass within sites. This suggests that variation in wintering body mass between sites was due to variation in food quality/availability and not adjustments in foraging activity to varying risks of predation.

Evolution and inheritance of early embryonic patterning in Drosophila simulans and D. sechellia.

PubMed

Lott, Susan E; Ludwig, Michael Z; Kreitman, Martin

2011-05-01

Pattern formation in Drosophila is a widely studied example of a robust developmental system. Such robust systems pose a challenge to adaptive evolution, as they mask variation that selection may otherwise act upon. Yet we find variation in the localization of expression domains (henceforth "stripe allometry") in the pattern formation pathway. Specifically, we characterize differences in the gap genes giant and Kruppel, and the pair-rule gene even-skipped, which differ between the sibling species Drosophila simulans and D. sechellia. In a double-backcross experiment, stripe allometry is consistent with maternal inheritance of stripe positioning and multiple genetic factors, with a distinct genetic basis from embryo length. Embryos produced by F1 and F2 backcross mothers exhibit novel spatial patterns of gene expression relative to the parental species, with no measurable increase in positional variance among individuals. Buffering of novel spatial patterns in the backcross genotypes suggests that robustness need not be disrupted in order for the trait to evolve, and perhaps the system is incapable of evolving to prevent the expression of all genetic variation. This limitation, and the ability of natural selection to act on minute genetic differences that are within the "margin of error" for the buffering mechanism, indicates that developmentally buffered traits can evolve without disruption of robustness. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Activation of c-jun N-terminal kinase upon influenza A virus (IAV) infection is independent of pathogen-related receptors but dependent on amino acid sequence variations of IAV NS1.

PubMed

Nacken, Wolfgang; Anhlan, Darisuren; Hrincius, Eike R; Mostafa, Ahmed; Wolff, Thorsten; Sadewasser, Anne; Pleschka, Stephan; Ehrhardt, Christina; Ludwig, Stephan

2014-08-01

A hallmark cell response to influenza A virus (IAV) infections is the phosphorylation and activation of c-jun N-terminal kinase (JNK). However, so far it is not fully clear which molecules are involved in the activation of JNK upon IAV infection. Here, we report that the transfection of influenza viral-RNA induces JNK in a retinoic acid-inducible gene I (RIG-I)-dependent manner. However, neither RIG-I-like receptors nor MyD88-dependent Toll-like receptors were found to be involved in the activation of JNK upon IAV infection. Viral JNK activation may be blocked by addition of cycloheximide and heat shock protein inhibitors during infection, suggesting that the expression of an IAV-encoded protein is responsible for JNK activation. Indeed, the overexpression of nonstructural protein 1 (NS1) of certain IAV subtypes activated JNK, whereas those of some other subtypes failed to activate JNK. Site-directed mutagenesis experiments using NS1 of the IAV H7N7, H5N1, and H3N2 subtypes identified the amino acid residue phenylalanine (F) at position 103 to be decisive for JNK activation. Cleavage- and polyadenylation-specific factor 30 (CPSF30), whose binding to NS1 is stabilized by the amino acids F103 and M106, is not involved in JNK activation. Conclusively, subtype-specific sequence variations in the IAV NS1 protein result in subtype-specific differences in JNK signaling upon IAV infection. Influenza A virus (IAV) infection leads to the activation or modulation of multiple signaling pathways. Here, we demonstrate for the first time that the c-jun N-terminal kinase (JNK), a long-known stress-activated mitogen-activated protein (MAP) kinase, is activated by RIG-I when cells are treated with IAV RNA. However, at the same time, nonstructural protein 1 (NS1) of IAV has an intrinsic JNK-activating property that is dependent on IAV subtype-specific amino acid variations around position 103. Our findings identify two different and independent pathways that result in the activation of JNK in the course of an IAV infection. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Activation of c-jun N-Terminal Kinase upon Influenza A Virus (IAV) Infection Is Independent of Pathogen-Related Receptors but Dependent on Amino Acid Sequence Variations of IAV NS1

PubMed Central

Nacken, Wolfgang; Anhlan, Darisuren; Hrincius, Eike R.; Mostafa, Ahmed; Wolff, Thorsten; Sadewasser, Anne; Pleschka, Stephan; Ehrhardt, Christina

2014-01-01

ABSTRACT A hallmark cell response to influenza A virus (IAV) infections is the phosphorylation and activation of c-jun N-terminal kinase (JNK). However, so far it is not fully clear which molecules are involved in the activation of JNK upon IAV infection. Here, we report that the transfection of influenza viral-RNA induces JNK in a retinoic acid-inducible gene I (RIG-I)-dependent manner. However, neither RIG-I-like receptors nor MyD88-dependent Toll-like receptors were found to be involved in the activation of JNK upon IAV infection. Viral JNK activation may be blocked by addition of cycloheximide and heat shock protein inhibitors during infection, suggesting that the expression of an IAV-encoded protein is responsible for JNK activation. Indeed, the overexpression of nonstructural protein 1 (NS1) of certain IAV subtypes activated JNK, whereas those of some other subtypes failed to activate JNK. Site-directed mutagenesis experiments using NS1 of the IAV H7N7, H5N1, and H3N2 subtypes identified the amino acid residue phenylalanine (F) at position 103 to be decisive for JNK activation. Cleavage- and polyadenylation-specific factor 30 (CPSF30), whose binding to NS1 is stabilized by the amino acids F103 and M106, is not involved in JNK activation. Conclusively, subtype-specific sequence variations in the IAV NS1 protein result in subtype-specific differences in JNK signaling upon IAV infection. IMPORTANCE Influenza A virus (IAV) infection leads to the activation or modulation of multiple signaling pathways. Here, we demonstrate for the first time that the c-jun N-terminal kinase (JNK), a long-known stress-activated mitogen-activated protein (MAP) kinase, is activated by RIG-I when cells are treated with IAV RNA. However, at the same time, nonstructural protein 1 (NS1) of IAV has an intrinsic JNK-activating property that is dependent on IAV subtype-specific amino acid variations around position 103. Our findings identify two different and independent pathways that result in the activation of JNK in the course of an IAV infection. PMID:24872593

The Physical and Athletic Performance Characteristics of Division I Collegiate Female Soccer Players by Position.

PubMed

Lockie, Robert G; Moreno, Matthew R; Lazar, Adrina; Orjalo, Ashley J; Giuliano, Dominic V; Risso, Fabrice G; Davis, DeShaun L; Crelling, Jeff B; Lockwood, John R; Jalilvand, Farzad

2018-02-01

Lockie, RG, Moreno, MR, Lazar, A, Orjalo, AJ, Giuliano, DV, Risso, FG, Davis, DL, Crelling, JB, Lockwood, JR, and Jalilvand, F. The physical and athletic performance characteristics of Division I collegiate female soccer players by position. J Strength Cond Res 32(2): 334-343, 2018-Playing positions in soccer can exhibit different movement demands during a match, contributing to variations in physical and performance characteristics. National Collegiate Athletic Association (NCAA) soccer features different substitution rules when compared to FIFA-sanctioned matches, which could influence each players' characteristics. Therefore, this study determined the athletic performance characteristics of Division I female soccer players. Twenty-six players (3 goalkeepers; 8 defenders; 10 midfielders; 5 forwards) from the same squad completed assessments of: lower-body power (vertical and standing broad jump); linear (0-5, 0-10, 0-30 meter [m] sprint intervals) and change-of-direction (pro-agility shuttle; arrowhead change-of-direction speed test) speed; and soccer-specific fitness (Yo-Yo Intermittent Recovery Test [YYIRT] levels 1 and 2). Players were split into position groups, and a Kruskal-Wallis H test with post hoc pairwise analyses (p ≤ 0.05) calculated significant between-group differences. There were no differences in age, height, or body mass between the positions. Midfielders had a faster 0-5 m time compared with the defenders (p = 0.017) and the goalkeepers (p = 0.030). The defenders (p = 0.011) and midfielders (p = 0.013) covered a greater YYIRT2 distance compared with the goalkeepers. There were no other significant between-position differences. Overall, Division I collegiate female players from the same squad demonstrated similar characteristics as measured by soccer-specific performance tests, which could allow for flexibility in position assignments. However, a relatively homogenous squad could also indicate commonality in training prescription, particularly regarding acceleration and high-intensity running. Strength and conditioning coaches may have to consider the specific movement demands of individual positions when training these capacities.

Air pollution exposure, cause-specific deaths and hospitalizations in a highly polluted Italian region.

PubMed

Carugno, Michele; Consonni, Dario; Randi, Giorgia; Catelan, Dolores; Grisotto, Laura; Bertazzi, Pier Alberto; Biggeri, Annibale; Baccini, Michela

2016-05-01

The Lombardy region in northern Italy ranks among the most air polluted areas of Europe. Previous studies showed air pollution short-term effects on all-cause mortality. We examine here the effects of particulate matter with aerodynamic diameter ≤10µm (PM10) and nitrogen dioxide (NO2) exposure on deaths and hospitalizations from specific causes, including cardiac, cerebrovascular and respiratory diseases. We considered air pollution, mortality and hospitalization data for a non-opportunistic sample of 18 highly polluted and most densely populated areas of the region in the years 2003-2006. We obtained area-specific effect estimates for PM10 and NO2 from a Poisson regression model on the daily number of total deaths or cause-specific hospitalizations and then combined them in a Bayesian random-effects meta-analysis. For cause-specific mortality, we applied a case-crossover analysis. Age- and season-specific analyses were also performed. Effect estimates were expressed as percent variation in mortality or hospitalizations associated with a 10µg/m(3) increase in PM10 or NO2 concentration. Natural mortality was positively associated with both pollutants (0.30%, 90% Credibility Interval [CrI]: -0.31; 0.78 for PM10; 0.70%, 90%CrI: 0.10; 1.27 for NO2). Cardiovascular deaths showed a higher percent variation in association with NO2 (1.12%, 90% Confidence Interval [CI]: 0.14; 2.11), while the percent variation for respiratory mortality was highest in association with PM10 (1.64%, 90%CI: 0.35; 2.93). The effect of both pollutants was more evident in the summer season. Air pollution was also associated to hospitalizations, the highest variations being 0.77% (90%CrI: 0.22; 1.43) for PM10 and respiratory diseases, and 1.70% (90%CrI: 0.39; 2.84) for NO2 and cerebrovascular diseases. The effect of PM10 on respiratory hospital admissions appeared to increase with age. For both pollutants, effects on cerebrovascular hospitalizations were more evident in subjects aged less than 75 years. Our study provided a sound characterization of air pollution exposure and its potential effects on human health in the most polluted, and also most populated and productive, Italian region, further documenting the need for effective public health policies. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Being born under adverse economic conditions leads to a higher cardiovascular mortality rate later in life: evidence based on individuals born at different stages of the business cycle.

PubMed

van den Berg, Gerard J; Doblhammer-Reiter, Gabriele; Christensen, Kaare

2011-05-01

We connect the recent medical and economic literatures on the long-run effects of early-life conditions by analyzing the effects of economic conditions on the individual cardiovascular (CV) mortality rate later in life, using individual data records from the Danish Twin Registry covering births since the 1870s and including the cause of death. To capture exogenous variation of conditions early in life, we use the state of the business cycle around birth. We find significant negative effects of economic conditions around birth on the individual CV mortality rate at higher ages. There is no effect on the cancer-specific mortality rate. From variation within and between monozygotic and dizygotic twin pairs born under different conditions, we conclude that the fate of an individual is more strongly determined by genetic and household-environmental factors if early-life conditions are poor. Individual-specific qualities come more to fruition if the starting position in life is better.

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

Harris, Michael D.; Dater, Manasi; Whitaker, Ross

In this study, statistical shape modeling (SSM) was used to quantify three-dimensional (3D) variation and morphologic differences between femurs with and without cam femoroacetabular impingement (FAI). 3D surfaces were generated from CT scans of femurs from 41 controls and 30 cam FAI patients. SSM correspondence particles were optimally positioned on each surface using a gradient descent energy function. Mean shapes for control and patient groups were defined from the resulting particle configurations. Morphological differences between group mean shapes and between the control mean and individual patients were calculated. Principal component analysis was used to describe anatomical variation present in bothmore » groups. The first 6 modes (or principal components) captured statistically significant shape variations, which comprised 84% of cumulative variation among the femurs. Shape variation was greatest in femoral offset, greater trochanter height, and the head-neck junction. The mean cam femur shape protruded above the control mean by a maximum of 3.3 mm with sustained protrusions of 2.5-3.0 mm along the anterolateral head-neck junction and distally along the anterior neck, corresponding well with reported cam lesion locations and soft-tissue damage. This study provides initial evidence that SSM can describe variations in femoral morphology in both controls and cam FAI patients and may be useful for developing new measurements of pathological anatomy. SSM may also be applied to characterize cam FAI severity and provide templates to guide patient-specific surgical resection of bone.« less

Running vacuum in the Universe and the time variation of the fundamental constants of Nature

NASA Astrophysics Data System (ADS)

Fritzsch, Harald; Solà, Joan; Nunes, Rafael C.

2017-03-01

We compute the time variation of the fundamental constants (such as the ratio of the proton mass to the electron mass, the strong coupling constant, the fine-structure constant and Newton's constant) within the context of the so-called running vacuum models (RVMs) of the cosmic evolution. Recently, compelling evidence has been provided that these models are able to fit the main cosmological data (SNIa+BAO+H(z)+LSS+BBN+CMB) significantly better than the concordance Λ CDM model. Specifically, the vacuum parameters of the RVM (i.e. those responsible for the dynamics of the vacuum energy) prove to be nonzero at a confidence level ≳ 3σ . Here we use such remarkable status of the RVMs to make definite predictions on the cosmic time variation of the fundamental constants. It turns out that the predicted variations are close to the present observational limits. Furthermore, we find that the time evolution of the dark matter particle masses should be crucially involved in the total mass variation of our Universe. A positive measurement of this kind of effects could be interpreted as strong support to the "micro-macro connection" (viz. the dynamical feedback between the evolution of the cosmological parameters and the time variation of the fundamental constants of the microscopic world), previously proposed by two of us (HF and JS).

Revisiting Darwin's hypothesis: Does greater intraspecific variability increase species' ecological breadth?

PubMed

Sides, Colby B; Enquist, Brian J; Ebersole, James J; Smith, Marielle N; Henderson, Amanda N; Sloat, Lindsey L

2014-01-01

Darwin first proposed that species with larger ecological breadth have greater phenotypic variation. We tested this hypothesis by comparing intraspecific variation in specific leaf area (SLA) to species' local elevational range and by assessing how external (abiotic) filters may influence observed differences in ecological breadth among species. Understanding the patterns of individual variation within and between populations will help evaluate differing hypotheses for structuring of communities and distribution of species. We selected 21 species with varying elevational ranges and compared the coefficient of variation of SLA for each species against its local elevational range. We examined the influence of external filters on local trait composition by determining if intraspecific changes in SLA with elevation have the same direction and similar rates of change as the change in community mean SLA value. In support of Darwin's hypothesis, we found a positive relationship between species' coefficient of variation for SLA with species' local elevational range. Intraspecific changes in SLA had the same sign, but generally lower magnitude than the community mean SLA. The results indicate that wide-ranging species are indeed characterized by greater intraspecific variation and that species' phenotypes shift along environmental gradients in the same direction as the community phenotypes. However, across species, the rate of intraspecific trait change, reflecting plastic and/or adaptive changes across populations, is limited and prevents species from adjusting to environmental gradients as quickly as interspecific changes resulting from community assembly.

Multi-fingered haptic palpation utilizing granular jamming stiffness feedback actuators

NASA Astrophysics Data System (ADS)

Li, Min; Ranzani, Tommaso; Sareh, Sina; Seneviratne, Lakmal D.; Dasgupta, Prokar; Wurdemann, Helge A.; Althoefer, Kaspar

2014-09-01

This paper describes a multi-fingered haptic palpation method using stiffness feedback actuators for simulating tissue palpation procedures in traditional and in robot-assisted minimally invasive surgery. Soft tissue stiffness is simulated by changing the stiffness property of the actuator during palpation. For the first time, granular jamming and pneumatic air actuation are combined to realize stiffness modulation. The stiffness feedback actuator is validated by stiffness measurements in indentation tests and through stiffness discrimination based on a user study. According to the indentation test results, the introduction of a pneumatic chamber to granular jamming can amplify the stiffness variation range and reduce hysteresis of the actuator. The advantage of multi-fingered palpation using the proposed actuators is proven by the comparison of the results of the stiffness discrimination performance using two-fingered (sensitivity: 82.2%, specificity: 88.9%, positive predicative value: 80.0%, accuracy: 85.4%, time: 4.84 s) and single-fingered (sensitivity: 76.4%, specificity: 85.7%, positive predicative value: 75.3%, accuracy: 81.8%, time: 7.48 s) stiffness feedback.

Position-specific 13C distributions within propane from experiments and natural gas samples

NASA Astrophysics Data System (ADS)

Piasecki, Alison; Sessions, Alex; Lawson, Michael; Ferreira, A. A.; Santos Neto, E. V.; Ellis, Geoffrey S.; Lewan, Michael D.; Eiler, John M.

2018-01-01

Site-specific carbon isotope measurements of organic compounds potentially recover information that is lost in a conventional, 'bulk' isotopic analysis. Such measurements are useful because isotopically fractionating processes may have distinct effects at different molecular sites, and thermodynamically equilibrated populations of molecules tend to concentrate heavy isotopes in one molecular site versus another. Most recent studies of site-specific 13C in organics use specialized Nuclear Magnetic Resonance (NMR) techniques or complex chemical degradations prior to mass spectrometric measurements. Herein we present the first application of a new mass spectrometric technique that reconstructs the site-specific carbon isotope composition of propane based on measurements of the 13C/12C ratios of two or more fragment ions that sample different proportions of the terminal and central carbon sites. We apply this method to propane from laboratory experiments and natural gas samples to explore the relationships between site-specific carbon isotope composition, full-molecular δ13C, thermal maturity, and variation in organic matter precursors. Our goal is to advance the understanding of the sources and histories of short-chain alkanes within geologic systems. Our findings suggest that propane varies in its site-specific carbon isotope structure, which is correlated with increasing thermal maturity, first increasing in terminal position δ13C and then increasing in both center and terminal position δ13C. This pattern is observed in both experimental and natural samples, and is plausibly explained by a combination of site-specific, temperature-dependent isotope effects associated with conversion of different precursor molecules (kerogen, bitumen, and/or oil) to propane, differences in site-specific isotopic contents of those precursors, and possibly distillation of reactive components of those precursors with increasing maturity. We hypothesize that the largest changes in site-specific isotopic content of propane occur when bitumen and/or oil replace kerogen as the dominant precursors. If correct, this phenomenon could have significant utility for understanding gas generation in thermogenic petroleum systems.

Position-specific 13C distributions within propane from experiments and natural gas samples

USGS Publications Warehouse

Piasecki, Alison; Sessions, Alex L.; Lawson, Michael; Ferreira, A.A.; Santos Neto, E. V.; Ellis, Geoffrey S.; Lewan, Michael; Eilers, J.M.

2018-01-01

Site-specific carbon isotope measurements of organic compounds potentially recover information that is lost in a conventional, ‘bulk’ isotopic analysis. Such measurements are useful because isotopically fractionating processes may have distinct effects at different molecular sites, and thermodynamically equilibrated populations of molecules tend to concentrate heavy isotopes in one molecular site versus another. Most recent studies of site-specific 13C in organics use specialized Nuclear Magnetic Resonance (NMR) techniques or complex chemical degradations prior to mass spectrometric measurements. Herein we present the first application of a new mass spectrometric technique that reconstructs the site-specific carbon isotope composition of propane based on measurements of the 13C/12C ratios of two or more fragment ions that sample different proportions of the terminal and central carbon sites. We apply this method to propane from laboratory experiments and natural gas samples to explore the relationships between site-specific carbon isotope composition, full-molecular δ13C, thermal maturity, and variation in organic matter precursors. Our goal is to advance the understanding of the sources and histories of short-chain alkanes within geologic systems. Our findings suggest that propane varies in its site-specific carbon isotope structure, which is correlated with increasing thermal maturity, first increasing in terminal position δ13C and then increasing in both center and terminal position δ13C. This pattern is observed in both experimental and natural samples, and is plausibly explained by a combination of site-specific, temperature-dependent isotope effects associated with conversion of different precursor molecules (kerogen, bitumen, and/or oil) to propane, differences in site-specific isotopic contents of those precursors, and possibly distillation of reactive components of those precursors with increasing maturity. We hypothesize that the largest changes in site-specific isotopic content of propane occur when bitumen and/or oil replace kerogen as the dominant precursors. If correct, this phenomenon could have significant utility for understanding gas generation in thermogenic petroleum systems.

Accuracy of FDG-PET to diagnose lung cancer in a region of endemic granulomatous disease.

PubMed

Deppen, Stephen; Putnam, Joe B; Andrade, Gabriela; Speroff, Theodore; Nesbitt, Jonathan C; Lambright, Eric S; Massion, Pierre P; Walker, Ron; Grogan, Eric L

2011-08-01

The 18 F-fluorodeoxyglucose-positron emission tomography (FDG-PET) is used to evaluate suspicious pulmonary lesions due to its diagnostic accuracy. The southeastern United States has a high prevalence of infectious granulomatous lung disease, and the accuracy of FDG-PET may be reduced in this population. We examined the diagnostic accuracy of FDG-PET in patients with known or suspected non-small cell lung cancer treated at our institution. A total of 279 patients, identified through our prospective database, underwent an operation for known or suspected lung cancer. Preoperative FDG-PET in 211 eligible patients was defined by standardized uptake value greater than 2.5 or by description ("moderate" or "intense") as avid. Sensitivity, specificity, positive and negative predictive values, likelihood ratios, and decision diagrams were calculated for FDG-PET in all patients and in patients with indeterminate nodules. In all eligible patients (n=211), sensitivity and specificity of FDG-PET were 92% and 40%, respectively. Positive and negative predictive values were 86% and 55%. Overall FDG-PET accuracy to diagnose lung cancer was 81%. Preoperative positive likelihood ratio for FDG-PET diagnosis of lung cancer in this population was 1.5 compared with previously published values of 7.1. In 113 indeterminate lesions, 65% had lung cancer and the sensitivity and specificity were 89% and 40%, respectively. Twenty-four benign nodules (60%) had false positive FDG-PET scans. Twenty-two of 43 benign nodules (51%) were granulomas. In a region with endemic granulomatous diseases, the specificity of FDG-PET for diagnosis of lung cancer was 40%. Clinical decisions and future clinical predictive models for lung cancer must accommodate regional variation of FDG-PET scan results. Copyright © 2011 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

A survey of the population genetic variation in the human kinome.

PubMed

Zhang, Wei; Catenacci, Daniel V T; Duan, Shiwei; Ratain, Mark J

2009-08-01

Protein kinases are key regulators of various biological processes, such as control of cell growth, metabolism, differentiation and apoptosis. Therefore, protein kinases have been an important class of targets for anticancer drugs. Health-related disparities such as differential drug response have been observed between human populations. A survey of the human kinases and their ligand genes for those containing population-specific genetic variants could provide new insights into the mechanisms of these health disparities and suggest novel targets for ethnicity-specific personalized medicine. Using the International HapMap Project genotypic data on single-nucleotide polymorphisms (SNPs), the protein kinase complement of the human genome (kinome) and some experimentally verified ligand genes were scanned for the existence of population-specific SNPs (eSNPs). In general, protein kinases were found to contain a much higher proportion of eSNPs than the whole genome background, indicating a stronger pressure for adaptation in individual populations. In contrast, the proportion of ligand genes containing eSNPs was not different from that of the whole genome background. Although with some important limitations, our results suggest that human kinases are more likely to be under recent positive selection than ligands. Our findings suggest that the health-related disparities associated with kinase signaling pathways are more likely to be driven by the genetic variation in the kinase genes than their cognate ligands. Illustrating the role of molecular evolution in the genetic variation of the human kinome could provide a promising route to understand the ethnic differences in cancer and facilitate the realization of ethnicity-based individualized medicine.

Adaptive diversification of growth allometry in the plant Arabidopsis thaliana.

PubMed

Vasseur, François; Exposito-Alonso, Moises; Ayala-Garay, Oscar J; Wang, George; Enquist, Brian J; Vile, Denis; Violle, Cyrille; Weigel, Detlef

2018-03-27

Seed plants vary tremendously in size and morphology; however, variation and covariation in plant traits may be governed, at least in part, by universal biophysical laws and biological constants. Metabolic scaling theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near-constant allometric scaling exponents across species. However, the observed variation in scaling exponents calls into question the evolutionary drivers and the universality of allometric equations. We have measured growth scaling and fitness traits of 451 Arabidopsis thaliana accessions with sequenced genomes. Variation among accessions around the scaling exponent predicted by MST was correlated with relative growth rate, seed production, and stress resistance. Genomic analyses indicate that growth allometry is affected by many genes associated with local climate and abiotic stress response. The gene with the strongest effect, PUB4 , has molecular signatures of balancing selection, suggesting that intraspecific variation in growth scaling is maintained by opposing selection on the trade-off between seed production and abiotic stress resistance. Our findings suggest that variation in allometry contributes to local adaptation to contrasting environments. Our results help reconcile past debates on the origin of allometric scaling in biology and begin to link adaptive variation in allometric scaling to specific genes. Copyright © 2018 the Author(s). Published by PNAS.

Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

PubMed Central

Vasseur, François; Ayala-Garay, Oscar J.; Wang, George; Enquist, Brian J.; Vile, Denis; Violle, Cyrille

2018-01-01

Seed plants vary tremendously in size and morphology; however, variation and covariation in plant traits may be governed, at least in part, by universal biophysical laws and biological constants. Metabolic scaling theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near-constant allometric scaling exponents across species. However, the observed variation in scaling exponents calls into question the evolutionary drivers and the universality of allometric equations. We have measured growth scaling and fitness traits of 451 Arabidopsis thaliana accessions with sequenced genomes. Variation among accessions around the scaling exponent predicted by MST was correlated with relative growth rate, seed production, and stress resistance. Genomic analyses indicate that growth allometry is affected by many genes associated with local climate and abiotic stress response. The gene with the strongest effect, PUB4, has molecular signatures of balancing selection, suggesting that intraspecific variation in growth scaling is maintained by opposing selection on the trade-off between seed production and abiotic stress resistance. Our findings suggest that variation in allometry contributes to local adaptation to contrasting environments. Our results help reconcile past debates on the origin of allometric scaling in biology and begin to link adaptive variation in allometric scaling to specific genes. PMID:29540570

The microgeographical patterns of morphological and molecular variation of a mixed ploidy population in the species complex Actinidia chinensis.

PubMed

Liu, Yifei; Li, Dawei; Yan, Ling; Huang, Hongwen

2015-01-01

Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches.

Lateralization of infant holding by mothers: A longitudinal evaluation of variations over the first 12 weeks.

PubMed

Todd, Brenda K; Banerjee, Robin

2016-01-01

The maternal preference to hold infants on the left rather than right side of the body was examined longitudinally, with attention to 4 explanations: maternal monitoring of infant state, maternal handedness, infant proximity to the mother's heartbeat, and preferred infant head position. The side and site of holding were measured over the first 12 weeks of the lives of 24 infants. Information about group and individual consistency in holding side allowed novel evaluation of the theories. A strong bias to hold on the left dropped below significance when the infants were aged 12 weeks and was limited to specific holding positions. Findings were generally consistent with the monitoring hypothesis, and little support was found for the 3 alternative explanations.

Stratification based on reproductive state reveals contrasting patterns of age-related variation in demographic parameters in the kittiwake

USGS Publications Warehouse

Cam, E.; Monnat, J.-Y.

2000-01-01

Heterogeneity in individual quality can be a major obstacle when interpreting age-specific variation in life-history traits. Heterogeneity is likely to lead to within-generation selection, and patterns observed at the population level may result from the combination of hidden patterns specific to subpopulations. Population-level patterns are not relevant to hypotheses concerning the evolution of age-specific reproductive strategies if they differ from patterns at the individual level. We addressed the influence of age and a variable used as a surrogate of quality (yearly reproductive state) on survival and breeding probability in the kittiwake. We found evidence of an effect of age and quality on both demographic parameters. Patterns observed in breeders are consistent with the selection hypothesis, which predicts age-related increases in survival and traits positively correlated with survival. Our results also reveal unexpected age effects specific to subgroups: the influence of age on survival and future breeding probability is not the same in nonbreeders and breeders. These patterns are observed in higher-quality breeding habitats, where the influence of extrinsic factors on breeding state is the weakest. Moreover, there is slight evidence of an influence of sex on breeding probability (not on survival), but the same overall pattern is observed in both sexes. Our results support the hypothesis that age-related variation in demographic parameters observed at the population level is partly shaped by heterogeneity among individuals. They also suggest processes specific to subpopulations. Recent theoreticaI developments lay emphasis on integration of sources of heterogeneity in optimization models to account for apparently 'sub-optimal' empirical patterns. Incorporation of sources of heterogeneity is also the key to investigation of age-related reproductive strategies in heterogeneous populations. Thwarting 'heterogeneity's ruses' has become a major challenge: for detecting and understanding natural processes, and a constructive confrontation between empirical and theoretical studies.

When your face describes your memories: facial expressions during retrieval of autobiographical memories.

PubMed

El Haj, Mohamad; Daoudi, Mohamed; Gallouj, Karim; Moustafa, Ahmed A; Nandrino, Jean-Louis

2018-05-11

Thanks to the current advances in the software analysis of facial expressions, there is a burgeoning interest in understanding emotional facial expressions observed during the retrieval of autobiographical memories. This review describes the research on facial expressions during autobiographical retrieval showing distinct emotional facial expressions according to the characteristics of retrieved memoires. More specifically, this research demonstrates that the retrieval of emotional memories can trigger corresponding emotional facial expressions (e.g. positive memories may trigger positive facial expressions). Also, this study demonstrates the variations of facial expressions according to specificity, self-relevance, or past versus future direction of memory construction. Besides linking research on facial expressions during autobiographical retrieval to cognitive and affective characteristics of autobiographical memory in general, this review positions this research within the broader context research on the physiologic characteristics of autobiographical retrieval. We also provide several perspectives for clinical studies to investigate facial expressions in populations with deficits in autobiographical memory (e.g. whether autobiographical overgenerality in neurologic and psychiatric populations may trigger few emotional facial expressions). In sum, this review paper demonstrates how the evaluation of facial expressions during autobiographical retrieval may help understand the functioning and dysfunctioning of autobiographical memory.

Interleukin (IL)-1A and IL-6: Applications to the predictive diagnostic testing of radiation pneumonitis

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

Chen Yuhchyau; Hyrien, Ollivier; Williams, Jacqueline

2005-05-01

Purpose: To explore the application of interleukin (IL)-1{alpha} and IL-6 measurements in the predictive diagnostic testing for symptomatic radiation pneumonitis (RP). Methods and materials: In a prospective protocol investigating RP and cytokines, IL-1{alpha} and IL-6 values were analyzed by enzyme-linked immunosorbent assay from serial weekly blood samples of patients receiving chest radiation. We analyzed sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) over selected threshold values for both cytokines in the application to diagnostic testing. Results: The average coefficient of variation was 51% of the weekly mean IL-1{alpha} level and 39% of the weekly mean IL-6 value.more » Interleukin 1{alpha} and IL-6 became positively correlated with time. Specificity for both cytokines was better than sensitivity. IL-6 globally outperformed IL-1{alpha} in predicting RP, with higher PPV and NPV. Conclusions: Our data demonstrate the feasibility of applying IL-1{alpha} and IL-6 measurements of blood specimens to predict RP. Interleukin-6 measurements offer stronger positive predictive value than IL-1{alpha}. This application might be further explored in a larger sample of patients.« less

Medical audit of rectal biopsy diagnosis of inflammatory bowel disease.

PubMed

Frei, J V; Morson, B C

1982-03-01

The records of the rectal biopsy diagnoses of ulcerative colitis and Crohn's disease in the Department of Pathology, St Mark's Hospital, London, were reviewed. The biopsy diagnoses were compared to subsequent resection diagnoses on the same patients, and annual and seasonal variations in the frequency of these and related diagnoses were studied. The accuracy rate for the biopsy diagnosis of ulcerative colitis was about 70% and for Crohn's disease about 40% each time a biopsy was read. The low figure for the accuracy rate for Crohn's disease could be attributed to sampling error inherent in the diagnosis of a disease which is essentially patchy, showing discontinuous pathology. Also, many patients with Crohn's disease have a normal rectum which is biopsied to demonstrate the distinction from ulcerative colitis. In practical terms therefore a 40% accuracy rate in Crohn's disease is probably adequate. The rate of "false-positive" diagnoses was about 5%. There was a seasonal variation in the frequency of these two diagnoses, but no variation attributable to changes in observers, as pathology trainees in the Department change regularly. The frequency of diagnoses of non-specific inflammation and of normal colon did show such non-random variations.

Voltage contrast X-ray photoelectron spectroscopy reveals graphene-substrate interaction in graphene devices fabricated on the C- and Si- faces of SiC

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

Aydogan, Pinar; Suzer, Sefik, E-mail: suzer@fen.bilkent.edu.tr; Arslan, Engin

2015-09-21

We report on an X-ray photoelectron spectroscopy (XPS) study of two graphene based devices that were analyzed by imposing a significant current under +3 V bias. The devices were fabricated as graphene layers(s) on hexagonal SiC substrates, either on the C- or Si-terminated faces. Position dependent potential distributions (IR-drop), as measured by variations in the binding energy of a C1s peak are observed to be sporadic for the C-face graphene sample, but very smooth for the Si-face one, although the latter is less conductive. We attribute these sporadic variations in the C-face device to the incomplete electrical decoupling between the graphenemore » layer(s) with the underlying buffer and/or substrate layers. Variations in the Si2p and O1s peaks of the underlayer(s) shed further light into the electrical interaction between graphene and other layers. Since the potential variations are amplified only under applied bias (voltage-contrast), our methodology gives unique, chemically specific electrical information that is difficult to obtain by other techniques.« less

Evolutionary potential of upper thermal tolerance: biogeographic patterns and expectations under climate change.

PubMed

Diamond, Sarah E

2017-02-01

How will organisms respond to climate change? The rapid changes in global climate are expected to impose strong directional selection on fitness-related traits. A major open question then is the potential for adaptive evolutionary change under these shifting climates. At the most basic level, evolutionary change requires the presence of heritable variation and natural selection. Because organismal tolerances of high temperature place an upper bound on responding to temperature change, there has been a surge of research effort on the evolutionary potential of upper thermal tolerance traits. Here, I review the available evidence on heritable variation in upper thermal tolerance traits, adopting a biogeographic perspective to understand how heritability of tolerance varies across space. Specifically, I use meta-analytical models to explore the relationship between upper thermal tolerance heritability and environmental variability in temperature. I also explore how variation in the methods used to obtain these thermal tolerance heritabilities influences the estimation of heritable variation in tolerance. I conclude by discussing the implications of a positive relationship between thermal tolerance heritability and environmental variability in temperature and how this might influence responses to future changes in climate. © 2016 New York Academy of Sciences.

Detection of autoantibodies to 3-hydroxy-3-methylglutaryl-coenzyme a reductase by ELISA in a reference laboratory setting.

PubMed

Jaskowski, Troy D; La'ulu, Sonia L; Mahler, Michael; Tebo, Anne E

2017-09-01

We investigated the performance of an ELISA for the detection of 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGCR) IgG antibodies in immune-mediated necrotizing myopathies (IMNM). Patients positive for HMGCR antibodies (n=61) or negative (n=78) by protein immunoprecipitation (IP), and healthy controls (n=100) were used to evaluate the ELISA. Unique consecutive serum samples (n=155) received at ARUP Laboratories for HMGCR IgG testing by ELISA were also investigated and analysed for serum muscle enzymes (aldolase, creatine kinase, and myoglobin). The ELISA's sensitivity, specificity, and percentage agreement were assessed relative to IP. Correlation between specific muscle enzyme concentration and the presence of HMGCR antibody was determined. Overall agreement between ELISA and IP was 93.4%. Using the IP as reference, the sensitivity and specificity of the ELISA was 95.1%, and 100%, respectively. Inter- and intra-assay coefficient of variation of the ELISA was <10.0%, and ≤15.0%, respectively. In the consecutive cohort, 21 (13.6%) samples tested positive for HMGCR IgG. Concentrations of aldolase, creatine kinase, and myoglobin were significantly higher (all p<0.0001) in patients positive for HMGCR antibodies at the time of evaluation. We confirm significant reliability of HMGCR antibodies as measured by the ELISA for the evaluation of IMNM. Copyright © 2017 Elsevier B.V. All rights reserved.

Common themes and cell type specific variations of higher order chromatin arrangements in the mouse

PubMed Central

Mayer, Robert; Brero, Alessandro; von Hase, Johann; Schroeder, Timm; Cremer, Thomas; Dietzel, Steffen

2005-01-01

Background Similarities as well as differences in higher order chromatin arrangements of human cell types were previously reported. For an evolutionary comparison, we now studied the arrangements of chromosome territories and centromere regions in six mouse cell types (lymphocytes, embryonic stem cells, macrophages, fibroblasts, myoblasts and myotubes) with fluorescence in situ hybridization and confocal laser scanning microscopy. Both species evolved pronounced differences in karyotypes after their last common ancestors lived about 87 million years ago and thus seem particularly suited to elucidate common and cell type specific themes of higher order chromatin arrangements in mammals. Results All mouse cell types showed non-random correlations of radial chromosome territory positions with gene density as well as with chromosome size. The distribution of chromosome territories and pericentromeric heterochromatin changed during differentiation, leading to distinct cell type specific distribution patterns. We exclude a strict dependence of these differences on nuclear shape. Positional differences in mouse cell nuclei were less pronounced compared to human cell nuclei in agreement with smaller differences in chromosome size and gene density. Notably, the position of chromosome territories relative to each other was very variable. Conclusion Chromosome territory arrangements according to chromosome size and gene density provide common, evolutionary conserved themes in both, human and mouse cell types. Our findings are incompatible with a previously reported model of parental genome separation. PMID:16336643

Climate, soil and plant functional types as drivers of global fine-root trait variation

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

Freschet, Grégoire T.; Valverde-Barrantes, Oscar J.; Tucker, Caroline M.

Ecosystem functioning relies heavily on below-ground processes, which are largely regulated by plant fine-roots and their functional traits. However, our knowledge of fine-root trait distribution relies to date on local- and regional-scale studies with limited numbers of species, growth forms and environmental variation. We compiled a world-wide fine-root trait dataset, featuring 1115 species from contrasting climatic areas, phylogeny and growth forms to test a series of hypotheses pertaining to the influence of plant functional types, soil and climate variables, and the degree of manipulation of plant growing conditions on species fine-root trait variation. Most particularly, we tested the competing hypothesesmore » that fine-root traits typical of faster return on investment would be most strongly associated with conditions of limiting versus favourable soil resource availability. We accounted for both data source and species phylogenetic relatedness. We demonstrate that: (i) Climate conditions promoting soil fertility relate negatively to fine-root traits favouring fast soil resource acquisition, with a particularly strong positive effect of temperature on fine-root diameter and negative effect on specific root length (SRL), and a negative effect of rainfall on root nitrogen concentration; (ii) Soil bulk density strongly influences species fine-root morphology, by favouring thicker, denser fine-roots; (iii) Fine-roots from herbaceous species are on average finer and have higher SRL than those of woody species, and N 2-fixing capacity positively relates to root nitrogen; and (iv) Plants growing in pots have higher SRL than those grown in the field. Synthesis. This study reveals both the large variation in fine-root traits encountered globally and the relevance of several key plant functional types and soil and climate variables for explaining a substantial part of this variation. Climate, particularly temperature, and plant functional types were the two strongest predictors of fine-root trait variation. High trait variation occurred at local scales, suggesting that wide-ranging below-ground resource economics strategies are viable within most climatic areas and soil conditions.« less

Climate, soil and plant functional types as drivers of global fine-root trait variation

DOE PAGES

Freschet, Grégoire T.; Valverde-Barrantes, Oscar J.; Tucker, Caroline M.; ...

2017-03-08

Ecosystem functioning relies heavily on below-ground processes, which are largely regulated by plant fine-roots and their functional traits. However, our knowledge of fine-root trait distribution relies to date on local- and regional-scale studies with limited numbers of species, growth forms and environmental variation. We compiled a world-wide fine-root trait dataset, featuring 1115 species from contrasting climatic areas, phylogeny and growth forms to test a series of hypotheses pertaining to the influence of plant functional types, soil and climate variables, and the degree of manipulation of plant growing conditions on species fine-root trait variation. Most particularly, we tested the competing hypothesesmore » that fine-root traits typical of faster return on investment would be most strongly associated with conditions of limiting versus favourable soil resource availability. We accounted for both data source and species phylogenetic relatedness. We demonstrate that: (i) Climate conditions promoting soil fertility relate negatively to fine-root traits favouring fast soil resource acquisition, with a particularly strong positive effect of temperature on fine-root diameter and negative effect on specific root length (SRL), and a negative effect of rainfall on root nitrogen concentration; (ii) Soil bulk density strongly influences species fine-root morphology, by favouring thicker, denser fine-roots; (iii) Fine-roots from herbaceous species are on average finer and have higher SRL than those of woody species, and N 2-fixing capacity positively relates to root nitrogen; and (iv) Plants growing in pots have higher SRL than those grown in the field. Synthesis. This study reveals both the large variation in fine-root traits encountered globally and the relevance of several key plant functional types and soil and climate variables for explaining a substantial part of this variation. Climate, particularly temperature, and plant functional types were the two strongest predictors of fine-root trait variation. High trait variation occurred at local scales, suggesting that wide-ranging below-ground resource economics strategies are viable within most climatic areas and soil conditions.« less

Seasonal and spatial community dynamics in the meromictic Lake Cadagno.

PubMed

Bosshard, P P; Stettler, R; Bachofen, R

2000-09-01

The seasonal and spatial variations in the community structure of bacterioplankton in the meromictic alpine Lake Cadagno were examined by temporal temperature gradient gel electrophoresis (TTGE) of PCR-amplified 16S rDNA fragments. Two different amplifications were performed, one specific for the domain Bacteria (Escherichia coli positions 8-536) and another specific for the family Chromatiaceae (E. coli positions 8-1005). The latter was followed by semi-nested reamplification with the bacterial primer set, allowing comparison of the two PCR approaches by TTGE. The TTGE patterns of samples from the chemocline and the anoxic monimolimnion were essentially identical, whereas the oxic mixolimnion displayed distinctively different banding patterns. For samples from the chemocline and the monimolimnion, dominant bands in the Bacteria-specific TTGE profiles comigrated with bands obtained by the semi-nested PCR approach specific for Chromatiaceae. This observation suggested that Chromatiaceae are in high abundance in the anoxic water layer. All dominant bands were excised and sequenced. Changes in the community structure, as indicated by changes in the TTGE profiles, were observed in samples taken at different times of the year. In the chemocline, Chomatium okenii was dominant in the summer months, whereas Amoebobacter purpureus populations dominated in autumn and winter. This change was confirmed by fluorescent in situ hybridization.

Human Facial Shape and Size Heritability and Genetic Correlations.

PubMed

Cole, Joanne B; Manyama, Mange; Larson, Jacinda R; Liberton, Denise K; Ferrara, Tracey M; Riccardi, Sheri L; Li, Mao; Mio, Washington; Klein, Ophir D; Santorico, Stephanie A; Hallgrímsson, Benedikt; Spritz, Richard A

2017-02-01

The human face is an array of variable physical features that together make each of us unique and distinguishable. Striking familial facial similarities underscore a genetic component, but little is known of the genes that underlie facial shape differences. Numerous studies have estimated facial shape heritability using various methods. Here, we used advanced three-dimensional imaging technology and quantitative human genetics analysis to estimate narrow-sense heritability, heritability explained by common genetic variation, and pairwise genetic correlations of 38 measures of facial shape and size in normal African Bantu children from Tanzania. Specifically, we fit a linear mixed model of genetic relatedness between close and distant relatives to jointly estimate variance components that correspond to heritability explained by genome-wide common genetic variation and variance explained by uncaptured genetic variation, the sum representing total narrow-sense heritability. Our significant estimates for narrow-sense heritability of specific facial traits range from 28 to 67%, with horizontal measures being slightly more heritable than vertical or depth measures. Furthermore, for over half of facial traits, >90% of narrow-sense heritability can be explained by common genetic variation. We also find high absolute genetic correlation between most traits, indicating large overlap in underlying genetic loci. Not surprisingly, traits measured in the same physical orientation (i.e., both horizontal or both vertical) have high positive genetic correlations, whereas traits in opposite orientations have high negative correlations. The complex genetic architecture of facial shape informs our understanding of the intricate relationships among different facial features as well as overall facial development. Copyright © 2017 by the Genetics Society of America.

SNP in Chalcone Synthase gene is associated with variation of 6-gingerol content in contrasting landraces of Zingiber officinale.Roscoe.

PubMed

Ghosh, Subhabrata; Mandi, Swati Sen

2015-07-25

Zingiber officinale, medicinally the most important species within Zingiber genus, contains 6-gingerol as the active principle. This compound obtained from rhizomes of Z.officinale, has immense medicinal importance and is used in various herbal drug formulations. Our record of variation in content of this active principle, viz. 6-gingerol, in land races of this drug plant collected from different locations correlated with our Gene expression studies exhibiting high Chalcone Synthase gene (Chalcone Synthase is the rate limiting enzyme of 6-gingerol biosynthesis pathway) expression in high 6-gingerol containing landraces than in the low 6-gingerol containing landraces. Sequencing of Chalcone Synthase cDNA and subsequent multiple sequence alignment revealed seven SNPs between these contrasting genotypes. Converting this nucleotide sequence to amino acid sequence, alteration of two amino acids becomes evident; one amino acid change (asparagine to serine at position 336) is associated with base change (A→G) and another change (serine to leucine at position 142) is associated with the base change (C→T). Since asparagine at position 336 is one of the critical amino acids of the catalytic triad of Chalcone Synthase enzyme, responsible for substrate binding, our study suggests that landraces with a specific amino acid change viz. Asparagine (found in high 6-gingerol containing landraces) to serine causes low 6-gingerol content. This is probably due to a weak enzyme substrate association caused by the absence of asparagine in the catalytic triad. Detailed study of this finding could also help to understand molecular mechanism associated with variation in 6-gingerol content in Z.officinale genotypes and thereby strategies for developing elite genotypes containing high 6-gingerol content. Copyright © 2015 Elsevier B.V. All rights reserved.

Evaluation of on-line pyrolysis coupled to isotope ratio mass spectrometry for the determination of position-specific (13)C isotope composition of short chain n-alkanes (C6-C12).

PubMed

Gilbert, Alexis; Yamada, Keita; Yoshida, Naohiro

2016-06-01

We measured (13)C intramolecular isotopic composition of commercially available short-chain hydrocarbons (n-C6-n-C12) using (13)C-NMR. Results show that the main variation is between the terminal and the sub-terminal C-atom positions. Site-preference (difference in δ(13)C values between terminal and sub-terminal C-atom positions) among all the samples varies between -12.2‰ and +8.4‰. Comparison of these results with those obtained using on-line pyrolysis coupled with GC-C-IRMS show that the thermal cracking of hydrocarbons occurs with a good isotopic fidelity between terminal and sub-terminal C-atom positions of the starting material and the related pyrolysis products (methane and ethylene). On-line pyrolysis coupled with GC-C-IRMS can thus be used for tracing hydrocarbons biogeochemical processes. Copyright © 2016 Elsevier B.V. All rights reserved.

Variation of isomer distribution in electrophilic nitration of toluene, anisole, and o-xylene: Independence of high regioselectivity from reactivity of reagent*

PubMed Central

Olah, George A.; Lin, Henry C.; Olah, Judith A.; Narang, Subhash C.

1978-01-01

The nitration of toluene and anisole was studied with nitrating systems of varying reactivity. High regioselectivity of ortho-para over meta substitution was maintained in all nitrations, regardless of the reactivity of the nitrating system. At the same time, the amount of meta substitution stayed low (3% or less), even when the fast reactions may have reached the encounter-controlled limit. Because the nitration of o-xylene, in which both ring positions are activated by the effect of a methyl group, also does not show any diminishing of regioselectivity, the possibility of a dual mechanistic pathway, in which the activated position would react by a fast, encounter-controlled path, whereas the nonactivated meta position by a slower σ-type path, can be ruled out. The data unambiguously prove that the high regioselectivity of electrophilic aromatic nitration is independent of the reactivity of the reagent, because no significant increase of meta substitution of toluene or anisole was observed, regardless of the activity of the nitrating system. No selectivity-reactivity relationship is thus evident and the ortho-para directing effect of primary substituents over meta substitution is always maintained. The variation in the amount of the meta isomer, up to the observed limit of about 3% in the case of toluene and <2% for anisole, is probably significant but, at the present time, cannot be quantitatively evaluated with the ±0.5% overall reproducible accuracy of the nitrations. Steric factors, such as increasing bulkiness of the nitrating agent, also can affect the ortho-para isomer ratios but are not considered to be the only reason for the observed variations, which reflect the specific nitrating systems, affecting the nature and position of the transition state of highest energy on the reaction pathway. PMID:16592489

Genetic variation of pfhrp2 in Plasmodium falciparum isolates from Yemen and the performance of HRP2-based malaria rapid diagnostic test.

PubMed

Atroosh, Wahib M; Al-Mekhlafi, Hesham M; Al-Jasari, Adel; Sady, Hany; Al-Delaimy, Ahmed K; Nasr, Nabil A; Dawaki, Salwa; Abdulsalam, Awatif M; Ithoi, Init; Lau, Yee Ling; Fong, Mun Yik; Surin, Johari

2015-07-22

The genetic variation in the Plasmodium falciparum histidine-rich protein 2 (pfhrp2) gene that may compromise the use of pfhrp2-based rapid diagnostic tests (RDTs) for the diagnosis of malaria was assessed in P. falciparum isolates from Yemen. This study was conducted in Hodeidah and Al-Mahwit governorates, Yemen. A total of 622 individuals with fever were examined for malaria by CareStart malaria HRP2-RDT and Giemsa-stained thin and thick blood films. The Pfhrp2 gene was amplified and sequenced from 180 isolates, and subjected to amino acid repeat types analysis. A total of 188 (30.2%) participants were found positive for P. falciparum by the RDT. Overall, 12 different amino acid repeat types were identified in Yemeni isolates. Six repeat types were detected in all the isolates (100%) namely types 1, 2, 6, 7, 10 and 12 while types 9 and 11 were not detected in any of the isolates. Moreover, the sensitivity and specificity of the used PfHRP2-based RDTs were high (90.5% and 96.1%, respectively). The present study provides data on the genetic variation within the pfhrp2 gene, and its potential impact on the PfHRP2-based RDTs commonly used in Yemen. CareStart Malaria HRP2-based RDT showed high sensitivity and specificity in endemic areas of Yemen.

Functional Roles of Neural Preparatory Processes in a Cued Stroop Task Revealed by Linking Electrophysiology with Behavioral Performance.

PubMed

Wang, Chao; Ding, Mingzhou; Kluger, Benzi M

2015-01-01

It is well established that cuing facilitates behavioral performance and that different aspects of instructional cues evoke specific neural preparatory processes in cued task-switching paradigms. To deduce the functional role of these neural preparatory processes the majority of studies vary aspects of the experimental paradigm and describe how these variations alter markers of neural preparatory processes. Although these studies provide important insights, they also have notable limitations, particularly in terms of understanding the causal or functional relationship of neural markers to cognitive and behavioral processes. In this study, we sought to address these limitations and uncover the functional roles of neural processes by examining how variability in the amplitude of neural preparatory processes predicts behavioral performance to subsequent stimuli. To achieve this objective 16 young adults were recruited to perform a cued Stroop task while their brain activity was measured using high-density electroencephalography. Four temporally overlapping but functionally and topographically distinct cue-triggered event related potentials (ERPs) were identified: 1) A left-frontotemporal negativity (250-700 ms) that was positively associated with word-reading performance; 2) a midline-frontal negativity (450-800 ms) that was positively associated with color-naming and incongruent performance; 3) a left-frontal negativity (450-800 ms) that was positively associated with switch trial performance; and 4) a centroparietal positivity (450-800 ms) that was positively associated with performance for almost all trial types. These results suggest that at least four dissociable cognitive processes are evoked by instructional cues in the present task, including: 1) domain-specific task facilitation; 2) switch-specific task-set reconfiguration; 3) preparation for response conflict; and 4) proactive attentional control. Examining the relationship between ERPs and behavioral performance provides a functional link between neural markers and the cognitive processes they index.

Quantifying the performance of in vivo portal dosimetry in detecting four types of treatment parameter variations

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

Bojechko, C.; Ford, E. C., E-mail: eford@uw.edu

Purpose: To quantify the ability of electronic portal imaging device (EPID) dosimetry used during treatment (in vivo) in detecting variations that can occur in the course of patient treatment. Methods: Images of transmitted radiation from in vivo EPID measurements were converted to a 2D planar dose at isocenter and compared to the treatment planning dose using a prototype software system. Using the treatment planning system (TPS), four different types of variability were modeled: overall dose scaling, shifting the positions of the multileaf collimator (MLC) leaves, shifting of the patient position, and changes in the patient body contour. The gamma passmore » rate was calculated for the modified and unmodified plans and used to construct a receiver operator characteristic (ROC) curve to assess the detectability of the different parameter variations. The detectability is given by the area under the ROC curve (AUC). The TPS was also used to calculate the impact of the variations on the target dose–volume histogram. Results: Nine intensity modulation radiation therapy plans were measured for four different anatomical sites consisting of 70 separate fields. Results show that in vivo EPID dosimetry was most sensitive to variations in the machine output, AUC = 0.70 − 0.94, changes in patient body habitus, AUC = 0.67 − 0.88, and systematic shifts in the MLC bank positions, AUC = 0.59 − 0.82. These deviations are expected to have a relatively small clinical impact [planning target volume (PTV) D{sub 99} change <7%]. Larger variations have even higher detectability. Displacements in the patient’s position and random variations in MLC leaf positions were not readily detectable, AUC < 0.64. The D{sub 99} of the PTV changed by up to 57% for the patient position shifts considered here. Conclusions: In vivo EPID dosimetry is able to detect relatively small variations in overall dose, systematic shifts of the MLC’s, and changes in the patient habitus. Shifts in the patient’s position which can introduce large changes in the target dose coverage were not readily detected.« less

Variation in false-positive rates of mammography reading among 1067 radiologists: a population-based assessment.

PubMed

Tan, Alai; Freeman, Daniel H; Goodwin, James S; Freeman, Jean L

2006-12-01

The accuracy of mammography reading varies among radiologists. We conducted a population-based assessment on radiologist variation in false- positive rates of screening mammography and its associated radiologist characteristics. About 27,394 screening mammograms interpreted by 1067 radiologists were identified from a 5% non-cancer sample of Medicare claims during 1998-1999. The data were linked to the American Medical Association Masterfile to obtain radiologist characteristics. Multilevel logistic regression models were used to examine the radiologist variation in false-positive rates of screening mammography and the associated radiologist characteristics. Radiologists varied substantially in the false-positive rates of screening mammography (ranging from 1.5 to 24.1%, adjusting for patient characteristics). A longer time period since graduation is associated with lower false-positive rates (odds ratio [OR] for every 10 years increase: 0.87, 95% Confidence Interval [CI], 0.81-0.94) and female radiologists had higher false-positive rates than male radiologists (OR = 1.25, 95% CI, 1.05-1.49), adjusting for patient and other radiologist characteristics. The unmeasured factors contributed to about 90% of the between-radiologist variance. Radiologists varied greatly in accuracy of mammography reading. Female and more recently trained radiologists had higher false-positive rates. The variation among radiologists was largely due to unmeasured factors, especially unmeasured radiologist factors. If our results are confirmed in further studies, they suggest that system-level interventions would be required to reduce variation in mammography interpretation.

Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

PubMed Central

Juul, Malene; Bertl, Johanna; Guo, Qianyun; Nielsen, Morten Muhlig; Świtnicki, Michał; Hornshøj, Henrik; Madsen, Tobias; Hobolth, Asger; Pedersen, Jakob Skou

2017-01-01

Non-coding mutations may drive cancer development. Statistical detection of non-coding driver regions is challenged by a varying mutation rate and uncertainty of functional impact. Here, we develop a statistically founded non-coding driver-detection method, ncdDetect, which includes sample-specific mutational signatures, long-range mutation rate variation, and position-specific impact measures. Using ncdDetect, we screened non-coding regulatory regions of protein-coding genes across a pan-cancer set of whole-genomes (n = 505), which top-ranked known drivers and identified new candidates. For individual candidates, presence of non-coding mutations associates with altered expression or decreased patient survival across an independent pan-cancer sample set (n = 5454). This includes an antigen-presenting gene (CD1A), where 5’UTR mutations correlate significantly with decreased survival in melanoma. Additionally, mutations in a base-excision-repair gene (SMUG1) correlate with a C-to-T mutational-signature. Overall, we find that a rich model of mutational heterogeneity facilitates non-coding driver identification and integrative analysis points to candidates of potential clinical relevance. DOI: http://dx.doi.org/10.7554/eLife.21778.001 PMID:28362259

Development and validation of a real-time PCR assay for the detection of Toxoplasma gondii DNA in animal and meat samples.

PubMed

Marino, Anna Maria Fausta; Percipalle, Maurizio; Giunta, Renato Paolo; Salvaggio, Antonio; Caracappa, Giulia; Alfonzetti, Tiziana; Aparo, Alessandra; Reale, Stefano

2017-03-01

We report a rapid and reliable method for the detection of Toxoplasma gondii in meat and animal tissues based on real-time polymerase chain reaction (PCR). Samples were collected from cattle, small ruminants, horses, and pigs raised or imported into Sicily, Italy. All DNA preparations were assayed by real-time PCR tests targeted to a 98-bp long fragment in the AF 529-bp repeat element and to the B1 gene using specific primers. Diagnostic sensitivity (100%), diagnostic specificity (100%), limit of detection (0.01 pg), efficiency (92-109%), and precision (mean coefficient of variation = 0.60%), repeatability (100%), reproducibility (100%), and robustness were evaluated using 240 DNA extracted samples (120 positives and 120 negative as per the OIE nested PCR method) from different matrices. Positive results were confirmed by the repetition of both real-time and nested PCR assays. Our study demonstrates the viability of a reliable, rapid, and specific real-time PCR on a large scale to monitor contamination with Toxoplasma cysts in meat and animal specimens. This validated method can be used for postmortem detection in domestic and wild animals and for food safety purposes.

Novel, In-House, SYBR Green Based One-Step rRT-PCR: Rapid and Accurate Diagnosis of Crimean-Congo Hemorrhagic Fever Virus in Suspected Patients From Iran.

PubMed

Zahraei, Bentolhoda; Hashemzadeh, Mohammad Sadegh; Najarasl, Mohammad; Zahiriyeganeh, Samaneh; Tat, Mahdi; Metanat, Maliheh; Sepehri Rad, Nahid; Khansari-Nejad, Behzad; Zafari, Ehsan; Sharti, Mojtaba; Dorostkar, Ruhollah

2016-01-01

The Crimean-Congo hemorrhagic fever (CCHF) virus causes severe disease in humans, with a high mortality rate. Since, there is no approved vaccine or specific treatment for CCHF, an early and accurate diagnosis, as well as reliable surveillance, is essential for case management and patient improvement. For this research, our aim was to evaluate the application of a novel SYBR Green based one-step real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) assay for the in-house diagnosis of the CCHF virus. In this experimental study, the highly conserved S-region sequence of the CCHF viral genome was first adapted from GenBank, and the specific primers targeting this region were designed. Then, the viral RNA was extracted from 75 serum samples from different patients in eastern Iran. The sensitivity and specificity of the primers were also evaluated in positive serum samples previously confirmed to have the CCHF virus, by this one-step rRT-PCR assay, as well as a DNA sequencing analysis. From a total of 75 suspected serum samples, 42 were confirmed to be positive for CCHF virus, with no false-positives detected by the sequencing results. After 40 amplification cycles, the melting curve analysis revealed a mean melting temperature (Tm) of 86.5 ± 0.6°C (quite different from those of the primer-dimers), and the positive samples showed only a small variation in the parameters. In all of the positive samples, the predicted length of 420 bp was confirmed by electrophoresis. Moreover, the sensitivity test showed that this assay can detect less than 20 copies of viral RNA per reaction. This study showed that this novel one-step rRT-PCR assay is a rapid, reliable, repeatable, specific, sensitive, and simple tool for the detection of the CCHF virus.

Flower-level developmental plasticity to nutrient availability in Datura stramonium: implications for the mating system.

PubMed

Camargo, Iván Darío; Nattero, Julieta; Careaga, Sonia A; Núñez-Farfán, Juan

2017-10-17

Studies of phenotypic plasticity in plants have mainly focused on (1) the effect of environmental variation on whole-plant traits related to the number of modules rather than on (2) the phenotypic consequences of environmental variation in traits of individual modules. Since environmental and developmental factors can produce changes in traits related to the mating system, this study used the second approach to investigate whether within-individual variation in herkogamy-related traits is affected by the environment during plant development in two populations of Datura stramonium , an annual herb with a hypothesized persistent mixed mating system, and to determine which morphological traits may promote self-fertilization. Full-sib families of two Mexican populations of D. stramonium , with contrasting ecological histories, were grown under low, mid and high nutrient availability to investigate the effects of genetic, environmental and within-plant flower position on flower size, corolla, stamen and pistil lengths, and herkogamy. Populations showed differences in familial variation, plasticity and familial differences in plasticity in most floral traits analysed. In one population (Ticumán), the effect of flower position on trait variation varied among families, whereas in the other (Pedregal) the effect of flower position interacted with the nutrient environment. Flower size varied with the position of flowers, but in the opposite direction between populations in low nutrients; a systematic within-plant trend of reduction in flower size, pistil length and herkogamy with flower position increased the probability of self-fertilization in the Pedregal population. Besides genetic variation in floral traits between and within populations, environmental variation affects phenotypic floral trait values at the whole-plant level, as well as among flower positions. The interaction between flower position and nutrient environment can affect the plant's mating system, and this differs between populations. Thus, reductions in herkogamy with flower positions may be expected in environments with either low pollinator abundance or low nutrients. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Influence of analytical bias and imprecision on the number of false positive results using Guideline-Driven Medical Decision Limits.

PubMed

Hyltoft Petersen, Per; Klee, George G

2014-03-20

Diagnostic decisions based on decision limits according to medical guidelines are different from the majority of clinical decisions due to the strict dichotomization of patients into diseased and non-diseased. Consequently, the influence of analytical performance is more critical than for other diagnostic decisions where much other information is included. The aim of this opinion paper is to investigate consequences of analytical quality and other circumstances for the outcome of "Guideline-Driven Medical Decision Limits". Effects of analytical bias and imprecision should be investigated separately and analytical quality specifications should be estimated accordingly. Use of sharp decision limits doesn't consider biological variation and effects of this variation are closely connected with the effects of analytical performance. Such relationships are investigated for the guidelines for HbA1c in diagnosis of diabetes and in risk of coronary heart disease based on serum cholesterol. The effects of a second sampling in diagnosis give dramatic reduction in the effects of analytical quality showing minimal influence of imprecision up to 3 to 5% for two independent samplings, whereas the reduction in bias is more moderate and a 2% increase in concentration doubles the percentage of false positive diagnoses, both for HbA1c and cholesterol. An alternative approach comes from the current application of guidelines for follow-up laboratory tests according to clinical procedure orders, e.g. frequency of parathyroid hormone requests as a function of serum calcium concentrations. Here, the specifications for bias can be evaluated from the functional increase in requests for increasing serum calcium concentrations. In consequence of the difficulties with biological variation and the practical utilization of concentration dependence of frequency of follow-up laboratory tests already in use, a kind of probability function for diagnosis as function of the key-analyte is proposed. Copyright © 2013 Elsevier B.V. All rights reserved.

Reprint of "Influence of analytical bias and imprecision on the number of false positive results using Guideline-Driven Medical Decision Limits".

PubMed

Hyltoft Petersen, Per; Klee, George G

2014-05-15

Diagnostic decisions based on decision limits according to medical guidelines are different from the majority of clinical decisions due to the strict dichotomization of patients into diseased and non-diseased. Consequently, the influence of analytical performance is more critical than for other diagnostic decisions where much other information is included. The aim of this opinion paper is to investigate consequences of analytical quality and other circumstances for the outcome of "Guideline-Driven Medical Decision Limits". Effects of analytical bias and imprecision should be investigated separately and analytical quality specifications should be estimated accordingly. Use of sharp decision limits doesn't consider biological variation and effects of this variation are closely connected with the effects of analytical performance. Such relationships are investigated for the guidelines for HbA1c in diagnosis of diabetes and in risk of coronary heart disease based on serum cholesterol. The effects of a second sampling in diagnosis give dramatic reduction in the effects of analytical quality showing minimal influence of imprecision up to 3 to 5% for two independent samplings, whereas the reduction in bias is more moderate and a 2% increase in concentration doubles the percentage of false positive diagnoses, both for HbA1c and cholesterol. An alternative approach comes from the current application of guidelines for follow-up laboratory tests according to clinical procedure orders, e.g. frequency of parathyroid hormone requests as a function of serum calcium concentrations. Here, the specifications for bias can be evaluated from the functional increase in requests for increasing serum calcium concentrations. In consequence of the difficulties with biological variation and the practical utilization of concentration dependence of frequency of follow-up laboratory tests already in use, a kind of probability function for diagnosis as function of the key-analyte is proposed. Copyright © 2014. Published by Elsevier B.V.

Binding of ring-substituted indole-3-acetic acids to human serum albumin.

PubMed

Soskić, Milan; Magnus, Volker

2007-07-01

The plant hormone, indole-3-acetic acid (IAA), and its ring-substituted derivatives have recently attracted attention as promising pro-drugs in cancer therapy. Here we present relative binding constants to human serum albumin for IAA and 34 of its derivatives, as obtained using the immobilized protein bound to a support suitable for high-performance liquid chromatography. We also report their octanol-water partition coefficients (logK(ow)) computed from retention data on a C(18) coated silica gel column. A four-parameter QSPR (quantitative structure-property relationships) model, based on physico-chemical properties, is put forward, which accounts for more than 96% of the variations in the binding affinities of these compounds. The model confirms the importance of lipophilicity as a global parameter governing interaction with serum albumin, but also assigns significant roles to parameters specifically related to the molecular topology of ring-substituted IAAs. Bulky substituents at ring-position 6 increase affinity, those at position 2 obstruct binding, while no steric effects were noted at other ring-positions. Electron-withdrawing substituents at position 5 enhance binding, but have no obvious effect at other ring positions.

Mood, motives, and gambling in young adults: an examination of within- and between-person variations using experience sampling.

PubMed

Goldstein, Abby L; Stewart, Sherry H; Hoaken, Peter N S; Flett, Gordon L

2014-03-01

It is well established that young adults are a population at risk for problem gambling and that young adults gamble for various reasons, including positive mood enhancement and negative mood reduction. Although these motives have been identified as important proximal predictors of gambling, the research to date has focused on between-subjects relationships. What is missing is a process-level understanding of the specific within-subjects relations between mood-regulation motives for gambling, mood states, and gambling behaviors. The current study used experience sampling to assess the specific link between gambling motives, mood states, and gambling behavior. Participants were 108 young adults (ages 19-24 years), who completed baseline measures of gambling motives and gambling problems and then reported on their mood states and gambling behavior three times a day for 30 days. Multilevel modeling analyses revealed a significant positive moderating effect for enhancement motives on the relationship between positive mood and amount of time spent gambling and number of drinks consumed while gambling. In addition, problem gambling status was associated with consuming fewer drinks while gambling at higher levels of positive mood, and spending more money than intended at higher levels of negative mood. Unexpectedly, there was only one moderating effect for coping motives on the mood-gambling relationship; low coping motivated gamblers consumed more alcohol while gambling at higher levels of positive mood, whereas high coping motivated gamblers did not change their drinking in response to positive mood. The current findings highlight enhancement motives as risky motives for young adult gambling, particularly in the context of positive mood, and suggest that gambling interventions should include strategies to address positive mood management.

Association Between the Built Environment in School Neighborhoods With Physical Activity Among New York City Children, 2012

PubMed Central

Gray, Heewon Lee; Quinn, James; Rundle, Andrew G.; Contento, Isobel R.; Koch, Pamela A.

2016-01-01

Introduction The benefits of physical activity for health and well-being are well established, yet built environment characteristics in the school neighborhood may constrain students’ ability to engage in physical activity and contribute to the considerable variation in physical activity among students at different schools. Methods Baseline data from the Food, Health and Choices obesity prevention trial were used to create multilevel linear models of the relationship between fifth-grade students’ (n = 952) physical activity and related psychosocial factors and characteristics of the built environment of the school’s neighborhood (park access, public transportation density, total crime, and walkability), controlling for age and body mass index z scores. Results Total crime was inversely associated with boys’ light physical activity duration (β = −0.189; P = .02) and behavioral intention for physical activity (β = −0.178; P = .03). Boys’ habit strength for physical activity was positively associated with public transportation density (β = 0.375; P = .02) and negatively associated with total crime (β = −0.216; P = .01), explaining 67% of between-school variation. Girls’ frequency of light physical activity was positively associated with park access (β = 0.188; P = .04). Built environment characteristics explained 97% of the between-school variation in girls’ self-efficacy in walking for exercise. Conclusions Characteristics of the built environment surrounding schools were associated with and explain between-school variation in students’ physical activity and several theory-based psychosocial factors. Partnerships between public health practitioners, policy makers, and school administrators may be warranted to shape the school neighborhood, specifically to decrease crime rates and increase park access, to encourage physical activity in youth. PMID:27536902

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

NASA Astrophysics Data System (ADS)

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13C NMR spectrometry (irm-13C NMR) provides the complete 13C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13C natural abundance values (50‰), irm-13C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13C NMR. Until now, the conventional strategy to determine the position-specific abundance xi relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1H NMR pulse sequence (named DWET) with a 13C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T1, which forms a serious limitation for irm-13C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T1 variations. Their performance is evaluated on the determination of the 13C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-13C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time.

Specific Gravity Variation in a Lower Mississippi Valley Cottonwood Population

Treesearch

R. E. Farmer; J. R. Wilcox

1966-01-01

Specific gravity varied from 0,32 to 0.46, averaging 0.38. Most of the variation was associated with individual trees; samples within locations accounted for a smaller, but statistically significant, portion of the variation. Variation between locatians was not significant. It was concluded that individual high-density trees' should be sought throughout the...

The emergence of human-evolutionary medical genomics

PubMed Central

Crespi, Bernard J

2011-01-01

In this review, I describe how evolutionary genomics is uniquely suited to spearhead advances in understanding human disease risk, owing to the privileged position of genes as fundamental causes of phenotypic variation, and the ability of population genetic and phylogenetic methods to robustly infer processes of natural selection, drift, and mutation from genetic variation at the levels of family, population, species, and clade. I first provide an overview of models for the origins and maintenance of genetically based disease risk in humans. I then discuss how analyses of genetic disease risk can be dovetailed with studies of positive and balancing selection, to evaluate the degree to which the ‘genes that make us human’ also represent the genes that mediate risk of polygenic disease. Finally, I present four basic principles for the nascent field of human evolutionary medical genomics, each of which represents a process that is nonintuitive from a proximate perspective. Joint consideration of these principles compels novel forms of interdisciplinary analyses, most notably studies that (i) analyze tradeoffs at the level of molecular genetics, and (ii) identify genetic variants that are derived in the human lineage or in specific populations, and then compare individuals with derived versus ancestral alleles. PMID:25567974

Marketing analysis of a positive technology app for the self-management of psychological stress.

PubMed

Wiederhold, Brenda K; Boyd, Chelsie; Sulea, Camelia; Gaggioli, Andrea; Riva, Giuseppe

2014-01-01

The INTERSTRESS project developed a completely new concept in the treatment of psychological stress: Interreality, a concept that combines cognitive behavioral therapy with a hybrid, closed-loop empowering experience bridging real and virtual worlds. This model provides the opportunity for individual citizens to become active participants in their own health and well-being. This article contains the results of the Marketing Trial and analysis of the opinions of individual consumers/end users of the INTERSTRESS product. The specific objective of this study was to evaluate the feasibility, efficacy and user acceptance of a novel mobile-based relaxation training tool in combination with biofeedback exercises and wearable biosensors. Relaxation was aided through immersion in a mobile virtual scenario (a virtual island) featuring pre-recorded audio narratives guiding a series of relaxation exercises. During biofeedback exercises, a wearable biosensor system provided data which directly modified the virtual reality experience in real-time. Thirty-six participants evaluated the product and overall feedback from users was positive, with some variation seen based on participant gender. A larger market study is now underway to understand if there are cultural variations in acceptability of the device.

Splenomegaly Segmentation using Global Convolutional Kernels and Conditional Generative Adversarial Networks

PubMed Central

Huo, Yuankai; Xu, Zhoubing; Bao, Shunxing; Bermudez, Camilo; Plassard, Andrew J.; Liu, Jiaqi; Yao, Yuang; Assad, Albert; Abramson, Richard G.; Landman, Bennett A.

2018-01-01

Spleen volume estimation using automated image segmentation technique may be used to detect splenomegaly (abnormally enlarged spleen) on Magnetic Resonance Imaging (MRI) scans. In recent years, Deep Convolutional Neural Networks (DCNN) segmentation methods have demonstrated advantages for abdominal organ segmentation. However, variations in both size and shape of the spleen on MRI images may result in large false positive and false negative labeling when deploying DCNN based methods. In this paper, we propose the Splenomegaly Segmentation Network (SSNet) to address spatial variations when segmenting extraordinarily large spleens. SSNet was designed based on the framework of image-to-image conditional generative adversarial networks (cGAN). Specifically, the Global Convolutional Network (GCN) was used as the generator to reduce false negatives, while the Markovian discriminator (PatchGAN) was used to alleviate false positives. A cohort of clinically acquired 3D MRI scans (both T1 weighted and T2 weighted) from patients with splenomegaly were used to train and test the networks. The experimental results demonstrated that a mean Dice coefficient of 0.9260 and a median Dice coefficient of 0.9262 using SSNet on independently tested MRI volumes of patients with splenomegaly.

An Embedded Stress Sensor for Concrete SHM Based on Amorphous Ferromagnetic Microwires

PubMed Central

Olivera, Jesús; González, Margarita; Fuente, José Vicente; Varga, Rastislav; Zhukov, Arkady; Anaya, José Javier

2014-01-01

A new smart concrete aggregate design as a candidate for applications in structural health monitoring (SHM) of critical elements in civil infrastructure is proposed. The cement-based stress/strain sensor was developed by utilizing the stress/strain sensing properties of a magnetic microwire embedded in cement-based composite (MMCC). This is a contact-less type sensor that measures variations of magnetic properties resulting from stress variations. Sensors made of these materials can be designed to satisfy the specific demand for an economic way to monitor concrete infrastructure health. For this purpose, we embedded a thin magnetic microwire in the core of a cement-based cylinder, which was inserted into the concrete specimen under study as an extra aggregate. The experimental results show that the embedded MMCC sensor is capable of measuring internal compressive stress around the range of 1–30 MPa. Two stress sensing properties of the embedded sensor under uniaxial compression were studied: the peak amplitude and peak position of magnetic switching field. The sensitivity values for the amplitude and position within the measured range were 5 mV/MPa and 2.5 μs/MPa, respectively. PMID:25347582

Determinants of PCR performance (Xpert MTB/RIF), including bacterial load and inhibition, for TB diagnosis using specimens from different body compartments

PubMed Central

Theron, Grant; Peter, Jonny; Calligaro, Greg; Meldau, Richard; Hanrahan, Colleen; Khalfey, Hoosain; Matinyenya, Brian; Muchinga, Tapuwa; Smith, Liezel; Pandie, Shaheen; Lenders, Laura; Patel, Vinod; Mayosi, Bongani M.; Dheda, Keertan

2014-01-01

The determinants of Xpert MTB/RIF sensitivity, a widely used PCR test for the diagnosis of tuberculosis (TB) are poorly understood. We compared culture time-to-positivity (TTP; a surrogate of bacterial load), MTB/RIF TB-specific and internal positive control (IPC)-specific CT values, and clinical characteristics in patients with suspected TB who provided expectorated (n = 438) or induced sputum (n = 128), tracheal aspirates (n = 71), bronchoalveolar lavage fluid (n = 152), pleural fluid (n = 76), cerebral spinal fluid (CSF; n = 152), pericardial fluid (n = 131), or urine (n = 173) specimens. Median bacterial load (TTP in days) was the strongest associate of MTB/RIF positivity in each fluid. TTP correlated with CT values in pulmonary specimens but not extrapulmonary specimens (Spearman's coefficient 0.5043 versus 0.1437; p = 0.030). Inhibition affected a greater proportion of pulmonary specimens than extrapulmonary specimens (IPC CT > 34: 6% (47/731) versus 1% (4/381; p < 0.0001). Pulmonary specimens had greater load than extrapulmonary specimens [TTPs (interquartile range) of 11 (7–16) versus 22 (18–33.5) days; p < 0.0001]. HIV-infection was associated with a decreased likelihood of MTB/RIF-positivity in pulmonary specimens but an increased likelihood in extrapulmonary specimens. Mycobacterial load, which displays significant variation across different body compartments, is the main determinant of MTB/RIF-positivity rather than PCR inhibition. MTB/RIF CT is a poor surrogate of load in extrapulmonary specimens. PMID:25014250

Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle.

PubMed

Nayeri, Shadi; Sargolzaei, Mehdi; Abo-Ismail, Mohammed K; May, Natalie; Miller, Stephen P; Schenkel, Flavio; Moore, Stephen S; Stothard, Paul

2016-06-10

Genome-wide association studies (GWAS) are a powerful tool for detecting genomic regions explaining variation in phenotype. The objectives of the present study were to identify or refine the positions of genomic regions affecting milk production, milk components and fertility traits in Canadian Holstein cattle, and to use these positions to identify genes and pathways that may influence these traits. Several QTL regions were detected for milk production (MILK), fat production (FAT), protein production (PROT) and fat and protein deviation (FATD, PROTD respectively). The identified QTL regions for production traits (including milk production) support previous findings and some overlap with genes with known relevant biological functions identified in earlier studies such as DGAT1 and CPSF1. A significant region on chromosome 21 overlapping with the gene FAM181A and not previous linked to fertility in dairy cattle was identified for the calving to first service interval and days open. A functional enrichment analysis of the GWAS results yielded GO terms consistent with the specific phenotypes tested, for example GO terms GO:0007595 (lactation) and GO:0043627 (response to estrogen) for milk production (MILK), GO:0051057 (positive regulation of small GTPase mediated signal transduction) for fat production (FAT), GO:0040019 (positive regulation of embryonic development) for first service to calving interval (CTFS) and GO:0043268 (positive regulation of potassium ion transport) for days open (DO). In other cases the connection between the enriched GO terms and the traits were less clear, for example GO:0003279 (cardiac septum development) for FAT and GO:0030903 (notochord development) for DO trait. The chromosomal regions and enriched pathways identified in this study confirm several previous findings and highlight new regions and pathways that may contribute to variation in production or fertility traits in dairy cattle.

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites

PubMed Central

Grievink, Liat Shavit; Penny, David; Hendy, Mike D; Holland, Barbara R

2009-01-01

Correction to Shavit Grievink L, Penny D, Hendy MD, Holland BR: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol 2008, 8(1):317.

Position-specific isotope modeling of organic micropollutants transformations through different reaction pathways

NASA Astrophysics Data System (ADS)

Jin, Biao; Rolle, Massimo

2016-04-01

Organic compounds are produced in vast quantities for industrial and agricultural use, as well as for human and animal healthcare [1]. These chemicals and their metabolites are frequently detected at trace levels in fresh water environments where they undergo degradation via different reaction pathways. Compound specific stable isotope analysis (CSIA) is a valuable tool to identify such degradation pathways in different environmental systems. Recent advances in analytical techniques have promoted the fast development and implementation of multi-element CSIA. However, quantitative frameworks to evaluate multi-element stable isotope data and incorporating mechanistic information on the degradation processes [2,3] are still lacking. In this study we propose a mechanism-based modeling approach to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. We validate the proposed approach with the concentration and multi-element isotope data of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model precisely captures the dual element isotope trends characteristic of different reaction pathways and their range of variation consistent with observed multi-element (C, N) bulk isotope fractionation. The proposed approach can also be used as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. [1] Schwarzenbach, R.P., Egli, T., Hofstetter, T.B., von Gunten, U., Wehrli, B., 2010. Global Water Pollution and Human Health. Annu. Rev. Environ. Resour. doi:10.1146/annurev-environ-100809-125342. [2] Jin, B., Haderlein, S.B., Rolle, M., 2013. Integrated carbon and chlorine isotope modeling: Applications to chlorinated aliphatic hydrocarbons dechlorination. Environ. Sci. Technol. 47, 1443-1451. doi:10.1021/es304053h. [3] Jin, B., Rolle, M., 2014. Mechanistic approach to multi-element isotope modeling of organic contaminant degradation. Chemosphere 95, 131-139. doi:10.1016/j.chemosphere.2013.08.050.

Genovar: a detection and visualization tool for genomic variants.

PubMed

Jung, Kwang Su; Moon, Sanghoon; Kim, Young Jin; Kim, Bong-Jo; Park, Kiejung

2012-05-08

Along with single nucleotide polymorphisms (SNPs), copy number variation (CNV) is considered an important source of genetic variation associated with disease susceptibility. Despite the importance of CNV, the tools currently available for its analysis often produce false positive results due to limitations such as low resolution of array platforms, platform specificity, and the type of CNV. To resolve this problem, spurious signals must be separated from true signals by visual inspection. None of the previously reported CNV analysis tools support this function and the simultaneous visualization of comparative genomic hybridization arrays (aCGH) and sequence alignment. The purpose of the present study was to develop a useful program for the efficient detection and visualization of CNV regions that enables the manual exclusion of erroneous signals. A JAVA-based stand-alone program called Genovar was developed. To ascertain whether a detected CNV region is a novel variant, Genovar compares the detected CNV regions with previously reported CNV regions using the Database of Genomic Variants (DGV, http://projects.tcag.ca/variation) and the Single Nucleotide Polymorphism Database (dbSNP). The current version of Genovar is capable of visualizing genomic data from sources such as the aCGH data file and sequence alignment format files. Genovar is freely accessible and provides a user-friendly graphic user interface (GUI) to facilitate the detection of CNV regions. The program also provides comprehensive information to help in the elimination of spurious signals by visual inspection, making Genovar a valuable tool for reducing false positive CNV results. http://genovar.sourceforge.net/.

An integrated signal conditioner for high-frequency inductive position sensors

NASA Astrophysics Data System (ADS)

Rahal, Mohamad; Demosthenous, Andreas

2010-01-01

This paper describes the design, implementation and evaluation of a signal conditioner application-specific integrated circuit (ASIC) for high-frequency inductive non-contact position sensors. These sensors employ a radio frequency technology based on an antenna planar arrangement and a resonant target, have a high inherent resolution (0.1% of antenna length) and can measure target position over a wide distance range (<0.1 mm to >10 m). However, due to the relatively high-frequency excitation (1 MHz typically) and to the specific layouts of these sensors, there is unwanted capacitive coupling between the transmitter and receiver coils; this type of distortion reduces linearity and resolution. The ASIC, which is the first generation of its kind for this type of sensor, employs a differential mixer topology which suppresses the capacitive coupling offsets. The system architecture and circuit details are presented. The ASIC was fabricated in a 0.6 µm high-voltage CMOS technology occupying an area of 8 mm2. It dissipates about 30 mA from a 24 V power supply. The ASIC was tested with a high-frequency inductive position sensor (with an antenna length of 10.8 cm). The measured input-referred offset due to transmitter crosstalk is on average about 22 µV over a wide phase difference variation (-99° to +117°) between the transmitter and demodulating signals.

Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing.

PubMed

Goossens, Dirk; Moens, Lotte N; Nelis, Eva; Lenaerts, An-Sofie; Glassee, Wim; Kalbe, Andreas; Frey, Bruno; Kopal, Guido; De Jonghe, Peter; De Rijk, Peter; Del-Favero, Jurgen

2009-03-01

We evaluated multiplex PCR amplification as a front-end for high-throughput sequencing, to widen the applicability of massive parallel sequencers for the detailed analysis of complex genomes. Using multiplex PCR reactions, we sequenced the complete coding regions of seven genes implicated in peripheral neuropathies in 40 individuals on a GS-FLX genome sequencer (Roche). The resulting dataset showed highly specific and uniform amplification. Comparison of the GS-FLX sequencing data with the dataset generated by Sanger sequencing confirmed the detection of all variants present and proved the sensitivity of the method for mutation detection. In addition, we showed that we could exploit the multiplexed PCR amplicons to determine individual copy number variation (CNV), increasing the spectrum of detected variations to both genetic and genomic variants. We conclude that our straightforward procedure substantially expands the applicability of the massive parallel sequencers for sequencing projects of a moderate number of amplicons (50-500) with typical applications in resequencing exons in positional or functional candidate regions and molecular genetic diagnostics. 2008 Wiley-Liss, Inc.

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs

PubMed Central

2013-01-01

Background The field of cancer genomics has rapidly adopted next-generation sequencing (NGS) in order to study and characterize malignant tumors with unprecedented resolution. In particular for cancer, one is often trying to identify somatic mutations – changes specific to a tumor and not within an individual’s germline. However, false positive and false negative detections often result from lack of sufficient variant evidence, contamination of the biopsy by stromal tissue, sequencing errors, and the erroneous classification of germline variation as tumor-specific. Results We have developed a generalized Bayesian analysis framework for matched tumor/normal samples with the purpose of identifying tumor-specific alterations such as single nucleotide mutations, small insertions/deletions, and structural variation. We describe our methodology, and discuss its application to other types of paired-tissue analysis such as the detection of loss of heterozygosity as well as allelic imbalance. We also demonstrate the high level of sensitivity and specificity in discovering simulated somatic mutations, for various combinations of a) genomic coverage and b) emulated heterogeneity. Conclusion We present a Java-based implementation of our methods named Seurat, which is made available for free academic use. We have demonstrated and reported on the discovery of different types of somatic change by applying Seurat to an experimentally-derived cancer dataset using our methods; and have discussed considerations and practices regarding the accurate detection of somatic events in cancer genomes. Seurat is available at https://sites.google.com/site/seuratsomatic. PMID:23642077

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs.

PubMed

Christoforides, Alexis; Carpten, John D; Weiss, Glen J; Demeure, Michael J; Von Hoff, Daniel D; Craig, David W

2013-05-04

The field of cancer genomics has rapidly adopted next-generation sequencing (NGS) in order to study and characterize malignant tumors with unprecedented resolution. In particular for cancer, one is often trying to identify somatic mutations--changes specific to a tumor and not within an individual's germline. However, false positive and false negative detections often result from lack of sufficient variant evidence, contamination of the biopsy by stromal tissue, sequencing errors, and the erroneous classification of germline variation as tumor-specific. We have developed a generalized Bayesian analysis framework for matched tumor/normal samples with the purpose of identifying tumor-specific alterations such as single nucleotide mutations, small insertions/deletions, and structural variation. We describe our methodology, and discuss its application to other types of paired-tissue analysis such as the detection of loss of heterozygosity as well as allelic imbalance. We also demonstrate the high level of sensitivity and specificity in discovering simulated somatic mutations, for various combinations of a) genomic coverage and b) emulated heterogeneity. We present a Java-based implementation of our methods named Seurat, which is made available for free academic use. We have demonstrated and reported on the discovery of different types of somatic change by applying Seurat to an experimentally-derived cancer dataset using our methods; and have discussed considerations and practices regarding the accurate detection of somatic events in cancer genomes. Seurat is available at https://sites.google.com/site/seuratsomatic.

Variation of Specific Gravity in Plantation-Grown Trees of Bigleaf Mahogany

Treesearch

C. B. Briscoe; J. B. Harris; D. Wyckoff

1963-01-01

As a prelude to tree improvement work in the genus Swietenia, a study was made of specific gravity variation within the bole of six plantation-grown trees of bigleaf mahogany. Variation was appreciable, from 0.36 to 0.65 , and several patterns were determined. Specific gravity of the tree increased with growth rate, as expressed in diameter at breast height, but not...

Skeletal morphology of the forefoot in shrews (Mammalia: Soricidae) of the genus Cryptotis, as revealed by digital x-rays

USGS Publications Warehouse

Woodman, N.; Morgan, J.P.J.

2005-01-01

Variation in the forefoot skeleton of small-eared shrews (family Soricidae, genus Cryptotis) has been previously documented, but the paucity of available skeletons for most taxa makes assessment of the degrees of intraspecific and interspecific variation difficult. We used a digital X-ray system to extract images of the forefoot skeleton from 101 dried skins of eight taxa (seven species, including two subspecies of one species) of these shrews. Lengths and widths of each of the four bones of digit III were measured directly from the digital images, and we used these data to quantify variation within and among taxa. Analysis of the images and measurements showed that interspecific variation exceeds intraspecific variation. In fact, most taxa could be distinguished in multivariate and some bivariate plots. Our quantitative data helped us define a number of specific forefoot characters that we subsequently used to hypothesize evolutionary relationships among the taxa using the exhaustive search option in PAUP, a computer program for phylogenetic analysis. The resulting trees generally concur with previously published evolutionary hypotheses for small-eared shrews. Cryptotis meridensis, a taxon not previously examined in recent phylogenies, is rooted at the base of the branch leading to the C. mexicana group of species. The position of this species suggests that the mostly South American C. thomasi group shares an early ancestor with the C. mexicana group.

Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster

PubMed Central

He, Bing; Caudy, Amy; Parsons, Lance; Rosebrock, Adam; Pane, Attilio; Raj, Sandeep; Wieschaus, Eric

2012-01-01

Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions. By excluding sequences that can be mapped to the assembled euchromatic arms, we identified sequences that are specific to heterochromatin and used them to design heterochromatin specific probes (“H-probes”) for microarray. By comparative genomic hybridization (CGH) analyses of embryos deficient for each chromosome or chromosome arm, we were able to map most of our H-probes to specific chromosome arms. We also positioned sequences mapped to the second and X chromosomes to finer intervals by analyzing smaller deletions with breakpoints in heterochromatin. Using this approach, we were able to map >40% (13.9 Mb) of the previously unmapped heterochromatin sequences assembled by the whole-genome sequencing effort on arm U and arm Uextra to specific locations. We also identified and mapped 110 kb of novel heterochromatic sequences. Subsequent analyses revealed that sequences located within different heterochromatic regions have distinct properties, such as sequence composition, degree of repetitiveness, and level of underreplication in polytenized tissues. Surprisingly, although heterochromatin is generally considered to be transcriptionally silent, we detected region-specific temporal patterns of transcription in heterochromatin during oogenesis and early embryonic development. Our study provides a useful approach to elucidate the molecular organization and function of heterochromatin and reveals region-specific variation of heterochromatin. PMID:22745230

Impact of head morphology on local brain specific absorption rate from exposure to mobile phone radiation.

PubMed

Adibzadeh, Fatemeh; Bakker, Jurriaan F; Paulides, Margarethus M; Verhaart, René F; van Rhoon, Gerard C

2015-01-01

Among various possible health effects of mobile phone radiation, the risk of inducing cancer has the strongest interest of laymen and health organizations. Recently, the Interphone epidemiological study investigated the association between the estimated Radio Frequency (RF) dose from mobile phones and the risk of developing a brain tumor. Their dosimetric analysis included over 100 phone models but only two homogeneous head phantoms. So, the potential impact of individual morphological features on global and local RF absorption in the brain was not investigated. In this study, we performed detailed dosimetric simulations for 20 head models and quantified the variation of RF dose in different brain regions as a function of head morphology. Head models were exposed to RF fields from generic mobile phones at 835 and 1900 MHz in the "tilted" and "cheek" positions. To evaluate the local RF dose variation, we used and compared two different post-processing methods, that is, averaging specific absorption rate (SAR) over Talairach regions and over sixteen predefined 1 cm(3) cube-shaped field-sensors. The results show that the variation in the averaged SAR among the heads can reach up to 16.4 dB at a 1 cm(3) cube inside the brain (field-sensor method) and alternatively up to 15.8 dB in the medulla region (Talairach method). In conclusion, we show head morphology as an important uncertainty source for dosimetric studies of mobile phones. Therefore, any dosimetric analysis dealing with RF dose at a specific region in the brain (e.g., tumor risk analysis) should be based upon real morphology. © 2014 Wiley Periodicals, Inc.

Specific Polymorphic Variation in the Mitochondrial Genome and Increased In-Hospital Mortality After Severe Trauma

PubMed Central

Canter, Jeffrey A.; Norris, Patrick R.; Moore, Jason H.; Jenkins, Judith M.; Morris, John A.

2007-01-01

Objective: To determine whether specific genetic variations in the mtDNA that impact energy production and free-radical generation are potential new risk factors for in-hospital mortality after severe trauma. Summary Background Data: Each of the 3 mitochondrial DNA polymorphisms selected for this study (at positions 4216, 10398, 4917) alter the amino acid sequence of different key subunits of Complex I in the electron transport chain. They have been previously implicated in phenotypes involving tissues with high-energy demand, such as the brain and retina. Methods: Seven hundred forty-five consecutive patients admitted to the trauma intensive care unit at Vanderbilt University Medical Center between April 11, 2005, and February 27, 2006, were potentially eligible for this study. Under an Institutional Review Board-approved protocol (which excluded patients <18 years of age and prisoners), 666 patients had DNA extracted from a blood sample. Detailed demographic and clinical covariates were also obtained (including age, gender, ethnicity, lactate measurements, and injury severity score). A flurogenic 5′ nuclease allelic discrimination Taqman assay and the ABI 7900HT Sequence Detection System (v2.1) was used to genotype the T4216C, A10398G, and A4917G polymorphisms. The primary outcome was in-hospital mortality. Results: Multivariate logistic regression analysis revealed that the 4216T allele was a significant independent predictor of in-hospital mortality (OR = 2.63, 95% CI 1.14–6.07, P = 0.02) after adjustment for age, gender, injury severity score, highest lactate level, mechanism of injury, and the 10398 polymorphism. Conclusions: Variation in the mtDNA, specifically the 4216T allele, appears to increase the risk of in-hospital mortality after severe injury. PMID:17717444

Decoupled leaf and root carbon economics is a key component in the ecological diversity and evolutionary divergence of deciduous and evergreen lineages of genus Rhododendron.

PubMed

Medeiros, Juliana S; Burns, Jean H; Nicholson, Jaynell; Rogers, Louisa; Valverde-Barrantes, Oscar

2017-06-01

We explored trait-trait and trait-climate relationships for 27 Rhododendron species while accounting for phylogenetic relationships and within-species variation to investigate whether leaf and root traits are coordinated across environments and over evolutionary time, as part of a whole-plant economics spectrum. We examined specific leaf area (SLA) and four root traits: specific root length (SRL), specific root tip abundance (SRTA), first order diameter, and link average length, for plants growing in a cold, seasonal climate (Kirtland, Ohio) and a warmer, less seasonal climate (Federal Way, Washington) in the United States. We estimated a phylogeny and species' climate of origin, determined phylogenetic signal on mean traits and within-species variation, and used phylogenetically informed analysis to compare trait-trait and trait-climate relationships for deciduous and evergreen lineages. Mean SLA and within-species variation in SRL were more similar between close relatives than expected by chance. SLA and root traits differed according to climate of origin and across growth environments, though SLA differed within- and among-species less than roots. A negative SRL-SRTA correlation indicates investment in foraging scale vs. precision as a fundamental trade-off defining the root economic spectrum. Also, the deciduous clade exhibited a strong negative relationship between SLA and SRL, while evergreen clades showed a weaker positive or no relationship. Our work suggests that natural selection has shaped relationships between above- and belowground traits in genus Rhododendron and that leaf and root traits may evolve independently. Morphological decoupling may help explain habitat diversity among Rhododendron species, as well as the changes accompanying the divergence of deciduous and evergreen lineages. © 2017 Botanical Society of America.

Climate sensitivity of reproduction in a mast-seeding boreal conifer across its distributional range from lowland to treeline forests.

PubMed

Roland, Carl A; Schmidt, Joshua H; Johnstone, Jill F

2014-03-01

Mast-seeding conifers such as Picea glauca exhibit synchronous production of large seed crops over wide areas, suggesting climate factors as possible triggers for episodic high seed production. Rapidly changing climatic conditions may thus alter the tempo and spatial pattern of masting of dominant species with potentially far-reaching ecological consequences. Understanding the future reproductive dynamics of ecosystems including boreal forests, which may be dominated by mast-seeding species, requires identifying the specific cues that drive variation in reproductive output across landscape gradients and among years. Here we used annual data collected at three sites spanning an elevation gradient in interior Alaska, USA between 1986 and 2011 to produce the first quantitative models for climate controls over both seedfall and seed viability in P. glauca, a dominant boreal conifer. We identified positive associations between seedfall and increased summer precipitation and decreased summer warmth in all years except for the year prior to seedfall. Seed viability showed a contrasting response, with positive correlations to summer warmth in all years analyzed except for one, and an especially positive response to warm and wet conditions in the seedfall year. Finally, we found substantial reductions in reproductive potential of P. glauca at high elevation due to significantly reduced seed viability there. Our results indicate that major variation in the reproductive potential of this species may occur in different landscape positions in response to warming, with decreasing reproductive success in areas prone to drought stress contrasted with increasing success in higher elevation areas currently limited by cool summer temperatures.

Facing the facts: The Runx2 gene is associated with variation in facial morphology in primates.

PubMed

Ritzman, Terrence B; Banovich, Nicholas; Buss, Kaitlin P; Guida, Jennifer; Rubel, Meagan A; Pinney, Jennifer; Khang, Bao; Ravosa, Matthew J; Stone, Anne C

2017-10-01

The phylogenetic and adaptive factors that cause variation in primate facial form-including differences among the major primate clades and variation related to feeding and/or social behavior-are relatively well understood. However, comparatively little is known about the genetic mechanisms that underlie diversity in facial form in primates. Because it is essential for osteoblastic differentiation and skeletal development, the runt-related transcription factor 2 (Runx2) is one gene that may play a role in these genetic mechanisms. Specifically, polymorphisms in the QA ratio (determined by the ratio of the number of polyglutamines to polyalanines in one functional domain of Runx2) have been shown to be correlated with variation in facial length and orientation in other mammal groups. However, to date, the relationship between variation in this gene and variation in facial form in primates has not been explicitly tested. To test the hypothesis that the QA ratio is correlated with facial form in primates, the current study quantified the QA ratio, facial length, and facial angle in a sample of 33 primate species and tested for correlation using phylogenetic generalized least squares. The results indicate that the QA ratio of the Runx2 gene is positively correlated with variation in relative facial length in anthropoid primates. However, no correlation was found in strepsirrhines, and there was no correlation between facial angle and the QA ratio in any groups. These results suggest that, in primates, the QA ratio of the Runx2 gene may play a role in modulating facial size, but not facial orientation. This study therefore provides important clues about the genetic and developmental mechanisms that may underlie variation in facial form in primates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Common variant in OXTR predicts growth in positive emotions from loving-kindness training.

PubMed

Isgett, Suzannah F; Algoe, Sara B; Boulton, Aaron J; Way, Baldwin M; Fredrickson, Barbara L

2016-11-01

Ample research suggests that social connection reliably generates positive emotions. Oxytocin, a neuropeptide implicated in social cognition and behavior, is one biological mechanism that may influence an individual's capacity to extract positive emotions from social contexts. Because variation in certain genes may indicate underlying neurobiological differences, we tested whether several SNPs in two genes related to oxytocin signaling would show effects on positive emotions that were context-specific, depending on sociality. For six weeks, a sample of mid-life adults (N=122) participated in either socially-focused loving-kindness training or mindfulness training. During this timespan they reported their positive emotions daily. Five SNPs within OXTR and CD38 were assayed, and each was tested for its individual effect on daily emotions. The hypothesized three-way interaction between time, training type, and genetic variability emerged: Individuals homozygous for the G allele of OXTR rs1042778 experienced gains in daily positive emotions from loving-kindness training, whereas individuals with the T allele did not experience gains in positive emotions with either training. These findings are among the first to show how genetic differences in oxytocin signaling may influence an individual's capacity to experience positive emotions as a result of a socially-focused intervention. Copyright © 2016 Elsevier Ltd. All rights reserved.

Common variant in OXTR predicts growth in positive emotions from loving-kindness training

PubMed Central

Isgett, Suzannah F.; Algoe, Sara B.; Boulton, Aaron J.; Way, Baldwin M.

2017-01-01

Ample research suggests that social connection reliably generates positive emotions. Oxytocin, a neuropeptide implicated in social cognition and behavior, is one biological mechanism that may influence an individual’s capacity to extract positive emotions from social contexts. Because variation in certain genes may indicate underlying neurobiological differences, we tested whether several SNPs in two genes related to oxytocin signaling would show effects on positive emotions that were context-specific, depending on sociality. For six weeks, a sample of mid-life adults (N = 122) participated in either socially-focused loving-kindness training or mindfulness training. During this timespan they reported their positive emotions daily. Five SNPs within OXTR and CD38 were assayed, and each was tested for its individual effect on daily emotions. The hypothesized three-way interaction between time, training type, and genetic variability emerged: Individuals homozygous for the G allele of OXTR rs1042778 experienced gains in daily positive emotions from loving-kindness training, whereas individuals with the T allele did not experience gains in positive emotions with either training. These findings are among the first to show how genetic differences in oxytocin signaling may influence an individual’s capacity to experience positive emotions as a result of a socially-focused intervention. PMID:27543885

Positive benefits of caring on nurses' motivation and well-being: a diary study about the role of emotional regulation abilities at work.

PubMed

Donoso, Luis Manuel Blanco; Demerouti, Evangelia; Garrosa Hernández, Eva; Moreno-Jiménez, Bernardo; Carmona Cobo, Isabel

2015-04-01

Recent research reveals that not all job demands have negative effects on workers' well-being and suggests that the negative or positive effects of specific job demands depend on the occupational sector. Specifically, emotional job demands form the heart of the work for nurses and for this reason they can be interpreted by nurses as a challenge that promotes motivation and well-being among these professionals, especially if personal and job resources become available. The study had two objectives. First, to examine whether daily emotional demands within a nursing work context have a positive effect on nurses' daily motivation at work (vigour) and well-being at home (vitality and positive affect). Second, to explore whether this positive effect could be enhanced by nurses' emotional regulation abilities. This research used a diary design to explore daily experiences and to analyze how variations in specific job or personal characteristics can affect levels of motivation and well-being across days. Fifty-three nurses working in different Spanish hospitals and primary health care centres completed a general questionnaire and a diary booklet over 5 consecutive working days in two different moments, after work and at night (N=53 participants and N=265 observations). In line with our hypotheses, multi-level analyses revealed that, on the one hand, day-level emotional demands at work had a positive effect on vigour at work and on vitality at home. On the other hand, analyses showed that nurses with higher emotional regulation abilities have more motivation at work and well-being at home when they have to face high emotional demands at work, showing a spill over effect after work. These findings support the idea that emotional demands from the nursing profession can act as challenges which promote motivation and well-being, especially if internal emotional resources become available. Copyright © 2015 Elsevier Ltd. All rights reserved.

Usefulness of multiplex PCR methods and respiratory viruses’ distribution in children below 15 years old according to age, seasons and clinical units in France: A 3 years retrospective study

PubMed Central

Collin, Gilles; Ichou, Houria; Charpentier, Charlotte; Bendhafer, Samia; Dumitrescu, Madalina; Allal, Lahcene; Cojocaru, Bogdan; Desfrère, Luc; Descamps, Diane; Mandelbrot, Laurent; Houhou-Fidouh, Nadhira

2017-01-01

Background To date, only influenza and RSV testing are recommended for respiratory viruses’ detection in paediatric units. In this study, we described, according to seasons, ages and clinical units, the results obtained in children (<15 years old) by multiplex-PCR (mPCR) tests allowing a quick and wide range detection of all respiratory viruses. These results were also compared with RSV specific detection. Methods All nasopharyngeal mPCR and RSV tests requested by clinicians in our French teaching hospitals group between 2011 and 2014 were retrospectively included. All repeated samples for the same children in the same month were discarded. Results Of the 381 mPCR tests (344 children) performed, 51.4% were positive. Positivity and viral co-infection rates were higher in the 6–36 months old strata (81% and 25%, p<0.0001 and p = 0.04, respectively). Viral distribution showed strong variations across ages. During specific influenza epidemic periods, only 1/39 (2.5%) mPCR tests were positive for influenza and 19/39 (48.7%) for other viruses. During specific RSV epidemic periods, only 8/46 (17.4%) mPCR tests were positive for RSV and 14/46 (30.4%) for other viruses. 477/1529 (31.2%) of RSV immunochromatography-tests were positive. Among the negatives immunochromatography-test also explored by mPCR, 28/62 (31%) were positive for other respiratory viruses. Conclusion This study provides a wide description of respiratory viruses’ distribution among children in hospital settings using mPCR over 3 years. It emphasizes the number of undiagnosed respiratory viruses according to the current diagnosis practice in France and gives a better picture of respiratory viruses identified in hospital settings by mPCR all over the year in France. PMID:28235002

Are medication restrictions before FOBT necessary?

PubMed Central

Konrad, Gerald; Katz, Alan

2012-01-01

Abstract Objective To determine whether medication interventions enhance the sensitivity and specificity of guaiac-based fecal occult blood testing (FOBT) when screening for colorectal cancer (CRC). Data sources We searched PubMed-MEDLINE, CINAHL, and the Cochrane databases using the MeSH headings occult blood, feces/analysis, and guaiac/analysis, linking them to variations of anticoagulants, heparin, warfarin, iron, aspirin, nonsteroidal anti-inflammatory drugs (NSAIDs), clopidogrel, cyclooxygenase-2 inhibitors, and ascorbic acid (vitamin C). Study selections were limited to English studies involving humans. Study selection All resulting titles and abstracts were reviewed for studies that included manipulation of medications associated with guaiac-based FOBT. If the study’s relevance was unclear from the abstract, the full article was reviewed. The search resulted in 31 pertinent studies. Synthesis No studies addressed the effects of medication interventions on the sensitivity or specificity of FOBT screening. Randomized controlled trials, however, showed no increase in the rate of positive results among those taking NSAIDs. The literature is mixed regarding the effect of NSAIDs on the positive predictive value of a positive FOBT result, although no change in positive predictive value has been shown for warfarin. Iron will not affect FOBT results in vivo. Ascorbic acid might inhibit positive FOBT results both in vitro and in vivo, but it has not been studied in screening populations. Conclusion Studies evaluating the effects of medication intervention on FOBT screening for CRC are limited by their lower quality and because they do not address sensitivity and specificity. Available evidence, however, does not suggest a benefit from withholding NSAIDs, anticoagulant medications, or iron during the screening period. These recommendations should be abandoned in order to maximize adherence to screening. Positive FOBT results obtained among patients taking these medications deserve full evaluation for CRC. Until further studies clarify the effect of ascorbic acid on FOBT screening, withholding this medication before testing seems prudent. PMID:22972722

QTL mapping for sexually dimorphic fitness-related traits in wild bighorn sheep

PubMed Central

Poissant, J; Davis, C S; Malenfant, R M; Hogg, J T; Coltman, D W

2012-01-01

Dissecting the genetic architecture of fitness-related traits in wild populations is key to understanding evolution and the mechanisms maintaining adaptive genetic variation. We took advantage of a recently developed genetic linkage map and phenotypic information from wild pedigreed individuals from Ram Mountain, Alberta, Canada, to study the genetic architecture of ecologically important traits (horn volume, length, base circumference and body mass) in bighorn sheep. In addition to estimating sex-specific and cross-sex quantitative genetic parameters, we tested for the presence of quantitative trait loci (QTLs), colocalization of QTLs between bighorn sheep and domestic sheep, and sex × QTL interactions. All traits showed significant additive genetic variance and genetic correlations tended to be positive. Linkage analysis based on 241 microsatellite loci typed in 310 pedigreed animals resulted in no significant and five suggestive QTLs (four for horn dimension on chromosomes 1, 18 and 23, and one for body mass on chromosome 26) using genome-wide significance thresholds (Logarithm of odds (LOD) >3.31 and >1.88, respectively). We also confirmed the presence of a horn dimension QTL in bighorn sheep at the only position known to contain a similar QTL in domestic sheep (on chromosome 10 near the horns locus; nominal P<0.01) and highlighted a number of regions potentially containing weight-related QTLs in both species. As expected for sexually dimorphic traits involved in male–male combat, loci with sex-specific effects were detected. This study lays the foundation for future work on adaptive genetic variation and the evolutionary dynamics of sexually dimorphic traits in bighorn sheep. PMID:21847139

Tissue-Specific and Cation/Anion-Specific DNA Methylation Variations Occurred in C. virgata in Response to Salinity Stress

PubMed Central

Gao, Xiang; Cao, Donghui; Liu, Jie; Wang, Xiaoping; Geng, Shujuan; Liu, Bao; Shi, Decheng

2013-01-01

Salinity is a widespread environmental problem limiting productivity and growth of plants. Halophytes which can adapt and resist certain salt stress have various mechanisms to defend the higher salinity and alkalinity, and epigenetic mechanisms especially DNA methylation may play important roles in plant adaptability and plasticity. In this study, we aimed to investigate the different influences of various single salts (NaCl, Na2SO4, NaHCO3, Na2CO3) and their mixed salts on halophyte Chloris. virgata from the DNA methylation prospective, and discover the underlying relationships between specific DNA methylation variations and specific cations/anions through the methylation-sensitive amplification polymorphism analysis. The results showed that the effects on DNA methylation variations of single salts were ranked as follows: Na2CO3> NaHCO3> Na2SO4> NaCl, and their mixed salts exerted tissue-specific effects on C. virgata seedlings. Eight types of DNA methylation variations were detected and defined in C. virgata according to the specific cations/anions existed in stressful solutions; in addition, mix-specific and higher pH-specific bands were the main type in leaves and roots independently. These findings suggested that mixed salts were not the simple combination of single salts. Furthermore, not only single salts but also mixed salts showed tissue-specific and cations/anions-specific DNA methylation variations. PMID:24223802

Tissue-specific and cation/anion-specific DNA methylation variations occurred in C. virgata in response to salinity stress.

PubMed

Gao, Xiang; Cao, Donghui; Liu, Jie; Wang, Xiaoping; Geng, Shujuan; Liu, Bao; Shi, Decheng

2013-01-01

Salinity is a widespread environmental problem limiting productivity and growth of plants. Halophytes which can adapt and resist certain salt stress have various mechanisms to defend the higher salinity and alkalinity, and epigenetic mechanisms especially DNA methylation may play important roles in plant adaptability and plasticity. In this study, we aimed to investigate the different influences of various single salts (NaCl, Na2SO4, NaHCO3, Na2CO3) and their mixed salts on halophyte Chloris. virgata from the DNA methylation prospective, and discover the underlying relationships between specific DNA methylation variations and specific cations/anions through the methylation-sensitive amplification polymorphism analysis. The results showed that the effects on DNA methylation variations of single salts were ranked as follows: Na2CO3> NaHCO3> Na2SO4> NaCl, and their mixed salts exerted tissue-specific effects on C. virgata seedlings. Eight types of DNA methylation variations were detected and defined in C. virgata according to the specific cations/anions existed in stressful solutions; in addition, mix-specific and higher pH-specific bands were the main type in leaves and roots independently. These findings suggested that mixed salts were not the simple combination of single salts. Furthermore, not only single salts but also mixed salts showed tissue-specific and cations/anions-specific DNA methylation variations.

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.

Genetic variation in transmission success of the Lyme borreliosis pathogen Borrelia afzelii.

PubMed

Tonetti, Nicolas; Voordouw, Maarten J; Durand, Jonas; Monnier, Séverine; Gern, Lise

2015-04-01

The vector-to-host and host-to-vector transmission steps are the two critical events that define the life cycle of any vector-borne pathogen. We expect negative genetic correlations between these two transmission phenotypes, if parasite genotypes specialized at invading the vector are less effective at infecting the vertebrate host and vice versa. We used the tick-borne bacterium Borrelia afzelii, a causative agent of Lyme borreliosis in Europe, to test whether genetic trade-offs exist between tick-to-host, systemic (host-to-tick), and a third mode of co-feeding (tick-to-tick) transmission. We worked with six strains of B. afzelii that were differentiated according to their ospC gene. We compared the three components of transmission among the B. afzelii strains using laboratory rodents as the vertebrate host and a laboratory colony of Ixodes ricinus as the tick vector. We used next generation matrix models to combine these transmission components into a single estimate of the reproductive number (R0) for each B. afzelii strain. We also tested whether these strain-specific estimates of R0 were correlated with the strain-specific frequencies in the field. We found significant genetic variation in the three transmission components among the B. afzelii strains. This is the first study to document genetic variation in co-feeding transmission for any tick-borne pathogen. We found no evidence of trade-offs as the three pairwise correlations of the transmission rates were all positive. The R0 values from our laboratory study explained 45% of the variation in the frequencies of the B. afzelii ospC strains in the field. Our study suggests that laboratory estimates of pathogen fitness can predict the distribution of pathogen strains in nature. Copyright © 2015 Elsevier GmbH. All rights reserved.

Neuropsychological Correlates of Normal Variation in Emotional Response to Visual Stimuli

PubMed Central

Robinson, Robert G.; Paradiso, Sergio; Mizrahi, Romina; Fiedorowicz, Jess G.; Kouzoukas, Dimitrios E.; Moser, David J.

2007-01-01

Although the neural substrates of induced emotion have been the focus of numerous investigations, the factors related to individual variation in emotional experience have rarely been investigated in older adults. Twenty-six older normal subjects (mean age, 54) were shown color slides to elicit emotions of sadness, fear, or happiness and asked to rate the intensity of their emotional responses. Subjects who experienced negative emotion most intensely showed relative impairment on every aspect of the Wisconsin Card Sorting Test. Intense positive emotion was associated with relatively impaired performance on the Rey Complex Figure Test. The volume of frontal brain structures, however, was not associated with emotion responses. Hemisphere-specific executive dysfunction was associated with greater intensity of emotional experience in normal older subjects. The role of these differences in intensity of induced emotion and impairment in executive function in daily social and vocational activity should be investigated. PMID:17299297

Regional Variation in the Correlation of Antibody and T-Cell Responses to Trypanosoma cruzi

PubMed Central

Martin, Diana L.; Marks, Morgan; Galdos-Cardenas, Gerson; Gilman, Robert H.; Goodhew, Brook; Ferrufino, Lisbeth; Halperin, Anthony; Sanchez, Gerardo; Verastegui, Manuela; Escalante, Patricia; Naquira, Cesar; Levy, Michael Z.; Bern, Caryn

2014-01-01

Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, is a major cause of morbidity and mortality in Central and South America. Geographic variations in the sensitivity of serologic diagnostic assays to T. cruzi may reflect differences in T. cruzi exposure. We measured parasite-specific T-cell responses among seropositive individuals in two populations from South America with widely varying antibody titers against T. cruzi. Antibody titers among seropositive individuals were significantly lower in Arequipa, Peru compared with Santa Cruz, Bolivia. Similarly, the proportion of seropositive individuals with positive T-cell responses was lower in Peru than Bolivia, resulting in overall lower frequencies of interferon-γ (IFNγ)-secreting cells from Peruvian samples. However, the magnitude of the IFNγ response was similar among the IFNγ responders in both locations. These data indicate that immunological discrepancies based on geographic region are reflected in T-cell responses as well as antibody responses. PMID:24710614

Environmental controls of temporal and spatial variability in CO2 and CH4 fluxes in a neotropical peatland.

PubMed

Wright, Emma L; Black, Colin R; Turner, Benjamin L; Sjögersten, Sofie

2013-12-01

Tropical peatlands play an important role in the global storage and cycling of carbon (C) but information on carbon dioxide (CO2) and methane (CH4) fluxes from these systems is sparse, particularly in the Neotropics. We quantified short and long-term temporal and small scale spatial variation in CO2 and CH4 fluxes from three contrasting vegetation communities in a domed ombrotrophic peatland in Panama. There was significant variation in CO2 fluxes among vegetation communities in the order Campnosperma panamensis > Raphia taedigera > Cyperus. There was no consistent variation among sites and no discernible seasonal pattern of CH4 flux despite the considerable range of values recorded (e.g. -1.0 to 12.6 mg m(-2) h(-1) in 2007). CO2 fluxes varied seasonally in 2007, being greatest in drier periods (300-400 mg m(-2) h(-1)) and lowest during the wet period (60-132 mg m(-2) h(-1)) while very high emissions were found during the 2009 wet period, suggesting that peak CO2 fluxes may occur following both low and high rainfall. In contrast, only weak relationships between CH4 flux and rainfall (positive at the C. panamensis site) and solar radiation (negative at the C. panamensis and Cyperus sites) was found. CO2 fluxes showed a diurnal pattern across sites and at the Cyperus sp. site CO2 and CH4 fluxes were positively correlated. The amount of dissolved carbon and nutrients were strong predictors of small scale within-site variability in gas release but the effect was site-specific. We conclude that (i) temporal variability in CO2 was greater than variation among vegetation communities; (ii) rainfall may be a good predictor of CO2 emissions from tropical peatlands but temporal variation in CH4 does not follow seasonal rainfall patterns; and (iii) diurnal variation in CO2 fluxes across different vegetation communities can be described by a Fourier model. © 2013 John Wiley & Sons Ltd.

Interfraction variation in lung tumor position with abdominal compression during stereotactic body radiotherapy

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

Mampuya, Wambaka Ange; Nakamura, Mitsuhiro; Matsuo, Yukinori

2013-09-15

Purpose: To assess the effect of abdominal compression on the interfraction variation in tumor position in lung stereotactic body radiotherapy (SBRT) using cone-beam computed tomography (CBCT) in a larger series of patients with large tumor motion amplitude.Methods: Thirty patients with lung tumor motion exceeding 8 mm who underwent SBRT were included in this study. After translational and rotational initial setup error was corrected based on bone anatomy, CBCT images were acquired for each fraction. The residual interfraction variation was defined as the difference between the centroid position of the visualized target in three dimensions derived from CBCT scans and thosemore » derived from averaged intensity projection images. The authors compared the magnitude of the interfraction variation in tumor position between patients treated with [n= 16 (76 fractions)] and without [n= 14 (76 fractions)] abdominal compression.Results: The mean ± standard deviation (SD) of the motion amplitude in the longitudinal direction before abdominal compression was 19.9 ± 7.3 (range, 10–40) mm and was significantly (p < 0.01) reduced to 12.4 ± 5.8 (range, 5–30) mm with compression. The greatest variance of the interfraction variation with abdominal compression was observed in the longitudinal direction, with a mean ± SD of 0.79 ± 3.05 mm, compared to −0.60 ± 2.10 mm without abdominal compression. The absolute values of the 95th percentile of the interfraction variation for one side in each direction were 3.97/6.21 mm (posterior/anterior), 4.16/3.76 mm (caudal/cranial), and 2.90/2.32 mm (right/left) without abdominal compression, and 2.14/5.03 mm (posterior/anterior), 3.93/9.23 mm (caudal/cranial), and 2.37/5.45 mm (right/left) with abdominal compression. An absolute interfraction variation greater than 5 mm was observed in six (9.2%) fractions without and 13 (17.1%) fractions with abdominal compression.Conclusions: Abdominal compression was effective for reducing the amplitude of tumor motion. However, in most of the authors’ patients, the use of abdominal compression seemed to increase the interfraction variation in tumor position, despite reducing lung tumor motion. The daily tumor position deviated more systematically from the tumor position in the planning CT scan in the lateral and longitudinal directions in patients treated with abdominal compression compared to those treated without compression. Therefore, target matching is required to correct or minimize the interfraction variation.« less

Development of type 2 diabetes caused by a deficiency of a tRNA(lys) modification.

PubMed

Wei, Fan-Yan; Tomizawa, Kazuhito

2012-01-01

Genetic variations in the cdk5 regulator associated protein 1-like 1 (cdkal1) gene have been identified in whole genome association studies as a risk factor for the development of type 2 diabetes (T2D). A recent study showed that Cdkal1 was a mammalian methythiotransferase, which specifically synthesizes 2-methylthio-N (6)-threonylcarbamoyladenosine (ms (2)t (6)A) at position 37 of tRNA(lys)(UUU). The ms (2)t (6)A modification in tRNA(lys)(UUU) was important for the accurate decoding of its cognate codon. In pancreatic β-cell-specific Cdkal1 knockout (Cdkal1 KO) mice, a deficiency of ms (2)t (6)A caused the mistranslation of a Lys codon in proinsulin, resulting in improper processing. The mice showed a decrease in insulin secretion and glucose intolerance. In addition, the mistranslation contributed to the expression of the endoplasmic reticulum (ER) stress response in Cdkal1-deficient β-cells. Furthermore, Cdkal1 KO mice were hypersensitive to high-fat diet-induced glucose intolerance, as well as the ER stress response. These findings might potentially explain the molecular pathogenesis of T2D in patients carrying Cdkal1 variations.

Morphological and Molecular Identification of Globodera pallida Associated with Potato in Idaho

PubMed Central

Skantar, A. M.; Handoo, Z. A.; Carta, L. K.; Chitwood, D. J.

2007-01-01

The identity of a newly discovered population of pale potato cyst nematode Globodera pallida associated with potato in eastern Idaho was established by morphological and molecular methods. Morphometrics of cysts and second-stage juveniles were generally within the expected ranges for G. pallida with some variations noted. The Idaho population and paratype material from Epworth, Lincolnshire, England, both showed variations in tail shape, with bluntly rounded to finely pointed tail termini. Compared to literature values for the paratypes, second-stage juveniles of the Idaho population had a somewhat shorter mean body length, and cysts had a slightly higher mean distance from the anus to the nearest edge of the fenestra. PCR-RFLP of the rDNA ITS region, sequence-specific multiplex PCR and DNA sequence comparisons all confirmed the identity of the Idaho population as G. pallida. The ITS rDNA sequence of the Idaho isolate was identical to those from York, England, and the Netherlands. Species-specific primers that can positively identify the tobacco cyst nematode Globodera tabacum were also developed, providing a new assay for distinguishing this species from G. pallida and the golden potato cyst nematode Globodera rostochiensis. PMID:19259482

Lagrangian Turbulence and Transport in Semi-Enclosed Basins and Coastal Regions

DTIC Science & Technology

2008-09-30

P.M. Poulain, R. Signell, J. Chiggiato , S. Carniel, 2008: Variational analysis of drifter positions and model outputs for the reconstruction of... Chiggiato , S. Carniel, 2008: Variational analysis of drifter positions and model outputs for the reconstruction of surface currents in the Central

What drives interaction strengths in complex food webs? A test with feeding rates of a generalist stream predator.

PubMed

Preston, Daniel L; Henderson, Jeremy S; Falke, Landon P; Segui, Leah M; Layden, Tamara J; Novak, Mark

2018-05-08

Describing the mechanisms that drive variation in species interaction strengths is central to understanding, predicting, and managing community dynamics. Multiple factors have been linked to trophic interaction strength variation, including species densities, species traits, and abiotic factors. Yet most empirical tests of the relative roles of multiple mechanisms that drive variation have been limited to simplified experiments that may diverge from the dynamics of natural food webs. Here, we used a field-based observational approach to quantify the roles of prey density, predator density, predator-prey body-mass ratios, prey identity, and abiotic factors in driving variation in feeding rates of reticulate sculpin (Cottus perplexus). We combined data on over 6,000 predator-prey observations with prey identification time functions to estimate 289 prey-specific feeding rates at nine stream sites in Oregon. Feeding rates on 57 prey types showed an approximately log-normal distribution, with few strong and many weak interactions. Model selection indicated that prey density, followed by prey identity, were the two most important predictors of prey-specific sculpin feeding rates. Feeding rates showed a positive relationship with prey taxon densities that was inconsistent with predator saturation predicted by current functional response models. Feeding rates also exhibited four orders-of-magnitude in variation across prey taxonomic orders, with the lowest feeding rates observed on prey with significant anti-predator defenses. Body-mass ratios were the third most important predictor variable, showing a hump-shaped relationship with the highest feeding rates at intermediate ratios. Sculpin density was negatively correlated with feeding rates, consistent with the presence of intraspecific predator interference. Our results highlight how multiple co-occurring drivers shape trophic interactions in nature and underscore ways in which simplified experiments or reliance on scaling laws alone may lead to biased inferences about the structure and dynamics of species-rich food webs. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

The Impact of Anxiety-Inducing Distraction on Cognitive Performance: A Combined Brain Imaging and Personality Investigation

PubMed Central

Denkova, Ekaterina; Wong, Gloria; Dolcos, Sanda; Sung, Keen; Wang, Lihong; Coupland, Nicholas; Dolcos, Florin

2010-01-01

Background Previous investigations revealed that the impact of task-irrelevant emotional distraction on ongoing goal-oriented cognitive processing is linked to opposite patterns of activation in emotional and perceptual vs. cognitive control/executive brain regions. However, little is known about the role of individual variations in these responses. The present study investigated the effect of trait anxiety on the neural responses mediating the impact of transient anxiety-inducing task-irrelevant distraction on cognitive performance, and on the neural correlates of coping with such distraction. We investigated whether activity in the brain regions sensitive to emotional distraction would show dissociable patterns of co-variation with measures indexing individual variations in trait anxiety and cognitive performance. Methodology/Principal Findings Event-related fMRI data, recorded while healthy female participants performed a delayed-response working memory (WM) task with distraction, were investigated in conjunction with behavioural measures that assessed individual variations in both trait anxiety and WM performance. Consistent with increased sensitivity to emotional cues in high anxiety, specific perceptual areas (fusiform gyrus - FG) exhibited increased activity that was positively correlated with trait anxiety and negatively correlated with WM performance, whereas specific executive regions (right lateral prefrontal cortex - PFC) exhibited decreased activity that was negatively correlated with trait anxiety. The study also identified a role of the medial and left lateral PFC in coping with distraction, as opposed to reflecting a detrimental impact of emotional distraction. Conclusions These findings provide initial evidence concerning the neural mechanisms sensitive to individual variations in trait anxiety and WM performance, which dissociate the detrimental impact of emotion distraction and the engagement of mechanisms to cope with distracting emotions. Our study sheds light on the neural correlates of emotion-cognition interactions in normal behaviour, which has implications for understanding factors that may influence susceptibility to affective disorders, in general, and to anxiety disorders, in particular. PMID:21152391

Effect of Plasmid Design and Type of Integration Event on Recombinant Protein Expression in Pichia pastoris.

PubMed

Vogl, Thomas; Gebbie, Leigh; Palfreyman, Robin W; Speight, Robert

2018-03-15

Pichia pastoris (syn. Komagataella phaffii ) is one of the most common eukaryotic expression systems for heterologous protein production. Expression cassettes are typically integrated in the genome to obtain stable expression strains. In contrast to Saccharomyces cerevisiae , where short overhangs are sufficient to target highly specific integration, long overhangs are more efficient in P. pastoris and ectopic integration of foreign DNA can occur. Here, we aimed to elucidate the influence of ectopic integration by high-throughput screening of >700 transformants and whole-genome sequencing of 27 transformants. Different vector designs and linearization approaches were used to mimic the most common integration events targeted in P. pastoris Fluorescence of an enhanced green fluorescent protein (eGFP) reporter protein was highly uniform among transformants when the expression cassettes were correctly integrated in the targeted locus. Surprisingly, most nonspecifically integrated transformants showed highly uniform expression that was comparable to specific integration, suggesting that nonspecific integration does not necessarily influence expression. However, a few clones (<10%) harboring ectopically integrated cassettes showed a greater variation spanning a 25-fold range, surpassing specifically integrated reference strains up to 6-fold. High-expression strains showed a correlation between increased gene copy numbers and high reporter protein fluorescence levels. Our results suggest that for comparing expression levels between strains, the integration locus can be neglected as long as a sufficient numbers of transformed strains are compared. For expression optimization of highly expressible proteins, increasing copy number appears to be the dominant positive influence rather than the integration locus, genomic rearrangements, deletions, or single-nucleotide polymorphisms (SNPs). IMPORTANCE Yeasts are commonly used as biotechnological production hosts for proteins and metabolites. In the yeast Saccharomyces cerevisiae , expression cassettes carrying foreign genes integrate highly specifically at the targeted sites in the genome. In contrast, cassettes often integrate at random genomic positions in nonconventional yeasts, such as Pichia pastoris (syn. Komagataella phaffii ). Hence, cells from the same transformation event often behave differently, with significant clonal variation necessitating the screening of large numbers of strains. The importance of this study is that we systematically investigated the influence of integration events in more than 700 strains. Our findings provide novel insight into clonal variation in P. pastoris and, thus, how to avoid pitfalls and obtain reliable results. The underlying mechanisms may also play a role in other yeasts and hence could be generally relevant for recombinant yeast protein production strains. Copyright © 2018 American Society for Microbiology.

Impact of Parental Bos taurus and Bos indicus Origins on Copy Number Variation in Traditional Chinese Cattle Breeds

PubMed Central

Zhang, Liangzhi; Jia, Shangang; Plath, Martin; Huang, Yongzhen; Li, Congjun; Lei, Chuzhao; Zhao, Xin; Chen, Hong

2015-01-01

Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also in domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here, we of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal single nucleotide polymorphisms to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y1, Y2; B. indicus: Y3), whereas 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression. PMID:26260653

Sex-dependent selection differentially shapes genetic variation on and off the guppy Y chromosome.

PubMed

Postma, Erik; Spyrou, Nicolle; Rollins, Lee Ann; Brooks, Robert C

2011-08-01

Because selection is often sex-dependent, alleles can have positive effects on fitness in one sex and negative effects in the other, resulting in intralocus sexual conflict. Evolutionary theory predicts that intralocus sexual conflict can drive the evolution of sex limitation, sex-linkage, and sex chromosome differentiation. However, evidence that sex-dependent selection results in sex-linkage is limited. Here, we formally partition the contribution of Y-linked and non-Y-linked quantitative genetic variation in coloration, tail, and body size of male guppies (Poecilia reticulata)-traits previously implicated as sexually antagonistic. We show that these traits are strongly genetically correlated, both on and off the Y chromosome, but that these correlations differ in sign and magnitude between both parts of the genome. As predicted, variation in attractiveness was found to be associated with the Y-linked, rather than with the non-Y-linked component of genetic variation in male ornamentation. These findings show how the evolution of Y-linkage may be able to resolve sexual conflict. More generally, they provide unique insight into how sex-specific selection has the potential to differentially shape the genetic architecture of fitness traits across different parts of the genome. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Differences in protein expression among five species of stream stonefly (Plecoptera) along a latitudinal gradient in Japan.

PubMed

Gamboa, Maribet; Tsuchiya, Maria Claret; Matsumoto, Suguru; Iwata, Hisato; Watanabe, Kozo

2017-11-01

Proteome variation among natural populations along an environmental gradient may provide insights into how the biological functions of species are related to their local adaptation. We investigated protein expression in five stream stonefly species from four geographic regions along a latitudinal gradient in Japan with varying climatic conditions. The extracted proteins were separated by two-dimensional gel electrophoresis and identified by matrix-assisted laser desorption/ionization of time-of-flight (MALDI TOF/TOF), yielding 446 proteins. Low interspecies variation in the proteome profiles was observed among five species within geographical regions, presumably due to the co-occurring species sharing the environments. However, large spatial variations in protein expression were found among four geographic regions, suggesting strong regulation of protein expression in heterogeneous environments, where the spatial variations were positively correlated with water temperature. We identified 21 unique proteins expressed specifically in a geographical region and six common proteins expressed throughout all regions. In warmer regions, metabolic proteins were upregulated, whereas proteins related to cold stress, the photoperiod, and mating were downregulated. Oxygen-related and energy-production proteins were upregulated in colder regions with higher altitudes. Thus, our proteomic approach is useful for identifying and understanding important biological functions related to local adaptations by populations of stoneflies. © 2017 Wiley Periodicals, Inc.

Plant reproductive allocation predicts herbivore dynamics across spatial and temporal scales.

PubMed

Miller, Tom E X; Tyre, Andrew J; Louda, Svata M

2006-11-01

Life-history theory suggests that iteroparous plants should be flexible in their allocation of resources toward growth and reproduction. Such plasticity could have consequences for herbivores that prefer or specialize on vegetative versus reproductive structures. To test this prediction, we studied the response of the cactus bug (Narnia pallidicornis) to meristem allocation by tree cholla cactus (Opuntia imbricata). We evaluated the explanatory power of demographic models that incorporated variation in cactus relative reproductive effort (RRE; the proportion of meristems allocated toward reproduction). Field data provided strong support for a single model that defined herbivore fecundity as a time-varying, increasing function of host RRE. High-RRE plants were predicted to support larger insect populations, and this effect was strongest late in the season. Independent field data provided strong support for these qualitative predictions and suggested that plant allocation effects extend across temporal and spatial scales. Specifically, late-season insect abundance was positively associated with interannual changes in cactus RRE over 3 years. Spatial variation in insect abundance was correlated with variation in RRE among five cactus populations across New Mexico. We conclude that plant allocation can be a critical component of resource quality for insect herbivores and, thus, an important mechanism underlying variation in herbivore abundance across time and space.

Temporal changes of 210Po in temperate coastal waters.

PubMed

Wildgust, M A; McDonald, P; White, K N

1998-06-18

The temporal variation of Polonium-210 (210Po) was examined in coastal sea water, the mussel Mytilus edulis, the winkle Littorina littorea and green alga Ulva lactuca in order to investigate the entry of 210Po into the marine food chain. More than 99% of 210Po in the water column occurred in the particulate phase. Dissolved 210Po concentrations peaked during the spring phytoplankton bloom and it is suggested this is related to preferential scavenging of 210Po by the increased numbers of bacteria, viruses and small dissolved particulates. Changes in L. littorea 210Po specific activity are thought not to be related to food, but to a drop in body weight following spawning. Much of the 210Po accumulated by M. edulis was located in the digestive gland. The specific activity of 210Po in the digestive gland of M. edulis was shown to be strongly correlated with changes in sea water suspended particulate specific activity. Examination of other trace metal (Ag, Al, As, Ca, Cd, Cr, Co, Cu, Fe, Hg, K, Mg, Mn, Na, Ni, Sb, Se, Sn and Zn) variations in the digestive gland revealed that class B and borderline metals had a strong positive correlation with 210Po. On-going work is investigating whether the accumulation and loss of 210Po is affected by the presence of metallothioneins.

Experimental Null Method to Guide the Development of Technical Procedures and to Control False-Positive Discovery in Quantitative Proteomics.

PubMed

Shen, Xiaomeng; Hu, Qiang; Li, Jun; Wang, Jianmin; Qu, Jun

2015-10-02

Comprehensive and accurate evaluation of data quality and false-positive biomarker discovery is critical to direct the method development/optimization for quantitative proteomics, which nonetheless remains challenging largely due to the high complexity and unique features of proteomic data. Here we describe an experimental null (EN) method to address this need. Because the method experimentally measures the null distribution (either technical or biological replicates) using the same proteomic samples, the same procedures and the same batch as the case-vs-contol experiment, it correctly reflects the collective effects of technical variability (e.g., variation/bias in sample preparation, LC-MS analysis, and data processing) and project-specific features (e.g., characteristics of the proteome and biological variation) on the performances of quantitative analysis. To show a proof of concept, we employed the EN method to assess the quantitative accuracy and precision and the ability to quantify subtle ratio changes between groups using different experimental and data-processing approaches and in various cellular and tissue proteomes. It was found that choices of quantitative features, sample size, experimental design, data-processing strategies, and quality of chromatographic separation can profoundly affect quantitative precision and accuracy of label-free quantification. The EN method was also demonstrated as a practical tool to determine the optimal experimental parameters and rational ratio cutoff for reliable protein quantification in specific proteomic experiments, for example, to identify the necessary number of technical/biological replicates per group that affords sufficient power for discovery. Furthermore, we assessed the ability of EN method to estimate levels of false-positives in the discovery of altered proteins, using two concocted sample sets mimicking proteomic profiling using technical and biological replicates, respectively, where the true-positives/negatives are known and span a wide concentration range. It was observed that the EN method correctly reflects the null distribution in a proteomic system and accurately measures false altered proteins discovery rate (FADR). In summary, the EN method provides a straightforward, practical, and accurate alternative to statistics-based approaches for the development and evaluation of proteomic experiments and can be universally adapted to various types of quantitative techniques.

Development and evaluation of the quantitative real-time PCR assay in detection and typing of herpes simplex virus in swab specimens from patients with genital herpes.

PubMed

Liu, Junlian; Yi, Yong; Chen, Wei; Si, Shaoyan; Yin, Mengmeng; Jin, Hua; Liu, Jianjun; Zhou, Jinlian; Zhang, Jianzhong

2015-01-01

Genital herpes (GH), which is caused mainly by herpes simplex virus (HSV)-2 and HSV-1, remains a worldwide problem. Laboratory confirmation of GH is important, particularly as there are other conditions which present similarly to GH, while atypical presentations of GH also occur. Currently, virus culture is the classical method for diagnosis of GH, but it is time consuming and with low sensitivity. A major advance for diagnosis of GH is to use Real-time polymerase chain reaction (PCR). In this study, to evaluate the significance of the real-time PCR method in diagnosis and typing of genital HSV, the primers and probes targeted at HSV-1 DNA polymerase gene and HSV-2 glycoprotein D gene fraction were designed and applied to amplify DNA from HSV-1 or HSV-2 by employing the real-time PCR technique. Then the PCR reaction system was optimized and evaluated. HSV in swab specimens from patients with genital herpes was detected by real-time PCR. The real-time PCR assay showed good specificity for detection and typing of HSV, with good linear range (5×10(2)~5×10(8) copies/ml, r=0.997), a sensitivity of 5×10(2) copies/ml, and good reproducibility (intra-assay coefficients of variation 2.29% and inter-assay coefficients of variation 4.76%). 186 swab specimens were tested for HSV by real-time PCR, and the positive rate was 23.7% (44/186). Among the 44 positive specimens, 8 (18.2%) were positive for HSV-1 with a viral load of 8.5546×10(6) copies/ml and 36 (81.2%) were positive for HSV-2 with a viral load of 1.9861×10(6) copies/ml. It is concluded that the real-time PCR is a specific, sensitive and rapid method for the detection and typing of HSV, which can be widely used in clinical diagnosis of GH.

Differential Evolution and Neofunctionalization of Snake Venom Metalloprotease Domains*

PubMed Central

Brust, Andreas; Sunagar, Kartik; Undheim, Eivind A.B.; Vetter, Irina; Yang, Daryl C.; Casewell, Nicholas R.; Jackson, Timothy N. W.; Koludarov, Ivan; Alewood, Paul F.; Hodgson, Wayne C.; Lewis, Richard J.; King, Glenn F.; Antunes, Agostinho; Hendrikx, Iwan; Fry, Bryan G.

2013-01-01

Snake venom metalloproteases (SVMP) are composed of five domains: signal peptide, propeptide, metalloprotease, disintegrin, and cysteine-rich. Secreted toxins are typically combinatorial variations of the latter three domains. The SVMP-encoding genes of Psammophis mossambicus venom are unique in containing only the signal and propeptide domains. We show that the Psammophis SVMP propeptide evolves rapidly and is subject to a high degree of positive selection. Unlike Psammophis, some species of Echis express both the typical multidomain and the unusual monodomain (propeptide only) SVMP, with the result that a lower level of variation is exerted upon the latter. We showed that most mutations in the multidomain Echis SVMP occurred in the protease domain responsible for proteolytic and hemorrhagic activities. The cysteine-rich and disintegrin-like domains, which are putatively responsible for making the P-III SVMPs more potent than the P-I and P-II forms, accumulate the remaining variation. Thus, the binding sites on the molecule's surface are evolving rapidly whereas the core remains relatively conserved. Bioassays conducted on two post-translationally cleaved novel proline-rich peptides from the P. mossambicus propeptide domain showed them to have been neofunctionalized for specific inhibition of mammalian a7 neuronal nicotinic acetylcholine receptors. We show that the proline rich postsynaptic specific neurotoxic peptides from Azemiops feae are the result of convergent evolution within the precursor region of the C-type natriuretic peptide instead of the SVMP. The results of this study reinforce the value of studying obscure venoms for biodiscovery of novel investigational ligands. PMID:23242553

Differential evolution and neofunctionalization of snake venom metalloprotease domains.

PubMed

Brust, Andreas; Sunagar, Kartik; Undheim, Eivind A B; Vetter, Irina; Yang, Daryl C; Yang, Dary C; Casewell, Nicholas R; Jackson, Timothy N W; Koludarov, Ivan; Alewood, Paul F; Hodgson, Wayne C; Lewis, Richard J; King, Glenn F; Antunes, Agostinho; Hendrikx, Iwan; Fry, Bryan G

2013-03-01

Snake venom metalloproteases (SVMP) are composed of five domains: signal peptide, propeptide, metalloprotease, disintegrin, and cysteine-rich. Secreted toxins are typically combinatorial variations of the latter three domains. The SVMP-encoding genes of Psammophis mossambicus venom are unique in containing only the signal and propeptide domains. We show that the Psammophis SVMP propeptide evolves rapidly and is subject to a high degree of positive selection. Unlike Psammophis, some species of Echis express both the typical multidomain and the unusual monodomain (propeptide only) SVMP, with the result that a lower level of variation is exerted upon the latter. We showed that most mutations in the multidomain Echis SVMP occurred in the protease domain responsible for proteolytic and hemorrhagic activities. The cysteine-rich and disintegrin-like domains, which are putatively responsible for making the P-III SVMPs more potent than the P-I and P-II forms, accumulate the remaining variation. Thus, the binding sites on the molecule's surface are evolving rapidly whereas the core remains relatively conserved. Bioassays conducted on two post-translationally cleaved novel proline-rich peptides from the P. mossambicus propeptide domain showed them to have been neofunctionalized for specific inhibition of mammalian a7 neuronal nicotinic acetylcholine receptors. We show that the proline rich postsynaptic specific neurotoxic peptides from Azemiops feae are the result of convergent evolution within the precursor region of the C-type natriuretic peptide instead of the SVMP. The results of this study reinforce the value of studying obscure venoms for biodiscovery of novel investigational ligands.

Monthly Estimates of Alcohol Drinking During Pregnancy: United States, 2002-2011.

PubMed

Alshaarawy, Omayma; Breslau, Naomi; Anthony, James C

2016-03-01

Taking a step beyond prior alcohol research on pregnancy trimesters, we produced pregnancy month-specific drinking estimates for women in the United States in order to shed light on time variations of alcohol drinking during pregnancy, as might be determined by alcohol dependence. We posited that (a) pregnancy might prompt cessation of drinking soon after pregnancy status is discovered, a finding obscured in trimester-specific estimates, and (b) a possible alcohol-dependence effect on drinking persistence among pregnant women might be observed via the monthly approach. Data are from the 2002-2011 National Surveys on Drug Use and Health (Restricted-Data Analysis System [R-DAS]), with large nationally representative samples of U.S. civilians, including 12- to 44-year-old females stratified by pregnancy status and month of pregnancy, and with assessment of recent alcohol dependence as well as heavy episodic drinking (HED). Pregnancy's possibly protective constraints on drinking can be seen as early as Month 2. We observed considerable variability of drinking prevalence (%) before Trimester 1 ended, with no appreciable variation across Months 4-9. A possible alcohol-dependence effect on drinking persistence is seen when the contrast is made in relation to expected values for pregnant women without alcohol dependence. We detected a possibly ameliorative pregnancy effect on alcohol use and HED, with variation in drinking prevalence across the months of the first trimester. Alcohol dependence might be affecting drinking persistence among pregnant women, but this effect cannot account for the drinking persistence observed here.

Analytical performance specifications for changes in assay bias (Δbias) for data with logarithmic distributions as assessed by effects on reference change values.

PubMed

Petersen, Per H; Lund, Flemming; Fraser, Callum G; Sölétormos, György

2016-11-01

Background The distributions of within-subject biological variation are usually described as coefficients of variation, as are analytical performance specifications for bias, imprecision and other characteristics. Estimation of specifications required for reference change values is traditionally done using relationship between the batch-related changes during routine performance, described as Δbias, and the coefficients of variation for analytical imprecision (CV A ): the original theory is based on standard deviations or coefficients of variation calculated as if distributions were Gaussian. Methods The distribution of between-subject biological variation can generally be described as log-Gaussian. Moreover, recent analyses of within-subject biological variation suggest that many measurands have log-Gaussian distributions. In consequence, we generated a model for the estimation of analytical performance specifications for reference change value, with combination of Δbias and CV A based on log-Gaussian distributions of CV I as natural logarithms. The model was tested using plasma prolactin and glucose as examples. Results Analytical performance specifications for reference change value generated using the new model based on log-Gaussian distributions were practically identical with the traditional model based on Gaussian distributions. Conclusion The traditional and simple to apply model used to generate analytical performance specifications for reference change value, based on the use of coefficients of variation and assuming Gaussian distributions for both CV I and CV A , is generally useful.

Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

PubMed Central

Carvalho, Alexandra T P; Gouveia, Leonor; Kanna, Charan Raju; Wärmländer, Sebastian K T S; Platts, Jamie A; Kamerlin, Shina Caroline Lynn

2014-01-01

We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding. PMID:25625845

Toward rules relating zinc finger protein sequences and DNA binding site preferences.

PubMed

Desjarlais, J R; Berg, J M

1992-08-15

Zinc finger proteins of the Cys2-His2 type consist of tandem arrays of domains, where each domain appears to contact three adjacent base pairs of DNA through three key residues. We have designed and prepared a series of variants of the central zinc finger within the DNA binding domain of Sp1 by using information from an analysis of a large data base of zinc finger protein sequences. Through systematic variations at two of the three contact positions (underlined), relatively specific recognition of sequences of the form 5'-GGGGN(G or T)GGG-3' has been achieved. These results provide the basis for rules that may develop into a code that will allow the design of zinc finger proteins with preselected DNA site specificity.

Near real-time monitoring and mapping of specific conductivity levels across Lake Texoma, USA

USGS Publications Warehouse

Atkinson, S.F.; Mabe, J.A.

2006-01-01

A submersible sonde equipped with a specific conductivity probe, linked with a global positioning satellite receiver was developed, deployed on a small boat, and used to map spatial and temporal variations in specific conductivity in a large reservoir. 7,695 sample points were recorded during 8 sampling trips. Specific conductivity ranged from 442 uS/cm to 3,378 uS/cm over the nine-month study. The data showed five statistically different zones in the reservoir: 2 different riverine zones, 2 different riverine transition zones, and a lacustrine zone (the main lake zone). These data were imported to a geographic information system where they were spatially interpolated to generate 8 maps showing specific conductivity levels across the entire surface of the lake. The highly dynamic nature of water quality, due to the widely differing nature of the rivers that flow into the reservoir and the effect of large inflows of fresh water during winter storms is easily captured and visualized using this approach. ?? Springer Science+Business Media, Inc. 2006.

A cross-sectional study of the influence of neighborhood environment on childhood overweight and obesity: Variation by age, gender, and environment characteristics.

PubMed

Yang, Yong; Jiang, Yu; Xu, Yanqing; Mzayek, Fawaz; Levy, Marian

2018-03-01

To examine the influence of neighborhood environment on childhood overweight and obesity in Shelby County Schools, Tennessee, and whether and to what extent that influence varies by age, gender, and the specific environment characteristics. 41,283 students were surveyed covering both individual-level covariates and several objective measures of neighborhood environment. Multilevel logistic regressions were used to examine the influence of neighborhood-level variables on overweight+obesity and obesity with adjustment of individual-level covariates. Further, a stratified analysis for each of the six groups by school level and gender. For both overweight+obesity and obesity, younger children were less sensitive to neighborhood characteristics than older children, and boys are less sensitive than girls. For girls in middle and high schools, the risk of overweight+obesity and obesity were positively associated with population density, and negatively associated with percent of poverty and percent of unhealthy food. Boys' risk of overweight+obesity and obesity were positively associated with distance to park. Neighborhood environment plays an important role in childhood overweight and obesity, and the effects vary by age, gender, and the specific neighborhood characteristic. Intervention programs tailored to specific groups may be more effective than ones targeted to children as a whole. Copyright © 2018 Elsevier Inc. All rights reserved.

The effect of the hot oxygen corona on the interaction of the solar wind with Venus

NASA Technical Reports Server (NTRS)

Belotserkovskii, O. M.; Mitnitskii, V. IA.; Breus, T. K.; Krymskii, A. M.; Nagy, A. F.

1987-01-01

A numerical gasdynamic model, which includes the effects of mass loading of the shocked solar wind, was used to calculate the density and magnetic field variations in the magnetosheath of Venus. These calculations were carried out for conditions corresponding to a specific orbit of the Pioneer Venus Orbiter (PVO orbit 582). A comparison of the model predictions and the measured shock position, density and magnetic field values showed a reasonable agreement, indicating that a gasdynamic model that includes the effects of mass loading can be used to predict these parameters.

The genetic basis of adaptive pigmentation variation in Drosophila melanogaster.

PubMed

Pool, John E; Aquadro, Charles F

2007-07-01

In a broad survey of Drosophila melanogaster population samples, levels of abdominal pigmentation were found to be highly variable and geographically differentiated. A strong positive correlation was found between dark pigmentation and high altitude, suggesting adaptation to specific environments. DNA sequence polymorphism at the candidate gene ebony revealed a clear association with the pigmentation of homozygous third chromosome lines. The darkest lines sequenced had nearly identical haplotypes spanning 14.5 kb upstream of the protein-coding exons of ebony. Thus, natural selection may have elevated the frequency of an allele that confers dark abdominal pigmentation by influencing the regulation of ebony.

The effect of the hot oxygen corona on the interaction of the solar wind with Venus

NASA Astrophysics Data System (ADS)

Belotserkovskii, O. M.; Breus, T. K.; Krymskii, A. M.; Mitnitskii, V. Ya.; Nagey, A. F.; Gombosi, T. I.

1987-05-01

A numerical gas dynamic model, which includes the effects of mass loading of the shocked solar wind, was used to calculate the density and magnetic field variations in the magnetosheath of Venus. These calculations were carried out for conditions corresponding to a specific orbit of the Pioneer Venus Orbiter (PVO orbit 582). A comparison of the model predictions and the measured shock position, density and magnetic field values showed a reasonable agreement, indicating that a gas dynamic model that includes the effects of mass loading can be used to predict these parameters.

Ablation characteristics of carbon-doped glycerol irradiated by a 1064 nm nanosecond pulse laser

NASA Astrophysics Data System (ADS)

Jing, QI; Siqi, ZHANG; Tian, LIANG; Ke, XIAO; Weichong, TANG; Zhiyuan, ZHENG

2018-03-01

The ablation characteristics of carbon-doped glycerol were investigated in laser plasma propulsion using a pulse laser with 10 ns pulse width and 1064 nm wavelength. The results showed that with the incident laser intensity increasing, the target momentum decreased. Results still indicated that the strong plasma shielded the consumption loss and resulted in a low coupling coefficient. Furthermore, the carbon-doping gave rise to variations in the laser focal position and laser intensity, which in turn reduced the glycerol splashing. Based on the glycerol viscosity and the carbon doping, a high specific impulse is anticipated.

Healthy Dietary Patterns and Oxidative Stress as Measured by Fluorescent Oxidation Products in Nurses' Health Study.

PubMed

Jung, Seungyoun; Smith-Warner, Stephanie A; Willett, Walter C; Wang, Molin; Wu, Tianying; Jensen, Majken; Hankinson, Susan E; Eliassen, A Heather

2016-09-21

Healthy diets may lower oxidative stress and risk of chronic diseases. However, no previous studies examined associations between diet and fluorescent oxidation products (FlOP), a global marker of oxidative stress. We evaluated associations between healthy eating patterns (Alternative Healthy Eating Index (AHEI), Dietary Approach to Stop Hypertension (DASH), and Alternate Mediterranean Diet (aMED)) and FlOP, measured at three excitation/emission wavelengths (FlOP_360, FlOP_320, FlOP_400) from 2021 blood samples collected from 1688 women within the Nurses' Health Study. AHEI, DASH, and aMED scores were significantly positively associated with FlOP_360 and FlOP_320 concentrations ( p -trend ≤ 0.04), but not associated with FlOP_400. Among specific food groups that contribute to these diet scores, significantly positive associations were observed with legumes and vegetables for FlOP_360, vegetables and fruits for FlOP_320, and legumes and alcohol for FlOP_400. Inverse associations were observed with nuts, sweets or desserts, and olive oil for FlOP_360, nuts for FlOP_320 and sweets or desserts for FlOP_400 (all p -trend ≤ 0.05). However, FlOP variation due to diet was small compared to overall FlOP variation. In conclusion, AHEI, DASH, and aMED scores were unexpectedly positively, but weakly, associated with FlOP_360 and FlOP_320. However, these findings should be interpreted cautiously as the determinants of FlOP concentrations are not fully understood.

Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes.

PubMed

Yeo, Zhen Xuan; Wong, Joshua Chee Leong; Rozen, Steven G; Lee, Ann Siew Gek

2014-06-24

The Ion Torrent PGM is a popular benchtop sequencer that shows promise in replacing conventional Sanger sequencing as the gold standard for mutation detection. Despite the PGM's reported high accuracy in calling single nucleotide variations, it tends to generate many false positive calls in detecting insertions and deletions (indels), which may hinder its utility for clinical genetic testing. Recently, the proprietary analytical workflow for the Ion Torrent sequencer, Torrent Suite (TS), underwent a series of upgrades. We evaluated three major upgrades of TS by calling indels in the BRCA1 and BRCA2 genes. Our analysis revealed that false negative indels could be generated by TS under both default calling parameters and parameters adjusted for maximum sensitivity. However, indel calling with the same data using the open source variant callers, GATK and SAMtools showed that false negatives could be minimised with the use of appropriate bioinformatics analysis. Furthermore, we identified two variant calling measures, Quality-by-Depth (QD) and VARiation of the Width of gaps and inserts (VARW), which substantially reduced false positive indels, including non-homopolymer associated errors without compromising sensitivity. In our best case scenario that involved the TMAP aligner and SAMtools, we achieved 100% sensitivity, 99.99% specificity and 29% False Discovery Rate (FDR) in indel calling from all 23 samples, which is a good performance for mutation screening using PGM. New versions of TS, BWA and GATK have shown improvements in indel calling sensitivity and specificity over their older counterpart. However, the variant caller of TS exhibits a lower sensitivity than GATK and SAMtools. Our findings demonstrate that although indel calling from PGM sequences may appear to be noisy at first glance, proper computational indel calling analysis is able to maximize both the sensitivity and specificity at the single base level, paving the way for the usage of this technology for future clinical genetic testing.

Socioeconomic inequalities in cause-specific mortality in 15 European cities.

PubMed

Marí-Dell'Olmo, Marc; Gotsens, Mercè; Palència, Laia; Burström, Bo; Corman, Diana; Costa, Giuseppe; Deboosere, Patrick; Díez, Èlia; Domínguez-Berjón, Felicitas; Dzúrová, Dagmar; Gandarillas, Ana; Hoffmann, Rasmus; Kovács, Katalin; Martikainen, Pekka; Demaria, Moreno; Pikhart, Hynek; Rodríguez-Sanz, Maica; Saez, Marc; Santana, Paula; Schwierz, Cornelia; Tarkiainen, Lasse; Borrell, Carme

2015-05-01

Socioeconomic inequalities are increasingly recognised as an important public health issue, although their role in the leading causes of mortality in urban areas in Europe has not been fully evaluated. In this study, we used data from the INEQ-CITIES study to analyse inequalities in cause-specific mortality in 15 European cities at the beginning of the 21st century. A cross-sectional ecological study was carried out to analyse 9 of the leading specific causes of death in small areas from 15 European cities. Using a hierarchical Bayesian spatial model, we estimated smoothed Standardized Mortality Ratios, relative risks and 95% credible intervals for cause-specific mortality in relation to a socioeconomic deprivation index, separately for men and women. We detected spatial socioeconomic inequalities for most causes of mortality studied, although these inequalities differed markedly between cities, being more pronounced in Northern and Central-Eastern Europe. In the majority of cities, most of these causes of death were positively associated with deprivation among men, with the exception of prostatic cancer. Among women, diabetes, ischaemic heart disease, chronic liver diseases and respiratory diseases were also positively associated with deprivation in most cities. Lung cancer mortality was positively associated with deprivation in Northern European cities and in Kosice, but this association was non-existent or even negative in Southern European cities. Finally, breast cancer risk was inversely associated with deprivation in three Southern European cities. The results confirm the existence of socioeconomic inequalities in many of the main causes of mortality, and reveal variations in their magnitude between different European cities. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

[Effects of canopy position and leaf age on photosynthesis and transpiration of Pinus koraiensis].

PubMed

Huo, Hong; Wang, Chuan-kuan

2007-06-01

The photosynthesis and transpiration of Pinus koraiensis needles at different canopy positions and of different leaf ages were measured in the field with a Li-6400 portable CO2/H2O infrared gas analyzer. The results showed that canopy position and leaf age had significant effects on the maximum net photosynthetic rate (Pmax), light saturation point (LSP), light compensation point (LCP), maximum apparent quantum efficiency (alpha), transpiration rate (T(r)), and specific leaf area (SLA), but no effects on water use efficiency (WUE). The Pmax decreased with the decrease of canopy position and the increase of leaf age, ranging in 6.55-9.05 micromol.m(-2).s(-1) on average. There were great variations in LSP and LCP among different canopy positions and leaf ages. The needles at middle canopy position had the greatest capacity of utilizing both weak and strong radiation. The T(r) decreased with canopy position decreasing, and varied from 1.37 to 1.59 mmol.m(-2).s(-1) across different leaf ages. There was a significant positive correlation between T(r) and photosynthetically active radiation (R2 = 0.967), and between WUE and net photosynthetic rate (R2 = 0.860). The SLA decreased with canopy position and leaf age increasing, ranging in 6.61-8.41 m2.kg(-1) and 6.65-8.38 m2.kg(-1), respectively.

An exploratory study of knowledge brokering in hospital settings: facilitating knowledge sharing and learning for patient safety?

PubMed

Waring, Justin; Currie, Graeme; Crompton, Amanda; Bishop, Simon

2013-12-01

This paper reports on an exploratory study of intra-organisational knowledge brokers working within three large acute hospitals in the English National Health Services. Knowledge brokering is promoted as a strategy for supporting knowledge sharing and learning in healthcare, especially in the diffusion of research evidence into practice. Less attention has been given to brokers who support knowledge sharing and learning within healthcare organisations. With specific reference to the need for learning around patient safety, this paper focuses on the structural position and role of four types of intra-organisational brokers. Through ethnographic research it examines how variations in formal role, location and relationships shape how they share and support the use of knowledge across organisational and occupational boundaries. It suggests those occupying hybrid organisational roles, such as clinical-managers, are often best positioned to support knowledge sharing and learning because of their 'ambassadorial' type position and legitimacy to participate in multiple communities through dual-directed relationships. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genetic and epigenetic variation in the lineage specification of regulatory T cells

PubMed Central

Arvey, Aaron; van der Veeken, Joris; Plitas, George; Rich, Stephen S; Concannon, Patrick; Rudensky, Alexander Y

2015-01-01

Regulatory T (Treg) cells, which suppress autoimmunity and other inflammatory states, are characterized by a distinct set of genetic elements controlling their gene expression. However, the extent of genetic and associated epigenetic variation in the Treg cell lineage and its possible relation to disease states in humans remain unknown. We explored evolutionary conservation of regulatory elements and natural human inter-individual epigenetic variation in Treg cells to identify the core transcriptional control program of lineage specification. Analysis of single nucleotide polymorphisms in core lineage-specific enhancers revealed disease associations, which were further corroborated by high-resolution genotyping to fine map causal polymorphisms in lineage-specific enhancers. Our findings suggest that a small set of regulatory elements specify the Treg lineage and that genetic variation in Treg cell-specific enhancers may alter Treg cell function contributing to polygenic disease. DOI: http://dx.doi.org/10.7554/eLife.07571.001 PMID:26510014

[Hypothesis of the correlation of personality characteristics and the clinical history of bronchogenic cancer].

PubMed

Beltrami, V; Buonsanto, A; Di Nuzzo, D; Lattanzio, R

1995-01-01

A correlation between the personality profile and the clinical history in lung cancer patients was studied. Selection of cases included in the sample only surgical patients with a medium educational level and a tested capability to understand a specific questionnaire. One hundred and seventy patients were selected and the so-called C.R.I.C.S. (Clinical-Rated Inventory of Character Style) was applied. Score variations were recorded after curative resection as well as during relapse. Changes in the character profile pattern were found in all subjects who experienced the disease and its surgical treatment. These changes occurred either in "regression"-with an increase of schizoid, narcissistic or hysterical aspects-or in a "positive evolution", with a decrease of paranoid traits and into a depressive position. The two groups of responses demonstrated a similar percentage.

Instant screening and verification of carbapenemase activity in Bacteroides fragilis in positive blood culture, using matrix-assisted laser desorption ionization--time of flight mass spectrometry.

PubMed

Johansson, Åsa; Nagy, Elisabeth; Sóki, József

2014-08-01

Rapid identification of isolates in positive blood cultures are of great importance to secure correct treatment of septicaemic patients. As antimicrobial resistance is increasing, rapid detection of resistance is crucial. Carbapenem resistance in Bacteroides fragilis associated with cfiA-encoded class B metallo-beta-lactamase is emerging. In our study we spiked blood culture bottles with 26 B. fragilis strains with various cfiA-status and ertapenem MICs. By using main spectra specific for cfiA-positive and cfiA-negative B. fragilis strains, isolates could be screened for resistance. To verify strains that were positive in the screening, a carbapenemase assay was performed where the specific peaks of intact and hydrolysed ertapenem were analysed with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). We show here that it is possible to correctly identify B. fragilis and to screen for enzymic carbapenem resistance directly from the pellet of positive blood cultures. The carbapenemase assay to verify the presence of the enzyme was successfully performed on the pellet from the direct identification despite the presence of blood components. The result of the procedure was achieved in 3 h. Also the Bruker mass spectrometric β-lactamase assay (MSBL assay) prototype software was proven not only to be based on an algorithm that correlated with the manual inspection of the spectra, but also to improve the interpretation by showing the variation in the dataset. © 2014 The Authors.

Allelic Variation of Risk for Anxiety Symptoms Moderates the Relation Between Adolescent Safety Behaviors and Social Anxiety Symptoms

PubMed Central

Thomas, Sarah A.; Weeks, Justin W.; Dougherty, Lea R.; Lipton, Melanie F.; Daruwala, Samantha E.; Kline, Kathryn

2015-01-01

Social anxiety often develops in adolescence, and precedes the onset of depression and substance use disorders. The link between social anxiety and use of behaviors to minimize distress in social situations (i.e., safety behaviors) is strong and for some patients, this link poses difficulty for engaging in, and benefiting from, exposure-based treatment. Yet, little is known about whether individual differences may moderate links between social anxiety and safety behaviors, namely variations in genetic alleles germane to anxiety. We examined the relation between adolescent social anxiety and expressions of safety behaviors, and whether allelic variation for anxiety moderates this relation. Adolescents (n=75; ages 14–17) were recruited from two larger studies investigating measurement of family relationships or adolescent social anxiety. Adolescents completed self-report measures about social anxiety symptoms and use of safety behaviors. They also provided saliva samples to assess allelic variations for anxiety from two genetic polymorphisms (BDNF rs6265; TAQ1A rs1800497). Controlling for adolescent age and gender, we observed a significant interaction between social anxiety symptoms and allelic variation (β=0.37, t=2.41, p=.02). Specifically, adolescents carrying allelic variations for anxiety evidenced a statistically significant and relatively strong positive relation between social anxiety symptoms and safety behaviors (β=0.73), whereas adolescents not carrying allelic variation evidenced a statistically non-significant and relatively weak relation (β=0.22). These findings have important implications for treating adolescent social anxiety, in that we identified an individual difference variable that can be used to identify people who evidence a particularly strong link between use of safety behaviors and expressing social anxiety. PMID:26692635

[Analysis of allergens characteristic in 1172 patients with allergic rhinitis in Changzhou area].

PubMed

Shi, Mei; Yao, Lina; Yang, Xiaojun; Chen, Jian; Zhang, Lirong; Sun, Jing; Xu, Xiaopeng

2016-01-01

To determine the distribution of allergens in patients with allergic rhinitis during from 2008 to 2015 in Changzhou area. Allergy Screen method was used to detect the specifical-allergen IgE levels of 1172 patients with allergic rhinitis. Among the patients, the distribution of all allergens was analyzed. The positive rate was compared with age, gender, season and so on. The most common allergens in allergic rhinitis patients in Changzhou were dust mite, fungus, house dust, milk, dander of dog, weed mixture, farina and dander of cat. The more higher positive rates of dust mite, fungus, house dust, milk, dander of dog, dander of cat, eggs were found in teenager group than adult group (P < 0.05). There were more higer positive rates of weed mixture, farina, cashew, cockroaches and crab in teenager group than adult group (P < 0.05). There was no significant difference of positive rate between female group and male group. There was significant difference of variation with seasons. Dust mite, fungus and house dust were the most common allergens among patiens with allergic rhinitis in Changzhou area. The positive rates of allergens varied with ages and seasons.

Differences in within- and between-person factor structure of positive and negative affect: analysis of two intensive measurement studies using multilevel structural equation modeling.

PubMed

Rush, Jonathan; Hofer, Scott M

2014-06-01

The Positive and Negative Affect Schedule (PANAS) is a widely used measure of emotional experience. The factor structure of the PANAS has been examined predominantly with cross-sectional designs, which fails to disaggregate within-person variation from between-person differences. There is still uncertainty as to the factor structure of positive and negative affect and whether they constitute 2 distinct independent factors. The present study examined the within-person and between-person factor structure of the PANAS in 2 independent samples that reported daily affect over 7 and 14 occasions, respectively. Results from multilevel confirmatory factor analyses revealed that a 2-factor structure at both the within-person and between-person levels, with correlated specific factors for overlapping items, provided good model fit. The best-fitting solution was one where within-person factors of positive and negative affect were inversely correlated, but between-person factors were independent. The structure was further validated through multilevel structural equation modeling examining the effects of cognitive interference, daily stress, physical symptoms, and physical activity on positive and negative affect factors.

Single crystal CVD diamond membranes as Position Sensitive X-ray Detector

NASA Astrophysics Data System (ADS)

Desjardins, K.; Menneglier, C.; Pomorski, M.

2017-12-01

Transparent X-ray Beam Position Monitor (XBPM) has been specifically developed for low energy X-ray beamlines (1.4 keV < E < 5 keV) allowing to transmit more than 80% of 2 keV energy beam. The detector is based on a free-standing single crystal CVD diamond membrane of 4 μm thickness with position-sensitive DLC (Diamond-Like Carbon) resistive electrodes in duo-lateral configuration. The measured X-ray beam induced current (XBIC) due to the interaction of X-rays with diamond membrane allows precise monitoring of the absolute beam flux and the beam position (by the reconstruction of its center-of-gravity) at beam transmissions reaching 95%. This detector has been installed at SOLEIL synchrotron on the SIRIUS beamline monochromator output and it has shown charge collection efficiency (CCE) reaching 100% with no lag-effects and excellent beam intensity sensitivity monitoring. X-ray beam mapping of the detector showed an XBIC response inhomogeneity of less than 10% across the membrane, corresponding mainly to the measured variation of the diamond plate thickness. The measured beam position resolution is at sub-micron level depending on the beam flux and the readout electronics bandwidth.

Evaluation of the Enhanced Integrated Climatic Model for modulus-based construction specification for Oklahoma pavements.

DOT National Transportation Integrated Search

2013-07-01

The study provides estimation of site specific variation in environmental factors that can be : used in predicting seasonal and long-term variations in moduli of unbound materials. Using : these site specific estimates, the EICM climatic input files ...

Normal Genetic Variation, Cognition, and Aging

PubMed Central

Greenwood, P. M.; Parasuraman, Raja

2005-01-01

This article reviews the modulation of cognitive function by normal genetic variation. Although the heritability of “g” is well established, the genes that modulate specific cognitive functions are largely unidentified. Application of the allelic association approach to individual differences in cognition has begun to reveal the effects of single nucleotide polymorphisms on specific and general cognitive functions. This article proposes a framework for relating genotype to cognitive phenotype by considering the effect of genetic variation on the protein product of specific genes within the context of the neural basis of particular cognitive domains. Specificity of effects is considered, from genes controlling part of one receptor type to genes controlling agents of neuronal repair, and evidence is reviewed of cognitive modulation by polymorphisms in dopaminergic and cholinergic receptor genes, dopaminergic enzyme genes, and neurotrophic genes. Although allelic variation in certain genes can be reliably linked to cognition—specifically to components of attention, working memory, and executive function in healthy adults—the specificity, generality, and replicability of the effects are not fully known. PMID:15006290

Comparing intra- and inter-specific effects on litter decomposition in an old-field ecosystem

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

Crutsinger, Greg; Sanders, Dr. Nathan James; Classen, Aimee T

2009-09-01

Plant species can differ in the quantity and quality of leaf litter they produce, and many studies have examined whether plant species diversity affects leaf-litter decomposition and nutrient release. A growing number of studies have indicated that intra-specific variation within plant species can also affect key ecosystem processes. However, the relative importance of intra- versus inter-specific variation for the functioning of ecosystems remains poorly known. Here, we investigate the effects of intra-specific variation in a dominant old-field plant species, tall goldenrod (Solidago altissima), and inter-specific variation among goldenrod species on litter quality, decomposition, and nitrogen (N) release. We found thatmore » the nutrient concentration of leaf litter varied among genotypes, which translated into 50% difference in decomposition rates. Variation among other goldenrod species in decomposition rate was more than twice that of genetic variation within S. altissima. Furthermore, by manipulating litterbags to contain 1, 3, 6, or 9 genotypes, we found that S. altissima genotype identity had much stronger effects than did genotypic diversity on leaf-litter quality, decomposition, and N release. Taken together, these results suggest that the order of ecological importance for controlling leaf-litter decomposition and N release dynamics is plant species identitygenotype identity>genotypic diversity.« less

Genovariation Study of Hantavirus in Main Endemic Areas of Hemorrhagic Fever with Renal Syndrome in Hebei Province, China.

PubMed

Li, Qi; Cai, Yanan; Wei, Yamei; Han, Xu; Han, Zhanying; Zhang, Yanbo; Qi, Shunxiang; Xu, Yonggang

2016-01-01

Hemorrhagic fever with renal syndrome (HFRS) is an important infectious disease in Hebei Province. At present, cases from the northeast regions of the province account for >80% of the total incidences. However, studies that examine the region-specific genetic variations of the Hantavirus (HV), the causative pathogen for HFRS, have been lacking. Rodents were collected in northeast Hebei Province from 2004 to 2013, and the HV strains used in this study were isolated in 1993. Lung tissues were isolated from the rodents and HV antigen was detected by indirect immunofluorescence. The M1 and M2 fragments of HV M region were amplified by reverse transcription polymerase chain reaction (RT-PCR), cloned into pMDl9-T vector, sequenced and compared with representative standard stains for homology and phylogenetic analysis. A total of 21 samples of HV antigen-positive were collected. Real-time PCR analysis revealed that the 19 rodent lungs and two HV strains were positive for the SEO virus. 11 samples were chosen to sequence, and they shared 95.8%-99.8% in nucleotide homology, and 83.6%-99.2% when compared to the standard strains of SEO virus. Phylogenetic analysis demonstrated that all strains were grouped into the same S3 subtype. SEO was the major epidemic genotype of HV in the main HFRS endemic areas in Hebei Province, and S3 was the major subtype. There was minor genetic variation in HV over short term periods, while long term variations were higher.

Isolation and molecular characterization of partial FSH and LH receptor genes in Arabian camels (Camelus dromedarius)

PubMed Central

Jelokhani-Niaraki, Saber; Tahmoorespur, Mojtaba; Bitaraf-Sani, Morteza

2015-01-01

Very little is known about LHR and FSHR genes of domestic dromedary camels. The main objective of this study was to determine and analyze partial genomic regions of FSHR and LHR genes in dromedary camels for the first time. To this end, a total of50 DNA samples belonging to dromedary camels raised in Iran were sent for sequencing (25 samples of each gene). We compared the nucleotide sequences of Camelus dromedarius with corresponding sequences of previously published FSHR and LHR genes in bactrian camels and other species. According to the data, the same nucleotide variation was identified in both regions of the two camel species. The alignment of deduced protein sequences of the two different species revealed an amino acid variation at the FSHR region. No evidence of amino acid variation was observed, however, in LHR sequences. Phylogenetic analysis indicated that both camel species had a close relationship and clustered together in a separate branch. This was further confirmed by genetic distance values illustrating significant sequence identity between Camelus dromedarius and Camelus bactrianus. Interestingly, sequence comparisons revealed heterozygote patterns in FSHR sequences isolated from dromedary camels of Iran. In comparison to other species, this camel contains three amino acid substitutions at 5, 67, and 105 positions in the FSHR coding region. These positions are found exclusively in camels and can be considered as species specific. The results of our study can be used for hormone functionality research (FSHR and LHR) as well as reproduction-linked polymorphisms and breeding programs. PMID:27844002

Isolation and molecular characterization of partial FSH and LH receptor genes in Arabian camels (Camelus dromedarius).

PubMed

Jelokhani-Niaraki, Saber; Tahmoorespur, Mojtaba; Bitaraf-Sani, Morteza

2015-06-01

Very little is known about LHR and FSHR genes of domestic dromedary camels. The main objective of this study was to determine and analyze partial genomic regions of FSHR and LHR genes in dromedary camels for the first time. To this end, a total of50 DNA samples belonging to dromedary camels raised in Iran were sent for sequencing (25 samples of each gene). We compared the nucleotide sequences of Camelus dromedarius with corresponding sequences of previously published FSHR and LHR genes in bactrian camels and other species. According to the data, the same nucleotide variation was identified in both regions of the two camel species. The alignment of deduced protein sequences of the two different species revealed an amino acid variation at the FSHR region. No evidence of amino acid variation was observed, however, in LHR sequences. Phylogenetic analysis indicated that both camel species had a close relationship and clustered together in a separate branch. This was further confirmed by genetic distance values illustrating significant sequence identity between Camelus dromedarius and Camelus bactrianus . Interestingly, sequence comparisons revealed heterozygote patterns in FSHR sequences isolated from dromedary camels of Iran. In comparison to other species, this camel contains three amino acid substitutions at 5, 67, and 105 positions in the FSHR coding region. These positions are found exclusively in camels and can be considered as species specific. The results of our study can be used for hormone functionality research ( FSHR and LHR ) as well as reproduction-linked polymorphisms and breeding programs.

A developmental basis for stochasticity in floral organ numbers

PubMed Central

Kitazawa, Miho S.; Fujimoto, Koichi

2014-01-01

Stochasticity ubiquitously inevitably appears at all levels from molecular traits to multicellular, morphological traits. Intrinsic stochasticity in biochemical reactions underlies the typical intercellular distributions of chemical concentrations, e.g., morphogen gradients, which can give rise to stochastic morphogenesis. While the universal statistics and mechanisms underlying the stochasticity at the biochemical level have been widely analyzed, those at the morphological level have not. Such morphological stochasticity is found in foral organ numbers. Although the floral organ number is a hallmark of floral species, it can distribute stochastically even within an individual plant. The probability distribution of the floral organ number within a population is usually asymmetric, i.e., it is more likely to increase rather than decrease from the modal value, or vice versa. We combined field observations, statistical analysis, and mathematical modeling to study the developmental basis of the variation in floral organ numbers among 50 species mainly from Ranunculaceae and several other families from core eudicots. We compared six hypothetical mechanisms and found that a modified error function reproduced much of the asymmetric variation found in eudicot floral organ numbers. The error function is derived from mathematical modeling of floral organ positioning, and its parameters represent measurable distances in the floral bud morphologies. The model predicts two developmental sources of the organ-number distributions: stochastic shifts in the expression boundaries of homeotic genes and a semi-concentric (whorled-type) organ arrangement. Other models species- or organ-specifically reproduced different types of distributions that reflect different developmental processes. The organ-number variation could be an indicator of stochasticity in organ fate determination and organ positioning. PMID:25404932

Positive and negative variations in capacitive images for given defects under varying experimental conditions

NASA Astrophysics Data System (ADS)

Li, Chen; Yin, Xiaokang; Li, Zhen; Li, Wei; Chen, Guoming

2018-04-01

Capacitive imaging (CI) technique is a novel electromagnetic NDE technique. The Quasi-static electromagnetic field from the carefully designed electrode pair will vary when the electrical properties of the sample change, leading to the possibility of imaging. It is observed that for a given specimen, the targeted features appear as different variations in capacitive images under different experimental conditions. In some cases, even opposite variations occur, which brings confusion to indication interpretation. It is thus thought interesting to embark on investigations into the cause and effects of the negative variation phenomenon. In this work, the positive and negative variations were first explained from the measurement sensitivity distribution perspective. This was then followed by a detailed analysis using finite element models in COMSOL. A parametric experimental study on a glass fiber composite plate with artificial defects was then carried out to investigate how the experimental conditions affect the variation.

Alcohol outlet density and violence: A geographically weighted regression approach.

PubMed

Cameron, Michael P; Cochrane, William; Gordon, Craig; Livingston, Michael

2016-05-01

We investigate the relationship between outlet density (of different types) and violence (as measured by police activity) across the North Island of New Zealand, specifically looking at whether the relationships vary spatially. We use New Zealand data at the census area unit (approximately suburb) level, on police-attended violent incidents and outlet density (by type of outlet), controlling for population density and local social deprivation. We employed geographically weighted regression to obtain both global average and locally specific estimates of the relationships between alcohol outlet density and violence. We find that bar and night club density, and licensed club density (e.g. sports clubs) have statistically significant and positive relationships with violence, with an additional bar or night club is associated with nearly 5.3 additional violent events per year, and an additional licensed club associated with 0.8 additional violent events per year. These relationships do not show significant spatial variation. In contrast, the effects of off-licence density and restaurant/café density do exhibit significant spatial variation. However, the non-varying effects of bar and night club density are larger than the locally specific effects of other outlet types. The relationships between outlet density and violence vary significantly across space for off-licences and restaurants/cafés. These results suggest that in order to minimise alcohol-related harms, such as violence, locally specific policy interventions are likely to be necessary. [Cameron MP, Cochrane W, Gordon C, Livingston M. Alcohol outlet density and violence: A geographically weighted regression approach. Drug Alcohol Rev 2016;35:280-288]. © 2015 Australasian Professional Society on Alcohol and other Drugs.

Testing the mate-choice hypothesis of the female orgasm: disentangling traits and behaviours.

PubMed

Sherlock, James M; Sidari, Morgan J; Harris, Emily Ann; Barlow, Fiona Kate; Zietsch, Brendan P

2016-01-01

The evolution of the female orgasm in humans and its role in romantic relationships is poorly understood. Whereas the male orgasm is inherently linked to reproduction, the female orgasm is not linked to obvious reproductive or survival benefits. It also occurs less consistently during penetrative sex than does the male orgasm. Mate-choice hypotheses posit that the wide variation in female orgasm frequency reflects a discriminatory mechanism designed to select high-quality mates. We aimed to determine (1) whether women report that their orgasm frequency varies between partners, (2) whether this variation reflects mates' personal characteristics, and (3) whether this variation reflects own and partner sexual behaviour during intercourse. We collected survey data from 103 women who rated (1) the extent to which their orgasm frequency varied between partners, (2) the characteristics of previous sexual partners who induced high-orgasm frequency and those who induced low-orgasm frequency, and (3) the specific behaviours during sex with those partners. This is the first study to test within-woman variation in orgasm and partner traits. Overall, women reported variation in their orgasm rates with different partners. Partners who induced high-orgasm rates were rated as more humorous, creative, warm, faithful, and better smelling than partners who induced low-orgasm rates, and also engaged in greater efforts to induce partner orgasm. Some assumptions and predictions of mate-choice hypotheses of female orgasm were supported, while other aspects of our findings provide reasons to remain sceptical.

Testing the mate-choice hypothesis of the female orgasm: disentangling traits and behaviours

PubMed Central

Sherlock, James M.; Sidari, Morgan J.; Harris, Emily Ann; Barlow, Fiona Kate; Zietsch, Brendan P.

2016-01-01

Background The evolution of the female orgasm in humans and its role in romantic relationships is poorly understood. Whereas the male orgasm is inherently linked to reproduction, the female orgasm is not linked to obvious reproductive or survival benefits. It also occurs less consistently during penetrative sex than does the male orgasm. Mate-choice hypotheses posit that the wide variation in female orgasm frequency reflects a discriminatory mechanism designed to select high-quality mates. Objective We aimed to determine (1) whether women report that their orgasm frequency varies between partners, (2) whether this variation reflects mates' personal characteristics, and (3) whether this variation reflects own and partner sexual behaviour during intercourse. Design We collected survey data from 103 women who rated (1) the extent to which their orgasm frequency varied between partners, (2) the characteristics of previous sexual partners who induced high-orgasm frequency and those who induced low-orgasm frequency, and (3) the specific behaviours during sex with those partners. This is the first study to test within-woman variation in orgasm and partner traits. Results Overall, women reported variation in their orgasm rates with different partners. Partners who induced high-orgasm rates were rated as more humorous, creative, warm, faithful, and better smelling than partners who induced low-orgasm rates, and also engaged in greater efforts to induce partner orgasm. Conclusions Some assumptions and predictions of mate-choice hypotheses of female orgasm were supported, while other aspects of our findings provide reasons to remain sceptical. PMID:27791967

Jet outflow and gamma-ray emission correlations in S5 0716+714

DOE PAGES

Rani, B.; Krichbaum, T. P.; Marscher, A. P.; ...

2014-11-06

Here, using millimeter very long baseline interferometry (VLBI) observations of the BL Lac object S5 0716+714 from August 2008 to September 2013, we investigate variations in the core flux density and orientation of the sub-parsec scale jet, i.e. position angle. The γ-ray data obtained by the Fermi Large Area Telescope are used to investigate the high-energy flux variations over the same time period. For the first time in any blazar, we report a significant correlation between the γ-ray flux variations and the position angle variations in the VLBI jet. The cross-correlation analysis also indicates a positive correlation such that themore » mm-VLBI core flux density variations are delayed with respect to the γ-ray flux by 82±32 days. This suggests that the high-energy emission is coming from a region located ≥(3.8±1.9) parsecs upstream of the mm-VLBI core (closer to the central black hole). Lastly, these results imply that the observed inner jet morphology has a strong connection with the observed γ-ray flares.« less

Threshold voltage variation depending on single grain boundary and stored charges in an adjacent cell for vertical silicon–oxide–nitride–oxide–silicon NAND flash memory

NASA Astrophysics Data System (ADS)

Oh, Hyeongwan; Kim, Jiwon; Baek, Rock-Hyun; Lee, Jeong-Soo

2018-04-01

The effects of single grain boundary (SGB) position and stored electron charges in an adjacent cell in silicon–oxide–nitride–oxide–silicon (SONOS) structures on the variations of threshold voltage (V th) were investigated using technology computer-aided design (TCAD) simulation. As the bit line voltage increases, the SGB position causing the maximum V th variation was shifted from the center to the source side in the channel, owing to the drain-induced grain barrier lowering effect. When the SGB is located in the spacer region, the potential interaction from both the SGB and the stored electron charges in the adjacent cell becomes significant and thus resulting in larger V th variation. In contrast, when the SGB is located at the center of the channel, the peak position of potential barrier is shifted to the center, so that the influence of the adjacent cell is diminished. As the gate length is scaled down to 20 nm, the influence of stored charges in adjacent cells becomes significant, resulting in larger V th variations.

Jet outflow and gamma-ray emission correlations in S5 0716+714

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

Rani, B.; Krichbaum, T. P.; Marscher, A. P.

Here, using millimeter very long baseline interferometry (VLBI) observations of the BL Lac object S5 0716+714 from August 2008 to September 2013, we investigate variations in the core flux density and orientation of the sub-parsec scale jet, i.e. position angle. The γ-ray data obtained by the Fermi Large Area Telescope are used to investigate the high-energy flux variations over the same time period. For the first time in any blazar, we report a significant correlation between the γ-ray flux variations and the position angle variations in the VLBI jet. The cross-correlation analysis also indicates a positive correlation such that themore » mm-VLBI core flux density variations are delayed with respect to the γ-ray flux by 82±32 days. This suggests that the high-energy emission is coming from a region located ≥(3.8±1.9) parsecs upstream of the mm-VLBI core (closer to the central black hole). Lastly, these results imply that the observed inner jet morphology has a strong connection with the observed γ-ray flares.« less

Dietary biomagnification of organochlorine contaminants in Alaskan polar bears

USGS Publications Warehouse

Bentzen, T.W.; Follmann, Erich H.; Amstrup, Steven C.; York, G.S.; Wooller, M.J.; Muir, D.C.G.; O'Hara, T. M.

2008-01-01

Concentrations of organochlorine contaminants in the adipose tissue of polar bears (Ursus maritimus Phipps, 1774) vary throughout the Arctic. The range in concentrations has not been explained fully by bear age, sex, condition, location, or reproductive status. Dietary pathways expose polar bears to a variety of contaminant profiles and concentrations. Prey range from lower trophic level bowhead whales (Balaena mysticetus L., 1758), one of the least contaminated marine mammals, to highly contaminated upper trophic level ringed seals (Phoca hispida (Schreber, 1775)). We used ??15N and ??13C signatures to estimate the trophic status of 42 polar bears sampled along Alaska's Beaufort Sea coast to determine the relationship between organochlorine concentration and trophic level. The ?? 15N values in the cellular portions of blood ranged from 18.2% to 20.7%. We found strong positive relationships between concentrations of the most recalcitrant polychlorinated biphenyls (PCBs) and ??15N values in models incorporating age, lipid content, and ??13C value. Specifically these models accounted for 67% and 76% of the variation in PCB153 and oxychlordane concentration in male polar bears and 85% and 93% in females, respectively. These results are strong indicators of variation in diet and biomagnification of organochlorines among polar bears related to their sex, age, and trophic position. ?? 2008 NRC.

Neural signals of selective attention are modulated by subjective preferences and buying decisions in a virtual shopping task.

PubMed

Goto, Nobuhiko; Mushtaq, Faisal; Shee, Dexter; Lim, Xue Li; Mortazavi, Matin; Watabe, Motoki; Schaefer, Alexandre

2017-09-01

We investigated whether well-known neural markers of selective attention to motivationally-relevant stimuli were modulated by variations in subjective preference towards consumer goods in a virtual shopping task. Specifically, participants viewed and rated pictures of various goods on the extent to which they wanted each item, which they could potentially purchase afterwards. Using the event-related potentials (ERP) method, we found that variations in subjective preferences for consumer goods strongly modulated positive slow waves (PSW) from 800 to 3000 milliseconds after stimulus onset. We also found that subjective preferences modulated the N200 and the late positive potential (LPP). In addition, we found that both PSW and LPP were modulated by subsequent buying decisions. Overall, these findings show that well-known brain event-related potentials reflecting selective attention processes can reliably index preferences to consumer goods in a shopping environment. Based on a large body of previous research, we suggest that early ERPs (e.g. the N200) to consumer goods could be indicative of preferences driven by unconditional and automatic processes, whereas later ERPs such as the LPP and the PSW could reflect preferences built upon more elaborative and conscious cognitive processes. Copyright © 2017 Elsevier B.V. All rights reserved.

Functional group diversity of bee pollinators increases crop yield

PubMed Central

Hoehn, Patrick; Tscharntke, Teja; Tylianakis, Jason M; Steffan-Dewenter, Ingolf

2008-01-01

Niche complementarity is a commonly invoked mechanism underlying the positive relationship between biodiversity and ecosystem functioning, but little empirical evidence exists for complementarity among pollinator species. This study related differences in three functional traits of pollinating bees (flower height preference, daily time of flower visitation and within-flower behaviour) to the seed set of the obligate cross-pollinated pumpkin Cucurbita moschata Duch. ex Poir. across a land-use intensity gradient from tropical rainforest and agroforests to grassland in Indonesia. Bee richness and abundance changed with habitat variables and we used this natural variation to test whether complementary resource use by the diverse pollinator community enhanced final yield. We found that pollinator diversity, but not abundance, was positively related to seed set of pumpkins. Bees showed species-specific spatial and temporal variation in flower visitation traits and within-flower behaviour, allowing for classification into functional guilds. Diversity of functional groups explained even more of the variance in seed set (r2=45%) than did species richness (r2=32%) highlighting the role of functional complementarity. Even though we do not provide experimental, but rather correlative evidence, we can link spatial and temporal complementarity in highly diverse pollinator communities to pollination success in the field, leading to enhanced crop yield without any managed honeybees. PMID:18595841

Quantitative Evaluation of Stereo Visual Odometry for Autonomous Vessel Localisation in Inland Waterway Sensing Applications

PubMed Central

Kriechbaumer, Thomas; Blackburn, Kim; Breckon, Toby P.; Hamilton, Oliver; Rivas Casado, Monica

2015-01-01

Autonomous survey vessels can increase the efficiency and availability of wide-area river environment surveying as a tool for environment protection and conservation. A key challenge is the accurate localisation of the vessel, where bank-side vegetation or urban settlement preclude the conventional use of line-of-sight global navigation satellite systems (GNSS). In this paper, we evaluate unaided visual odometry, via an on-board stereo camera rig attached to the survey vessel, as a novel, low-cost localisation strategy. Feature-based and appearance-based visual odometry algorithms are implemented on a six degrees of freedom platform operating under guided motion, but stochastic variation in yaw, pitch and roll. Evaluation is based on a 663 m-long trajectory (>15,000 image frames) and statistical error analysis against ground truth position from a target tracking tachymeter integrating electronic distance and angular measurements. The position error of the feature-based technique (mean of ±0.067 m) is three times smaller than that of the appearance-based algorithm. From multi-variable statistical regression, we are able to attribute this error to the depth of tracked features from the camera in the scene and variations in platform yaw. Our findings inform effective strategies to enhance stereo visual localisation for the specific application of river monitoring. PMID:26694411

Are Eyes a Mirror of the Soul? What Eye Wrinkles Reveal about a Horse’s Emotional State

PubMed Central

Hintze, Sara; Smith, Samantha; Patt, Antonia; Bachmann, Iris; Würbel, Hanno

2016-01-01

Finding valid indicators of emotional states is one of the biggest challenges in animal welfare science. Here, we investigated in horses whether variation in the expression of eye wrinkles caused by contraction of the inner eyebrow raiser reflects emotional valence. By confronting horses with positive and negative conditions, we aimed to induce positive and negative emotional states, hypothesising that positive emotions would reduce whereas negative emotions would increase eye wrinkle expression. Sixteen horses were individually exposed in a balanced order to two positive (grooming, food anticipation) and two negative conditions (food competition, waving a plastic bag). Each condition lasted for 60 seconds and was preceded by a 60 second control phase. Throughout both phases, pictures of the eyes were taken, and for each horse four pictures per condition and phase were randomly selected. Pictures were scored in random order and by two experimenters blind to condition and phase for six outcome measures: qualitative impression, eyelid shape, markedness of the wrinkles, presence of eye white, number of wrinkles, and the angle between the line through the eyeball and the highest wrinkle. The angle decreased during grooming and increased during food competition compared to control phases, whereas the two phases did not differ during food anticipation and the plastic bag condition. No effects on the other outcome measures were detected. Taken together, we have defined a set of measures to assess eye wrinkle expression reliably, of which one measure was affected by the conditions the horses were exposed to. Variation in eye wrinkle expression might provide valuable information on horse welfare but further validation of specific measures across different conditions is needed. PMID:27732647

Mutations in the quinolone resistance determining region conferring resistance to fluoroquinolones in Mycoplasma agalactiae.

PubMed

Tatay-Dualde, Juan; Prats-van der Ham, Miranda; de la Fe, Christian; Paterna, Ana; Sánchez, Antonio; Corrales, Juan Carlos; Contreras, Antonio; Gómez-Martín, Ángel

2017-08-01

M. agalactiae is the main causative agent of contagious agalactia, against which antimicrobial treatment is the main applied control measure. Quinolones are an effective group of antimicrobials inhibiting the growth of M. agalactiae, but in the last years, various reports have demonstrated an increase of resistance in field isolates due to its massive use. Nevertheless, the molecular mechanisms involved in the acquisition of fluoroquinolones resistance in M. agalactiae have not been elucidated yet. Therefore, the aim of this work was to analyze the presence of DNA variations that could be related to changes in fluoroquinolone susceptibility. For this purpose, three M. agalactiae strains were selected to obtain in vitro resistant mutants against enrofloxacin, marbofloxacin and moxifloxacin and afterwards, partial sequences of their gyrA, gyrB, parC and parE genes were analyzed. In addition, a set of field isolates with different MIC values were also studied. Changes related to variations in fluoroquinolones susceptibility were found in gyrB, parC and parE. Specifically, gyrB genes were affected at the predicted amino acid position 424, four amino acid changes were detected in parC (positions 78, 79, 80 and 84) and two substitutions were reported in parE (amino acid positions 429 and 459). Mutations at predicted positions 424 of gyrB and 429 of parE are novel DNA changes which had not been previously described and, on the whole, parC was the first gene showing alterations when changes in susceptibility to fluoroquinolones occurred. Thus, this gene is the most suitable target for a rapid study of fluoroquinolone resistance in field isolates of M. agalactiae. Copyright © 2017 Elsevier B.V. All rights reserved.

KBA62 and PNL2: 2 new melanoma markers-immunohistochemical analysis of 1563 tumors including metastatic, desmoplastic, and mucosal melanomas and their mimics.

PubMed

Aung, Phyu Phyu; Sarlomo-Rikala, Maarit; Lasota, Jerzy; Lai, Jin-Ping; Wang, Zeng-Feng; Miettinen, Markku

2012-02-01

Identification of metastatic melanoma can be difficult because of its considerable morphologic variation and mimicry of a wide variety of other tumors. The more melanoma-specific melanoma markers, MelanA/MART-1, HMB45, and tyrosinase, used in addition to S100 protein, all have limitations in sensitivity and specificity. In this study, we evaluated 2 new melanoma markers, monoclonal antibodies KBA62 and PNL2 to yet unidentified antigens, using a large panel of metastatic melanomas (n=214), desmoplastic melanomas (n=34), gastrointestinal mucosal melanomas (n=54), benign nevi (n=27), clear cell sarcomas (n=16), and nonmelanocytic tumors (n=1218). Immunoreactivity for KBA62 and PNL2 was found in all pigmented nevi and in 86% and 90% of metastatic melanomas, respectively. Mucosal melanomas showed a similar rate of PNL2 immunoreactivity but somewhat less frequent KBA62 positivity (72%). In addition, KBA62 was found to be a sensitive diagnostic marker for desmoplastic melanoma (28 of 34; 82%), whereas PNL2 was only rarely positive (2 of 34; 6%). KBA62-positive normal tissues included pericytes, vascular and parenchymal smooth muscles, and basal cells of complex epithelia, including myoepithelia, whereas PNL2 labeled only melanocytes and neutrophils. Among nonmelanocytic tumors, those that were KBA62 positive were nodular fasciitis, leiomyoma and leiomyosarcoma, gastrointestinal stromal tumors, benign and malignant nerve sheath tumors, synovial sarcoma, and subsets of various carcinomas, especially those with squamous cell/stratified epithelial differentiation. PNL2 positivity in nonmelanocytic tumors was more restricted but occurred consistently in angiomyolipoma and other perivascular epitheloid cell tumor and in chronic myeloid leukemia tissue infiltrates. KBA62 may assist in the identification of desmoplastic melanomas, but its widespread occurrence in nonmelanomas limits utility. PNL2 is highly specific for melanomas but lacks reactivity with desmoplastic melanomas. It is also an excellent supplementary marker for perivascular epitheloid cell tumor at various sites.

Functional Roles of Neural Preparatory Processes in a Cued Stroop Task Revealed by Linking Electrophysiology with Behavioral Performance

PubMed Central

Wang, Chao; Ding, Mingzhou; Kluger, Benzi M.

2015-01-01

It is well established that cuing facilitates behavioral performance and that different aspects of instructional cues evoke specific neural preparatory processes in cued task-switching paradigms. To deduce the functional role of these neural preparatory processes the majority of studies vary aspects of the experimental paradigm and describe how these variations alter markers of neural preparatory processes. Although these studies provide important insights, they also have notable limitations, particularly in terms of understanding the causal or functional relationship of neural markers to cognitive and behavioral processes. In this study, we sought to address these limitations and uncover the functional roles of neural processes by examining how variability in the amplitude of neural preparatory processes predicts behavioral performance to subsequent stimuli. To achieve this objective 16 young adults were recruited to perform a cued Stroop task while their brain activity was measured using high-density electroencephalography. Four temporally overlapping but functionally and topographically distinct cue-triggered event related potentials (ERPs) were identified: 1) A left-frontotemporal negativity (250-700 ms) that was positively associated with word-reading performance; 2) a midline-frontal negativity (450-800 ms) that was positively associated with color-naming and incongruent performance; 3) a left-frontal negativity (450-800 ms) that was positively associated with switch trial performance; and 4) a centroparietal positivity (450-800 ms) that was positively associated with performance for almost all trial types. These results suggest that at least four dissociable cognitive processes are evoked by instructional cues in the present task, including: 1) domain-specific task facilitation; 2) switch-specific task-set reconfiguration; 3) preparation for response conflict; and 4) proactive attentional control. Examining the relationship between ERPs and behavioral performance provides a functional link between neural markers and the cognitive processes they index. PMID:26230662

Positive selection on human gamete-recognition genes

PubMed Central

Stover, Daryn A.; Guerra, Vanessa; Mozaffari, Sahar V.; Ober, Carole; Mugal, Carina F.; Kaj, Ingemar

2018-01-01

Coevolution of genes that encode interacting proteins expressed on the surfaces of sperm and eggs can lead to variation in reproductive compatibility between mates and reproductive isolation between members of different species. Previous studies in mice and other mammals have focused in particular on evidence for positive or diversifying selection that shapes the evolution of genes that encode sperm-binding proteins expressed in the egg coat or zona pellucida (ZP). By fitting phylogenetic models of codon evolution to data from the 1000 Genomes Project, we identified candidate sites evolving under diversifying selection in the human genes ZP3 and ZP2. We also identified one candidate site under positive selection in C4BPA, which encodes a repetitive protein similar to the mouse protein ZP3R that is expressed in the sperm head and binds to the ZP at fertilization. Results from several additional analyses that applied population genetic models to the same data were consistent with the hypothesis of selection on those candidate sites leading to coevolution of sperm- and egg-expressed genes. By contrast, we found no candidate sites under selection in a fourth gene (ZP1) that encodes an egg coat structural protein not directly involved in sperm binding. Finally, we found that two of the candidate sites (in C4BPA and ZP2) were correlated with variation in family size and birth rate among Hutterite couples, and those two candidate sites were also in linkage disequilibrium in the same Hutterite study population. All of these lines of evidence are consistent with predictions from a previously proposed hypothesis of balancing selection on epistatic interactions between C4BPA and ZP3 at fertilization that lead to the evolution of co-adapted allele pairs. Such patterns also suggest specific molecular traits that may be associated with both natural reproductive variation and clinical infertility. PMID:29340252

MAGNETIC ACTIVITY ANALYSIS FOR A SAMPLE OF G-TYPE MAIN SEQUENCE KEPLER TARGETS

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

Mehrabi, Ahmad; He, Han; Khosroshahi, Habib, E-mail: mehrabi@basu.ac.ir

2017-01-10

The variation of a stellar light curve owing to rotational modulation by magnetic features (starspots and faculae) on the star’s surface can be used to investigate the magnetic properties of the host star. In this paper, we use the periodicity and magnitude of the light-curve variation as two proxies to study the stellar magnetic properties for a large sample of G-type main sequence Kepler targets, for which the rotation periods were recently determined. By analyzing the correlation between the two magnetic proxies, it is found that: (1) the two proxies are positively correlated for most of the stars in ourmore » sample, and the percentages of negative, zero, and positive correlations are 4.27%, 6.81%, and 88.91%, respectively; (2) negative correlation stars cannot have a large magnitude of light-curve variation; and (3) with the increase of rotation period, the relative number of positive correlation stars decreases and the negative correlation one increases. These results indicate that stars with shorter rotation period tend to have positive correlation between the two proxies, and a good portion of the positive correlation stars have a larger magnitude of light-curve variation (and hence more intense magnetic activities) than negative correlation stars.« less

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

PubMed Central

Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O’Connor, Timothy D.; Abecasis, Gonçalo R.; Wojcik, Genevieve L; Gignoux, Christopher R.; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E.; Bustamante, Carlos; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.; Qin, Zhaohui S.; Preethi Boorgula, Meher; Campbell, Monica; Chavan, Sameer; Ford, Jean G.; Foster, Cassandra; Gao, Li; Hansel, Nadia N.; Horowitz, Edward; Huang, Lili; Ortiz, Romina; Potee, Joseph; Rafaels, Nicholas; Ruczinski, Ingo; Scott, Alan F.; Taub, Margaret A.; Vergara, Candelaria; Levin, Albert M.; Padhukasahasram, Badri; Williams, L. Keoki; Dunston, Georgia M.; Faruque, Mezbah U.; Gietzen, Kimberly; Deshpande, Aniket; Grus, Wendy E.; Locke, Devin P.; Foreman, Marilyn G.; Avila, Pedro C.; Grammer, Leslie; Kim, Kwang-Youn A.; Kumar, Rajesh; Schleimer, Robert; De La Vega, Francisco M.; Shringarpure, Suyash S.; Musharoff, Shaila; Burchard, Esteban G.; Eng, Celeste; Hernandez, Ryan D.; Pino-Yanes, Maria; Torgerson, Dara G.; Szpiech, Zachary A.; Torres, Raul; Nicolae, Dan L.; Ober, Carole; Olopade, Christopher O; Olopade, Olufunmilayo; Oluwole, Oluwafemi; Arinola, Ganiyu; Song, Wei; Correa, Adolfo; Musani, Solomon; Wilson, James G.; Lange, Leslie A.; Akey, Joshua; Bamshad, Michael; Chong, Jessica; Fu, Wenqing; Nickerson, Deborah; Reiner, Alexander; Hartert, Tina; Ware, Lorraine B.; Bleecker, Eugene; Meyers, Deborah; Ortega, Victor E.; Maul, Pissamai; Maul, Trevor; Watson, Harold; Ilma Araujo, Maria; Riccio Oliveira, Ricardo; Caraballo, Luis; Marrugo, Javier; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Francisco Herrera-Paz, Edwin; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Alvaro; Mayorga, Luis F.; Mejia-Mejia, Delmy-Aracely; Ramos, Hector; Saenz, Allan; Varela, Gloria; Marina Vasquez, Olga; Ferguson, Trevor; Knight-Madden, Jennifer; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Yazdanbakhsh, Maria

2017-01-01

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an ‘African Diaspora Power Chip’ (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry. PMID:28429804

The effect of increase in dielectric values on specific absorption rate (SAR) in eye and head tissues following 900, 1800 and 2450 MHz radio frequency (RF) exposure

NASA Astrophysics Data System (ADS)

Keshvari, Jafar; Keshvari, Rahim; Lang, Sakari

2006-03-01

Numerous studies have attempted to address the question of the RF energy absorption difference between children and adults using computational methods. They have assumed the same dielectric parameters for child and adult head models in SAR calculations. This has been criticized by many researchers who have stated that child organs are not fully developed, their anatomy is different and also their tissue composition is slightly different with higher water content. Higher water content would affect dielectric values, which in turn would have an effect on RF energy absorption. The objective of this study was to investigate possible variation in specific absorption rate (SAR) in the head region of children and adults by applying the finite-difference time-domain (FDTD) method and using anatomically correct child and adult head models. In the calculations, the conductivity and permittivity of all tissues were increased from 5 to 20% but using otherwise the same exposure conditions. A half-wave dipole antenna was used as an exposure source to minimize the uncertainties of the positioning of a real mobile device and making the simulations easily replicable. Common mobile telephony frequencies of 900, 1800 and 2450 MHz were used in this study. The exposures of ear and eye regions were investigated. The SARs of models with increased dielectric values were compared to the SARs of the models where dielectric values were unchanged. The analyses suggest that increasing the value of dielectric parameters does not necessarily mean that volume-averaged SAR would increase. Under many exposure conditions, specifically at higher frequencies in eye exposure, volume-averaged SAR decreases. An increase of up to 20% in dielectric conductivity or both conductivity and permittivity always caused a SAR variation of less than 20%, usually about 5%, when it was averaged over 1, 5 or 10 g of cubic mass for all models. The thickness and composition of different tissue layers in the exposed regions within the human head play a more significant role in SAR variation compared to the variations (5-20%) of the tissue dielectric parameters.

Ethnic Variation in Depressive Symptoms in a Community Sample in Hawai‘i

PubMed Central

Kanazawa, Asako; White, Patricia M.; Hampson, Sarah E.

2008-01-01

A modified CES-D was administered to a community sample of 176 European Americans (EA), 209 Native Hawaiians (NH), and 357 Japanese Americans (JA), yielding measures of depression, positive affect, depressed affect, somatic disturbance and disturbed interpersonal relations. Positive affect was lower in JA relative to EA, consistent with findings among Native Japanese, a pattern attributed to cultural variation in emotion regulation. NH reported lower positive affect than EA, accompanied by elevated negative affect and somatic disturbance, suggesting generally higher levels of depressive symptoms. The three ethnic groups varied in mental healthcare usage with differing associations between depressive symptoms and experiences of stressful life events. Taken together, these results suggest ethnic variation in depressive symptoms may arise from differing cultural beliefs. PMID:17227175

Specific variations of air temperature and relative humidity around the time of Michoacan earthquake M8.1 Sept. 19, 1985 as a possible indicator of interaction between tectonic plates

NASA Astrophysics Data System (ADS)

Pulinets, S. A.; Dunajecka, M. A.

2007-02-01

The recent development of the Lithosphere-Atmosphere-Ionosphere (LAI) coupling model and experimental data of remote sensing satellites on thermal anomalies before major strong earthquakes have demonstrated that radon emanations in the area of earthquake preparation can produce variations of the air temperature and relative humidity. Specific repeating pattern of humidity and air temperature variations was revealed as a result of analysis of the meteorological data for several tens of strong earthquakes all over the world. The main physical process responsible for the observed variations is the latent heat release due to water vapor condensation on ions produced as a result of air ionization by energetic α-particles emitted by 222Rn. The high effectiveness of this process was proved by the laboratory and field experiments; hence the specific variations of air humidity and temperature can be used as indicator of radon variations before earthquakes. We analyzed the historical meteorological data all over the Mexico around the time of one of the most destructive earthquakes (Michoacan earthquake M8.1) that affected the Mexico City on September 19, 1985. Several distinct zones of specific variations of the air temperature and relative humidity were revealed that may indicate the different character of radon variations in different parts of Mexico before the Michoacan earthquake. The most interesting result on the specific variations of atmosphere parameters was obtained at Baja California region close to the border of Cocos and Rivera tectonic plates. This result demonstrates the possibility of the increased radon variations not only in the vicinity of the earthquake source but also at the border of interacting tectonic plates. Recent results on Thermal InfraRed (TIR) anomalies registered by Meteosat 5 before the Gujarat earthquake M7.9 on 26 of January 2001 supports the idea on the possibility of thermal effects at the border of interacting tectonic plates.

Culturally diverse health care students' experiences with teaching strategies in Finland: a national survey.

PubMed

Pitkajarvi, Marianne; Eriksson, Elina; Pitkala, Kaisu

2013-06-01

All over the world, current health care students come from a variety of cultural, linguistic and educational backgrounds. Their expectations and learning needs vary, yet little is known about how our current education system meets their needs. The purpose of this study was to explore culturally diverse health care students' experiences of teaching strategies in polytechnic faculties of health care in Finland. Specifically, we aimed to compare how international students and Finnish students experience the same curriculum. A cross sectional survey. Ten polytechnic faculties of health care in Finland offering English-Language-Taught Degree Programmess (ELTDPs). 283 students studying nursing, public health nursing, or physiotherapy in English. Of these, 166 were international students and 112 were Finnish students. The data were collected using a questionnaire designed specifically for this study. The survey included items grouped into seven dimensions: 1. concreteness of theoretical instruction, 2. encouragement of student activity, 3. use of skills labs, 4. variation among teaching strategies, 5. assessment, 6. interaction in the English-Language-Taught Degree Programmes, and 7. approach to diversity in the English-Language-Taught Degree Programmes. The most positive experiences for all students were with the approach to cultural diversity and the concreteness of theoretical instruction, whereas the most negative experiences were with assessment. International students' experiences were more positive than Finnish students' in the following dimensions: encouragement of student activity (p=0.005), variation among teaching strategies (p<0.001), and assessment (p<0.001). Compared to the Finnish students, more than double the number of international students were dissatisfied with their lives (p<0.001). The implications for education include the strengthening teachers' leadership role in small group activities, providing individual and detailed feedback, and ensuring appropriate support mechanisms for all students. Copyright © 2012 Elsevier Ltd. All rights reserved.

Long-term feeding ecology and habitat use in harbour porpoises Phocoena phocoena from Scandinavian waters inferred from trace elements and stable isotopes.

PubMed

Fontaine, Michaël C; Tolley, Krystal A; Siebert, Ursula; Gobert, Sylvie; Lepoint, Gilles; Bouquegneau, Jean-Marie; Das, Krishna

2007-01-17

We investigated the feeding ecology and habitat use of 32 harbour porpoises by-caught in 4 localities along the Scandinavian coast from the North Sea to the Barents Sea using time-integrative markers: stable isotopes (delta13C, delta15N) and trace elements (Zn, Cu, Fe, Se, total Hg and Cd), in relation to habitat characteristics (bathymetry) and geographic position (latitude). Among the trace elements analysed, only Cd, with an oceanic specific food origin, was found to be useful as an ecological tracer. All other trace elements studied were not useful, most likely because of physiological regulation and/or few specific sources in the food web. The delta13C, delta15N signatures and Cd levels were highly correlated with each other, as well as with local bathymetry and geographic position (latitude). Variation in the isotopic ratios indicated a shift in harbour porpoise's feeding habits from pelagic prey species in deep northern waters to more coastal and/or demersal prey in the relatively shallow North Sea and Skagerrak waters. This result is consistent with stomach content analyses found in the literature. This shift was associated with a northward Cd-enrichment which provides further support to the Cd 'anomaly' previously reported in polar waters and suggests that porpoises in deep northern waters include Cd-contaminated prey in their diet, such as oceanic cephalopods. As stable isotopes and Cd provide information in the medium and the long term respectively, the spatial variation found, shows that harbour porpoises experience different ecological regimes during the year along the Scandinavian coasts, adapting their feeding habits to local oceanographic conditions, without performing extensive migration.

School District Variation in Parental Influence on Underage Drinking Behaviors.

PubMed

Tseng, Fang-Yi; Chen, Kuang-Hung; Liu, Chieh-Yu; Chen, Wei J; Chen, Chuan-Yu

2017-09-01

We examined the relationship between alcohol-specific and nonalcohol-specific parental characteristics with occasional alcohol drinking in early adolescence and probed potential school district variation. A total of 1,581 fourth and sixth graders (age range: 10-12 years) were ascertained from 17 elementary schools in a cohort study conducted in northern Taiwan in 2006, with three waves of follow-up between 2007 and 2009. Information on alcohol-specific and nonalcohol-specific parental attributes was obtained from the first two waves of self-administered paper-and-pencil questionnaires; occasional drinking, defined by having drunk on three or more occasions in the past year, was assessed at fourth wave. School district characteristics were retrieved from official statistics and self-report. Multilevel analyses were used to evaluate strength of association, with stratification by disadvantaged status of school districts. Thirteen percent (95% confidence interval [CI] = 10.1%-15.8%) of young adolescents reported to drink occasionally; higher grade level, childhood drinking experience, lower parental education, maternal drinking, and positive parental attitude toward drinking were significant predictors. Nonalcohol parental predictors, including not living with both parents (adjusted odds ratio [aOR] = 2.34, 95% CI = 1.21-4.53) and parental involvement/reinforcement (aOR = .44; 95% CI = .22-.87), were only significant for the children of socioeconomically disadvantaged school districts. As to alcohol-specific parental characteristics, the effects of maternal drinking appear more salient in socioeconomically advantaged school districts (aOR = 2.63; 95% CI = 1.66-4.18). Alcohol-specific and nonalcohol-specific parental influence may operate differentially across school districts sub-grouped by socioeconomic attributes. Preventive strategies raising the awareness of underage drinking and strengthening parenting skills should be devised and implemented in the perspective of social context. Copyright © 2017 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas.

PubMed

Lu, Hong; Patil, Prabhu; Van Sluys, Marie-Anne; White, Frank F; Ryan, Robert P; Dow, J Maxwell; Rabinowicz, Pablo; Salzberg, Steven L; Leach, Jan E; Sonti, Ramesh; Brendel, Volker; Bogdanove, Adam J

2008-01-01

Xanthomonas is a large genus of plant-associated and plant-pathogenic bacteria. Collectively, members cause diseases on over 392 plant species. Individually, they exhibit marked host- and tissue-specificity. The determinants of this specificity are unknown. To assess potential contributions to host- and tissue-specificity, pathogenesis-associated gene clusters were compared across genomes of eight Xanthomonas strains representing vascular or non-vascular pathogens of rice, brassicas, pepper and tomato, and citrus. The gum cluster for extracellular polysaccharide is conserved except for gumN and sequences downstream. The xcs and xps clusters for type II secretion are conserved, except in the rice pathogens, in which xcs is missing. In the otherwise conserved hrp cluster, sequences flanking the core genes for type III secretion vary with respect to insertion sequence element and putative effector gene content. Variation at the rpf (regulation of pathogenicity factors) cluster is more pronounced, though genes with established functional relevance are conserved. A cluster for synthesis of lipopolysaccharide varies highly, suggesting multiple horizontal gene transfers and reassortments, but this variation does not correlate with host- or tissue-specificity. Phylogenetic trees based on amino acid alignments of gum, xps, xcs, hrp, and rpf cluster products generally reflect strain phylogeny. However, amino acid residues at four positions correlate with tissue specificity, revealing hpaA and xpsD as candidate determinants. Examination of genome sequences of xanthomonads Xylella fastidiosa and Stenotrophomonas maltophilia revealed that the hrp, gum, and xcs clusters are recent acquisitions in the Xanthomonas lineage. Our results provide insight into the ancestral Xanthomonas genome and indicate that differentiation with respect to host- and tissue-specificity involved not major modifications or wholesale exchange of clusters, but subtle changes in a small number of genes or in non-coding sequences, and/or differences outside the clusters, potentially among regulatory targets or secretory substrates.

Morphological variations of papillary muscles in the mitral valve complex in human cadaveric hearts.

PubMed

Gunnal, Sandhya Arvind; Wabale, Rajendra Namdeo; Farooqui, Mujeebuddin Samsamuddin

2013-01-01

Papillary muscle rupture and dysfunction can lead to complications of prolapsed mitral valve and mitral regurgitation. Multiple operative procedures of the papillary muscles, such as resection, repositioning and realignment, are carried out to restore normal physiological function. Therefore, it is important to know both the variations and the normal anatomy of papillary muscles. This study was carried out on 116 human cadaveric hearts. The left ventricles were opened along the left border in order to view the papillary muscles. The number, shape, position and pattern of the papillary muscles were observed. In this series, the papillary muscles were mostly found in groups instead of in twos, as is described in standard textbooks. Four different shapes of papillary muscles were identified - conical, broad-apexed, pyramidal and fan-shaped. We also discovered various patterns of papillary muscles. No two mitral valve complexes have the same architectural arrangement. Each case seems to be unique. Therefore, it is important for scientists worldwide to study the variations in the mitral valve complex in order to ascertain the reason behind each specific architectural arrangement. This will enable cardiothoracic surgeons to tailor the surgical procedures according to the individual papillary muscle pattern.

Performance assessment of low pressure nuclear thermal propulsion

NASA Technical Reports Server (NTRS)

Gerrish, H. P., Jr.; Doughty, G. E.

1993-01-01

A low pressure nuclear thermal propulsion (LPNTP) system, which takes advantage of hydrogen dissociation/recombination, was proposed as a means of increasing engine specific impulse (Isp). The effect of hydrogen dissociation/recombination on LPNTP Isp is examined. A two-dimensional computer model was used to show that the optimum chamber pressure is approximately 100 psia (at a chamber temperature of 3,000 K), with an Isp approximately 15 s higher than at 1,000 psia. At high chamber temperatures and low chamber pressures, the increase in Isp is due to both lower average molecular weights caused by dissociation and added kinetic energy from monatomic hydrogen recombination. Monatomic hydrogen recombination increases the Isp more then hydrogen dissociation. Variations in the mole fraction of monatomic hydrogen are similar to variations in static pressure along the axial nozzle position. Most recombination occurs close to the nozzle throat. Practical variations in nozzle geometry have minimal impact on recombination. Other models which can simulate a wider range of nozzle designs should be used in the future. The uncertainty of the hydrogen kinetic reaction rates at high temperatures (approximately 3,000 K) affects the accuracy of the analysis and should be verified with simple bench tests.

Diffraction Effects in the SOFIA Telescope and Cavity Door

NASA Astrophysics Data System (ADS)

Erickson, E. F.; Haas, M. R.; Davis, P. K.

2005-12-01

Calculations of diffraction phenomena for SOFIA (the Stratospheric Observatory for Infrared Astronomy) are described. The analyses establish the diffraction-limited point-spread function for the planned central obscuration of the telescope, confirm the specification for the oversized primary mirror diameter, evaluate spider diffraction effects, and determine the variation in focal-plane flux with position of the telescope relative to the cavity door. The latter is a concern because motion between the door aperture and the telescope can vary the flux from a point source and the sky background by diffraction (even when the door aperture does not physically obstruct the geometrical beam). We find all these effects to be acceptable in terms of observatory performance, with the possible exception of fractional background variations 3E-3 at wavelengths 1mm. Fractional background variations larger than 1E-6 can exceed photon shot noise in one second for broad-band, background-limited infrared detectors systems. However, we expect that synchronous signal demodulation using the telescope's chopping secondary mirror will obviate this effect, assuming modulation of the diffracted sky radiation by the relative motion of the door and telescope occurs at frequencies well below the chopoper frequency. This work is supported by the National Aeronautics and Space Administration.

Geographic variation in the association between exploratory behavior and physiology in rufous-collared sparrows.

PubMed

Maldonado, Karin; van Dongen, Wouter F D; Vásquez, Rodrigo A; Sabat, Pablo

2012-01-01

Increasing research has attempted to clarify the links between animal personality and physiology. However, the mechanisms driving this association remain largely unknown, and knowledge of how ecological factors may affect its direction and strength is scant. In this study, we quantified variation in the association between exploratory behavior, basal metabolic rate (BMR), and total evaporative water loss (TEWL) in rufous-collared sparrows (Zonotrichia capensis) inhabiting desert, Mediterranean, and cold-temperate climates. We found that the exploratory behavior score was highest in birds from the cold-temperate site, which was characterized by a moderate level of ecological variability (seasonality). Moreover, the association between exploratory behavior and physiological variables differed among localities. Only birds from the Mediterranean site showed a positive correlation between exploratory behavior and BMR. We found no association between exploration and TEWL at any study site. Our findings suggest that differences in the ecological conditions experienced by each sparrow population result in a particular combination of behavioral and physiological traits. An understanding of this intraspecific variation along ecological gradients provides unique insights into how specific ecological conditions affect the coupling of behavioral and physiological traits and the mechanisms underlying that relationship.

Effects of region, demography, and protection from fishing on batch fecundity of common coral trout ( Plectropomus leopardus)

NASA Astrophysics Data System (ADS)

Carter, Alex B.; Davies, Campbell R.; Mapstone, Bruce D.; Russ, Garry R.; Tobin, Andrew J.; Williams, Ashley J.

2014-09-01

Batch fecundity of female Plectropomus leopardus, a coral reef fish targeted by commercial and recreational fishing, was compared between reefs open to fishing and reefs within no-take marine reserves within three regions of the Great Barrier Reef (GBR), Australia. Length, weight, and age had positive effects on batch fecundity of spawners from northern and central reefs but negligible effects on spawners from southern reefs. Females were least fecund for a given length, weight, and age in the southern GBR. Batch fecundity of a 500-mm fork length female was 430 % greater on central reefs and 207 % greater on northern reefs than on southern reefs. The effects of length and age on batch fecundity did not differ significantly between reserve and fished reefs in any region, but weight-specific fecundity was 100 % greater for large 2.0 kg females on reserve reefs compared with fished reefs in the central GBR. We hypothesize that regional variation in batch fecundity is likely driven by water temperature and prey availability. Significant regional variation in batch fecundity highlights the need for understanding spatial variation in reproductive output where single conservation or fishery management strategies cover large, potentially diverse, spatial scales.

Local Time Variation of Water Vapor on Mars using TES Aerobraking Spectra

NASA Astrophysics Data System (ADS)

AlShamsi, M. R.; AlJanaahi, A. A.; Smith, M. D.; Altunaiji, E. S.; Edwards, C. S.

2016-12-01

During the Mars Global Surveyor (MGS) aerobraking phase, the spacecraft was in a large elliptical orbit that enabled the Thermal Emission Spectrometer (TES) instrument to sample many local times of Mars. The observed TES aerobraking spectra during that phase cover the time range between Mars Year 23, Ls=180° and Mars Year 24, Ls=30°. These TES aerobraking spectra have never been analyzed to study local time variations on Mars. Through radiative transfer modeling of the spectra, surface and atmospheric temperature, dust and water ice optical depth, and water vapor were retrieved. Specifically, the water vapor retrievals during aerobraking have similar seasonal and latitudinal trends to those in other Mars years observed by TES. These retrievals show somewhat higher water vapor during the morning hours (09:00-12:00) than in the afternoon (12:00-17:00) during southern summer (Ls=270°-330°) and little variation as a function of local time for southern fall (Ls=0°-30°). These retrievals show water vapor has a positive correlation with surface pressure (or negative correlation with altitude) indicating that water vapor is mixed in the lowest 10-20 km.

Colony-specific calcification and mortality under ocean acidification in the branching coral Montipora digitata.

PubMed

Kavousi, Javid; Tanaka, Yasuaki; Nishida, Kozue; Suzuki, Atsushi; Nojiri, Yukihiro; Nakamura, Takashi

2016-08-01

Ocean acidification (OA) threatens calcifying marine organisms including reef-building corals. In this study, we examined the OA responses of individual colonies of the branching scleractinian coral Montipora digitata. We exposed nubbins of unique colonies (n = 15) to ambient or elevated pCO2 under natural light and temperature regimes for 110 days. Although elevated pCO2 exposure on average reduced calcification, individual colonies showed unique responses ranging from declines in positive calcification to negative calcification (decalcification) to no change. Similarly, mortality was greater on average in elevated pCO2, but also showed colony-specific patterns. High variation in colony responses suggests the possibility that ongoing OA may lead to natural selection of OA-tolerant colonies within a coral population. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ab-initio study of thermodynamic properties of boron nanowire at atomic scale

NASA Astrophysics Data System (ADS)

Bhuyan, Prabal D.; Gupta, Sanjeev K.; Sonvane, Y.; Gajjar, P. N.

2018-04-01

In the present work, we have optimized ribbon like zigzag structure of boron (B) nanowire (NW) and investigated vibrational and thermodynamic properties using quasi-harmonic approximations (QHA). All positive phonon in the phonon dispersive curve have confirmed dynamical stability of ribbon B-NW. The thermodynamic properties, like Debye temperature, internal energy and specific heat, are calculated as a function of temperature. The variation of specific heat is proportional to T3 Debye law at lower temperature for B-NW, while it becomes constant above room temperature at 1200K; obeys Dulong-Petit's law. The high Debye temperature of 1120K is observed at ambient temperature, which can be attributed to high thermal conductivity. Our study shows that B-NW with high thermal conductivity could be the next generation electron connector for nanoscale electronic devices.

RPS8—a New Informative DNA Marker for Phylogeny of Babesia and Theileria Parasites in China

PubMed Central

Tian, Zhan-Cheng; Liu, Guang-Yuan; Yin, Hong; Luo, Jian-Xun; Guan, Gui-Quan; Luo, Jin; Xie, Jun-Ren; Shen, Hui; Tian, Mei-Yuan; Zheng, Jin-feng; Yuan, Xiao-song; Wang, Fang-fang

2013-01-01

Piroplasmosis is a serious debilitating and sometimes fatal disease. Phylogenetic relationships within piroplasmida are complex and remain unclear. We compared the intron–exon structure and DNA sequences of the RPS8 gene from Babesia and Theileria spp. isolates in China. Similar to 18S rDNA, the 40S ribosomal protein S8 gene, RPS8, including both coding and non-coding regions is a useful and novel genetic marker for defining species boundaries and for inferring phylogenies because it tends to have little intra-specific variation but considerable inter-specific difference. However, more samples are needed to verify the usefulness of the RPS8 (coding and non-coding regions) gene as a marker for the phylogenetic position and detection of most Babesia and Theileria species, particularly for some closely related species. PMID:24244571

Serial-position effects for items and relations in short-term memory.

PubMed

Jones, Tim; Oberauer, Klaus

2013-04-01

Two experiments used immediate probed recall of words to investigate serial-position effects. Item memory was tested through probing with a semantic category. Relation memory was tested through probing with the word's spatial location of presentation. Input order and output order were deconfounded by presenting and probing items in different orders. Primacy and recency effects over input position were found for both item memory and relation memory. Both item and relation memory declined over output position. The finding of a U-shaped input position function for item memory rules out an explanation purely in terms of positional confusions (e.g., edge effects). Either these serial-position effects arise from variations in the intrinsic memory strength of the items, or they arise from variations in the strength of item-position bindings, together with retrieval by scanning.

Functional Incompatibility between the Generic NF-κB Motif and a Subtype-Specific Sp1III Element Drives the Formation of the HIV-1 Subtype C Viral Promoter

PubMed Central

Verma, Anjali; Rajagopalan, Pavithra; Lotke, Rishikesh; Varghese, Rebu; Selvam, Deepak; Kundu, Tapas K.

2016-01-01

ABSTRACT Of the various genetic subtypes of human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) and simian immunodeficiency virus (SIV), only in subtype C of HIV-1 is a genetically variant NF-κB binding site found at the core of the viral promoter in association with a subtype-specific Sp1III motif. How the subtype-associated variations in the core transcription factor binding sites (TFBS) influence gene expression from the viral promoter has not been examined previously. Using panels of infectious viral molecular clones, we demonstrate that subtype-specific NF-κB and Sp1III motifs have evolved for optimal gene expression, and neither of the motifs can be replaced by a corresponding TFBS variant. The variant NF-κB motif binds NF-κB with an affinity 2-fold higher than that of the generic NF-κB site. Importantly, in the context of an infectious virus, the subtype-specific Sp1III motif demonstrates a profound loss of function in association with the generic NF-κB motif. An additional substitution of the Sp1III motif fully restores viral replication, suggesting that the subtype C-specific Sp1III has evolved to function with the variant, but not generic, NF-κB motif. A change of only two base pairs in the central NF-κB motif completely suppresses viral transcription from the provirus and converts the promoter into heterochromatin refractory to tumor necrosis factor alpha (TNF-α) induction. The present work represents the first demonstration of functional incompatibility between an otherwise functional NF-κB motif and a unique Sp1 site in the context of an HIV-1 promoter. Our work provides important leads as to the evolution of the HIV-1 subtype C viral promoter with relevance for gene expression regulation and viral latency. IMPORTANCE Subtype-specific genetic variations provide a powerful tool to examine how these variations offer a replication advantage to specific viral subtypes, if any. Only in subtype C of HIV-1 are two genetically distinct transcription factor binding sites positioned at the most critical location of the viral promoter. Since a single promoter regulates viral gene expression, the promoter variations can play a critical role in determining the replication fitness of the viral strains. Our work for the first time provides a scientific explanation for the presence of a unique NF-κB binding motif in subtype C, a major HIV-1 genetic family responsible for half of the global HIV-1 infections. The results offer compelling evidence that the subtype C viral promoter not only is stronger but also is endowed with a qualitative gain-of-function advantage. The genetically variant NF-κB and the Sp1III motifs may be respond differently to specific cell signal pathways, and these mechanisms must be examined. PMID:27194770

Testing the niche variation hypothesis with a measure of body condition

EPA Science Inventory

Individual variation and fitness are cornerstones of evolution by natural selection. The niche variation hypothesis (NVH) posits that when interspecific competition is relaxed, intraspecific competition should drive niche expansion by selection favoring use of novel resources. Po...

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method.

PubMed

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13 C NMR spectrometry (irm- 13 C NMR) provides the complete 13 C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13 C natural abundance values (50‰), irm- 13 C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13 C NMR. Until now, the conventional strategy to determine the position-specific abundance x i relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13 C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13 C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1 H NMR pulse sequence (named DWET) with a 13 C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T 1 , which forms a serious limitation for irm- 13 C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T 1 variations. Their performance is evaluated on the determination of the 13 C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm- 13 C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time. Copyright © 2018 Elsevier Inc. All rights reserved.

Selection for population-specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post-glacial colonization.

PubMed

Mattila, Tiina M; Aalto, Esa A; Toivainen, Tuomas; Niittyvuopio, Anne; Piltonen, Susanna; Kuittinen, Helmi; Savolainen, Outi

2016-01-01

Spatially varying selection can lead to population-specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location-specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population-specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population-specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species. © 2015 John Wiley & Sons Ltd.

Application of rRNA probes and fluorescence in situ hybridization for rapid detection of the toxic dinoflagellate Alexandrium minutum

NASA Astrophysics Data System (ADS)

Tang, Xianghai; Yu, Rencheng; Zhou, Mingjiang; Yu, Zhigang

2012-03-01

The dinoflagellate Alexandrium minutum is often associated with harmful algal blooms (HABs). This species consists of many strains that differ in their ability to produce toxins but have similar morphology, making identification difficult. In this study, species-specific rRNA probes were designed for whole-cell fluorescence in situ hybridization (FISH) to distinguish A. minutum from two phylogenetic clades. We acquired the complete SSU to LSU rDNA sequences (GenBank accession numbers JF906989-JF906999) of 11 Alexandrium strains and used these to design rRNA targeted oligonucleotide probes. Three ribotype-specific probes, M-GC-1, M-PC-2, and M-PC-3, were designed. The former is specific for the GC clade ("Global clade") of A. minutum, the majority of which have been found non-toxic, and the latter two are specific for the PSP (paralytic shellfish poisoning)-producing PC clade ("Pacific clade"). The specificity of these three probes was confirmed by FISH. All cells in observed fields of view were fluorescently labeled when probes and target species were incubated under optimized FISH conditions. However, the accessibility of rRNA molecules in ribosomes varied among the probe binding positions. Thus, there was variation in the distribution of positive signals in labeled cells within nucleolus and cytosol (M-GC-1, M-PC-3), or just nucleolus (M-PC-2). Our results provide a methodological basis for studying the biogeography and population dynamics of A. minutum, and providing an early warning of toxic HABs.

Modeling of patient's blood pressure variation during ambulance transportation

NASA Astrophysics Data System (ADS)

Sakatani, Kenji; Ono, Takahiko; Kobayasi, Yasuhide; Hikita, Shinichi; Saito, Mitsuyuki

2007-12-01

In an emergency transportation by ambulance, a patient is transported in a supine position. In this position, a patient's blood pressure (BP) variation depending on an inertial force which occurs when an ambulance accelerates or decelerates. This BP variation causes a critical damage for a patent with brain disorder. In order to keep a patient stable during transportation, it is required to maintain small BP variation. To analyze the BP variation during transportation, a model of the BP variation has so far been made. But, it can estimate the BP variation only in braking. The purpose of this paper is to make a dynamical model of the BP variation which can simulate it in both braking and accelerating. First, to obtain the data to construct the model, we used a tilting bed to measure a head-to-foot acceleration and BP of fingertip. Based on this data, we build a mathematical model whose input is the head-to-foot acceleration and output is the Mean BP variation. It is a switched model which switches two models depending on the jerk. We add baroreceptor reflex to the model as a offset value.

The Neurocognition of Conduct Disorder Behaviors: Specificity to Physical Aggression and Theft After Controlling for ADHD Symptoms

PubMed Central

Barker, Edward D.; Tremblay, Richard E.; van Lier, Pol A.C.; Vitaro, Frank; Nagin, Daniel S.; Assaad, Jean-Marc; Séguin, Jean R.

2012-01-01

There is growing evidence that among the different conduct disorder (CD) behaviors, physical aggression, but not theft, links to low neurocognitive abilities. Specifically, physical aggression has consistently been found to be negatively related to neurocognitive abilities, whereas theft has been shown to be either positively or not related to neurocognition. The specificity of these links needs further examination because attention deficit hyperactivity disorder (ADHD) links to both physical aggression and neurocognitive variation. The development of self-reported physical aggression and theft, from age 11 to 17 years, was studied in a prospective at-risk male cohort via a dual process latent growth curve model. Seven neurocognitive tests at age 20 were regressed on the growth parameters of physical aggression and theft. The links between neurocognition and the growth parameters of physical aggression and theft were adjusted for ADHD symptoms at ages 11 and 15 (parent, child and teacher reports). Results indicated that verbal abilities were negatively related to physical aggression while they were positively associated with theft. However, inductive reasoning was negatively associated with increases in theft across adolescence. Symptoms of ADHD accounted for part of the neurocognitive test links with physical aggression but did not account for the associations with theft. These differences emphasize the importance of examining specific CD behaviors to better understand their neurodevelopmental mechanisms. They also suggest that youth who engage in different levels of physical aggression or theft behaviors may require different preventive and corrective interventions. PMID:21046606

The neurocognition of conduct disorder behaviors: specificity to physical aggression and theft after controlling for ADHD symptoms.

PubMed

Barker, Edward D; Tremblay, Richard E; van Lier, Pol A C; Vitaro, Frank; Nagin, Daniel S; Assaad, Jean-Marc; Séguin, Jean R

2011-01-01

There is growing evidence that among the different conduct disorder (CD) behaviors, physical aggression, but not theft, links to low neurocognitive abilities. Specifically, physical aggression has consistently been found to be negatively related to neurocognitive abilities, whereas theft has been shown to be either positively or not related to neurocognition. The specificity of these links needs further examination because attention deficit hyperactivity disorder (ADHD) links to both physical aggression and neurocognitive variation. The development of self-reported physical aggression and theft, from age 11 to 17 years, was studied in a prospective at-risk male cohort via a dual process latent growth curve model. Seven neurocognitive tests at age 20 were regressed on the growth parameters of physical aggression and theft. The links between neurocognition and the growth parameters of physical aggression and theft were adjusted for ADHD symptoms at ages 11 and 15 (parent, child and teacher reports). Results indicated that verbal abilities were negatively related to physical aggression while they were positively associated with theft. However, inductive reasoning was negatively associated with increases in theft across adolescence. Symptoms of ADHD accounted for part of the neurocognitive test links with physical aggression but did not account for the associations with theft. These differences emphasize the importance of examining specific CD behaviors to better understand their neurodevelopmental mechanisms. They also suggest that youth who engage in different levels of physical aggression or theft behaviors may require different preventive and corrective interventions. © 2010 Wiley-Liss, Inc.

Choosing a design to fit the situation: how to improve specificity and positive predictive values using Bayesian lot quality assurance sampling.

PubMed

Olives, Casey; Pagano, Marcello

2013-02-01

Lot Quality Assurance Sampling (LQAS) is a provably useful tool for monitoring health programmes. Although LQAS ensures acceptable Producer and Consumer risks, the literature alleges that the method suffers from poor specificity and positive predictive values (PPVs). We suggest that poor LQAS performance is due, in part, to variation in the true underlying distribution. However, until now the role of the underlying distribution in expected performance has not been adequately examined. We present Bayesian-LQAS (B-LQAS), an approach to incorporating prior information into the choice of the LQAS sample size and decision rule, and explore its properties through a numerical study. Additionally, we analyse vaccination coverage data from UNICEF's State of the World's Children in 1968-1989 and 2008 to exemplify the performance of LQAS and B-LQAS. Results of our numerical study show that the choice of LQAS sample size and decision rule is sensitive to the distribution of prior information, as well as to individual beliefs about the importance of correct classification. Application of the B-LQAS approach to the UNICEF data improves specificity and PPV in both time periods (1968-1989 and 2008) with minimal reductions in sensitivity and negative predictive value. LQAS is shown to be a robust tool that is not necessarily prone to poor specificity and PPV as previously alleged. In situations where prior or historical data are available, B-LQAS can lead to improvements in expected performance.

Molecular Detection of 10 of the Most Unwanted Alien Forest Pathogens in Canada Using Real-Time PCR

PubMed Central

Lamarche, Josyanne; Potvin, Amélie; Pelletier, Gervais; Stewart, Don; Feau, Nicolas; Alayon, Dario I. O.; Dale, Angela L.; Coelho, Aaron; Uzunovic, Adnan; Bilodeau, Guillaume J.; Brière, Stephan C.; Hamelin, Richard C.; Tanguay, Philippe

2015-01-01

Invasive alien tree pathogens can cause significant economic losses as well as large-scale damage to natural ecosystems. Early detection to prevent their establishment and spread is an important approach used by several national plant protection organizations (NPPOs). Molecular detection tools targeting 10 of the most unwanted alien forest pathogens in Canada were developed as part of the TAIGA project (http://taigaforesthealth.com/). Forest pathogens were selected following an independent prioritization. Specific TaqMan real-time PCR detection assays were designed to function under homogeneous conditions so that they may be used in 96- or 384-well plate format arrays for high-throughput testing of large numbers of samples against multiple targets. Assays were validated for 1) specificity, 2) sensitivity, 3) precision, and 4) robustness on environmental samples. All assays were highly specific when evaluated against a panel of pure cultures of target and phylogenetically closely-related species. Sensitivity, evaluated by assessing the limit of detection (with a threshold of 95% of positive samples), was found to be between one and ten target gene region copies. Precision or repeatability of each assay revealed a mean coefficient of variation of 3.4%. All assays successfully allowed detection of target pathogen on positive environmental samples, without any non-specific amplification. These molecular detection tools will allow for rapid and reliable detection of 10 of the most unwanted alien forest pathogens in Canada. PMID:26274489

Geographic patterns of seed mass are associated with climate factors, but relationships vary between species.

PubMed

Soper Gorden, Nicole L; Winkler, Katharine J; Jahnke, Matthew R; Marshall, Elizabeth; Horky, Joshua; Huddelson, Colton; Etterson, Julie R

2016-01-01

Seed size is a critical life history attribute with fitness effects that cascade throughout the lifespan of plants. Interspecific studies repeatedly report a negative correlation between seed mass and latitude. Yet, despite its importance, little is known about geographic variation in seed size within species' ranges. To improve our understanding of intraspecific geographic variation in seed size, we collected and weighed seeds by maternal line from 8 to 17 populations of seven herbaceous plant species spanning large geographic areas, and measured a dispersal trait, awn length, for two grass species. We examined the overall relationship between seed mass and latitude, then divided the data into species-specific subsets to compare the fit of three models to explain seed mass and awn length: (1) latitude and longitude, (2) long-term climate, and (3) collection-year weather. Like previous work, we found a negative relationship between interspecific seed mass and latitude. However, the best-fit models explaining seed size and awn length differed between individual species and often included significant interaction terms. For all species, the best model was either long-term or collection-year climate data instead of latitude and longitude. Intraspecific geographic patterns for seed traits were remarkably inconsistent, covarying both negatively and positively with temperature and precipitation. The only apparent generalization is that annual species' seed mass corresponded more with collection-year weather while perennial species covaried more with long-term climate. Overall, this study suggests that the scale of climate variation that molds seed traits is highly species-specific. © 2016 Botanical Society of America.

Impact of Parental Bos taurus and Bos indicus Origins on Copy Number Variation in Traditional Chinese Cattle Breeds.

PubMed

Zhang, Liangzhi; Jia, Shangang; Plath, Martin; Huang, Yongzhen; Li, Congjun; Lei, Chuzhao; Zhao, Xin; Chen, Hong

2015-08-10

Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also in domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here, we of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal single nucleotide polymorphisms to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y1, Y2; B. indicus: Y3), whereas 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Microform-related community patterns of methane-cycling microbes in boreal Sphagnum bogs are site specific.

PubMed

Juottonen, Heli; Kotiaho, Mirkka; Robinson, Devin; Merilä, Päivi; Fritze, Hannu; Tuittila, Eeva-Stiina

2015-09-01

Vegetation and water table are important regulators of methane emission in peatlands. Microform variation encompasses these factors in small-scale topographic gradients of dry hummocks, intermediate lawns and wet hollows. We examined methane production and oxidization among microforms in four boreal bogs that showed more variation of vegetation within a bog with microform than between the bogs. Potential methane production was low and differed among bogs but not consistently with microform. Methane oxidation followed water table position with microform, showing higher rates closer to surface in lawns and hollows than in hummocks. Methanogen community, analysed by mcrA terminal restriction fragment length polymorphism and dominated by Methanoregulaceae or 'Methanoflorentaceae', varied strongly with bog. The extent of microform-related variation of methanogens depended on the bog. Methanotrophs identified as Methylocystis spp. in pmoA denaturing gradient gel electrophoresis similarly showed effect of bog, and microform patterns were stronger within individual bogs. Our results suggest that methane-cycling microbes in boreal Sphagnum bogs with seemingly uniform environmental conditions may show strong site-dependent variation. The bog-intrinsic factor may be related to carbon availability but contrary to expectations appears to be unrelated to current surface vegetation, calling attention to the origin of carbon substrates for microbes in bogs. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Response of data-driven artificial neural network-based TEC models to neutral wind for different locations, seasons, and solar activity levels from the Indian longitude sector

NASA Astrophysics Data System (ADS)

Sur, D.; Haldar, S.; Ray, S.; Paul, A.

2017-07-01

The perturbations imposed on transionospheric signals by the ionosphere are a major concern for navigation. The dynamic nature of the ionosphere in the low-latitude equatorial region and the Indian longitude sector has some specific characteristics such as sharp temporal and latitudinal variation of total electron content (TEC). TEC in the Indian longitude sector also undergoes seasonal variations. The large magnitude and sharp variation of TEC cause large and variable range errors for satellite-based navigation system such as Global Positioning System (GPS) throughout the day. For accurate navigation using satellite-based augmentation systems, proper prediction of TEC under certain geophysical conditions is necessary in the equatorial region. It has been reported in the literature that prediction accuracy of TEC has been improved using measured data-driven artificial neural network (ANN)-based vertical TEC (VTEC) models, compared to standard ionospheric models. A set of observations carried out in the Indian longitude sector have been reported in this paper in order to find the amount of improvement in performance accuracy of an ANN-based VTEC model after incorporation of neutral wind as model input. The variations of this improvement in prediction accuracy with respect to latitude, longitude, season, and solar activity have also been reported in this paper.

Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana

PubMed Central

Simon, Lauriane; Rabanal, Fernando A; Dubos, Tristan; Oliver, Cecilia; Lauber, Damien; Poulet, Axel; Vogt, Alexander; Mandlbauer, Ariane; Le Goff, Samuel; Sommer, Andreas; Duborjal, Hervé; Tatout, Christophe

2018-01-01

Abstract Organized in tandem repeat arrays in most eukaryotes and transcribed by RNA polymerase III, expression of 5S rRNA genes is under epigenetic control. To unveil mechanisms of transcriptional regulation, we obtained here in depth sequence information on 5S rRNA genes from the Arabidopsis thaliana genome and identified differential enrichment in epigenetic marks between the three 5S rDNA loci situated on chromosomes 3, 4 and 5. We reveal the chromosome 5 locus as the major source of an atypical, long 5S rRNA transcript characteristic of an open chromatin structure. 5S rRNA genes from this locus translocated in the Landsberg erecta ecotype as shown by linkage mapping and chromosome-specific FISH analysis. These variations in 5S rDNA locus organization cause changes in the spatial arrangement of chromosomes in the nucleus. Furthermore, 5S rRNA gene arrangements are highly dynamic with alterations in chromosomal positions through translocations in certain mutants of the RNA-directed DNA methylation pathway and important copy number variations among ecotypes. Finally, variations in 5S rRNA gene sequence, chromatin organization and transcripts indicate differential usage of 5S rDNA loci in distinct ecotypes. We suggest that both the usage of existing and new 5S rDNA loci resulting from translocations may impact neighboring chromatin organization. PMID:29518237

Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana.

PubMed

Simon, Lauriane; Rabanal, Fernando A; Dubos, Tristan; Oliver, Cecilia; Lauber, Damien; Poulet, Axel; Vogt, Alexander; Mandlbauer, Ariane; Le Goff, Samuel; Sommer, Andreas; Duborjal, Hervé; Tatout, Christophe; Probst, Aline V

2018-04-06

Organized in tandem repeat arrays in most eukaryotes and transcribed by RNA polymerase III, expression of 5S rRNA genes is under epigenetic control. To unveil mechanisms of transcriptional regulation, we obtained here in depth sequence information on 5S rRNA genes from the Arabidopsis thaliana genome and identified differential enrichment in epigenetic marks between the three 5S rDNA loci situated on chromosomes 3, 4 and 5. We reveal the chromosome 5 locus as the major source of an atypical, long 5S rRNA transcript characteristic of an open chromatin structure. 5S rRNA genes from this locus translocated in the Landsberg erecta ecotype as shown by linkage mapping and chromosome-specific FISH analysis. These variations in 5S rDNA locus organization cause changes in the spatial arrangement of chromosomes in the nucleus. Furthermore, 5S rRNA gene arrangements are highly dynamic with alterations in chromosomal positions through translocations in certain mutants of the RNA-directed DNA methylation pathway and important copy number variations among ecotypes. Finally, variations in 5S rRNA gene sequence, chromatin organization and transcripts indicate differential usage of 5S rDNA loci in distinct ecotypes. We suggest that both the usage of existing and new 5S rDNA loci resulting from translocations may impact neighboring chromatin organization.

Schooling and variation in the COMT gene: The devil is in the details

PubMed Central

Campbell, Daniel; Bick, Johanna; Yrigollen, Carolyn M.; Lee, Maria; Joseph, Antony; Chang, Joseph T.; Grigorenko, Elena L.

2013-01-01

Background Schooling is considered to be one of the major contributors to the development of intelligence within societies and individuals. Genetic variation might modulate the impact of schooling and explain, at least partially, the presence of individual differences in classrooms. Method We studied a sample of 1502 children (mean age = 11.7 years) from Zambia. Approximately 57% of these children were enrolled in school, and the rest were not. To quantify genetic variation, we investigated a number of common polymorphisms in the catechol-O-methyltransferase (COMT) gene that controls the production of the protein thought to account for >60% of the dopamine degradation in the prefrontal cortex. Results Haplotype analyses generated results ranging from the presence to absence of significant interactions between a number of COMT haplotypes and indicators of schooling (i.e., in- vs. out-of-school and grade completed) in the prediction of nonverbal intelligence, depending on the parameter specification. However, an investigation of the distribution of corresponding p-values suggested that these positive results were false. Conclusions Convincing evidence that the variation in the COMT gene is associated with individual differences in nonverbal intelligence either directly or through interactions with schooling was not found. P-values produced by the method of testing for haplotype effects employed here may be sensitive to parameter settings, invalid under default settings, and should be checked for validity through simulation. PMID:23952646

LC-MSMS assays of urinary cortisol, a comparison between four in-house assays.

PubMed

Brossaud, Julie; Leban, Monique; Corcuff, Jean-Benoit; Boux de Casson, Florence; Leloupp, Anne-Gaëlle; Masson, Damien; Moal, Valérie; Bach-Ngohou, Kalyane

2018-06-27

Twenty-four hour urinary free cortisol (UFC) determination can be used for screening and follow-up of Cushing syndrome (CS). As immunoassay methods lack specificity for UFC measurement, the use of high-performance liquid chromatography coupled to mass spectrometer (LC-MSMS) is recommended. The aim of our study was to compare UFC results using four LC-MSMS methods performed in four independent laboratories in order to evaluate interlaboratory agreement. Frozen aliquots of 24-h urine samples (78 healthy volunteers and 20 patients with CS) were sent to four different laboratories for analysis. Following liquid-liquid or solid-liquid extraction, UFC were determined using four different LC-MSMS assay. UFC intra- and interassays variation coefficients were lower than 10% for each centre. External quality control results were not significantly different. UFC normal ranges (established from healthy volunteers) were 17-126, 15-134, 12-118 and 27-157 nmol/day, respectively. Classification of UFC from healthy volunteers and patients with CS using a 95th percentile threshold was similar. However, for extreme UFC values (<50 or >270 nmol/day), negative or positive bias was noted. Even for highly specific methods such as LC-MSMS, variations of results can be found depending on analytical process. Validation of LC-MSMS methods including determination of the reference range is essential.

Influence of precipitation and crop germination on resource selection by mule deer (Odocoileus hemionus) in southwest Colorado

USGS Publications Warehouse

Carrollo, Emily M.; Johnson, Heather E.; Fischer, Justin W.; Hammond, Matthew; Dorsey, Patricia D.; Anderson, Charles; Vercauteren, Kurt C.; Walter, W. David

2017-01-01

Mule deer (Odocoileus hemionus) populations in the western United States provide many benefits to local economies but can also cause considerable damage to agriculture, particularly damage to lucrative crops. Limited information exists to understand resource selection of mule deer in response to annual variation in crop rotation and climatic conditions. We tested the hypothesis that mule deer select certain crops, and in particular sunflower, based on annual climatic variability. Our objective was to use movements, estimates of home range, and resource selection analysis to identify resources selected by mule deer. We used annually-derived crop-specific datasets along with Global Positioning System collars to monitor 14 mule deer in an agricultural area near public lands in southwestern Colorado, USA. We estimated home ranges for two winter seasons that ranged between 7.68 and 9.88 km2, and for two summer seasons that ranged between 5.51 and 6.24 km2. Mule deer selected areas closer to forest and alfalfa for most periods during 2012, but selected areas closer to sunflower in a majority of periods during 2013. Considerable annual variation in climate patterns and precipitation levels appeared to influence selection by mule deer because of variability in crop rotation and success of germination of specific crops.

Tempo-Spatial Variations of Ambient Ozone-Mortality Associations in the USA: Results from the NMMAPS Data.

PubMed

Liu, Tao; Zeng, Weilin; Lin, Hualiang; Rutherford, Shannon; Xiao, Jianpeng; Li, Xing; Li, Zhihao; Qian, Zhengmin; Feng, Baixiang; Ma, Wenjun

2016-08-26

Although the health effects of ambient ozone have been widely assessed, their tempo-spatial variations remain unclear. We selected 20 communities (ten each from southern and northern USA) based on the US National Morbidity, Mortality, and Air Pollution Study (NMMAPS) dataset. A generalized linear model (GLM) was used to estimate the season-specific association between each 10 ppb (lag0-2 day average) increment in daily 8 h maximum ozone concentration and mortality in every community. The results showed that in the southern communities, a 10 ppb increment in ozone was linked to an increment of mortality of -0.07%, -0.17%, 0.40% and 0.27% in spring, summer, autumn and winter, respectively. For the northern communities, the excess risks (ERs) were 0.74%, 1.21%, 0.52% and -0.65% in the spring, summer, autumn and winter seasons, respectively. City-specific ozone-related mortality effects were positively related with latitude, but negatively related with seasonal average temperature in the spring, summer and autumn seasons. However, a reverse relationship was found in the winter. We concluded that there were different seasonal patterns of ozone effects on mortality between southern and northern US communities. Latitude and seasonal average temperature were identified as modifiers of the ambient ozone-related mortality risks.

Tempo-Spatial Variations of Ambient Ozone-Mortality Associations in the USA: Results from the NMMAPS Data

PubMed Central

Liu, Tao; Zeng, Weilin; Lin, Hualiang; Rutherford, Shannon; Xiao, Jianpeng; Li, Xing; Li, Zhihao; Qian, Zhengmin; Feng, Baixiang; Ma, Wenjun

2016-01-01

Although the health effects of ambient ozone have been widely assessed, their tempo-spatial variations remain unclear. We selected 20 communities (ten each from southern and northern USA) based on the US National Morbidity, Mortality, and Air Pollution Study (NMMAPS) dataset. A generalized linear model (GLM) was used to estimate the season-specific association between each 10 ppb (lag0-2 day average) increment in daily 8 h maximum ozone concentration and mortality in every community. The results showed that in the southern communities, a 10 ppb increment in ozone was linked to an increment of mortality of −0.07%, −0.17%, 0.40% and 0.27% in spring, summer, autumn and winter, respectively. For the northern communities, the excess risks (ERs) were 0.74%, 1.21%, 0.52% and −0.65% in the spring, summer, autumn and winter seasons, respectively. City-specific ozone-related mortality effects were positively related with latitude, but negatively related with seasonal average temperature in the spring, summer and autumn seasons. However, a reverse relationship was found in the winter. We concluded that there were different seasonal patterns of ozone effects on mortality between southern and northern US communities. Latitude and seasonal average temperature were identified as modifiers of the ambient ozone-related mortality risks. PMID:27571094

Influence of Precipitation and Crop Germination on Resource Selection by Mule Deer (Odocoileus hemionus) in Southwest Colorado.

PubMed

Carrollo, Emily M; Johnson, Heather E; Fischer, Justin W; Hammond, Matthew; Dorsey, Patricia D; Anderson, Charles; Vercauteren, Kurt C; Walter, W David

2017-11-09

Mule deer (Odocoileus hemionus) populations in the western United States provide many benefits to local economies but can also cause considerable damage to agriculture, particularly damage to lucrative crops. Limited information exists to understand resource selection of mule deer in response to annual variation in crop rotation and climatic conditions. We tested the hypothesis that mule deer select certain crops, and in particular sunflower, based on annual climatic variability. Our objective was to use movements, estimates of home range, and resource selection analysis to identify resources selected by mule deer. We used annually-derived crop-specific datasets along with Global Positioning System collars to monitor 14 mule deer in an agricultural area near public lands in southwestern Colorado, USA. We estimated home ranges for two winter seasons that ranged between 7.68 and 9.88 km 2 , and for two summer seasons that ranged between 5.51 and 6.24 km 2 . Mule deer selected areas closer to forest and alfalfa for most periods during 2012, but selected areas closer to sunflower in a majority of periods during 2013. Considerable annual variation in climate patterns and precipitation levels appeared to influence selection by mule deer because of variability in crop rotation and success of germination of specific crops.

Environmental Adaptation Contributes to Gene Polymorphism across the Arabidopsis thaliana Genome

PubMed Central

Lee, Cheng-Ruei

2012-01-01

The level of within-species polymorphism differs greatly among genes in a genome. Many genomic studies have investigated the relationship between gene polymorphism and factors such as recombination rate or expression pattern. However, the polymorphism of a gene is affected not only by its physical properties or functional constraints but also by natural selection on organisms in their environments. Specifically, if functionally divergent alleles enable adaptation to different environments, locus-specific polymorphism may be maintained by spatially heterogeneous natural selection. To test this hypothesis and estimate the extent to which environmental selection shapes the pattern of genome-wide polymorphism, we define the "environmental relevance" of a gene as the proportion of genetic variation explained by environmental factors, after controlling for population structure. We found substantial effects of environmental relevance on patterns of polymorphism among genes. In addition, the correlation between environmental relevance and gene polymorphism is positive, consistent with the expectation that balancing selection among heterogeneous environments maintains genetic variation at ecologically important genes. Comparison of the gene ontology annotations shows that genes with high environmental relevance are enriched in unknown function categories. These results suggest an important role for environmental factors in shaping genome-wide patterns of polymorphism and indicate another direction of genomic study. PMID:22798389

Genetic Variation in Serotonin Transporter Modulates Tactile Hyperresponsiveness in ASD

PubMed Central

Schauder, Kimberly B.; Muller, Christopher L.; Veenstra-VanderWeele, Jeremy; Cascio, Carissa J.

2014-01-01

Several lines of evidence implicate dysfunction of the serotonin (5-HT) system in autism spectrum disorder (ASD). Specifically, the serotonin transporter (5-HTT, SERT) has been scrutinized as an ASD candidate risk gene. SERT plays key roles in the development of circuits that underlie sensory function, particularly in the somatosensory system. One previous study in ASD found association of a rare, hyperfunctional SERT variant with sensory aversion, but studies of common SERT variants have never examined sensory symptoms in ASD. Using standardized caregiver assessments of sensory function in children, we evaluated patterns of sensory responsiveness in 47 children with ASD and 38 typically developing (TD) children. Study participants were genotyped for the functional SERT promoter polymorphisms, 5-HTTLPR and rs25531, to test the hypothesis that the higher expressing genotypes would be associated with hyperresponsiveness to touch, a common sensory aversion in ASD. All measures of sensory hypo- and hyperresponsiveness were increased in children with ASD, with hyporesponsive sensory patterns negatively correlated to age and hyperresponsive sensory patterns positively correlated to repetitive behavior. Strikingly, high-expressing SERT genotypes were associated with increased tactile hyperresponsiveness in the ASD group. Our findings indicate genetic variation that increases SERT function may specifically impact somatosensory processing in ASD. PMID:25558276

Mutational load of the mitochondrial genome predicts pathological features and biochemical recurrence in prostate cancer.

PubMed

Kalsbeek, Anton M F; Chan, Eva F K; Grogan, Judith; Petersen, Desiree C; Jaratlerdsiri, Weerachai; Gupta, Ruta; Lyons, Ruth J; Haynes, Anne-Maree; Horvath, Lisa G; Kench, James G; Stricker, Phillip D; Hayes, Vanessa M

2016-10-05

Prostate cancer management is complicated by extreme disease heterogeneity, which is further limited by availability of prognostic biomarkers. Recognition of prostate cancer as a genetic disease has prompted a focus on the nuclear genome for biomarker discovery, with little attention given to the mitochondrial genome. While it is evident that mitochondrial DNA (mtDNA) mutations are acquired during prostate tumorigenesis, no study has evaluated the prognostic value of mtDNA variation. Here we used next-generation sequencing to interrogate the mitochondrial genomes from prostate tissue biopsies and matched blood of 115 men having undergone a radical prostatectomy for which there was a mean of 107 months clinical follow-up. We identified 74 unique prostate cancer specific somatic mtDNA variants in 50 patients, providing significant expansion to the growing catalog of prostate cancer mtDNA mutations. While no single variant or variant cluster showed recurrence across multiple patients, we observe a significant positive correlation between the total burden of acquired mtDNA variation and elevated Gleason Score at diagnosis and biochemical relapse. We add to accumulating evidence that total acquired genomic burden, rather than specific mtDNA mutations, has diagnostic value. This is the first study to demonstrate the prognostic potential of mtDNA mutational burden in prostate cancer.

Temperature compensated and self-calibrated current sensor using reference current

DOEpatents

Yakymyshyn, Christopher Paul [Seminole, FL; Brubaker, Michael Allen [Loveland, CO; Yakymyshyn, Pamela Jane [Seminole, FL

2008-01-22

A method is described to provide temperature compensation and self-calibration of a current sensor based on a plurality of magnetic field sensors positioned around a current carrying conductor. A reference electrical current carried by a conductor positioned within the sensing window of the current sensor is used to correct variations in the output signal due to temperature variations and aging.

Value analysis of postoperative staging imaging for asymptomatic, early-stage breast cancer: implications of clinical variation on utility and cost.

PubMed

Pellet, Andrew C; Erten, Mujde Z; James, Ted A

2016-06-01

Routine staging imaging for early-stage breast cancer is not recommended. Despite this, there is clinical practice variation with imaging studies obtained for asymptomatic patients with a positive sentinel node (SN+). We characterize the utility, cost, and clinical implications of imaging studies obtained in asymptomatic SN+ patients. A retrospective review was performed of asymptomatic, clinically node-negative patients who were found to have a positive sentinel node after surgery. The type of imaging, subsequent tests/interventions, frequency of additional malignancy detected, and costs were recorded. From April 2009 to April 2013, a total of 50 of 113 (44%) asymptomatic patients underwent staging imaging for a positive sentinel node; 11 (22%) patients had at least 1 subsequent imaging study or diagnostic intervention. No instance of metastatic breast cancer was identified, with a total cost of imaging calculated at $116,905. Staging imaging for asymptomatic SN+ breast cancer demonstrates clinical variation. These tests were associated with low utility, increased costs, and frequent false positives leading to subsequent testing/intervention. Evidence-based standardization may help increase quality by decreasing unnecessary variation and cost. Copyright © 2015 Elsevier Inc. All rights reserved.

Radial variation in sap velocity as a function of stem diameter and sapwood thickness in yellow-poplar trees.

PubMed

Wullschleger, Stan D.; King, Anthony W.

2000-04-01

Canopy transpiration and forest water use are frequently estimated as the product of sap velocity and cross-sectional sapwood area. Few studies, however, have considered whether radial variation in sap velocity and the proportion of sapwood active in water transport are significant sources of uncertainty in the extrapolation process. Therefore, radial profiles of sap velocity were examined as a function of stem diameter and sapwood thickness for yellow-poplar (Liriodendron tulipifera L.) trees growing on two adjacent watersheds in eastern Tennessee. The compensation heat pulse velocity technique was used to quantify sap velocity at four equal-area depths in 20 trees that ranged in stem diameter from 15 to 69 cm, and in sapwood thickness from 2.1 to 14.8 cm. Sap velocity was highly dependent on the depth of probe insertion into the sapwood. Rates of sap velocity were greatest for probes located in the two outer sapwood annuli (P1 and P2) and lowest for probes in closest proximity to the heartwood (P3 and P4). Relative sap velocities averaged 0.98 at P1, 0.66 at P2, 0.41 at P3 and 0.35 at P4. Tree-specific sap velocities measured at each of the four probe positions, divided by the maximum sap velocity measured (usually at P1 or P2), indicated that the fraction of sapwood functional in water transport (f(S)) varied between 0.49 and 0.96. There was no relationship between f(S) and sapwood thickness, or between f(S) and stem diameter. The fraction of functional sapwood averaged 0.66 +/- 0.13 for trees on which radial profiles were determined. No significant depth-related differences were observed for sapwood density, which averaged 469 kg m(-3) across all four probe positions. There was, however, a significant decline in sapwood water content between the two outer probe positions (1.04 versus 0.89 kg kg(-1)). This difference was not sufficient to account for the observed radial variation in sap velocity. A Monte-Carlo analysis indicated that the standard error in estimated mean f(S) declined rapidly with increasing sample size. At n = 10, the coefficient of variation in mean f(S) was 7% and at n = 15 it was slightly less than 5%. These observations indicate that radial variation in sap velocity is an important, albeit often overlooked, source of uncertainty in the scaling process. Failure to recognize that not all sapwood is functional in water transport will introduce systematic bias into estimates of both tree and stand water use. Future studies should devise sampling strategies for assessing radial variation in sap velocity and such strategies should be used to identify the magnitude of this variation in a range of non-, diffuse- and ring-porous trees.

Proposal 11913-IR Filter Wedge Check

NASA Astrophysics Data System (ADS)

Sabbi, E.; MacKenty, J.; Borders, T.

2010-08-01

Variations in the thickness of a filter alter the path of the incoming light beam, causing an apparent displacement of the observed sources. Proposal 11913 was designed to verify the coplanarity of the WFC3/ IR filters, i.e. whether any of them was wedged, and if so, to evaluate the impact on the astrometry. We found that, with the exception of the F098M and F126N filters, the positions of stars observed through different filters, without moving the telescope, differ on average by less then 0.14 ±0.06 pixels and match the CEI specifications. In addition we found that the positional shifts increase along the X-axis and decrease along the Y-axis as a function of wavelength. The observed shifts are consistent with the fact that the refractive corrector plate (RCP) is tilted ~8.6 degree to the center of the field center chief ray.

Cross-cultural correlates of life satisfaction and self-esteem.

PubMed

Diener, E; Diener, M

1995-04-01

College students in 31 nations (N = 13,118) completed measures of self-esteem, life satisfaction, and satisfaction with specific domains (friends, family, and finances). The authors assessed whether cross-cultural variations in the strength of associations were related to societal dimensions including income and individualism. At the national level, individualism correlated -.24 (ns) with heterogeneity and .71 (p < .001) with wealth. At the individual level, self-esteem and life satisfaction were correlated .47 for the entire sample. This relation, however, was moderated by the individualism of the society. The associations of financial, friend, and family satisfactions with life satisfaction and with self-esteem also varied across nations. Financial satisfaction was a stronger correlate of life satisfaction in poorer countries. It was found that life satisfaction and self-esteem were clearly discriminable constructs. Satisfaction ratings, except for financial satisfaction, varied between slightly positive and fairly positive.

In operando quantitation of Li concentration for a commercial Li-ion rechargeable battery using high-energy X-ray Compton scattering.

PubMed

Suzuki, Kosuke; Suzuki, Ayahito; Ishikawa, Taiki; Itou, Masayoshi; Yamashige, Hisao; Orikasa, Yuki; Uchimoto, Yoshiharu; Sakurai, Yoshiharu; Sakurai, Hiroshi

2017-09-01

Compton scattering is one of the most promising probes for quantitating Li under in operando conditions, since high-energy X-rays, which have high penetration power, are used as the incident beam and the Compton-scattered energy spectrum has specific line-shapes for each element. An in operando quantitation method to determine the Li composition in electrodes has been developed by using line-shape (S-parameter) analysis of the Compton-scattered energy spectrum. In this study, S-parameter analysis has been applied to a commercial coin cell Li-ion rechargeable battery and the variation of the S-parameters during the charge/discharge cycle at the positive and negative electrodes has been obtained. By using calibration curves for Li composition in the electrodes, the change in Li composition of the positive and negative electrodes has been determined using the S-parameters simultaneously.

Karyotype Analysis of Four Vicia Species using In Situ Hybridization with Repetitive Sequences

PubMed Central

NAVRÁTILOVÁ, ALICE; NEUMANN, PAVEL; MACAS, JIŘÍ

2003-01-01

Mitotic chromosomes of four Vicia species (V. sativa, V. grandiflora, V. pannonica and V. narbonensis) were subjected to in situ hybridization with probes derived from conserved plant repetitive DNA sequences (18S–25S and 5S rDNA, telomeres) and genus‐specific satellite repeats (VicTR‐A and VicTR‐B). Numbers and positions of hybridization signals provided cytogenetic landmarks suitable for unambiguous identification of all chromosomes, and establishment of the karyotypes. The VicTR‐A and ‐B sequences, in particular, produced highly informative banding patterns that alone were sufficient for discrimination of all chromosomes. However, these patterns were not conserved among species and thus could not be employed for identification of homologous chromosomes. This fact, together with observed variations in positions and numbers of rDNA loci, suggests considerable divergence between karyotypes of the species studied. PMID:12770847

Variability of the protein sequences of lcrV between epidemic and atypical rhamnose-positive strains of Yersinia pestis.

PubMed

Anisimov, Andrey P; Panfertsev, Evgeniy A; Svetoch, Tat'yana E; Dentovskaya, Svetlana V

2007-01-01

Sequencing of lcrV genes and comparison of the deduced amino acid sequences from ten Y. pestis strains belonging mostly to the group of atypical rhamnose-positive isolates (non-pestis subspecies or pestoides group) showed that the LcrV proteins analyzed could be classified into five sequence types. This classification was based on major amino acid polymorphisms among LcrV proteins in the four "hot points" of the protein sequences. Some additional minor polymorphisms were found throughout these sequence types. The "hot points" corresponded to amino acids 18 (Lys --> Asn), 72 (Lys --> Arg), 273 (Cys --> Ser), and 324-326 (Ser-Gly-Lys --> Arg) in the LcrV sequence of the reference Y. pestis strain CO92. One possible explanation for polymorphism in amino acid sequences of LcrV among different strains is that strain-specific variation resulted from adaptation of the plague pathogen to different rodent and lagomorph hosts.

Risk of Interval Cancer in Fecal Immunochemical Test Screening Significantly Higher During the Summer Months: Results from the National Cancer Screening Program in Korea.

PubMed

Cha, Jae Myung; Suh, Mina; Kwak, Min Seob; Sung, Na Young; Choi, Kui Son; Park, Boyoung; Jun, Jae Kwan; Hwang, Sang-Hyun; Lee, Do-Hoon; Kim, Byung Chang; Lee, You Kyoung; Han, Dong Soo

2018-04-01

This study aimed to evaluate the impact of seasonal variations in climate on the performance of the fecal immunochemical test (FIT) in screening for colorectal cancer in the National Cancer Screening Program in Korea. Data were extracted from the National Cancer Screening Program databases for participants who underwent FIT between 2009 and 2010. We compared positivity rates, cancer detection rates, interval cancer rates, positive predictive value, sensitivity, and specificity for FIT during the spring, summer, fall, and winter seasons in Korea. In total, 4,788,104 FIT results were analyzed. FIT positivity rate was lowest during the summer months. In the summer, the positive predictive value of FIT was about 1.1 times (adjusted odds ratio (aOR) 1.08, 95% confidence interval (CI) 1.00-1.16) higher in the overall FIT group and about 1.3 times (aOR 1.29, 95% CI 1.10-1.50) higher in the quantitative FIT group, compared to those in the other seasons. Cancer detection rates, however, were similar regardless of season. Interval cancer risk was significantly higher in the summer for both the overall FIT group (aOR 1.16, 95% CI 1.07-1.27) and the quantitative FIT group (aOR 1.31, 95% CI 1.12-1.52). In addition, interval cancers in the rectum and distal colon were more frequently detected in the summer and autumn than in the winter. The positivity rate of FIT was lower in the summer, and the performance of the FIT screening program was influenced by seasonal variations in Korea. These results suggest that more efforts to reduce interval cancer during the summer are needed in population-based screening programs using FIT, particularly in countries with high ambient temperatures.

Timothy-specific IgG antibody levels vary with the pollen seasons.

PubMed

Nordvall, S L; Larsson, P H; Johansson, S G

1986-11-01

Serum samples were collected from eight grass pollen hypersensitive children during a 4-year period. The sera were assayed for contents of timothy-specific IgE antibodies by RAST. Timothy-specific IgG and IgA antibodies were quantified by a refined ELISA in which covalent binding of the antigen to the polystyrene solid phase had been performed. IgG antibodies were also assayed by a Sepharose-protein-A technique with radiolabelled timothy allergens as the antigen. It was possible to register clearcut seasonal variations with postseasonally boosted antibody levels not only of timothy-specific IgE but also of IgG antibody. Both IgG1 and IgG4 antibodies specific for timothy showed seasonal variations of a similar degree. It was not possible to register seasonal variations of the same magnitude of timothy-specific IgA antibodies.

Trend and variability of atmospheric ozone over middle Indo-Gangetic Plain: impacts of seasonality and precursor gases.

PubMed

Shukla, K; Srivastava, Prashant K; Banerjee, T; Aneja, Viney P

2017-01-01

Ozone dynamics in two urban background atmospheres over middle Indo-Gangetic Plain (IGP) were studied in two contexts: total columnar and ground-level ozone. In terms of total columnar ozone (TCO), emphases were made to compare satellite-based retrieval with ground-based observation and existing trend in decadal and seasonal variation was also identified. Both satellite-retrieved (Aura Ozone Monitoring Instrument-Differential Optical Absorption Spectroscopy (OMI-DOAS)) and ground-based observations (IMD-O 3 ) revealed satisfying agreement with OMI-DOAS observation over predicting TCO with a positive bias of 7.24 % under all-sky conditions. Minor variation between daily daytime (r = 0.54; R 2  = 29 %; n = 275) and satellite overpass time-averaged TCO (r = 0.58; R 2  = 34 %; n = 208) was also recognized. A consistent and clear seasonal trend in columnar ozone (2005-2015) was noted with summertime (March-June) maxima (Varanasi, 290.9 ± 8.8; Lucknow, 295.6 ± 9.5 DU) and wintertime (December-February) minima (Varanasi, 257.4 ± 10.1; Lucknow, 258.8 ± 8.8 DU). Seasonal trend decomposition based on locally weighted regression smoothing technique identified marginally decreasing trend (Varanasi, 0.0084; Lucknow, 0.0096 DU year -1 ) especially due to reduction in monsoon time minima and summertime maxima. In continuation to TCO, variation in ground-level ozone in terms of seasonality and precursor gases were also analysed from September 2014 to August 2015. Both stations registered similar pattern of variation with Lucknow representing slightly higher annual mean (44.3 ± 30.6; range, 1.5-309.1 μg/m 3 ) over Varanasi (38.5 ± 17.7; range, 4.9-104.2 μg/m 3 ). Variation in ground-level ozone was further explained in terms water vapour, atmospheric boundary layer height and solar radiation. Ambient water vapour content was found to associate negatively (r = -0.28, n = 284) with ground-level ozone with considerable seasonal variation in Varanasi. Implication of solar radiation on formation of ground-level ozone was overall positive (Varanasi, 0.60; Lucknow, 0.26), while season-specific association was recorded in case of atmospheric boundary layer.

Variations on a theme: diversification of cuticular hydrocarbons in a clade of cactophilic Drosophila

PubMed Central

2011-01-01

Background We characterized variation and chemical composition of epicuticular hydrocarbons (CHCs) in the seven species of the Drosophila buzzatii cluster with gas chromatography/mass spectrometry. Despite the critical role of CHCs in providing resistance to desiccation and involvement in communication, such as courtship behavior, mating, and aggregation, few studies have investigated how CHC profiles evolve within and between species in a phylogenetic context. We analyzed quantitative differences in CHC profiles in populations of the D. buzzatii species cluster in order to assess the concordance of CHC differentiation with species divergence. Results Thirty-six CHC components were scored in single fly extracts with carbon chain lengths ranging from C29 to C39, including methyl-branched alkanes, n-alkenes, and alkadienes. Multivariate analysis of variance revealed that CHC amounts were significantly different among all species and canonical discriminant function (CDF) analysis resolved all species into distinct, non-overlapping groups. Significant intraspecific variation was found in different populations of D. serido suggesting that this taxon is comprised of at least two species. We summarized CHC variation using CDF analysis and mapped the first five CHC canonical variates (CVs) onto an independently derived period (per) gene + chromosome inversion + mtDNA COI gene for each sex. We found that the COI sequences were not phylogenetically informative due to introgression between some species, so only per + inversion data were used. Positive phylogenetic signal was observed mainly for CV1 when parsimony methods and the test for serial independence (TFSI) were used. These results changed when no outgroup species were included in the analysis and phylogenetic signal was then observed for female CV3 and/or CV4 and male CV4 and CV5. Finally, removal of divergent populations of D. serido significantly increased the amount of phylogenetic signal as up to four out of five CVs then displayed positive phylogenetic signal. Conclusions CHCs were conserved among species while quantitative differences in CHC profiles between populations and species were statistically significant. Most CHCs were species-, population-, and sex-specific. Mapping CHCs onto an independently derived phylogeny revealed that a significant portion of CHC variation was explained by species' systematic affinities indicating phylogenetic conservatism in the evolution of these hydrocarbon arrays, presumptive waterproofing compounds and courtship signals as in many other drosophilid species. PMID:21699713

Tree-stem diameter fluctuates with the lunar tides and perhaps with geomagnetic activity.

PubMed

Barlow, Peter W; Mikulecký, Miroslav; Střeštík, Jaroslav

2010-11-01

Our initial objective has been to examine the suggestion of Zürcher et al. (Nature 392:665–666, 1998) that the naturally occurring variations in stem diameter of two experimental trees of Picea alba were related to near simultaneous variations in the lunisolar tidal acceleration. The relationship was positive: Lunar peaks were roughly synchronous with stem diameter peaks. To extend the investigation of this putative relationship, additional data on stem diameter variations from six other tree species were gathered from published literature. Sixteen sets of data were analysed retrospectively using graphical representations as well as cosinor analysis, statistical cross-correlation and cross-spectral analysis, together with estimated values of the lunisolar tidal acceleration corresponding to the sites, dates and times of collection of the biological data. Positive relationships were revealed between the daily variations of stem diameter and the variations of the lunisolar tidal acceleration. Although this relationship could be mediated by a 24.8-h lunar rhythm, the presence of a solar rhythm of 24.0 h could not be ruled out. Studies of transpiration in two of the observed trees indicated that although this variable was not linked to stem diameter variation, it might also be subject to lunisolar gravitational regulation. In three cases, the geomagnetic Thule index showed a weak but reciprocal relationship with stem diameter variation, as well as a positive relationship with the lunisolar tidal force. In conclusion, it seems that lunar gravity alone could influence stem diameter variation and that, under certain circumstances, additional regulation may come from the geomagnetic flux.

Real-Time Polymerase Chain Reaction for Detection of Schistosoma DNA in Small-Volume Urine Samples Reflects Focal Distribution of Urogenital Schistosomiasis in Primary School Girls in KwaZulu Natal, South Africa

PubMed Central

Pillay, Pavitra; Taylor, Myra; Zulu, Siphosenkosi G.; Gundersen, Svein G.; Verweij, Jaco J.; Hoekstra, Pytsje; Brienen, Eric A. T.; Kleppa, Elisabeth; Kjetland, Eyrun F.; van Lieshout, Lisette

2014-01-01

Schistosoma haematobium eggs and Schistosoma DNA levels were measured in urine samples from 708 girls recruited from 18 randomly sampled primary schools in South Africa. Microscopic analysis of two 10-mL urine subsamples collected on three consecutive days confirmed high day-to-day variation; 103 (14.5%) girls had positive results at all six examinations, and at least one positive sample was seen in 225 (31.8%) girls. Schistosoma-specific DNA, which was measured in a 200-μL urine subsample by using real-time polymerase chain reaction, was detected in 180 (25.4%) cases, and levels of DNA corresponded significantly with average urine egg excretion. In concordance with microscopic results, polymerase chain reaction results were significantly associated with history of gynecologic symptoms and confirmed highly focal distribution of urogenital schistosomiasis. Parasite-specific DNA detection has a sensitivity comparable to single urine microscopy and could be used as a standardized high-throughput procedure to assess distribution of urogenital schistosomiasis in relatively large study populations by using small sample volumes. PMID:24470560

Use of assisted reproductive technology treatment as reported by mothers in comparison with registry data: the Upstate KIDS Study.

PubMed

Buck Louis, Germaine M; Druschel, Charlotte; Bell, Erin; Stern, Judy E; Luke, Barbara; McLain, Alexander; Sundaram, Rajeshwari; Yeung, Edwina

2015-06-01

To assess the validity of maternally reported assisted reproductive technologies (ART) use and to identify predictors of reporting errors. Linkage study. Not applicable. A total of 5,034 (27%) mothers enrolled, from whom 4,886 (97%) self-reported information about use of infertility treatment, including ART, for the index birth. None. Four measures of validity (sensitivity, specificity, positive and negative predictive values) and use of net reclassification improvement (NRI) methods to identify predictors associated with concordant/discordant maternal reporting. The Upstate New York Infant Development Screening Program (Update KIDS Study) was linked with the Society for Assisted Reproductive Technology Clinic Outcome Reporting System (SART CORS) using a defined algorithm for 2008-2010. The sensitivity, specificity, positive and negative predictive values were high (0.93, 0.99, 0.80, and 1.00, respectively). The validity of maternal report was high, reflecting few differences by participant characteristics except for maternal age dichotomized at 29 years as identified with NRI methods. Maternally reported ART is valid, with little variation across various characteristics. No strong predictors of discordant reporting were found, supporting the utility of population-based research with SART CORS linkage. Published by Elsevier Inc.

Comparison of the levels of intra-specific genetic variation within Giardia muris and Giardia intestinalis.

PubMed

Andrews, R H; Monis, P T; Ey, P L; Mayrhofer, G

1998-08-01

The extent of intra-specific genetic variation between isolates of Giardia muris was assessed by allozyme electrophoresis. Additionally, the levels of allozymic variation detected within G. muris were compared with those observed between members of the two major assemblages of the morphologically distinct species Giardia intestinalis. Four isolates of G. muris were analysed. Three (Ad-120, -150, -151) were isolated from mice in Australia, while the fourth (R-T) was isolated from a golden hamster in North America. The 11 isolates of G. intestinalis (Ad-1, -12, -2, -62, representing genetic Groups I and II of Assemblage A and BAH-12, BRIS/87/HEPU/694, Ad-19, -22, -28, -45, -52, representing genetic Groups III and IV of Assemblage B) were from humans in Australia. Intra-specific genetic variation was detected between G. muris isolates at four of the 23 enzyme loci examined. Similar levels of variation were found within the genetic groups that comprise Assemblages A and B of G. intestinalis. These levels of intra-specific variation are similar to those observed within other morphologically-distinct species of protozoan parasites. We suggest that the magnitude of the genetic differences detected within G. muris provides an indication of the range of genetic variation within other species of Giardia and that this can be used as a model to delineate morphologically similar but genetically distinct (cryptic) species within this genus.

Gondola for High Altitude Planetary Science (GHAPS) Telescope Secondary Mirror Positioning Hexapod Issues and Alternatives

NASA Technical Reports Server (NTRS)

Wells, Mark

2017-01-01

Active positioning of the GHAPS secondary telescope mirror is desired to correct for rigid body deflections due to temperature variations and gravity sag in the telescope structure that may impact optical performance. The current design concept for the secondary mirror mount uses a Commercial-Off -the-Shelf hexapod for mirror positioning and fine adjustment. The Hexapod specification states that motions as small as 0.1 microns along the optical axis and 2 microns perpendicular to the optical axis will cause optical aberrations that will require correction by repositioning the secondary mirror. In addition, the secondary mirror mount and positioning system must survive a 15g shock of parachute opening and landing during the instrument recovery operation. The secondary mirror positioning system must operate at a minimum specified temperature of -50 C. The telescope operates in the IR and the secondary mirror mount and positioning device is in the metering path between the primary and secondary mirrors. I2R losses in positioning system actuator devices, which may cause heating of the positioning system and secondary mirror, must be minimized due to the previously mentioned alignment sensitivity and the viewing spectrum of interest. The GHAPs project was cancelled on June 30, 2017. The purpose of this study is to address some of the issues identified with the hexapod secondary mirror positioning system and identify alternative approaches. This information may be used if the project is re-started at a later date.

The genetic basis of adaptive pigmentation variation in Drosophila melanogaster

PubMed Central

Pool, John E.; Aquadro, Charles F.

2009-01-01

In a broad survey of Drosophila melanogaster population samples, levels of abdominal pigmentation were found to be highly variable and geographically differentiated. A strong positive correlation was found between dark pigmentation and high altitude, suggesting adaptation to specific environments. DNA sequence polymorphism at the candidate gene ebony revealed a clear association with the pigmentation of homozygous third chromosome lines. The darkest lines sequenced had nearly identical haplotypes spanning 14.5 kilobases upstream of the protein-coding exons of ebony. Thus, natural selection may have elevated the frequency of an allele that confers dark abdominal pigmentation by influencing the regulation of ebony. PMID:17614900

Seasonal and spatial variations in fish and macrocrustacean assemblage structure in Mad Island Marsh estuary, Texas

NASA Astrophysics Data System (ADS)

Akin, S.; Winemiller, K. O.; Gelwick, F. P.

2003-05-01

Fish and macrocrustacean assemblage structure was analyzed along an estuarine gradient at Mad Island Marsh (MIM), Matagorda Bay, TX, during March 1998-August 1999. Eight estuarine-dependent fish species accounted for 94% of the individual fishes collected, and three species accounted for 96% of macrocrustacean abundance. Consistent with evidence from other Gulf of Mexico estuarine studies, species richness and abundance were highest during late spring and summer, and lowest during winter and early spring. Sites near the bay supported the most individuals and species. Associations between fish abundance and environmental variables were examined with canonical correspondence analysis. The dominant gradient was associated with water depth and distance from the bay. The secondary gradient reflected seasonal variation and was associated with temperature, salinity, dissolved oxygen, and vegetation cover. At the scales examined, estuarine biota responded to seasonal variation more than spatial variation. Estuarine-dependent species dominated the fauna and were common throughout the open waters of the shallow lake during winter-early spring when water temperature and salinity were low and dissolved oxygen high. During summer-early fall, sub-optimal environmental conditions (high temperature, low DO) in upper reaches accounted for strong spatial variation in assemblage composition. Small estuarine-resident fishes and the blue crab ( Callinectes sapidus) were common in warm, shallow, vegetated inland sites during summer-fall. Estuarine-dependent species were common at deeper, more saline locations near the bay during this period. During summer, freshwater species, such as gizzard shad ( Dorosoma cepedianum) and gars ( Lepisosteus spp.), were positively associated with water depth and proximity to the bay. The distribution and abundance of fishes in MIM appear to result from the combined effects of endogenous, seasonal patterns of reproduction and migration operating on large spatial scales, and species-specific response to local environmental variation.

Temporal Variation of Wood Density and Carbon in Two Elevational Sites of Pinus cooperi in Relation to Climate Response in Northern Mexico

PubMed Central

Pompa-García, Marín; Venegas-González, Alejandro

2016-01-01

Forest ecosystems play an important role in the global carbon cycle. Therefore, understanding the dynamics of carbon uptake in forest ecosystems is much needed. Pinus cooperi is a widely distributed species in the Sierra Madre Occidental in northern Mexico and future climatic variations could impact these ecosystems. Here, we analyze the variations of trunk carbon in two populations of P. cooperi situated at different elevational gradients, combining dendrochronological techniques and allometry. Carbon sequestration (50% biomass) was estimated from a specific allometric equation for this species based on: (i) variation of intra-annual wood density and (ii) diameter reconstruction. The results show that the population at a higher elevation had greater wood density, basal area, and hence, carbon accumulation. This finding can be explained by an ecological response of trees to adverse weather conditions, which would cause a change in the cellular structure affecting the within-ring wood density profile. The influence of variations in climate on the maximum density of chronologies showed a positive correlation with precipitation and the Multivariate El Niño Southern Oscillation Index during the winter season, and a negative correlation with maximum temperature during the spring season. Monitoring previous conditions to growth is crucial due to the increased vulnerability to extreme climatic variations on higher elevational sites. We concluded that temporal variability of wood density contributes to a better understanding of environmental historical changes and forest carbon dynamics in Northern Mexico, representing a significant improvement over previous studies on carbon sequestration. Assuming a uniform density according to tree age is incorrect, so this method can be used for environmental mitigation strategies, such as for managing P. cooperi, a dominant species of great ecological amplitude and widely used in forest industries. PMID:27272519

Temporal Variation of Wood Density and Carbon in Two Elevational Sites of Pinus cooperi in Relation to Climate Response in Northern Mexico.

PubMed

Pompa-García, Marín; Venegas-González, Alejandro

2016-01-01

Forest ecosystems play an important role in the global carbon cycle. Therefore, understanding the dynamics of carbon uptake in forest ecosystems is much needed. Pinus cooperi is a widely distributed species in the Sierra Madre Occidental in northern Mexico and future climatic variations could impact these ecosystems. Here, we analyze the variations of trunk carbon in two populations of P. cooperi situated at different elevational gradients, combining dendrochronological techniques and allometry. Carbon sequestration (50% biomass) was estimated from a specific allometric equation for this species based on: (i) variation of intra-annual wood density and (ii) diameter reconstruction. The results show that the population at a higher elevation had greater wood density, basal area, and hence, carbon accumulation. This finding can be explained by an ecological response of trees to adverse weather conditions, which would cause a change in the cellular structure affecting the within-ring wood density profile. The influence of variations in climate on the maximum density of chronologies showed a positive correlation with precipitation and the Multivariate El Niño Southern Oscillation Index during the winter season, and a negative correlation with maximum temperature during the spring season. Monitoring previous conditions to growth is crucial due to the increased vulnerability to extreme climatic variations on higher elevational sites. We concluded that temporal variability of wood density contributes to a better understanding of environmental historical changes and forest carbon dynamics in Northern Mexico, representing a significant improvement over previous studies on carbon sequestration. Assuming a uniform density according to tree age is incorrect, so this method can be used for environmental mitigation strategies, such as for managing P. cooperi, a dominant species of great ecological amplitude and widely used in forest industries.

Linking melanism to brain development: expression of a melanism-related gene in barn owl feather follicles covaries with sleep ontogeny

PubMed Central

2013-01-01

Background Intra-specific variation in melanocyte pigmentation, common in the animal kingdom, has caught the eye of naturalists and biologists for centuries. In vertebrates, dark, eumelanin pigmentation is often genetically determined and associated with various behavioral and physiological traits, suggesting that the genes involved in melanism have far reaching pleiotropic effects. The mechanisms linking these traits remain poorly understood, and the potential involvement of developmental processes occurring in the brain early in life has not been investigated. We examined the ontogeny of rapid eye movement (REM) sleep, a state involved in brain development, in a wild population of barn owls (Tyto alba) exhibiting inter-individual variation in melanism and covarying traits. In addition to sleep, we measured melanistic feather spots and the expression of a gene in the feather follicles implicated in melanism (PCSK2). Results As in mammals, REM sleep declined with age across a period of brain development in owlets. In addition, inter-individual variation in REM sleep around this developmental trajectory was predicted by variation in PCSK2 expression in the feather follicles, with individuals expressing higher levels exhibiting a more precocial pattern characterized by less REM sleep. Finally, PCSK2 expression was positively correlated with feather spotting. Conclusions We demonstrate that the pace of brain development, as reflected in age-related changes in REM sleep, covaries with the peripheral activation of the melanocortin system. Given its role in brain development, variation in nestling REM sleep may lead to variation in adult brain organization, and thereby contribute to the behavioral and physiological differences observed between adults expressing different degrees of melanism. PMID:23886007

Salivary Concentration of Progesterone and Cortisol Significantly Differs Across Individuals After Correcting for Blood Hormone Values

PubMed Central

Konishi, Shoko; Brindle, Eleanor; Guyton, Amanda; O’Connor, Kathleen A.

2014-01-01

Between-individual variation of salivary progesterone (P4) and cortisol levels does not always closely reflect blood hormone concentrations. This may be partly a function of individual differences in salivary hormone excretion. We tested whether time of day at sampling and ethnicity contributed to individual variation in salivary hormones after adjusting for blood hormone levels. Forty-three Caucasian and 15 Japanese women (18–34 years) collected four sets of matched dried blood spot (DBS) and saliva specimens across a menstrual cycle (N = 232 specimen sets). Linear fixed-effects (LFE) models were used to estimate the effects of diurnal variation and ethnicity on salivary P4 and cortisol while adjusting for DBS levels. For each hormone, women with exclusively positive or negative residuals (unexplained variance) from the LFE models were categorized as high- or low-saliva-to-DBS hormone ratio (SDR; high or low salivary secretors), respectively. We found that salivary P4 (P < 0.05) was significantly higher in early morning compared to the afternoon, after controlling for DBS levels, ethnicity, and BMI. After further adjusting for this diurnal effect, significant individual variation in salivary P4 and cortisol remained: sixteen and nine women, respectively were categorized as low or high salivary secretors for both hormones (P < 0.001), suggesting systematic individual-specific variation of salivary hormonal concentration. We conclude that when saliva is used to quantify P4 or cortisol levels, time of day at sampling should be controlled. Even with this adjustment, salivary P4 and cortisol do not closely mirror between-individual variation of serum P4 and cortisol in a substantial proportion of individuals. PMID:22826025

Attenuated total reflectance spectroscopy of plant leaves: A tool for ecological and botanical studies

USGS Publications Warehouse

Ribeiro da Luz, B.

2006-01-01

??? Attenuated total reflectance (ATR) spectra of plant leaves display complex absorption features related to organic constituents of leaf surfaces. The spectra can be recorded rapidly, both in the field and in the laboratory, without special sample preparation. ??? This paper explores sources of ATR spectral variation in leaves, including compositional, positional and temporal variations. Interspecific variations are also examined, including the use of ATR spectra as a tool for species identification. ??? Positional spectral variations generally reflected the abundance of cutin and the epicuticular wax thickness and composition. For example, leaves exposed to full sunlight commonly showed more prominent cutin- and wax-related absorption features compared with shaded leaves. Adaxial vs. abaxial leaf surfaces displayed spectral variations reflecting differences in trichome abundance and wax composition. Mature vs. young leaves showed changes in absorption band position and intensity related to cutin, polysaccharide, and possibly amorphous silica development on and near the leaf surfaces. ??? Provided that similar samples are compared (e.g. adaxial surfaces of mature, sun-exposed leaves) same-species individuals display practically identical ATR spectra. Using spectral matching procedures to analyze an ATR database containing 117 individuals, including 32 different tree species, 83% of the individuals were correctly identified. ?? The Authors (2006).

Pattern of morphological variation and diversity of Cocos nucifera (Arecaceae) in Mexico.

PubMed

Zizumbo-Villarreal, D; Piñero, D

1998-06-01

The pattern of morphological variation of Cocos nucifera in Mexico was statistically and numerically evaluated. Forty-one populations were analyzed, using 17 morphological fruit characters. Principal components and cluster analyses indicated four main groups of coconut populations that showed high similarity with four different genotypes recently imported into Mexico from areas that could be the origin of Mexican coconut populations. These four genotypes were evaluated with regard to the lethal yellowing disease in Jamaica and showed a differential susceptibility. Therefore it is possible to speculate upon a difference in susceptibility of the Mexican genotypes. The analysis of correlation between morphological and geographical distances showed a high positive correlation that supports: (1) historical evidence that indicates early introductions of coconut from different regions of the world, (2) that on both coasts of Mexico two different patterns of dispersal were involved: continuous and in jumps. Collectively these results suggest that the impact of the lethal yellowing disease on coconut populations will vary depending on the specific area and the origin of its coconuts.

An efficient deterministic-probabilistic approach to modeling regional groundwater flow: 2. Application to Owens Valley, California

USGS Publications Warehouse

Guymon, Gary L.; Yen, Chung-Cheng

1990-01-01

The applicability of a deterministic-probabilistic model for predicting water tables in southern Owens Valley, California, is evaluated. The model is based on a two-layer deterministic model that is cascaded with a two-point probability model. To reduce the potentially large number of uncertain variables in the deterministic model, lumping of uncertain variables was evaluated by sensitivity analysis to reduce the total number of uncertain variables to three variables: hydraulic conductivity, storage coefficient or specific yield, and source-sink function. Results demonstrate that lumping of uncertain parameters reduces computational effort while providing sufficient precision for the case studied. Simulated spatial coefficients of variation for water table temporal position in most of the basin is small, which suggests that deterministic models can predict water tables in these areas with good precision. However, in several important areas where pumping occurs or the geology is complex, the simulated spatial coefficients of variation are over estimated by the two-point probability method.

An efficient deterministic-probabilistic approach to modeling regional groundwater flow: 2. Application to Owens Valley, California

NASA Astrophysics Data System (ADS)

Guymon, Gary L.; Yen, Chung-Cheng

1990-07-01

The applicability of a deterministic-probabilistic model for predicting water tables in southern Owens Valley, California, is evaluated. The model is based on a two-layer deterministic model that is cascaded with a two-point probability model. To reduce the potentially large number of uncertain variables in the deterministic model, lumping of uncertain variables was evaluated by sensitivity analysis to reduce the total number of uncertain variables to three variables: hydraulic conductivity, storage coefficient or specific yield, and source-sink function. Results demonstrate that lumping of uncertain parameters reduces computational effort while providing sufficient precision for the case studied. Simulated spatial coefficients of variation for water table temporal position in most of the basin is small, which suggests that deterministic models can predict water tables in these areas with good precision. However, in several important areas where pumping occurs or the geology is complex, the simulated spatial coefficients of variation are over estimated by the two-point probability method.

Analysis of variation in virulence of Beauveria bassiana against insect pests of pigeonpea using qPCR.

PubMed

Senthilraja, Govindasamy; Anand, Theerthagiri; Mohankumar, Subbarayalu; Raguchander, Thiruvengadam; Samiyappan, Ramasamy

2018-03-01

Beauveria bassiana is a broad spectrum microbial bioagent used for the control of agriculturally important insect pests. However, in our experiments, two virulent isolates of B. bassiana (B2 and B10) showed specific preference toward Maruca vitrata and Helicoverpa armigera of pigeonpea. To better understand this feature, we developed a qPCR assay to quantify the chitinase (virulence factor) of B. bassiana during the infection process. Isolates of B. bassiana were grown on insect cuticle amended medium and minimal medium (without insect cuticle) to assess the induction of chitinase. Our results revealed a positive correlation between expression of chitinase by B. bassiana and the substrates (with or without cuticles of M. vitrata and H. armigera) used. This study showcases the methodology to quantify the chitinase and analysis of variation in virulence of B. bassiana (B2 and B10) against M. vitrata and H. armigera. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phosphorus K-edge XANES spectroscopy of mineral standards

PubMed Central

Ingall, Ellery D.; Brandes, Jay A.; Diaz, Julia M.; de Jonge, Martin D.; Paterson, David; McNulty, Ian; Elliott, W. Crawford; Northrup, Paul

2011-01-01

Phosphorus K-edge X-ray absorption near-edge structure (XANES) spectroscopy was performed on phosphate mineral specimens including (a) twelve specimens from the apatite group covering a range of compositional variation and crystallinity; (b) six non-apatite calcium-rich phosphate minerals; (c) 15 aluminium-rich phosphate minerals; (d) ten phosphate minerals rich in either reduced iron or manganese; (e) four phosphate minerals rich in either oxidized iron or manganese; (f) eight phosphate minerals rich in either magnesium, copper, lead, zinc or rare-earth elements; and (g) four uranium phosphate minerals. The identity of all minerals examined in this study was independently confirmed using X-ray powder diffraction. Minerals were distinguished using XANES spectra with a combination of pre-edge features, edge position, peak shapes and post-edge features. Shared spectral features were observed in minerals with compositions dominated by the same specific cation. Analyses of apatite-group minerals indicate that XANES spectral patterns are not strongly affected by variations in composition and crystallinity typical of natural mineral specimens. PMID:21335905

Hydrodynamics-induced variability in the USP apparatus II dissolution test.

PubMed

Baxter, Jennifer L; Kukura, Joseph; Muzzio, Fernando J

2005-03-23

The USP tablet dissolution test is an analytical tool used for the verification of drug release processes and formulation selection within the pharmaceutical industry. Given the strong impact of this test, it is surprising that operating conditions and testing devices have been selected empirically. In fact, the flow phenomena in the USP test have received little attention in the past. An examination of the hydrodynamics in the USP apparatus II shows that the device is highly vulnerable to mixing problems that can affect testing performance and consistency. Experimental and computational techniques reveal that the flow field within the device is not uniform, and dissolution results can vary dramatically with the position of the tablet within the vessel. Specifically, computations predict sharp variations in the shear along the bottom of the vessel where the tablet is most likely to settle. Experiments in which the tablet location was carefully controlled reveal that the variation of shear within the testing device can affect the measured dissolution rate.

Effects of pipette modulation and imaging distances on ion currents measured with scanning ion conductance microscopy (SICM).

PubMed

Chen, Chiao-Chen; Baker, Lane A

2011-01-07

Local conductance variations can be estimated by measuring ion current magnitudes with scanning ion conductance microscopy (SICM). Factors which influence image quality and quantitation of ion currents measured with SICM have been evaluated. Specifically, effects of probe-sample separation and pipette modulation have been systematically studied for the case of imaging conductance variations at pores in a polymer membrane under transmembrane concentration gradients. The influence of probe-sample separation on ion current images was evaluated using distance-modulated (ac) feedback. Approach curves obtained using non-modulated (dc) feedback were also recorded to determine the relative influence of pipette-generated convection by comparison of ion currents measured with both ac and dc feedback modes. To better interpret results obtained, comparison to a model based on a disk-shaped geometry for nanopores in the membrane, as well as relevant position-dependent parameters of the experiment is described. These results advance our current understanding of conductance measurements with SICM.

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.

Intersystem return on investment in public mental health: Positive externality of public mental health expenditure for the jail system in the U.S.

PubMed

Yoon, Jangho; Luck, Jeff

2016-12-01

This study examines the extent to which increased public mental health expenditures lead to a reduction in jail populations and computes the associated intersystem return on investment (ROI). We analyze unique panel data on 44 U.S. states and D.C. for years 2001-2009. To isolate the intersystem spillover effect, we exploit variations across states and over time within states in per capita public mental health expenditures and average daily jail inmates. Regression models control for a comprehensive set of determinants of jail incarcerations as well as unobserved determinants specific to state and year. Findings show a positive spillover benefit of increased public mental health spending on the jail system: a 10% increase in per capita public inpatient mental health expenditure on average leads to a 1.5% reduction in jail inmates. We also find that the positive intersystem externality of increased public inpatient mental health expenditure is greater when the level of community mental health spending is lower. Similarly, the intersystem spillover effect of community mental health expenditure is larger when inpatient mental health spending is lower. We compute that overall an extra dollar in public inpatient mental health expenditure by a state would yield an intersystem ROI of a quarter dollar for the jail system. There is significant cross-state variation in the intersystem ROI in both public inpatient and community mental health expenditures, and the ROI overall is greater for inpatient mental health spending than for community mental health spending. Copyright © 2016. Published by Elsevier Ltd.

Brazilian adults' sedentary behaviors by life domain: population-based study.

PubMed

Mielke, Grégore I; da Silva, Inácio C M; Owen, Neville; Hallal, Pedro C

2014-01-01

There is rapidly-emerging evidence on the harmful health effects of sedentary behaviors. The aim of this paper was to quantify time in sedentary behaviors and document socio-demographic variations in different life domains among adults. A population-based survey was carried out in 2012 through face-to-face interviews with Brazilian adults aged 20+ years (N = 2,927). Information about time spent sedentary in a typical weekday was collected for five different domains (workplace, commuting, school/university, watching TV, and computer use at home). Descriptive and bivariate analyses examined variations in overall and domain-specific sedentary time by gender, age, educational attainment and socioeconomic position. On average, participants reported spending 5.8 (SD 4.5) hours per day sitting. The median value was 4.5 (interquartile range: 2.5-8) hours. Men, younger adults, those with higher schooling and from the wealthiest socioeconomic groups had higher overall sedentary scores. TV time was higher in women, older adults and among those with low schooling and socioeconomic position. Sedentary time in transport was higher in men, younger adults, and participants with high schooling and high socioeconomic position. Computer use at home was more frequent among young adults and those from high socioeconomic groups. Sitting at work was higher in those with higher schooling and from the wealthiest socioeconomic groups. Sedentary behavior at school was related inversely to age and directly to schooling. Patterns of sedentary behavior are different by life domains. Initiatives to reduce prolonged sitting among Brazilian adults will be required on multiple levels for different life domains.

Psychopathic Traits Mediate the Association of Serotonin Transporter Genotype and Child Externalizing Behavior

PubMed Central

Brammer, Whitney A.; Jezior, Kristen L.; Lee, Steve S.

2016-01-01

Although the promoter polymorphism of the serotonin transporter (5-HTTLPR) gene is associated with externalizing behavior, its mediating pathways are unknown. Given their sensitivity to serotonin neurotransmission and unique association with attention-deficit/hyperactivity disorder (ADHD) and oppositional defiant disorder (ODD), we tested callous-unemotional (CU) traits and narcissism as separate mediators of the association of 5-HTTLPR with ADHD and ODD. We evaluated 209 5–9 year-old children with and without ADHD at baseline; approximately two years later (i.e., Wave 2), parents and teachers separately rated ADHD and ODD symptoms and youth self-reported antisocial behavior. Controlling for race-ethnicity and baseline ADHD/ODD, narcissism uniquely mediated predictions of multi-informant rated Wave 2 ADHD and ODD from variation in 5-HTTLPR; CU traits mediated predictions of Wave 2 ADHD from variations in 5-HTTLPR, but did not mediate the associations of 5-HTTLPR with ODD or youth self-reported antisocial behavior. Specifically, the number of 5-HTTLPR long alleles positively predicted CU traits and narcissism; narcissism was positively associated with Wave 2 ADHD and ODD symptoms, whereas CU traits were positively associated with Wave 2 ADHD. Child sex also moderated indirect effects of CU traits and narcissism, such that narcissism mediated predictions of ADHD/ODD in girls but not boys. Psychopathic traits may represent a relevant pathway underlying predictions of prospective change in ADHD and ODD from 5-HTTLPR, particularly in girls. We consider the role of psychopathic traits as a potential intermediate phenotype in genetically-sensitive studies of child psychopathology. PMID:26990675

Cardiac Position Sensitivity Study in the Electrocardiographic Forward Problem Using Stochastic Collocation and Boundary Element Methods

PubMed Central

Swenson, Darrell J.; Geneser, Sarah E.; Stinstra, Jeroen G.; Kirby, Robert M.; MacLeod, Rob S.

2012-01-01

The electrocardiogram (ECG) is ubiquitously employed as a diagnostic and monitoring tool for patients experiencing cardiac distress and/or disease. It is widely known that changes in heart position resulting from, for example, posture of the patient (sitting, standing, lying) and respiration significantly affect the body-surface potentials; however, few studies have quantitatively and systematically evaluated the effects of heart displacement on the ECG. The goal of this study was to evaluate the impact of positional changes of the heart on the ECG in the specific clinical setting of myocardial ischemia. To carry out the necessary comprehensive sensitivity analysis, we applied a relatively novel and highly efficient statistical approach, the generalized polynomial chaos-stochastic collocation method, to a boundary element formulation of the electrocardiographic forward problem, and we drove these simulations with measured epicardial potentials from whole-heart experiments. Results of the analysis identified regions on the body-surface where the potentials were especially sensitive to realistic heart motion. The standard deviation (STD) of ST-segment voltage changes caused by the apex of a normal heart, swinging forward and backward or side-to-side was approximately 0.2 mV. Variations were even larger, 0.3 mV, for a heart exhibiting elevated ischemic potentials. These variations could be large enough to mask or to mimic signs of ischemia in the ECG. Our results suggest possible modifications to ECG protocols that could reduce the diagnostic error related to postural changes in patients possibly suffering from myocardial ischemia. PMID:21909818

The Influence of the Manner of Performing the Thyroid Ultrasound Examination on the Reliability of the Assessment of the Thyroid Size in School-Aged Children.

PubMed

Zygmunt, Arkadiusz; Adamczewski, Zbigniew; Zygmunt, Agnieszka; Karbownik-Lewinska, Malgorzata; Lewinski, Andrzej

2017-01-01

Goitre incidence in school-aged children evaluated using ultrasonography is one of the essential indicators of iodine intake in a given area. The aim of the study was to examine what the difference is between the volume of the thyroid gland measured in the supine and sitting position and to determine the intra-observer, inter-observer, and inter-position variations. The survey was conducted among 87 children (56 girls and 31 boys aged 7-13 years, mean age 10.44 ± 1.72 years). The thyroid volume measured in a sitting position was significantly lower than that measured in the supine position. The intra-observer variations for the total thyroid volume equalled 9.56-9.65%. The inter-observer variations were significantly higher and amounted to 34.5-35.7%. The way in which ultrasound evaluation is performed is important for the analysis of the results. It is crucial to aim for the smallest inter-observer variation, which can be achieved by strictly defining the methods of the thyroid measurement and comparing one's measuring techniques with the reference method. The use of standards in ultrasound evaluation performed in the supine position, as well as the use of standards without a strict determination of the study method, can lead to erro-neous conclusions. © 2017 S. Karger AG, Basel.

Estimating the actual subject-specific genetic correlations in behavior genetics.

PubMed

Molenaar, Peter C M

2012-10-01

Generalization of the standard behavior longitudinal genetic factor model for the analysis of interindividual phenotypic variation to a genetic state space model for the analysis of intraindividual variation enables the possibility to estimate subject-specific heritabilities.

Escherichia coli twin arginine (Tat) mutant translocases possessing relaxed signal peptide recognition specificities.

PubMed

Kreutzenbeck, Peter; Kröger, Carsten; Lausberg, Frank; Blaudeck, Natascha; Sprenger, Georg A; Freudl, Roland

2007-03-16

The twin arginine (Tat) secretion pathway allows the translocation of folded proteins across the cytoplasmic membrane of bacteria. Tat-specific signal peptides contain a characteristic amino acid motif ((S/T)RRXFLK) including two highly conserved consecutive arginine residues that are thought to be involved in the recognition of the signal peptides by the Tat translocase. Here, we have analyzed the specificity of Tat signal peptide recognition by using a genetic approach. Replacement of the two arginine residues in a Tat-specific precursor protein by lysine-glutamine resulted in an export-defective mutant precursor that was no longer accepted by the wild-type translocase. Selection for restored export allowed for the isolation of Tat translocases possessing single mutations in either the amino-terminal domain of TatB or the first cytosolic domain of TatC. The mutant Tat translocases still efficiently accepted the unaltered precursor protein, indicating that the substrate specificity of the translocases was not strictly changed; rather, the translocases showed an increased tolerance toward variations of the amino acids occupying the positions of the twin arginine residues in the consensus motif of a Tat signal peptide.

Distinct activation phenotype of a highly conserved novel HLA-B57-restricted epitope during dengue virus infection

PubMed Central

Townsley, Elizabeth; Woda, Marcia; Thomas, Stephen J; Kalayanarooj, Siripen; Gibbons, Robert V; Nisalak, Ananda; Srikiatkhachorn, Anon; Green, Sharone; Stephens, Henry AF; Rothman, Alan L; Mathew, Anuja

2014-01-01

Variation in the sequence of T-cell epitopes between dengue virus (DENV) serotypes is believed to alter memory T-cell responses during second heterologous infections. We identified a highly conserved, novel, HLA-B57-restricted epitope on the DENV NS1 protein. We predicted higher frequencies of B57-NS126–34-specific CD8+ T cells in peripheral blood mononuclear cells from individuals undergoing secondary rather than primary DENV infection. However, high tetramer-positive T-cell frequencies during acute infection were seen in only one of nine subjects with secondary infection. B57-NS126–34-specific and other DENV epitope-specific CD8+ T cells, as well as total CD8+ T cells, expressed an activated phenotype (CD69+ and/or CD38+) during acute infection. In contrast, expression of CD71 was largely limited to DENV epitope-specific CD8+ T cells. In vitro stimulation of cell lines indicated that CD71 expression was differentially sensitive to stimulation by homologous and heterologous variant peptides. CD71 may represent a useful marker of antigen-specific T-cell activation. PMID:23941420

Distinct activation phenotype of a highly conserved novel HLA-B57-restricted epitope during dengue virus infection.

PubMed

Townsley, Elizabeth; Woda, Marcia; Thomas, Stephen J; Kalayanarooj, Siripen; Gibbons, Robert V; Nisalak, Ananda; Srikiatkhachorn, Anon; Green, Sharone; Stephens, Henry A F; Rothman, Alan L; Mathew, Anuja

2014-01-01

Variation in the sequence of T-cell epitopes between dengue virus (DENV) serotypes is believed to alter memory T-cell responses during second heterologous infections. We identified a highly conserved, novel, HLA-B57-restricted epitope on the DENV NS1 protein. We predicted higher frequencies of B57-NS1(26-34) -specific CD8(+) T cells in peripheral blood mononuclear cells from individuals undergoing secondary rather than primary DENV infection. However, high tetramer-positive T-cell frequencies during acute infection were seen in only one of nine subjects with secondary infection. B57-NS1(26-34) -specific and other DENV epitope-specific CD8(+) T cells, as well as total CD8(+) T cells, expressed an activated phenotype (CD69(+) and/or CD38(+)) during acute infection. In contrast, expression of CD71 was largely limited to DENV epitope-specific CD8(+) T cells. In vitro stimulation of cell lines indicated that CD71 expression was differentially sensitive to stimulation by homologous and heterologous variant peptides. CD71 may represent a useful marker of antigen-specific T-cell activation. © 2013 John Wiley & Sons Ltd.

Synchrony, compensatory dynamics, and the functional trait basis of phenological diversity in a tropical dry forest tree community: effects of rainfall seasonality

NASA Astrophysics Data System (ADS)

Lasky, Jesse R.; Uriarte, María; Muscarella, Robert

2016-11-01

Interspecific variation in phenology is a key axis of functional diversity, potentially mediating how communities respond to climate change. The diverse drivers of phenology act across multiple temporal scales. For example, abiotic constraints favor synchronous reproduction (positive covariance among species), while biotic interactions can favor synchrony or compensatory dynamics (negative covariance). We used wavelet analyses to examine phenology of community flower and seed production for 45 tree species across multiple temporal scales in a tropical dry forest in Puerto Rico with marked rainfall seasonality. We asked three questions: (1) do species exhibit synchronous or compensatory temporal dynamics in reproduction, (2) do interspecific differences in phenology reflect variable responses to rainfall, and (3) is interspecific variation in phenology and response to a major drought associated with functional traits that mediate responses to moisture? Community-level flowering was synchronized at seasonal scales (˜5-6 mo) and at short scales (˜1 mo, following rainfall). However, seed rain exhibited significant compensatory dynamics at intraseasonal scales (˜3 mo), suggesting interspecific variation in temporal niches. Species with large leaves (associated with sensitivity to water deficit) peaked in reproduction synchronously with the peak of seasonal rainfall (˜5 mo scale). By contrast, species with high wood specific gravity (associated with drought resistance) tended to flower in drier periods. Flowering of tall species and those with large leaves was most tightly linked to intraseasonal (˜2 mo scale) rainfall fluctuations. Although the 2015 drought dramatically reduced community-wide reproduction, functional traits were not associated with the magnitude of species-specific declines. Our results suggest opposing drivers of synchronous versus compensatory dynamics at different temporal scales. Phenology associations with functional traits indicated that distinct strategies for coping with seasonality underlie phenological diversity. Observed drought responses highlight the importance of non-linear community responses to climate. Community phenology exhibits scale-specific patterns highlighting the need for multi-scale approaches to community dynamics.

Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus.

PubMed

Botosso, Viviane F; Zanotto, Paolo M de A; Ueda, Mirthes; Arruda, Eurico; Gilio, Alfredo E; Vieira, Sandra E; Stewien, Klaus E; Peret, Teresa C T; Jamal, Leda F; Pardini, Maria I de M C; Pinho, João R R; Massad, Eduardo; Sant'anna, Osvaldo A; Holmes, Eddie C; Durigon, Edison L

2009-01-01

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a "flip-flop" phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites.

Directional rolling of positively charged nanoparticles along a flexibility gradient on long DNA molecules.

PubMed

Park, Suehyun; Joo, Heesun; Kim, Jun Soo

2018-01-31

Directing the motion of molecules/colloids in any specific direction is of great interest in many applications of chemistry, physics, and biological sciences, where regulated positioning or transportation of materials is highly desired. Using Brownian dynamics simulations of coarse-grained models of a long, double-stranded DNA molecule and positively charged nanoparticles, we observed that the motion of a single nanoparticle bound to and wrapped by the DNA molecule can be directed along a gradient of DNA local flexibility. The flexibility gradient is constructed along a 0.8 kilobase-pair DNA molecule such that local persistence length decreases gradually from 50 nm to 40 nm, mimicking a gradual change in sequence-dependent flexibility. Nanoparticles roll over a long DNA molecule from less flexible regions towards more flexible ones as a result of the decreasing energetic cost of DNA bending and wrapping. In addition, the rolling becomes slightly accelerated as the positive charge of nanoparticles decreases due to a lower free energy barrier of DNA detachment from charged nanoparticle for processive rolling. This study suggests that the variation in DNA local flexibility can be utilized in constructing and manipulating supramolecular assemblies of DNA molecules and nanoparticles in structural DNA nanotechnology.

The North Atlantic Oscillation as a driver of multidecadal variability of the AMOC, the AMO, and Northern Hemisphere climate

NASA Astrophysics Data System (ADS)

Delworth, T. L.; Zeng, F. J.; Yang, X.; Zhang, L.

2017-12-01

We use suites of simulations with coupled ocean-atmosphere models to show that multidecadal changes in the North Atlantic Oscillation (NAO) can drive multidecadal changes in the Atlantic Meridional Overturning Circulation (AMOC) and the Atlantic Multidecadal Oscillation (AMO), with associated hemispheric climatic impacts. These impacts include rapid changes in Arctic sea ice, hemispheric temperature, and modulation of Atlantic hurricane activity. We use models that incorporate either a fully dynamic ocean or a simple slab ocean to explore the role of ocean dynamics and ocean-atmosphere interactions. A positive phase of the NAO is associated with strengthened westerly winds over the North Atlantic. These winds extract more heat than normal from the subpolar ocean, thereby increasing upper ocean density, deepwater formation, and the strength of the AMOC and associated poleward ocean heat transport. This warming leads to a positive phase of the AMO. The enhanced oceanic heat transport extends to the Arctic where it causes a reduction of Arctic sea ice. Large-scale atmospheric warming reduces vertical wind shear in the tropical North Atlantic, creating an environment more favorable for tropical storms. We use models to further show that observed multidecadal variations of the NAO over the 20th and early 21st centuries may have led to multidecadal variations of simulated AMOC and the AMO. Specifically, negative NAO values from the late 1960s through the early 1980s led to a weakened AMOC/cold North Atlantic, whereas increasing NAO values from the late 1980s through the late 1990s increased the model AMOC and led to a positive (warm) phase of the AMO. The warm phase contributed to increases in tropical storm activity and decreases in Arctic sea ice after the mid 1990s. Ocean dynamics are essential for translating the observed NAO variations into ocean heat content variations for the extratropical North Atlantic, but appear less important in the tropical North Atlantic. The observed AMO has substantial SST amplitude in both the tropical and extratropical North Atlantic. These results suggest that additional factors, such as cloud feedback, dust feedback, and anthropogenic radiative forcing, may play a crucial role for the tropical expression of the AMO.

Detection, prevalence, and transmission of avian hematozoa in waterfowl at the Arctic/sub-Arctic interface: co-infections, viral interactions, and sources of variation.

USGS Publications Warehouse

Meixell, Brandt W.; Arnold, Todd W.; Lindberg, Mark S.; Smith, Matthew M.; Runstadler, Jonathan A.; Ramey, Andy M.

2016-01-01

Methods: We used molecular methods to screen blood samples and cloacal/oropharyngeal swabs collected from 1347 ducks of five species during May-August 2010, in interior Alaska, for the presence of hematozoa, Influenza A Virus (IAV), and IAV antibodies. Using models to account for imperfect detection of parasites, we estimated seasonal variation in prevalence of three parasite genera (Haemoproteus, Plasmodium, Leucocytozoon) and investigated how co-infection with parasites and viruses were related to the probability of infection. Results: We detected parasites from each hematozoan genus in adult and juvenile ducks of all species sampled. Seasonal patterns in detection and prevalence varied by parasite genus and species, age, and sex of duck hosts. The probabilities of infection for Haemoproteus and Leucocytozoon parasites were strongly positively correlated, but hematozoa infection was not correlated with IAV infection or serostatus. The probability of Haemoproteus infection was negatively related to body condition in juvenile ducks; relationships between Leucocytozoon infection and body condition varied among host species. Conclusions: We present prevalence estimates for Haemoproteus, Leucocytozoon, and Plasmodium infections in waterfowl at the interface of the sub-Arctic and Arctic and provide evidence for local transmission of all three parasite genera. Variation in prevalence and molecular detection of hematozoa parasites in wild ducks is influenced by seasonal timing and a number of host traits. A positive correlation in co-infection of Leucocytozoon and Haemoproteus suggests that infection probability by parasites in one or both genera is enhanced by infection with the other, or that encounter rates of hosts and genus-specific vectors are correlated. Using size-adjusted mass as an index of host condition, we did not find evidence for strong deleterious consequences of hematozoa infection in wild ducks.

Hydrological networks and associated topographic variation as templates for the spatial organization of tropical forest vegetation.

PubMed

Detto, Matteo; Muller-Landau, Helene C; Mascaro, Joseph; Asner, Gregory P

2013-01-01

An understanding of the spatial variability in tropical forest structure and biomass, and the mechanisms that underpin this variability, is critical for designing, interpreting, and upscaling field studies for regional carbon inventories. We investigated the spatial structure of tropical forest vegetation and its relationship to the hydrological network and associated topographic structure across spatial scales of 10-1000 m using high-resolution maps of LiDAR-derived mean canopy profile height (MCH) and elevation for 4930 ha of tropical forest in central Panama. MCH was strongly associated with the hydrological network: canopy height was highest in areas of positive convexity (valleys, depressions) close to channels draining 1 ha or more. Average MCH declined strongly with decreasing convexity (transition to ridges, hilltops) and increasing distance from the nearest channel. Spectral analysis, performed with wavelet decomposition, showed that the variance in MCH had fractal similarity at scales of ∼30-600 m, and was strongly associated with variation in elevation, with peak correlations at scales of ∼250 m. Whereas previous studies of topographic correlates of tropical forest structure conducted analyses at just one or a few spatial grains, our study found that correlations were strongly scale-dependent. Multi-scale analyses of correlations of MCH with slope, aspect, curvature, and Laplacian convexity found that MCH was most strongly related to convexity measured at scales of 20-300 m, a topographic variable that is a good proxy for position with respect to the hydrological network. Overall, our results support the idea that, even in these mesic forests, hydrological networks and associated topographical variation serve as templates upon which vegetation is organized over specific ranges of scales. These findings constitute an important step towards a mechanistic understanding of these patterns, and can guide upscaling and downscaling.

Exploring Environmental Variation in Residential Care Facilities for Older People.

PubMed

Nordin, Susanna; McKee, Kevin; Wijk, Helle; Elf, Marie

2017-01-01

The aim of this study was to explore variation in environmental quality in Swedish residential care facilities (RCFs) using the Swedish version of the Sheffield Care Environment Assessment Matrix (S-SCEAM). Well-designed physical environments can positively impact on health and well-being among older persons with frail health living in RCFs and are essential for supporting person-centered care. However, the evidence base for informing the design of RCFs is weak, partly due to a lack of valid and reliable instruments that could provide important information on the environmental quality. Twenty RCFs were purposively sampled from several regions, varying in their building design, year of construction, size, and geographic location. The RCFs were assessed using S-SCEAM and the data were analyzed to examine variation in environmental quality between and within facilities. There was substantial variation in the quality of the physical environment between and within RCFs, reflected in S-SCEAM scores related to specific facility locations and with regard to domains reflecting residents' needs. In general, private apartments and dining areas had high S-SCEAM scores, while gardens had lower scores. Scores on the safety domain were high in the majority of RCFs, whereas scores for cognitive support and privacy were relatively low. Despite high building standard requirements, the substantial variations regarding environmental quality between and within RCFs indicate the potential for improvements to support the needs of older persons. We conclude that S-SCEAM is a sensitive and unique instrument representing a valuable contribution to evidence-based design that can support person-centered care.

Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens: introducing the ecotype Reute.

PubMed

Hiss, Manuel; Meyberg, Rabea; Westermann, Jens; Haas, Fabian B; Schneider, Lucas; Schallenberg-Rüdinger, Mareike; Ullrich, Kristian K; Rensing, Stefan A

2017-05-01

Rich ecotype collections are used for several plant models to unravel the molecular causes of phenotypic differences, and to investigate the effects of environmental adaption and acclimation. For the model moss Physcomitrella patens collections of accessions are available, and have been used for phylogenetic and taxonomic studies, for example, but few have been investigated further for phenotypic differences. Here, we focus on the Reute accession and provide expression profiling and comparative developmental data for several stages of sporophyte development, as well as information on genetic variation via genomic sequencing. We analysed cross-technology and cross-laboratory data to define a confident set of 15 mature sporophyte-specific genes. We find that the standard laboratory strain Gransden produces fewer sporophytes than Reute or Villersexel, although gametangia develop with the same time course and do not show evident morphological differences. Reute exhibits less genetic variation relative to Gransden than Villersexel, yet we found variation between Gransden and Reute in the expression profiles of several genes, as well as variation hot spots and genes that appear to evolve under positive Darwinian selection. We analyzed expression differences between the ecotypes for selected candidate genes in the GRAS transcription factor family, the chalcone synthase family and in genes involved in cell wall modification that are potentially related to phenotypic differences. We confirm that Reute is a P. patens ecotype, and suggest its use for reverse-genetics studies that involve progression through the life cycle and multiple generations. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster.

PubMed

Lavington, Erik; Kern, Andrew D

2017-11-06

Chromosomal inversions are a ubiquitous feature of genetic variation. Theoretical models describe several mechanisms by which inversions can drive adaptation and be maintained as polymorphisms. While inversions have been shown previously to be under selection, or contain genetic variation under selection, the specific phenotypic consequences of inversions leading to their maintenance remain unclear. Here we use genomic sequence and expression data from the Drosophila Genetic Reference Panel (DGRP) to explore the effects of two cosmopolitan inversions, In ( 2L ) t and In ( 3R ) Mo , on patterns of transcriptional variation. We demonstrate that each inversion has a significant effect on transcript abundance for hundreds of genes across the genome. Inversion-affected loci (IAL) appear both within inversions as well as on unlinked chromosomes. Importantly, IAL do not appear to be influenced by the previously reported genome-wide expression correlation structure. We found that five genes involved with sterol uptake, four of which are Niemann-Pick Type 2 orthologs, are upregulated in flies with In ( 3R ) Mo but do not have SNPs in linkage disequilibrium (LD) with the inversion. We speculate that this upregulation is driven by genetic variation in mod ( mdg4 ) that is in LD with In ( 3R ) Mo We find that there is little evidence for a regional or position effect of inversions on gene expression at the chromosomal level, but do find evidence for the distal breakpoint of In ( 3R ) Mo interrupting one gene and possibly disassociating the two flanking genes from regulatory elements. Copyright © 2017 Lavington and Kern.

The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster

PubMed Central

Lavington, Erik; Kern, Andrew D.

2017-01-01

Chromosomal inversions are a ubiquitous feature of genetic variation. Theoretical models describe several mechanisms by which inversions can drive adaptation and be maintained as polymorphisms. While inversions have been shown previously to be under selection, or contain genetic variation under selection, the specific phenotypic consequences of inversions leading to their maintenance remain unclear. Here we use genomic sequence and expression data from the Drosophila Genetic Reference Panel (DGRP) to explore the effects of two cosmopolitan inversions, In(2L)t and In(3R)Mo, on patterns of transcriptional variation. We demonstrate that each inversion has a significant effect on transcript abundance for hundreds of genes across the genome. Inversion-affected loci (IAL) appear both within inversions as well as on unlinked chromosomes. Importantly, IAL do not appear to be influenced by the previously reported genome-wide expression correlation structure. We found that five genes involved with sterol uptake, four of which are Niemann-Pick Type 2 orthologs, are upregulated in flies with In(3R)Mo but do not have SNPs in linkage disequilibrium (LD) with the inversion. We speculate that this upregulation is driven by genetic variation in mod(mdg4) that is in LD with In(3R)Mo. We find that there is little evidence for a regional or position effect of inversions on gene expression at the chromosomal level, but do find evidence for the distal breakpoint of In(3R)Mo interrupting one gene and possibly disassociating the two flanking genes from regulatory elements. PMID:28916647

[Cost variation in care groups?

PubMed

Mohnen, S M; Molema, C C M; Steenbeek, W; van den Berg, M J; de Bruin, S R; Baan, C A; Struijs, J N

2017-01-01

Is the simple mean of the costs per diabetes patient a suitable tool with which to compare care groups? Do the total costs of care per diabetes patient really give the best insight into care group performance? Cross-sectional, multi-level study. The 2009 insurance claims of 104,544 diabetes patients managed by care groups in the Netherlands were analysed. The data were obtained from Vektis care information centre. For each care group we determined the mean costs per patient of all the curative care and diabetes-specific hospital care using the simple mean method, then repeated it using the 'generalized linear mixed model'. We also calculated for which proportion the differences found could be attributed to the care groups themselves. The mean costs of the total curative care per patient were €3,092 - €6,546; there were no significant differences between care groups. The mixed model method resulted in less variation (€2,884 - €3,511), and there were a few significant differences. We found a similar result for diabetes-specific hospital care and the ranking position of the care groups proved to be dependent on the method used. The care group effect was limited, although it was greater in the diabetes-specific hospital costs than in the total costs of curative care (6.7% vs. 0.4%). The method used to benchmark care groups carries considerable weight. Simply stated, determining the mean costs of care (still often done) leads to an overestimation of the differences between care groups. The generalized linear mixed model is more accurate and yields better comparisons. However, the fact remains that 'total costs of care' is a faulty indicator since care groups have little impact on them. A more informative indicator is 'costs of diabetes-specific hospital care' as these costs are more influenced by care groups.

A sensitive one-step TaqMan amplification approach for detection of rubella virus clade I and II genotypes in clinical samples.

PubMed

Claus, C; Bergs, S; Emmrich, N C; Hübschen, J M; Mankertz, A; Liebert, U G

2017-02-01

Although teratogenic rubella virus (RV) causes a vaccine-preventable disease, it is still endemic in several countries worldwide. Thus, there is a constant risk of RV importation into non-endemic areas. RV monitoring, especially during measles and Zika virus outbreaks, requires reliable diagnostic tools. For this study, a TaqMan-based one-step reverse transcription-quantitative PCR (RT-qPCR) assay, with the p90 gene as a novel and so far unexplored target for detection of clade I and II genotypes, was developed and evaluated. Automated nucleic acid extraction was carried out. Performance characteristics of the TaqMan RT-qPCR assay were determined for a RV plasmid standard and RNA extracted from virus-infected cell culture supernatants representing clade I and II genotypes. Diagnostic specificity and sensitivity were validated against other RNA and DNA viruses, relevant for RV diagnostic approaches and for RV-positive clinical samples, respectively. The assay is specific and highly sensitive with a limit of detection as low as five to one copies per reaction or 200 infectious virus particles per ml. The coefficients of variation (CV) were specified as intra- (within one run) and inter- (between different runs) assay variation, and calculated based on the standard deviations for the obtained Ct values of the respective samples. Intra- and inter-assay CV values were low, with a maximum of 3.4% and 2.4%, respectively. The assay was shown to be suitable and specific for the analysis of clinical samples. With p90 as a novel target, the highly sensitive and specific TaqMan assay outlined in this study is suitable for RV diagnosis worldwide.

Morphological dependency of cutaneous blood flow and sweating during compensable heat stress when heat-loss requirements are matched across participants.

PubMed

Notley, Sean R; Park, Joonhee; Tagami, Kyoko; Ohnishi, Norikazu; Taylor, Nigel A S

2016-07-01

Human heat loss is thought, in part, to be morphologically related. It was therefore hypothesized that when heat-loss requirements and body temperatures were matched, that the mass-specific surface area alone could significantly explain both cutaneous vascular and sudomotor responses during compensable exercise. These thermoeffector responses were examined in 36 men with widely varying mass-specific surface areas (range, 232.3-292.7 cm(2)/kg), but of similar age, aerobic fitness, and adiposity. Subjects completed two trials under compensable conditions (28.1°C, 36.8% relative humidity), each involving rest (20 min) and steady-state cycling (45 min) at two matched metabolic heat-production rates (light, ∼135 W/m(2); moderate, ∼200 W/m(2)). Following equivalent mean body temperature changes, forearm blood flow and vascular conductance (r = 0.63 and r = 0.65) shared significant, positive associations with the mass-specific surface area during light work (P < 0.05), explaining ∼45% of the vasomotor variation. Conversely, during light and moderate work, whole body sweat rate, as well as local sweat rate and sudomotor sensitivity at three of four measured sites, revealed moderate, negative relationships with the mass-specific surface area (correlation coefficient range -0.37 to -0.73, P < 0.05). Moreover, those relationships could uniquely account for between 10 and 53% of those sweating responses (P < 0.05). Therefore, both thermoeffector responses displayed a significant morphological dependency in the presence of equivalent thermoafferent drive. Indeed, up to half of the interindividual variation in these effector responses could now be explained through morphological differences and the first principles governing heat transfer. Copyright © 2016 the American Physiological Society.

Morphological dependency of cutaneous blood flow and sweating during compensable heat stress when heat-loss requirements are matched across participants

PubMed Central

Notley, Sean R.; Park, Joonhee; Tagami, Kyoko; Ohnishi, Norikazu

2016-01-01

Human heat loss is thought, in part, to be morphologically related. It was therefore hypothesized that when heat-loss requirements and body temperatures were matched, that the mass-specific surface area alone could significantly explain both cutaneous vascular and sudomotor responses during compensable exercise. These thermoeffector responses were examined in 36 men with widely varying mass-specific surface areas (range, 232.3-292.7 cm2/kg), but of similar age, aerobic fitness, and adiposity. Subjects completed two trials under compensable conditions (28.1°C, 36.8% relative humidity), each involving rest (20 min) and steady-state cycling (45 min) at two matched metabolic heat-production rates (light, ∼135 W/m2; moderate, ∼200 W/m2). Following equivalent mean body temperature changes, forearm blood flow and vascular conductance (r = 0.63 and r = 0.65) shared significant, positive associations with the mass-specific surface area during light work (P < 0.05), explaining ∼45% of the vasomotor variation. Conversely, during light and moderate work, whole body sweat rate, as well as local sweat rate and sudomotor sensitivity at three of four measured sites, revealed moderate, negative relationships with the mass-specific surface area (correlation coefficient range −0.37 to −0.73, P < 0.05). Moreover, those relationships could uniquely account for between 10 and 53% of those sweating responses (P < 0.05). Therefore, both thermoeffector responses displayed a significant morphological dependency in the presence of equivalent thermoafferent drive. Indeed, up to half of the interindividual variation in these effector responses could now be explained through morphological differences and the first principles governing heat transfer. PMID:27125845

Genes contributing to the development of alcoholism: an overview.

PubMed

Edenberg, Howard J

2012-01-01

Genetic factors (i.e., variations in specific genes) account for a substantial portion of the risk for alcoholism. However, identifying those genes and the specific variations involved is challenging. Researchers have used both case-control and family studies to identify genes related to alcoholism risk. In addition, different strategies such as candidate gene analyses and genome-wide association studies have been used. The strongest effects have been found for specific variants of genes that encode two enzymes involved in alcohol metabolism-alcohol dehydrogenase and aldehyde dehydrogenase. Accumulating evidence indicates that variations in numerous other genes have smaller but measurable effects.

Local and Landscape Factors Determining Occurrence of Phyllostomid Bats in Tropical Secondary Forests

PubMed Central

Avila-Cabadilla, Luis Daniel; Sanchez-Azofeifa, Gerardo Arturo; Stoner, Kathryn Elizabeth; Alvarez-Añorve, Mariana Yolotl; Quesada, Mauricio; Portillo-Quintero, Carlos Alonso

2012-01-01

Neotropical forests are being increasingly replaced by a mosaic of patches of different successional stages, agricultural fields and pasture lands. Consequently, the identification of factors shaping the performance of taxa in anthropogenic landscapes is gaining importance, especially for taxa playing critical roles in ecosystem functioning. As phyllostomid bats provide important ecological services through seed dispersal, pollination and control of animal populations, in this study we assessed the relationships between phyllostomid occurrence and the variation in local and landscape level habitat attributes caused by disturbance. We mist-netted phyllostomids in 12 sites representing 4 successional stages of a tropical dry forest (initial, early, intermediate and late). We also quantitatively characterized the habitat attributes at the local (vegetation structure complexity) and the landscape level (forest cover, area and diversity of patches). Two focal scales were considered for landscape characterization: 500 and 1000 m. During 142 sampling nights, we captured 606 individuals representing 15 species and 4 broad guilds. Variation in phyllostomid assemblages, ensembles and populations was associated with variation in local and landscape habitat attributes, and this association was scale-dependent. Specifically, we found a marked guild-specific response, where the abundance of nectarivores tended to be negatively associated with the mean area of dry forest patches, while the abundance of frugivores was positively associated with the percentage of riparian forest. These results are explained by the prevalence of chiropterophilic species in the dry forest and of chiropterochorous species in the riparian forest. Our results indicate that different vegetation classes, as well as a multi-spatial scale approach must be considered for evaluating bat response to variation in landscape attributes. Moreover, for the long-term conservation of phyllostomids in anthropogenic landscapes, we must realize that the management of the habitat at the landscape level is as important as the conservation of particular forest fragments. PMID:22529994

Local and landscape factors determining occurrence of phyllostomid bats in tropical secondary forests.

PubMed

Avila-Cabadilla, Luis Daniel; Sanchez-Azofeifa, Gerardo Arturo; Stoner, Kathryn Elizabeth; Alvarez-Añorve, Mariana Yolotl; Quesada, Mauricio; Portillo-Quintero, Carlos Alonso

2012-01-01

Neotropical forests are being increasingly replaced by a mosaic of patches of different successional stages, agricultural fields and pasture lands. Consequently, the identification of factors shaping the performance of taxa in anthropogenic landscapes is gaining importance, especially for taxa playing critical roles in ecosystem functioning. As phyllostomid bats provide important ecological services through seed dispersal, pollination and control of animal populations, in this study we assessed the relationships between phyllostomid occurrence and the variation in local and landscape level habitat attributes caused by disturbance. We mist-netted phyllostomids in 12 sites representing 4 successional stages of a tropical dry forest (initial, early, intermediate and late). We also quantitatively characterized the habitat attributes at the local (vegetation structure complexity) and the landscape level (forest cover, area and diversity of patches). Two focal scales were considered for landscape characterization: 500 and 1000 m. During 142 sampling nights, we captured 606 individuals representing 15 species and 4 broad guilds. Variation in phyllostomid assemblages, ensembles and populations was associated with variation in local and landscape habitat attributes, and this association was scale-dependent. Specifically, we found a marked guild-specific response, where the abundance of nectarivores tended to be negatively associated with the mean area of dry forest patches, while the abundance of frugivores was positively associated with the percentage of riparian forest. These results are explained by the prevalence of chiropterophilic species in the dry forest and of chiropterochorous species in the riparian forest. Our results indicate that different vegetation classes, as well as a multi-spatial scale approach must be considered for evaluating bat response to variation in landscape attributes. Moreover, for the long-term conservation of phyllostomids in anthropogenic landscapes, we must realize that the management of the habitat at the landscape level is as important as the conservation of particular forest fragments.

A positive-definite form of bounce-averaged quasilinear velocity diffusion for the parallel inhomogeneity in a tokamak

NASA Astrophysics Data System (ADS)

Lee, Jungpyo; Smithe, David; Wright, John; Bonoli, Paul

2018-02-01

In this paper, the analytical form of the quasilinear diffusion coefficients is modified from the Kennel-Engelmann diffusion coefficients to guarantee the positive definiteness of its bounce average in a toroidal geometry. By evaluating the parallel inhomogeneity of plasmas and magnetic fields in the trajectory integral, we can ensure the positive definiteness and help illuminate some non-resonant toroidal effects in the quasilinear diffusion. When the correlation length of the plasma-wave interaction is comparable to the magnetic field variation length, the variation becomes important and the parabolic variation at the outer-midplane, the inner-midplane, and trapping tips can be evaluated by Airy functions. The new form allows the coefficients to include both resonant and non-resonant contributions, and the correlations between the consecutive resonances and in many poloidal periods. The positive-definite form is implemented in a wave code TORIC and we present an example for ITER using this form.

Spatial distribution of SPAD value and determination of the suitable leaf for N diagnosis in cucumber

NASA Astrophysics Data System (ADS)

Hu, Jing; Li, Chenxiao; Wen, Yifang; Gao, Xinhao; Shi, Feifei; Han, Luhua

2018-01-01

To determine the best leaf position for nitrogen diagnosis in cucumber with SPAD meter, greenhouse experiments were carried out to study spatial distribution of SPAD value of different position of the 3rd fully expanded cucumber leaf in the effect of different nitrogen levels, and the correlations between SPAD values and nitrogen concentration of chlorophyll. The results show that there is remarkable different SPAD value in different positions of the 3rd fully expanded leaf in the flowering and fruiting stage. Comparing the coefficients of SPAD value variation, we find that the coefficient of variation of leaf edge was significantly higher than the edge of the main vein, and the coefficient of variation of triangular area of leaf tip is significantly higher than any other leaf area. There is a significant correlation between SPAD values and leaf nitrogen content. Preliminary study shows that triangular area of leaf tip from the 20% leaf tip to leaf edge is the best position for nitrogen diagnosis.

An intelligent position-specific training system for mission operations

NASA Technical Reports Server (NTRS)

Schneider, M. P.

1992-01-01

Marshall Space Flight Center's (MSFC's) payload ground controller training program provides very good generic training; however, ground controller position-specific training can be improved by including position-specific training systems in the training program. This report explains why MSFC needs to improve payload ground controller position-specific training. The report describes a generic syllabus for position-specific training systems, a range of system designs for position-specific training systems, and a generic development process for developing position-specific training systems. The report also describes a position-specific training system prototype that was developed for the crew interface coordinator payload operations control center ground controller position. The report concludes that MSFC can improve the payload ground controller training program by incorporating position-specific training systems for each ground controller position; however, MSFC should not develop position-specific training systems unless payload ground controller position experts will be available to participate in the development process.

Negative blood oxygen level dependent signals during speech comprehension.

PubMed

Rodriguez Moreno, Diana; Schiff, Nicholas D; Hirsch, Joy

2015-05-01

Speech comprehension studies have generally focused on the isolation and function of regions with positive blood oxygen level dependent (BOLD) signals with respect to a resting baseline. Although regions with negative BOLD signals in comparison to a resting baseline have been reported in language-related tasks, their relationship to regions of positive signals is not fully appreciated. Based on the emerging notion that the negative signals may represent an active function in language tasks, the authors test the hypothesis that negative BOLD signals during receptive language are more associated with comprehension than content-free versions of the same stimuli. Regions associated with comprehension of speech were isolated by comparing responses to passive listening to natural speech to two incomprehensible versions of the same speech: one that was digitally time reversed and one that was muffled by removal of high frequencies. The signal polarity was determined by comparing the BOLD signal during each speech condition to the BOLD signal during a resting baseline. As expected, stimulation-induced positive signals relative to resting baseline were observed in the canonical language areas with varying signal amplitudes for each condition. Negative BOLD responses relative to resting baseline were observed primarily in frontoparietal regions and were specific to the natural speech condition. However, the BOLD signal remained indistinguishable from baseline for the unintelligible speech conditions. Variations in connectivity between brain regions with positive and negative signals were also specifically related to the comprehension of natural speech. These observations of anticorrelated signals related to speech comprehension are consistent with emerging models of cooperative roles represented by BOLD signals of opposite polarity.

Negative Blood Oxygen Level Dependent Signals During Speech Comprehension

PubMed Central

Rodriguez Moreno, Diana; Schiff, Nicholas D.

2015-01-01

Abstract Speech comprehension studies have generally focused on the isolation and function of regions with positive blood oxygen level dependent (BOLD) signals with respect to a resting baseline. Although regions with negative BOLD signals in comparison to a resting baseline have been reported in language-related tasks, their relationship to regions of positive signals is not fully appreciated. Based on the emerging notion that the negative signals may represent an active function in language tasks, the authors test the hypothesis that negative BOLD signals during receptive language are more associated with comprehension than content-free versions of the same stimuli. Regions associated with comprehension of speech were isolated by comparing responses to passive listening to natural speech to two incomprehensible versions of the same speech: one that was digitally time reversed and one that was muffled by removal of high frequencies. The signal polarity was determined by comparing the BOLD signal during each speech condition to the BOLD signal during a resting baseline. As expected, stimulation-induced positive signals relative to resting baseline were observed in the canonical language areas with varying signal amplitudes for each condition. Negative BOLD responses relative to resting baseline were observed primarily in frontoparietal regions and were specific to the natural speech condition. However, the BOLD signal remained indistinguishable from baseline for the unintelligible speech conditions. Variations in connectivity between brain regions with positive and negative signals were also specifically related to the comprehension of natural speech. These observations of anticorrelated signals related to speech comprehension are consistent with emerging models of cooperative roles represented by BOLD signals of opposite polarity. PMID:25412406

Ionospheric variation observed in Oregon Real-time GNSS network during the total eclipse of 21 August 2017

NASA Astrophysics Data System (ADS)

Shahbazi, A.; Park, J.; Kim, S.; Oberg, R.

2017-12-01

As the ionospheric behavior is highly related to the solar activity, the total eclipse passing across the North America on 21 August 2017 is expected to significantly affect the electron density in the ionosphere along the path. Taking advantage of GNSS capability for observing total electron content (TEC), this study demonstrates the impact of the total eclipse not only on the TEC variation during the period of the event but also on GNSS positioning. Oregon Department of Transportation (ODOT) runs a dense real time GNSS network, referred to as Oregon Real-time GNSS network (ORGN). From the dual frequency GPS and GLONASS observations in ORGN, the TEC over the network area can be extracted. We observe the vertical TEC (VTEC) from the ORGN for analyzing the ionospheric condition in the local area affected by the eclipse. To observe the temporal variation, we also observe the slant TEC (STEC) in each ray path and analyze the short term variation in different geometry of each ray path. Although the STEC is dependent quantity upon the changing geometry of a satellite, this approach provides insight to the ionospheric behavior of the total eclipse because the STEC does not involve the projection error, which is generated by VTEC computation. During the period of eclipse, the abnormal variations on VTEC and STEC are expected. The experimental results will be presented in time series plots for selected stations as well as the regional TEC map in Oregon. In addition to the TEC monitoring, we also test the positioning result of ORGN stations through Precise Point Positioning (PPP) and relative positioning. The expected result is that the both positioning results are degraded during the solar eclipse due to the instable ionospheric condition over short time.

Climate alters intraspecific variation in copepod effect traits through pond food webs.

PubMed

Charette, Cristina; Derry, Alison M

2016-05-01

Essential fatty acids (EFAs) are primarily generated by phytoplankton in aquatic ecosystems, and can limit the growth, development, and reproduction of higher consumers. Among the most critical of the EFAs are highly unsaturated fatty acids (HUFAs), which are only produced by certain groups of phytoplankton. Changing environmental conditions can alter phytoplankton community and fatty acid composition and affect the HUFA content of higher trophic levels. Almost no research has addressed intraspecific variation in HUFAs in zooplankton, nor intraspecific relationships of HUFAs with body size and fecundity. This is despite that intraspecific variation in HUFAs can exceed interspecific variation and that intraspecific trait variation in body size and fecundity is increasingly recognized to have an important role in food web ecology (effect traits). Our study addressed the relative influences of abiotic selection and food web effects associated with climate change on intraspecific differences and interrelationships between HUFA content, body size, and fecundity of freshwater copepods. We applied structural equation modeling and regression analyses to intraspecific variation in a dominant calanoid copepod, Leptodiatomus minutus, among a series of shallow north-temperate ponds. Climate-driven diurnal temperature fluctuations favored the coexistence of diversity of phytoplankton groups with different temperature optima and nutritive quality. This resulted in unexpected positive relationships between temperature, copepod DHA content and body size. Temperature correlated positively with diatom biovolume, and mediated relationships between copepod HUFA content and body size, and between copepod body size and fecundity. The presence of brook trout further accentuated these positive effects in warm ponds, likely through nutrient cycling and stimulation of phytoplankton resources. Climate change may have previously unrecognized positive effects on freshwater copepod DHA content, body size, and fecundity in the small, shallow bodies of inland waters that are commonly found in north-temperate landscapes.

Changes in glycolytic enzyme activities in aging erythrocytes fractionated by counter-current distribution in aqueous polymer two-phase systems.

PubMed Central

Jimeno, P; Garcia-Perez, A I; Luque, J; Pinilla, M

1991-01-01

Human and rat erythrocytes were fractionated by counter-current distribution in charge-sensitive dextran/poly(ethylene glycol) two-phase systems. The specific activities of the key glycolytic enzymes (hexokinase, phosphofructokinase and pyruvate kinase) declined along the distribution profiles, although the relative positions of the activity profiles were reversed in the two species. These enzymes maintained their normal response to specific regulatory effectors in all cell fractions. No variations were observed for phosphoglycerate kinase and bisphosphoglycerate mutase activities. Some correlations between enzyme activities (pyruvate kinase/hexokinase, pyruvate kinase/phosphofructokinase, pyruvate kinase/pyruvate kinase plus phosphoglycerate kinase, pyruvate kinase/bisphosphoglycerate mutase and phosphoglycerate kinase/bisphosphoglycerate mutase ratios) were studied in whole erythrocyte populations as well as in cell fractions. These results strongly support the fractionation of human erythrocytes according to cell age, as occurs with rat erythrocytes. PMID:1656939

Application of plasma electrolysis method for simultaneous phenol and Cr(VI) wastewater degradation using Na2SO4 electrolyte

NASA Astrophysics Data System (ADS)

Harianti, Aulia Rahmi; Saksono, Nelson

2017-11-01

Phenol and Cr (VI) are two types of wastewater known as dangerous and difficult to degrade. Through this study, phenol and Cr (VI) metal wastewater were degraded simultaneously using plasma electrolysis method by reactive species, •OH and H•. The variation of anode depth and position of plasma formation as independent variables correlated with yield of hydroxyl radical, percentage of phenol and Cr (VI) degradation, and specific energy. Within 30 minutes, phenol was degraded to 98.4% and Cr (VI) was degraded to 93.35% with 171.05 kJ/mmol in specific energy, and 174.53 ppm in COD. The optimum condition was obtained in anodic plasma and 1.5 cm in anode depth. The highest degradation percentage of phenol and Cr (VI) were 99.79% and 97.33% achieved during 180 minutes of plasma electrolysis process.

Motivation, working memory, and decision making: a cognitive-motivational theory of personality vulnerability to alcoholism.

PubMed

Finn, Peter R

2002-09-01

This article presents a cognitive-motivational theory (CMT) of the mechanisms associated with three basic dimensions of personality vulnerability to alcoholism, impulsivity/novelty seeking, harm avoidance, and excitement seeking. CMT describes the interrelationships between activity in basic motivational systems and attentional, decision-making and working memory processes as the mechanisms associated with variation in each personality trait. Impulsivity/novelty seeking reflects activity in both appetitive and inhibitory motivational systems, greater attention to reward cues, and increased emotional reactivity to reward and frustration. Harm avoidance reflects individual differences in fearfulness and activity in specific inhibitory systems. Excitement seeking reflects the need to engage in appetitive behaviors in less predictable environments to experience positive affect. CMT also describes the impact of working memory and the specific motivational processes underlying each trait dimension on the dynamics of decision making from the perspective of decision field theory.

Support Vector Machines to improve physiologic hot flash measures: application to the ambulatory setting.

PubMed

Thurston, Rebecca C; Hernandez, Javier; Del Rio, Jose M; De La Torre, Fernando

2011-07-01

Most midlife women have hot flashes. The conventional criterion (≥2 μmho rise/30 s) for classifying hot flashes physiologically has shown poor performance. We improved this performance in the laboratory with Support Vector Machines (SVMs), a pattern classification method. We aimed to compare conventional to SVM methods to classify hot flashes in the ambulatory setting. Thirty-one women with hot flashes underwent 24 h of ambulatory sternal skin conductance monitoring. Hot flashes were quantified with conventional (≥2 μmho/30 s) and SVM methods. Conventional methods had low sensitivity (sensitivity=.57, specificity=.98, positive predictive value (PPV)=.91, negative predictive value (NPV)=.90, F1=.60), with performance lower with higher body mass index (BMI). SVMs improved this performance (sensitivity=.87, specificity=.97, PPV=.90, NPV=.96, F1=.88) and reduced BMI variation. SVMs can improve ambulatory physiologic hot flash measures. Copyright © 2010 Society for Psychophysiological Research.

Daily positive events and diurnal cortisol rhythms: Examination of between-person differences and within-person variation.

PubMed

Sin, Nancy L; Ong, Anthony D; Stawski, Robert S; Almeida, David M

2017-09-01

Growing evidence from field studies has linked daily stressors to dysregulated patterns of diurnal cortisol. Less is known about whether naturally-occurring positive events in everyday life are associated with diurnal cortisol. The objectives of this study were to evaluate daily positive events as predictors of between-person differences and within-person (day-to-day) variations in diurnal cortisol parameters, in addition to daily positive events as buffers against the associations between daily stressors and cortisol. In the National Study of Daily Experiences, 1657 adults ages 33-84 (57% female) reported daily experiences during telephone interviews on 8 consecutive evenings. Saliva samples were collected 4 times per day on 4 interview days and assayed for cortisol. Multilevel models were used to estimate associations of daily positive events with cortisol awakening response (CAR), diurnal cortisol slope, and area under the curve (AUC). At the between-person level, people who experienced more frequent positive events exhibited a steeper diurnal cortisol slope, controlling for daily stressors, daily affect, and other covariates. At the within-person level, positive events in the morning (but not prior-night or afternoon/evening events) predicted steeper decline in cortisol across that day; positive events were also marginally associated with lower same-day AUC. Associations were not mediated by daily positive affect, and positive events did not buffer against stressor-related cortisol alterations. These findings indicate that individual differences and day-to-day variations in daily positive events are associated with diurnal cortisol patterns, independent of stressors and affect. Copyright © 2017 Elsevier Ltd. All rights reserved.

Relationship between seismic status of Earth and relative position of bodies in sun-earth-moon system

NASA Astrophysics Data System (ADS)

Kulanin, N. V.

1985-03-01

The time spectrum of variations in seismicity is quite broad. There are seismic seasons, as well as multiannual variations. The range of characteristic times of variation from days to about one year is studied. Seismic activity as a function of the position of the moon relative to the Earth and the direction toward the Sun is studied. The moments of strong earthquakes, over 5.8 on the Richter scale, between 1968 and June 1980 are plotted in time coordinates relating them to the relative positions of the three bodies in the sun-earth-moon system. Methods of mathematical statistics are applied to the points produced, indicating at least 99% probability that the distribution was not random. a periodicity of the earth's seismic state of 413 days is observed.

Life-history perspective of adaptive radiation in desmognathine salamanders

Treesearch

Richard C. Bruce

1996-01-01

This study investigates interspecific variation in age at first reproduction, fecundity, and body size in multispecies assemblages of desmognathine salamanders. The hypotheses tested are that interspecific differences in body size among desmognathines stem proximately from variation in age at first reproduction and that variation in the latter trait is positively...

Phonon dispersion evolution in uniaxially strained aluminum crystal

NASA Astrophysics Data System (ADS)

Parthasarathy, Ranganathan; Misra, Anil; Aryal, Sitaram; Ouyang, Lizhi

2018-04-01

The influence of loading upon the phonon dispersion of crystalline materials could be highly nonlinear with certain particular trends that depend upon the loading path. In this paper, we have calculated the influence of [100] uniaxial strain on the phonon dispersion and group velocities in fcc aluminum using second moments of position obtained from molecular dynamics (MD) simulation at 300 K. In contrast to nonlinear monotonic variation of both longitudinal and transverse phonon frequencies along the Δ , Λ and Σ lines of the first Brillouin zone under tension, transverse phonon branches along the Λ line show inflection at specific wavevectors when the compressive strain exceeds 5%. Further, the longitudinal group velocities along the high-symmetry Δ line vary non-monotonically with strain, reaching a minimum at 5% compressive strain. Throughout the strain range studied, the equilibrium positions of atoms displace in an affine manner preserving certain static structural symmetry. We attribute the anomalies in the phonon dispersion to the non-affine evolution of second moments of atomic position, and the associated plateauing of force constants under the applied strain path.

Sexual orientation and spatial position effects on selective forms of object location memory.

PubMed

Rahman, Qazi; Newland, Cherie; Smyth, Beatrice Mary

2011-04-01

Prior research has demonstrated robust sex and sexual orientation-related differences in object location memory in humans. Here we show that this sexual variation may depend on the spatial position of target objects and the task-specific nature of the spatial array. We tested the recovery of object locations in three object arrays (object exchanges, object shifts, and novel objects) relative to veridical center (left compared to right side of the arrays) in a sample of 35 heterosexual men, 35 heterosexual women, and 35 homosexual men. Relative to heterosexual men, heterosexual women showed better location recovery in the right side of the array during object exchanges and homosexual men performed better in the right side during novel objects. However, the difference between heterosexual and homosexual men disappeared after controlling for IQ. Heterosexual women and homosexual men did not differ significantly from each other in location change detection with respect to task or side of array. These data suggest that visual space biases in processing categorical spatial positions may enhance aspects of object location memory in heterosexual women. Copyright © 2010 Elsevier Inc. All rights reserved.

Development of an ELISA to detect circulating anti-asparaginase antibodies in dogs with lymphoid neoplasia treated with Escherichia coli l-asparaginase.

PubMed

Kidd, J A; Ross, P; Buntzman, A S; Hess, P R

2015-06-01

Resistance to Escherichia coli l-asparaginase in canine lymphoma occurs frequently with repeated administration, a phenomenon often attributed, without substantiation, to the induction of neutralizing antibodies. To test the hypothesis that treated dogs develop antibodies against the drug, we created an enzyme-linked immunosorbent assay (ELISA) to measure plasma anti-asparaginase immunoglobulin G responses. Using samples from dogs that had received multiple doses, specific reactivity against l-asparaginase was demonstrated, while naïve patients' samples were negative. The optimized ELISA appeared sensitive, with endpoint titers >1 600 000 in positive control dogs. Intra- and inter-assay coefficients of variation were 3.6 and 14.5%. The assay was supported by the observation that ELISA-positive plasma could immunoprecipitate asparaginase activity. When clinical patients were evaluated, 3/10 dogs developed titers after a single injection; with repeated administration, 4/7 dogs were positive. l-asparaginase antibodies showed reduced binding to the PEGylated drug formulation. The ELISA should prove useful in investigating the potential correlation of antibody responses with resistance. © 2012 Blackwell Publishing Ltd.

Development of an ELISA to detect circulating anti-asparaginase antibodies in dogs with lymphoid neoplasia treated with E. coli L-asparaginase*

PubMed Central

Kidd, Jason A.; Ross, Peter; Buntzman, Adam S.; Hess, Paul R.

2012-01-01

Resistance to E. coli L-asparaginase in canine lymphoma occurs frequently with repeated administration, a phenomenon often attributed, without substantiation, to the induction of neutralizing antibodies. To test the hypothesis that treated dogs develop antibodies against the drug, we created an ELISA to measure plasma anti-asparaginase IgG responses. Using samples from dogs that had received multiple doses, specific reactivity against L-asparaginase was demonstrated, while naïve patients’ samples were negative. The optimized ELISA appeared sensitive, with endpoint titers >1,600,000 in positive control dogs. Intra- and inter-assay coefficients of variation were 3.6 and 14.5%. The assay was supported by the observation that ELISA-positive plasma could immunoprecipitate asparaginase activity. When clinical patients were evaluated, 3/10 dogs developed titers after a single injection; with repeated administration, 4/7 dogs were positive. L-asparaginase antibodies showed reduced binding to the PEGylated drug formulation. The ELISA should prove useful in investigating the potential correlation of antibody responses with resistance. PMID:23253146

Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter.

PubMed

Morrissey, Ember M; Mau, Rebecca L; Schwartz, Egbert; McHugh, Theresa A; Dijkstra, Paul; Koch, Benjamin J; Marks, Jane C; Hungate, Bruce A

2017-08-01

Microorganisms perform most decomposition on Earth, mediating carbon (C) loss from ecosystems, and thereby influencing climate. Yet, how variation in the identity and composition of microbial communities influences ecosystem C balance is far from clear. Using quantitative stable isotope probing of DNA, we show how individual bacterial taxa influence soil C cycling following the addition of labile C (glucose). Specifically, we show that increased decomposition of soil C in response to added glucose (positive priming) occurs as a phylogenetically diverse group of taxa, accounting for a large proportion of the bacterial community, shift toward additional soil C use for growth. Our findings suggest that many microbial taxa exhibit C use plasticity, as most taxa altered their use of glucose and soil organic matter depending upon environmental conditions. In contrast, bacteria that exhibit other responses to glucose (reduced growth or reliance on glucose for additional growth) clustered strongly by phylogeny. These results suggest that positive priming is likely the prototypical response of bacteria to sustained labile C addition, consistent with the widespread occurrence of the positive priming effect in nature.

A variational approach to dynamics of flexible multibody systems

NASA Technical Reports Server (NTRS)

Wu, Shih-Chin; Haug, Edward J.; Kim, Sung-Soo

1989-01-01

This paper presents a variational formulation of constrained dynamics of flexible multibody systems, using a vector-variational calculus approach. Body reference frames are used to define global position and orientation of individual bodies in the system, located and oriented by position of its origin and Euler parameters, respectively. Small strain linear elastic deformation of individual components, relative to their body references frames, is defined by linear combinations of deformation modes that are induced by constraint reaction forces and normal modes of vibration. A library of kinematic couplings between flexible and/or rigid bodies is defined and analyzed. Variational equations of motion for multibody systems are obtained and reduced to mixed differential-algebraic equations of motion. A space structure that must deform during deployment is analyzed, to illustrate use of the methods developed.

Vitellogenin levels in hemolymph, ovary and hepatopancreas of the freshwater crayfish Cherax quadricarinatus (Decapoda: Parastacidae) during the reproductive cycle.

PubMed

Ferré, Lilian E; Medesani, Daniel A; García, C Fernando; Grodzielski, Matías; Rodríguez, Enrique M

2012-03-01

The freshwater crayfish Cherax quadricarinatus is a tropical species of great interest for aquaculture. Vitellogenin (Vg), a lipoprotein precursor of the vitellum accumulated in spawned eggs, can be synthesized in the ovary and/or hepatopancreas of most crustaceans, being the hemolymph the way for transporting Vg throughout the reproductive cycle. Concentration of Vg in hemolymph, ovary and hepatopancreas of Cherax quadricarinatus adult females was measured by means of ELISA, specifically developed after purifying the native Vg. Measurements were made at four periods of the reproductive cycle: pre-reproductive, mid-reproductive, late reproductive and post-reproductive. Besides, both hepatosomatic (HSI) and gonadosomatic (GSI) indexes were determined in each period. Significant variations in Vg levels were detected in both hemolymph and hepatopancreas, being the highest values observed during the mid-reproductive period. Besides, such variations were positively correlated to the HSI. A positive correlation between Vg levels in hepatopancreas and ovary was also seen. These results support previous evidences about the central role of the hepatopancreas as a site of Vg synthesis in the studied species, together with the relevancy of hemolymph for transporting Vg from the hepatopancreas to the ovary. For aquaculture purposes, Vg monitoring in hemolymph could be used as a non-injurious method, to check the reproductive activity of C. quadricarinatus females.

Analysis of percent density estimates from digital breast tomosynthesis projection images

NASA Astrophysics Data System (ADS)

Bakic, Predrag R.; Kontos, Despina; Zhang, Cuiping; Yaffe, Martin J.; Maidment, Andrew D. A.

2007-03-01

Women with dense breasts have an increased risk of breast cancer. Breast density is typically measured as the percent density (PD), the percentage of non-fatty (i.e., dense) tissue in breast images. Mammographic PD estimates vary, in part, due to the projective nature of mammograms. Digital breast tomosynthesis (DBT) is a novel radiographic method in which 3D images of the breast are reconstructed from a small number of projection (source) images, acquired at different positions of the x-ray focus. DBT provides superior visualization of breast tissue and has improved sensitivity and specificity as compared to mammography. Our long-term goal is to test the hypothesis that PD obtained from DBT is superior in estimating cancer risk compared with other modalities. As a first step, we have analyzed the PD estimates from DBT source projections since the results would be independent of the reconstruction method. We estimated PD from MLO mammograms (PD M) and from individual DBT projections (PD T). We observed good agreement between PD M and PD T from the central projection images of 40 women. This suggests that variations in breast positioning, dose, and scatter between mammography and DBT do not negatively affect PD estimation. The PD T estimated from individual DBT projections of nine women varied with the angle between the projections. This variation is caused by the 3D arrangement of the breast dense tissue and the acquisition geometry.

Trends in surface ozone over Europe, 1978-1990

NASA Technical Reports Server (NTRS)

Low, Pak Sum; Kelly, P. Michael; Davies, Trevor D.

1994-01-01

It has been suggested that surface ozone concentrations in rural areas of Europe have been increasing at a rate of 1 to 3 percent per year over the past two to three decades, presumably due to human influences (Feister and Warmbt, 1987; Bojkov, 1988; Penkett, 1989). Recently, we have analyzed surface ozone data from 20 European stations of differing character (remote, rural, suburban and urban) for a common period of 1978-1988 (Low et al., 1992). It was found that there were pronounced annual and seasonal variations in the linear trends in different areas, and there was no dominant region-wide trend. In spring and, most notably, summer, stations on the maritime fringe of the network generally exhibited negative trends whilst those located further into the continental interior exhibited positive trends. In winter, most of the stations in the network exhibited positive trends. Relatively few of these trends were statistically significant. This paper updates our earlier analysis by extending the data sets of the network up to the year 1990. The spatial variations in surface ozone trends over the extended period 1978-1990 are examined and discussed in comparison to the 1978-1988 patterns. The update confirms the overall conclusions of the earlier analysis, specifically that caution should be exercised in interpreting the results of trend analyses based on station data representative of a limited period of time and/or geographical area.

NPP VIIRS Geometric Performance Status

NASA Technical Reports Server (NTRS)

Lin, Guoqing; Wolfe, Robert E.; Nishihama, Masahiro

2011-01-01

Visible Infrared Imager Radiometer Suite (VIIRS) instrument on-board the National Polar-orbiting Operational Environmental Satellite System (NPOESS) Preparatory Project (NPP) satellite is scheduled for launch in October, 2011. It is to provide satellite measured radiance/reflectance data for both weather and climate applications. Along with radiometric calibration, geometric characterization and calibration of Sensor Data Records (SDRs) are crucial to the VIIRS Environmental Data Record (EDR) algorithms and products which are used in numerical weather prediction (NWP). The instrument geometric performance includes: 1) sensor (detector) spatial response, parameterized by the dynamic field of view (DFOV) in the scan direction and instantaneous FOV (IFOV) in the track direction, modulation transfer function (MTF) for the 17 moderate resolution bands (M-bands), and horizontal spatial resolution (HSR) for the five imagery bands (I-bands); 2) matrices of band-to-band co-registration (BBR) from the corresponding detectors in all band pairs; and 3) pointing knowledge and stability characteristics that includes scan plane tilt, scan rate and scan start position variations, and thermally induced variations in pointing with respect to orbital position. They have been calibrated and characterized through ground testing under ambient and thermal vacuum conditions, numerical modeling and analysis. This paper summarizes the results, which are in general compliance with specifications, along with anomaly investigations, and describes paths forward for characterizing on-orbit BBR and spatial response, and for improving instrument on-orbit performance in pointing and geolocation.

Genetic Characterization of Influenza A (H1N1) Pandemic 2009 Virus Isolates from Mumbai.

PubMed

Gohil, Devanshi; Kothari, Sweta; Shinde, Pramod; Meharunkar, Rhuta; Warke, Rajas; Chowdhary, Abhay; Deshmukh, Ranjana

2017-08-01

Pandemic influenza A (H1N1) 2009 virus was first detected in India in May 2009 which subsequently became endemic in many parts of the country. Influenza A viruses have the ability to evade the immune response through its ability of antigenic variations. The study aims to characterize influenza A (H1N1) pdm 09 viruses circulating in Mumbai during the pandemic and post-pandemic period. Nasopharyngeal swabs positive for influenza A (H1N1) pdm 09 viruses were inoculated on Madin-Darby canine kidney cell line for virus isolation. Molecular and phylogenetic analysis of influenza A (H1N1) pdm 09 isolates was conducted to understand the evolution and genetic diversity of the strains. Nucleotide and amino acid sequences of the HA gene of Mumbai isolates when compared to A/California/07/2009-vaccine strain revealed 14 specific amino acid differences located at the antigenic sites. Amino acid variations in HA and NA gene resulted in changes in the N-linked glycosylation motif which may lead to immune evasion. Phylogenetic analysis of the isolates revealed their evolutionary position with vaccine strain A/California/07/2009 but had undergone changes gradually. The findings in the present study confirm genetic variability of influenza viruses and highlight the importance of continuous surveillance during influenza outbreaks.

Spatiotemporal variation in survival rates: implications for population dynamics of yellow-bellied marmots.

PubMed

Ozgul, Arpat; Armitage, Kenneth B; Blumstein, Daniel T; Oli, Madan K

2006-04-01

Spatiotemporal variation in age-specific survival rates can profoundly influence population dynamics, but few studies of vertebrates have thoroughly investigated both spatial and temporal variability in age-specific survival rates. We used 28 years (1976-2003) of capture-mark-recapture (CMR) data from 17 locations to parameterize an age-structured Cormack-Jolly-Seber model, and investigated spatial and temporal variation in age-specific annual survival rates of yellow-bellied marmots (Marmota flaviventris). Survival rates varied both spatially and temporally, with survival of younger animals exhibiting the highest degree of variation. Juvenile survival rates varied from 0.52 +/- 0.05 to 0.78 +/- 0.10 among sites and from 0.15 +/- 0.14 to 0.89 +/- 0.06 over time. Adult survival rates varied from 0.62 +/- 0.09 to 0.80 +/- 0.03 among sites, but did not vary significantly over time. We used reverse-time CMR models to estimate the realized population growth rate (lamda), and to investigate the influence of the observed variation in age-specific survival rates on lamda. The realized growth rate of the population closely covaried with, and was significantly influenced by, spatiotemporal variation in juvenile survival rate. High variability in juvenile survival rates over space and time clearly influenced the dynamics of our study population and is also likely to be an important determinant of the spatiotemporal variation in the population dynamics of other mammals with similar life history characteristics.

Global variations in the level of cancer-related research activity and correlation to cancer-specific mortality: Proposal for a global curriculum.

PubMed

Are, C; Caniglia, A; Malik, Mohammed; Smith, L; Cummings, Charmaine; Lecoq, Carine; Berman, R; Audisio, R; Wyld, L

2018-01-01

The aim of this study was to analyze global variations in the level of cancer-related research activity and correlate this with cancer-specific mortality. The SCOPUS database was explored to obtain data relating to the number of cancer-related publications per country. Cancer-specific mortality rates were obtained from the World Health Organization. Global variations in the level of scholarly activity were analyzed and correlated with variations in cancer-specific mortality. Data for 142 countries were obtained and significant variations in the level of research activity was noted. The level of research activity increased with rising socio-economic status. The United States was the most prolific country with 222,300 publications followed by Japan and Germany. Several countries in different regions of the world had a low level of research activity. An inverse relationship between the level of research activity and cancer-specific mortality was noted. This relationship persisted even in countries with a low level of research activity. The socioeconomic status of a nation and geographic location (continent) had a mixed influence with an overall apparent correlation with cancer-related research activity. This study demonstrates significant global variation in the level of cancer-related research activity and a correlation with cancer-specific mortality. The presence of a minimum set of standards for research literacy, as proposed by the European Society of Surgical Oncology and the Society of Surgical Oncology may contribute to enhanced research activity and improve outcomes for cancer patients worldwide. Copyright © 2017 Society of Surgical Oncology, European Society of Surgical Oncology. Published by Elsevier Ltd.. All rights reserved.

Design and reliability analysis of DP-3 dynamic positioning control architecture

NASA Astrophysics Data System (ADS)

Wang, Fang; Wan, Lei; Jiang, Da-Peng; Xu, Yu-Ru

2011-12-01

As the exploration and exploitation of oil and gas proliferate throughout deepwater area, the requirements on the reliability of dynamic positioning system become increasingly stringent. The control objective ensuring safety operation at deep water will not be met by a single controller for dynamic positioning. In order to increase the availability and reliability of dynamic positioning control system, the triple redundancy hardware and software control architectures were designed and developed according to the safe specifications of DP-3 classification notation for dynamically positioned ships and rigs. The hardware redundant configuration takes the form of triple-redundant hot standby configuration including three identical operator stations and three real-time control computers which connect each other through dual networks. The function of motion control and redundancy management of control computers were implemented by software on the real-time operating system VxWorks. The software realization of task loose synchronization, majority voting and fault detection were presented in details. A hierarchical software architecture was planed during the development of software, consisting of application layer, real-time layer and physical layer. The behavior of the DP-3 dynamic positioning control system was modeled by a Markov model to analyze its reliability. The effects of variation in parameters on the reliability measures were investigated. The time domain dynamic simulation was carried out on a deepwater drilling rig to prove the feasibility of the proposed control architecture.

Dynamic Infrared Thermography Study of Blood Flow Relative to Lower Limp Position

NASA Astrophysics Data System (ADS)

Stathopoulos, I.; Skouroliakou, K.; Michail, C.; Valais, I.

2015-09-01

Thermography is an established method for studying skin temperature distribution. Temperature distribution on body surface is influenced by a variety of physiological mechanisms and has been proven a reliable indicator of various physiological disorders. Blood flow is an important factor that influences body heat diffusion and skin temperature. In an attempt to validate and further elucidate thermal models characterizing the human skin, dynamic thermography of the lower limp in horizontal and vertical position was performed, using a FLIR T460 thermographic camera. Temporal variation of temperature was recorded on five distinct points of the limp. Specific points were initially cooled by the means of an ice cube and measurements of the skin temperature were obtained every 30 seconds as the skin temperature was locally reduced and afterwards restored at its initial value. The return to thermal balance followed roughly the same pattern for all points of measurement, although the heating rate was faster when the foot was in horizontal position. Thermal balance was achieved faster at the spots that were positioned on a vein passage. Our results confirm the influence of blood flow on the thermal regulation of the skin. Spots located over veins exhibit different thermal behaviour due to thermal convection through blood flow. Changing the position of the foot from vertical to horizontal, effectively affects blood perfusion as in the vertical position blood circulation is opposed by gravity.

Faecal coliform bacteria in Febros river (northwest Portugal): temporal variation, correlation with water parameters, and species identification.

PubMed

Cabral, João Paulo; Marques, Cristina

2006-07-01

Febros river water was sampled weekly, during 35 successive weeks, and analyzed for microbiological (total coliforms, faecal coliforms, faecal streptococci and enterococci) and chemical-physical (ammonia and temperature) parameters. All microbiological parameters were highly correlated with each other and with ammonia, suggesting that the simultaneous determination of all variables currently in use in the evaluation of the microbiological quality of waters is probably redundant, and could be simplified, and that ammonia should be tested as a sentinel parameter of the microbiological pollution load of Febros river. From the strains isolated from positive tubes of the faecal coliforms test (multiple tube fermentation technique) and retested in this assay, Escherichia coli, Klebsiella oxytoca and Klebsiella pneumoniae subsp. pneumoniae strains were positive, indicating that the faecal coliforms test is not totally specific for Escherichia coli, and can detect other bacteria. Considering that these Klebsiella spp. are not necessarily of faecal origin, it was concluded that the faecal coliforms test can overestimate true faecal pollution. From the strains isolated from positive tubes of the faecal coliforms procedure, only Escherichia coli strains were clearly positive in the beta-D-glucuronidase test. All other species were negative or very weakly positive, suggesting that the assay of the beta-D-glucuronidase activity is less prone to false positives than the faecal coliforms test in the quantification of Escherichia coli in environmental waters.

Evaluation of the highly sensitive chemiluminescent enzyme immunoassay "Lumipulse HBsAg-HQ" for hepatitis B virus screening.

PubMed

Deguchi, Matsuo; Kagita, Masanori; Yoshioka, Nori; Tsukamoto, Hiroko; Takao, Miyuki; Tahara, Kazuko; Maeda, Ikuhiro; Hidaka, Yoh; Yamauchi, Satoshi; Kaneko, Atsushi; Miyakoshi, Hideo; Isomura, Mitsuo

2017-10-06

Ongoing efforts in the development of HBsAg detection kits are focused on improving sensitivity and specificity. The purpose of this study was to evaluate an improved, highly sensitive quantitative assay, "Lumipulse HBsAg-HQ", a chemiluminescent enzyme immunoassay designed for a fully automated instrument, the "Lumipulse G1200". Serum samples for reproducibility, dilution, correlation, sensitivity, and specificity studies were obtained from patients at the Osaka University Hospital. Seroconversion and sensitivity panels were purchased from a commercial vender. Subtype, sensitivity panels, and HBsAg recombinant proteins with one or two amino acid substitutions were prepared in-house. The coefficients of variation for the low, medium, and high concentration samples ranged from 1.93 to 2.55%. The HBsAg-HQ reagent for dilution testing showed good linearity in the 0.005-150 HBsAg IU/mL range and no prozone phenomenon. All 102 HBV carrier samples were positive by HBsAg-HQ, while other commercial reagents showed one or more to be negative. In the seroconversion panel, the 14-day blood sample was positive. The sensitivity against HBsAg-HQ "ad" and "ay" subtypes was 0.025 ng/mL. Comparisons among the HBsAg-HQ, HISCL, and Architect HBsAg reagents were performed using the Bland-Altman plot. Specificity for 1000 seronegative individuals was 99.7%. HBsAg-HQ detected 29 positive serum among 12 231 routinely obtained serum samples, which showed concentrations of 0.005-0.05 HBsAg IU/mL. According to these results, the Lumipulse HBsAg-HQ assay, with a highly sensitive limit of detection of 0.005 IU/mL, may facilitate the development of a better management strategy for a considerable proportion of infected patients. © 2017 Wiley Periodicals, Inc.

Heterogeneous genetic diversity pattern in Plasmodium vivax genes encoding merozoite surface proteins (MSP) -7E, -7F and -7L.

PubMed

Garzón-Ospina, Diego; Forero-Rodríguez, Johanna; Patarroyo, Manuel A

2014-12-13

The msp-7 gene has become differentially expanded in the Plasmodium genus; Plasmodium vivax has the highest copy number of this gene, several of which encode antigenic proteins in merozoites. DNA sequences from thirty-six Colombian clinical isolates from P. vivax (pv) msp-7E, -7F and -7L genes were analysed for characterizing and studying the genetic diversity of these pvmsp-7 members which are expressed during the intra-erythrocyte stage; natural selection signals producing the variation pattern so observed were evaluated. The pvmsp-7E gene was highly polymorphic compared to pvmsp-7F and pvmsp-7L which were seen to have limited genetic diversity; pvmsp-7E polymorphism was seen to have been maintained by different types of positive selection. Even though these copies seemed to be species-specific duplications, a search in the Plasmodium cynomolgi genome (P. vivax sister taxon) showed that both species shared the whole msp-7 repertoire. This led to exploring the long-term effect of natural selection by comparing the orthologous sequences which led to finding signatures for lineage-specific positive selection. The results confirmed that the P. vivax msp-7 family has a heterogeneous genetic diversity pattern; some members are highly conserved whilst others are highly diverse. The results suggested that the 3'-end of these genes encode MSP-7 proteins' functional region whilst the central region of pvmsp-7E has evolved rapidly. The lineage-specific positive selection signals found suggested that mutations occurring in msp-7s genes during host switch may have succeeded in adapting the ancestral P. vivax parasite population to humans.

Function of specific 2'-hydroxyl groups of guanosines in a hammerhead ribozyme probed by 2' modifications.

PubMed Central

Williams, D M; Pieken, W A; Eckstein, F

1992-01-01

The importance of the 2'-hydroxyl group of several guanosine residues for the catalytic efficiency of a hammerhead ribozyme has been investigated. Five ribozymes in which single guanosine residues were substituted with 2'-amino-, 2'-fluoro-, or 2'-deoxyguanosine were chemically synthesized. The comparison of the catalytic activity of the three 2' modifications at a specific position allows conclusions about the functional role of the parent 2'-hydroxyl group. Substitutions of nonconserved nucleotides within the ribozyme caused little alteration in the catalytic activity relative to that obtained with the unmodified ribozyme. In contrast, when either of the guanosines within the single-stranded loop between stem I and stem II of the ribozyme was replaced by 2'-deoxyguanosine or 2'-fluoro-2'-deoxyguanosine, the catalytic activities of the resulting ribozymes were reduced by factors of at least 150. The catalytic activities of the corresponding ribozymes containing 2'-amino-2'-deoxyguanosine substitutions at these positions, however, were both reduced by factors of 15. These effects resulted from decreases in the respective kcat values, whereas variations in the Km values were comparatively small. A different pattern of reactivity of the three 2' modifications was observed at the guanosine immediately 3' to stem II of the ribozyme. Whereas both 2'-deoxyguanosine and 2'-amino-2'-deoxyguanosine at this position showed catalytic activity similar to that of the unmodified ribozyme, the activity of the corresponding 2'-fluoro-2'-deoxyguanosine-containing ribozyme was reduced by a factor of 15. The implications of these substitution-specific reactivities on the functional role of the native 2'-hydroxyl groups are discussed. Images PMID:1736306

Cross-correlation map analyses show weather variation influences on mosquito abundance patterns in Saginaw County, Michigan, 1989-2005.

PubMed

Chuang, Ting-Wu; Ionides, Edward L; Knepper, Randall G; Stanuszek, William W; Walker, Edward D; Wilson, Mark L

2012-07-01

Weather is important determinant of mosquito abundance that, in turn, influences vectorborne disease dynamics. In temperate regions, transmission generally is seasonal as mosquito abundance and behavior varies with temperature, precipitation, and other meteorological factors. We investigated how such factors affected species-specific mosquito abundance patterns in Saginaw County, MI, during a 17-yr period. Systematic sampling was undertaken at 22 trapping sites from May to September, during 1989-2005, for 19,228 trap-nights and 300,770 mosquitoes in total. Aedes vexans (Meigen), Culex pipiens L. and Culex restuans Theobald, the most abundant species, were analyzed. Weather data included local daily maximum temperature, minimum temperature, total precipitation, and average relative humidity. In addition to standard statistical methods, cross-correlation mapping was used to evaluate temporal associations with various lag periods between weather variables and species-specific mosquito abundances. Overall, the average number of mosquitoes was 4.90 per trap-night for Ae. vexans, 2.12 for Cx. pipiens, and 1.23 for Cx. restuans. Statistical analysis of the considerable temporal variability in species-specific abundances indicated that precipitation and relative humidity 1 wk prior were significantly positively associated with Ae. vexans, whereas elevated maximum temperature had a negative effect during summer. Cx. pipiens abundance was positively influenced by the preceding minimum temperature in the early season but negatively associated with precipitation during summer and with maximum temperature in July and August. Cx. restuans showed the least weather association, with only relative humidity 2-24 d prior being linked positively during late spring-early summer. The recently developed analytical method applied in this study could enhance our understanding of the influences of weather variability on mosquito population dynamics.

Ab initio study of nitrogen and position-specific oxygen kinetic isotope effects in the NO + O3 reaction

NASA Astrophysics Data System (ADS)

Walters, Wendell W.; Michalski, Greg

2016-12-01

Ab initio calculations have been carried out to investigate nitrogen (k15/k14) and position-specific oxygen (k17/k16O & k18/k16) kinetic isotope effects (KIEs) for the reaction between NO and O3 using CCSD(T)/6-31G(d) and CCSD(T)/6-311G(d) derived frequencies in the complete Bigeleisen equations. Isotopic enrichment factors are calculated to be -6.7‰, -1.3‰, -44.7‰, -14.1‰, and -0.3‰ at 298 K for the reactions involving the 15N16O, 14N18O, 18O16O16O, 16O18O16O, and 16O16O18O isotopologues relative to the 14N16O and 16O3 isotopologues, respectively (CCSD(T)/6-311G(d)). Using our oxygen position-specific KIEs, a kinetic model was constructed using Kintecus, which estimates the overall isotopic enrichment factors associated with unreacted O3 and the oxygen transferred to NO2 to be -19.6‰ and -22.8‰, respectively, (CCSD(T)/6-311G(d)) which tends to be in agreement with previously reported experimental data. While this result may be fortuitous, this agreement suggests that our model is capturing the most important features of the underlying physics of the KIE associated with this reaction (i.e., shifts in zero-point energies). The calculated KIEs will useful in future NOx isotopic modeling studies aimed at understanding the processes responsible for the observed tropospheric isotopic variations of NOx as well as for tropospheric nitrate.

Colon tumor mutations and epigenetic changes associated with genetic polymorphism: Insight into disease pathways

PubMed Central

Slattery, Martha L.; Wolff, Roger K.; Curtin, Karen; Fitzpatrick, Frank; Herrick, Jennifer; Potter, John D.; Caan, Bette J.; Samowitz, Wade S.

2010-01-01

Variation in genes associated with serum levels of proteins may be useful for examining specific disease pathways. Using data from a large study of colon cancer, we examine genetic variants in insulin, inflammation, estrogen, metabolizing enzymes, and energy homeostasis genes to explore associations with microsatellite instability (MSI), CpG Island methylator phenotype (CIMP), mutations of p53 in exons 5 through 8, and mutations in codons 12 and 13 of Ki-ras. Insulin-related genes were associated with CIMP positive and MSI tumors, with the strongest associations among aspirin users. The Fok1 Vitamin D Receptor (VDR) polymorphism was associated with CIMP positive/Ki-ras mutated tumors; the Poly A and CDX2 VDR polymorphisms were associated only with Ki-ras mutated tumors. NAT2 was associated with CIMP positive/Ki-ras mutated tumors but not with MSI tumors. The TCF7L2 rs7903146 polymorphism was associated with p53 mutated tumors. Most associations varied by recent aspirin/NSAID use: IL6 rs1800796 and rs1800795 polymorphisms were associated inversely with tumor mutations in the presence of aspirin/NSAIDs; POMC significantly reduced risk of Ki-ras- mutated tumors when aspirin/NSAIDs were not used; the TCF7L2 rs7903146 was associated with reduced risk of Ki-ras-mutated tumors in the presence of aspirin and increased risk in the absence of aspirin. These data, although exploratory, identify specific tumor subsets that may be associated with specific exposures/polymorphism combinations. The important modifying effects of aspirin/NSAIDs on associations with genetic polymorphisms reinforce the underlying role of inflammation in the etiology of colon cancer. PMID:18992263

A comparative study of set up variations and bowel volumes in supine versus prone positions of patients treated with external beam radiation for carcinoma rectum.

PubMed

Rajeev, K R; Menon, Smrithy S; Beena, K; Holla, Raghavendra; Kumar, R Rajaneesh; Dinesh, M

2014-01-01

A prospective study was undertaken to evaluate the influence of patient positioning on the set up variations to determine the planning target volume (PTV) margins and to evaluate the clinical relevance volume assessment of the small bowel (SB) within the irradiated volume. During the period of months from December 2011 to April 2012, a computed tomography (CT) scan was done either in supine position or in prone position using a belly board (BB) for 20 consecutive patients. All the patients had histologically proven rectal cancer and received either post- or pre-operative pelvic irradiation. Using a three-dimensional planning system, the dose-volume histogram for SB was defined in each axial CT slice. Total dose was 46-50 Gy (2 Gy/fraction), delivered using the 4-field box technique. The set up variation of the study group was assessed from the data received from the electronic portal imaging device in the linear accelerator. The shift along X, Y, and Z directions were noted. Both systematic and random errors were calculated and using both these values the PTV margin was calculated. The systematic errors of patients treated in the supine position were 0.87 (X-mm), 0.66 (Y-mm), 1.6 (Z-mm) and in the prone position were 1.3 (X-mm), 0.59 (Y-mm), 1.17 (Z-mm). The random errors of patients treated in the supine positions were 1.81 (X-mm), 1.73 (Y-mm), 1.83 (Z-mm) and in prone position were 2.02 (X-mm), 1.21 (Y-mm), 3.05 (Z-mm). The calculated PTV margins in the supine position were 3.45 (X-mm), 2.87 (Y-mm), 5.31 (Z-mm) and in the prone position were 4.91 (X-mm), 2.32 (Y-mm), 5.08 (Z-mm). The mean volume of the peritoneal cavity was 648.65 cm 3 in the prone position and 1197.37 cm 3 in the supine position. The prone position using BB device was more effective in reducing irradiated SB volume in rectal cancer patients. There were no significant variations in the daily set up for patients treated in both supine and prone positions.

Statistical analysis of surface-water-quality data in and near the coal-mining region of southwestern Indiana, 1957-80

USGS Publications Warehouse

Martin, Jeffrey D.; Crawford, Charles G.

1987-01-01

The Surface Mining Control and Reclamation Act of 1977 requires that applications for coal-mining permits contain information about the water quality of streams at and near a proposed mine. To meet this need for information, streamflow, specific conductance, pH, and concentrations of total alkalinity, sulfate, dissolved solids, suspended solids, total iron, and total manganese at 37 stations were analyzed to determine the spatial and seasonal variations in water quality and to develop equations for predicting water quality. The season of lowest median streamflow was related to the size of the drainage area. Median streamflow was least during fall at 15 of 16 stations having drainage areas greater than 1,000 square miles but was least during summer at 17 of 21 stations having drainage areas less than 1,000 square miles. In general, the season of lowest median specific conductance occurred during the season of highest streamflow except at stations on the Wabash River. Median specific conductance was least during summer at 9 of 9 stations on the Wabash River, but was least during winter or spring (the seasons of highest streamflow) at 27 of the remaining 28 stations. Linear, inverse, semilog, log-log, and hyperbolic regression models were used to investigate the functional relations between water-quality characteristics and streamflow. Of 186 relations investigated, 143 were statistically significant. Specific conductance and concentrations of total alkalinity and sulfate were negatively related to streamflow at all stations except for a positive relation between total alkalinity concentration and streamflow at Patoka River near Princeton. Concentrations of total alkalinity and sulfate were positively related to specific conductance at all stations except for a negative relation at Patoka River near Princeton and for a positive and negative relation at Patoka River at Jasper. Most of these relations are good, have small confidence intervals, and will give reliable predictions of the water-quality variables listed above. The poorest relations are typically at stations in the Patoka River watershed. Suspended-solids concentration was positively related to streamflow at all but two stations on the Patoka River. These relations are poor, have large confidence intervals, and will give less reliable predictions of suspended-solids concentration. Predictive equations for the regional relations between dissolved-solids concentration and specific conductance and between sulfate concentration and specific conductance, and the seasonal patterns of water quality, are probably valid for the coal-mining regions of Illinois and western Kentucky.

The diagnostic accuracy of physical examination compared to lung ultrasound for determining lung congestion in hemodialysis patients who have reached their dry weight

NASA Astrophysics Data System (ADS)

Rahardjo, K. D.; Dharmaeizar; Nainggolan, G.; Harimurti, K.

2017-08-01

Research has shown that hemodialysis patients with lung congestion have high morbidity and mortality. Patients were assumed to be free of lung congestion if they had reached their post-dialysis dry weight. Most often, to determine if the patient was free of lung congestion, physical examination was used. However, the accuracy of physical examination in detecting lung congestion has not been established. To compare the capabilities of physical examination and lung ultrasound in detection of lung congestion, cross-sectional data collection was conducted on hemodialysis patients. Analysis was done to obtain proportion, sensitivity, specificity, positive predictive value, negative predictive value, and positive likelihood ratio. Sixty patients participated in this study. The inter observer variation of 20 patients revealed a kappa value of 0.828. When all 60 patients were taken into account, we found that 36 patients (57.1%) had lung congestion. Mild lung congestion was found in 24 (38.1%), and 12 (19%) had a moderate degree of congestion. In the analysis comparing jugular venous pressure to lung ultrasound, we found that sensitivity was 0.47 (0.31-0.63), specificity was 0.73 (0.54-0.86), positive predictive value (PPV) was 0.51 (0.36-0.67), negative predictive value (NPV) was 0.70 (0.49-0.84), positive likelihood ratio (PLR) was 1.75 (0.88-3.47), and the negative likelihood ratio (NLR) was 0.72 (0.47-1.12). In terms of lung auscultation, we found that sensitivity was 0.56 (0.39-0.71), specificity was 0.54 (0.35-0.71), PPV was 0.61 (0.44-0.76), NPV was 0.48 (0.31-0.66), PLR was 1.21 (0.73-2.0), and NLR was 0.82 (0.49-1.38). The results of our study showed that jugular venous distention and lung auscultation examination are not reliable means of detecting lung congestion.

FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications.

PubMed

Backenroth, Daniel; He, Zihuai; Kiryluk, Krzysztof; Boeva, Valentina; Pethukova, Lynn; Khurana, Ekta; Christiano, Angela; Buxbaum, Joseph D; Ionita-Laza, Iuliana

2018-05-03

We describe a method based on a latent Dirichlet allocation model for predicting functional effects of noncoding genetic variants in a cell-type- and/or tissue-specific way (FUN-LDA). Using this unsupervised approach, we predict tissue-specific functional effects for every position in the human genome in 127 different tissues and cell types. We demonstrate the usefulness of our predictions by using several validation experiments. Using eQTL data from several sources, including the GTEx project, Geuvadis project, and TwinsUK cohort, we show that eQTLs in specific tissues tend to be most enriched among the predicted functional variants in relevant tissues in Roadmap. We further show how these integrated functional scores can be used for (1) deriving the most likely cell or tissue type causally implicated for a complex trait by using summary statistics from genome-wide association studies and (2) estimating a tissue-based correlation matrix of various complex traits. We found large enrichment of heritability in functional components of relevant tissues for various complex traits, and FUN-LDA yielded higher enrichment estimates than existing methods. Finally, using experimentally validated functional variants from the literature and variants possibly implicated in disease by previous studies, we rigorously compare FUN-LDA with state-of-the-art functional annotation methods and show that FUN-LDA has better prediction accuracy and higher resolution than these methods. In particular, our results suggest that tissue- and cell-type-specific functional prediction methods tend to have substantially better prediction accuracy than organism-level prediction methods. Scores for each position in the human genome and for each ENCODE and Roadmap tissue are available online (see Web Resources). Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

The Dynamic Relationship Between Cognitive Function and Positive Well-Being in Older People: A Prospective Study Using the English Longitudinal Study of Aging

PubMed Central

2014-01-01

There is evidence that having a stronger sense of positive well-being may be a potential resource for healthier aging as represented by slower physical decline, reduced risk of frailty and longer survival. However, it is unclear whether positive well-being is protective of another crucial component of healthy aging, cognitive function, or whether it has a bidirectional relationship with cognitive function. We use multilevel models with within-person centering to estimate the within- and between-person association between cognitive function and positive well-being in 4 waves of data from the English Longitudinal Study of Ageing (ELSA), (N = 10985, aged 50–90 years at wave 1). Our findings show that, although most variation in cognitive function was explained by age, and most variation in well-being was explained by depression, small but significant associations between cognition and well-being remained after variation in age and depression were controlled. In models where cognition was the outcome, the association was mainly because of variation in mean levels of well-being between persons. In models where well-being was the outcome, the association was mainly because of within-person fluctuation in cognitive test performance. Exercise and depression were the most important moderating influences on the association between cognition and positive well-being. Depression had greater effect upon this association for those with higher well-being, but exercise protected cognitive performance against the adverse effects of lower well-being. PMID:24955999

Linkages Between Global Vegetation and Climate: An Analysis Based on NOAA Advanced Very High Resolution Radiometer Data. Degree awarded by Vrije Universiteit, Amsterdam, Netherlands

NASA Technical Reports Server (NTRS)

Los, Sietse Oene

1998-01-01

A monthly global 1 degree by 1 degree data set from 1982 until 1990 was derived from data collected by the Advanced Very High Resolution Radiometer on board the NOAA 7, 9, and 11 satellites. This data set was used to study the interactions between variations in climate and variations in the "greenness" of vegetation. Studies with the Colorado State University atmospheric general circulation model coupled to the Simple Biosphere model showed a large sensitivity of the hydrological balance to changes in vegetation at low latitudes. The depletion of soil moisture as a result of increased vegetation density provided a negative feedback in an otherwise positive association between increased vegetation, increased evaporation, and increased precipitation proposed by Charney and coworkers. Analysis of climate data showed, at temperate to high latitudes, a positive association between variation in land surface temperature, sea surface temperature and vegetation greenness. At low latitudes the data indicated a positive association between variations in sea surface temperature, rainfall and vegetation greenness. The variations in mid- to high latitude temperatures affected the global average greenness and this could provide an explanation for the increased carbon uptake by the terrestrial surface over the past couple of decades.

Sequence variations of the alpha-globin genes: scanning of high CG content genes with DHPLC and DG-DGGE.

PubMed

Lacerra, Giuseppina; Fiorito, Mirella; Musollino, Gennaro; Di Noce, Francesca; Esposito, Maria; Nigro, Vincenzo; Gaudiano, Carlo; Carestia, Clementina

2004-10-01

The alpha-globin chains are encoded by two duplicated genes (HBA2 and HBA1, 5'-3') showing overall sequence homology >96% and average CG content >60%. alpha-Thalassemia, the most prevalent worldwide autosomal recessive disorder, is a hereditary anemia caused by sequence variations of these genes in about 25% of carriers. We evaluated the overall sensitivity and suitability of DHPLC and DG-DGGE in scanning both the alpha-globin genes by carrying out a retrospective analysis of 19 variant alleles in 29 genotypes. The HBA2 alleles c.1A>G, c.79G>A, and c.281T>G, and the HBA1 allele c.475C>A were new. Three pathogenic sequence variations were associated in cis with nonpathogenic variations in all families studied; they were the HBA2 variation c.2T>C associated with c.-24C>G, and the HBA2 variations c.391G>C and c.427T>C, both associated with c.565G>A. We set up original experimental conditions for DHPLC and DG-DGGE and analyzed 10 normal subjects, 46 heterozygotes, seven homozygotes, seven compound heterozygotes, and six compound heterozygotes for a hybrid gene. Both the methodologies gave reproducible results and no false-positive was detected. DHPLC showed 100% sensitivity and DG-DGGE nearly 90%. About 100% of the sequence from the cap site to the polyA addition site could be scanned by DHPLC, about 87% by DG-DGGE. It is noteworthy that the three most common pathogenic sequence variations (HBA2 alleles c.2T>C, c.95+2_95+6del, and c.523A>G) were unambiguously detected by both the methodologies. Genotype diagnosis must be confirmed with PCR sequencing of single amplicons or with an allele-specific method. This study can be helpful for scanning genes with high CG content and offers a model suitable for duplicated genes with high homology. Copyright 2004 Wiley-Liss, Inc.

Respiratory sinus arrhythmia: opposite effects on systolic and mean arterial pressure in supine humans

NASA Technical Reports Server (NTRS)

Elstad, M.; Toska, K.; Chon, K. H.; Raeder, E. A.; Cohen, R. J.

2001-01-01

1. Are arterial blood pressure fluctuations buffered or reinforced by respiratory sinus arrhythmia (RSA)? There is still considerable debate about this simple question. Different results have been obtained, triggering a discussion as to whether or not the baroreflexes are responsible for RSA. We suspected that the measurements of different aspects of arterial pressure (mean arterial pressure (MAP) and systolic pressure (SP)) can explain the conflicting results. 2. Simultaneous recordings of beat-to-beat MAP, SP, left cardiac stroke volume (SV, pulsed ultrasound Doppler), heart rate (HR) and respiration (RE) were obtained in 10 healthy young adults during spontaneous respiration. In order to eliminate HR variations at respiratory frequency we used propranolol and atropine administration in the supine and tilted positions. Respiration-synchronous variation in the recorded variables was quantified by spectral analysis of the recordings of each of these variables, and the phase relations between them were determined by cross-spectral analysis. 3. MAP fluctuations increased after removing heart rate variations in both supine and tilted position, whereas SP fluctuations decreased in the supine position and increased in the head-up tilted position. 4. RSA buffers respiration-synchronous fluctuations in MAP in both positions. However, fluctuations in SP were reinforced by RSA in the supine and buffered in the tilted position.

The good, the bad and the plenty: interactive effects of food quality and quantity on the growth of different Daphnia species.

PubMed

Bukovinszky, Tibor; Verschoor, Antonie M; Helmsing, Nico R; Bezemer, T Martijn; Bakker, Elisabeth S; Vos, Matthijs; de Senerpont Domis, Lisette N

2012-01-01

Effects of food quality and quantity on consumers are neither independent nor interchangeable. Although consumer growth and reproduction show strong variation in relation to both food quality and quantity, the effects of food quality or food quantity have usually been studied in isolation. In two experiments, we studied the growth and reproduction in three filter-feeding freshwater zooplankton species, i.e. Daphnia galeata x hyalina, D. pulicaria and D. magna, on their algal food (Scenedesmus obliquus), varying in carbon to phosphorus (C∶P) ratios and quantities (concentrations). In the first experiment, we found a strong positive effect of the phosphorus content of food on growth of Daphnia, both in their early and late juvenile development. Variation in the relationship between the P-content of animals and their growth rate reflected interspecific differences in nutrient requirements. Although growth rates typically decreased as development neared maturation, this did not affect these species-specific couplings between growth rate and Daphnia P-content. In the second experiment, we examined the effects of food quality on Daphnia growth at different levels of food quantity. With the same decrease in P-content of food, species with higher estimated P-content at zero growth showed a larger increase in threshold food concentrations (i.e. food concentration sufficient to meet metabolic requirements but not growth). These results suggest that physiological processes such as maintenance and growth may in combination explain effects of food quality and quantity on consumers. Our study shows that differences in response to variation in food quality and quantity exist between species. As a consequence, species-specific effects of food quality on consumer growth will also determine how species deal with varying food levels, which has implications for resource-consumer interactions.

The Good, the Bad and the Plenty: Interactive Effects of Food Quality and Quantity on the Growth of Different Daphnia Species

PubMed Central

Bukovinszky, Tibor; Verschoor, Antonie M.; Helmsing, Nico R.; Bezemer, T. Martijn; Bakker, Elisabeth S.; Vos, Matthijs; de Senerpont Domis, Lisette N.

2012-01-01

Effects of food quality and quantity on consumers are neither independent nor interchangeable. Although consumer growth and reproduction show strong variation in relation to both food quality and quantity, the effects of food quality or food quantity have usually been studied in isolation. In two experiments, we studied the growth and reproduction in three filter-feeding freshwater zooplankton species, i.e. Daphnia galeata x hyalina, D. pulicaria and D. magna, on their algal food (Scenedesmus obliquus), varying in carbon to phosphorus (C∶P) ratios and quantities (concentrations). In the first experiment, we found a strong positive effect of the phosphorus content of food on growth of Daphnia, both in their early and late juvenile development. Variation in the relationship between the P-content of animals and their growth rate reflected interspecific differences in nutrient requirements. Although growth rates typically decreased as development neared maturation, this did not affect these species-specific couplings between growth rate and Daphnia P-content. In the second experiment, we examined the effects of food quality on Daphnia growth at different levels of food quantity. With the same decrease in P-content of food, species with higher estimated P-content at zero growth showed a larger increase in threshold food concentrations (i.e. food concentration sufficient to meet metabolic requirements but not growth). These results suggest that physiological processes such as maintenance and growth may in combination explain effects of food quality and quantity on consumers. Our study shows that differences in response to variation in food quality and quantity exist between species. As a consequence, species-specific effects of food quality on consumer growth will also determine how species deal with varying food levels, which has implications for resource-consumer interactions. PMID:23049734

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

PubMed Central

Degner, Jacob F.; Marioni, John C.; Pai, Athma A.; Pickrell, Joseph K.; Nkadori, Everlyne; Gilad, Yoav; Pritchard, Jonathan K.

2009-01-01

Motivation: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE). Results: We generated 16 million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias toward higher mapping rates of the allele in the reference sequence, compared with the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did not lead to more reliable results overall. We find that even after masking, ∼5–10% of SNPs still have an inherent bias toward more effective mapping of one allele. Filtering out inherently biased SNPs removes 40% of the top signals of ASE. The remaining SNPs showing ASE are enriched in genes previously known to harbor cis-regulatory variation or known to show uniparental imprinting. Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data. Availability: Scripts, written in Perl and R, for simulating short reads, masking SNP variation in a reference genome and analyzing the simulation output are available upon request from JFD. Raw short read data were deposited in GEO (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE18156. Contact: jdegner@uchicago.edu; marioni@uchicago.edu; gilad@uchicago.edu; pritch@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19808877

Rapid diversification of five Oryza AA genomes associated with rice adaptation.

PubMed

Zhang, Qun-Jie; Zhu, Ting; Xia, En-Hua; Shi, Chao; Liu, Yun-Long; Zhang, Yun; Liu, Yuan; Jiang, Wen-Kai; Zhao, You-Jie; Mao, Shu-Yan; Zhang, Li-Ping; Huang, Hui; Jiao, Jun-Ying; Xu, Ping-Zhen; Yao, Qiu-Yang; Zeng, Fan-Chun; Yang, Li-Li; Gao, Ju; Tao, Da-Yun; Wang, Yue-Ju; Bennetzen, Jeffrey L; Gao, Li-Zhi

2014-11-18

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.

Process contributions of Australian ecosystems to interannual variations in the carbon cycle

NASA Astrophysics Data System (ADS)

Haverd, Vanessa; Smith, Benjamin; Trudinger, Cathy

2016-05-01

New evidence is emerging that semi-arid ecosystems dominate interannual variability (IAV) of the global carbon cycle, largely via fluctuating water availability associated with El Niño/Southern Oscillation. Recent evidence from global terrestrial biosphere modelling and satellite-based inversion of atmospheric CO2 point to a large role of Australian ecosystems in global carbon cycle variability, including a large contribution from Australia to the record land sink of 2011. However the specific mechanisms governing this variability, and their bioclimatic distribution within Australia, have not been identified. Here we provide a regional assessment, based on best available observational data, of IAV in the Australian terrestrial carbon cycle and the role of Australia in the record land sink anomaly of 2011. We find that IAV in Australian net carbon uptake is dominated by semi-arid ecosystems in the east of the continent, whereas the 2011 anomaly was more uniformly spread across most of the continent. Further, and in contrast to global modelling results suggesting that IAV in Australian net carbon uptake is amplified by lags between production and decomposition, we find that, at continental scale, annual variations in production are dampened by annual variations in decomposition, with both fluxes responding positively to precipitation anomalies.

Comparative genomics of the mimicry switch in Papilio dardanus.

PubMed

Timmermans, Martijn J T N; Baxter, Simon W; Clark, Rebecca; Heckel, David G; Vogel, Heiko; Collins, Steve; Papanicolaou, Alexie; Fukova, Iva; Joron, Mathieu; Thompson, Martin J; Jiggins, Chris D; ffrench-Constant, Richard H; Vogler, Alfried P

2014-07-22

The African Mocker Swallowtail, Papilio dardanus, is a textbook example in evolutionary genetics. Classical breeding experiments have shown that wing pattern variation in this polymorphic Batesian mimic is determined by the polyallelic H locus that controls a set of distinct mimetic phenotypes. Using bacterial artificial chromosome (BAC) sequencing, recombination analyses and comparative genomics, we show that H co-segregates with an interval of less than 500 kb that is collinear with two other Lepidoptera genomes and contains 24 genes, including the transcription factor genes engrailed (en) and invected (inv). H is located in a region of conserved gene order, which argues against any role for genomic translocations in the evolution of a hypothesized multi-gene mimicry locus. Natural populations of P. dardanus show significant associations of specific morphs with single nucleotide polymorphisms (SNPs), centred on en. In addition, SNP variation in the H region reveals evidence of non-neutral molecular evolution in the en gene alone. We find evidence for a duplication potentially driving physical constraints on recombination in the lamborni morph. Absence of perfect linkage disequilibrium between different genes in the other morphs suggests that H is limited to nucleotide positions in the regulatory and coding regions of en. Our results therefore support the hypothesis that a single gene underlies wing pattern variation in P. dardanus.

Illness as a source of variation of laterality in lions (Panthera leo).

PubMed

Zucca, Paolo; Baciadonna, Luigi; Masci, Stefano; Mariscoli, Massimo

2011-05-01

Brain asymmetry--i.e. the specialisation of each cerebral hemisphere for sensorimotor processing mechanisms and for specific cognitive functions-is widely distributed among vertebrates. Several factors, such as embryological manipulations, sex, age, and breeds, can influence the maintenance, strength, and direction of laterality within a certain vertebrate species. Brain lateralisation is a universal phenomenon characterising not only cerebral control of cognitive or emotion-related functions but also cerebral regulation of somatic processes, and its evolution is strongly influenced by social selection pressure. Diseases are well known to be a cost of sociality but their role in influencing behaviour has received very little attention. The present study investigates the influence of illness conditions as a source of variation on laterality in a social keystone vertebrate predator model, the lion. In a preliminary stage, the clinical conditions of 24 adult lions were assessed. The same animals were scored for forelimb preference when in the quadrupedal standing position. Lions show a marked forelimb preference with a population bias towards the use of the right forelimb. Illness conditions strongly influenced the strength of laterality bias, with a significant difference between clinically healthy and sick lions. According to these results, health conditions should be recognised as an important source of variation in brain lateralisation.

Rapid diversification of five Oryza AA genomes associated with rice adaptation

PubMed Central

Zhang, Qun-Jie; Zhu, Ting; Xia, En-Hua; Shi, Chao; Liu, Yun-Long; Zhang, Yun; Liu, Yuan; Jiang, Wen-Kai; Zhao, You-Jie; Mao, Shu-Yan; Zhang, Li-Ping; Huang, Hui; Jiao, Jun-Ying; Xu, Ping-Zhen; Yao, Qiu-Yang; Zeng, Fan-Chun; Yang, Li-Li; Gao, Ju; Tao, Da-Yun; Wang, Yue-Ju; Bennetzen, Jeffrey L.; Gao, Li-Zhi

2014-01-01

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm. PMID:25368197

Mechanical Player Load™ using trunk-mounted accelerometry in football: Is it a reliable, task- and player-specific observation?

PubMed

Barreira, Paulo; Robinson, Mark A; Drust, Barry; Nedergaard, Niels; Raja Azidin, Raja Mohammed Firhad; Vanrenterghem, Jos

2017-09-01

The aim of the present study was to examine reliability and construct convergent validity of Player Load™ (PL) from trunk-mounted accelerometry, expressed as a cumulative measure and an intensity measure (PL · min - 1 ). Fifteen male participants twice performed an overground football match simulation that included four different multidirectional football actions (jog, side cut, stride and sprint) whilst wearing a trunk-mounted accelerometer inbuilt in a global positioning system unit. Results showed a moderate-to-high reliability as indicated by the intra-class correlation coefficient (0.806-0.949) and limits of agreement. Convergent validity analysis showed considerable between-participant variation (coefficient of variation range 14.5-24.5%), which was not explained from participant demographics despite a negative association with body height for the stride task. Between-task variations generally showed a moderate correlation between ranking of participants for PL (0.593-0.764) and PL · min - 1 (0.282-0.736). It was concluded that monitoring PL ® in football multidirectional actions presents moderate-to-high reliability, that between-participant variability most likely relies on the individual's locomotive skills and not their anthropometrics, and that the intensity of a task expressed by PL · min - 1 is largely related to the running velocity of the task.

Craniofacial variation and dietary adaptations of African colobines.

PubMed

Koyabu, Daisuke B; Endo, Hideki

2009-06-01

African colobine monkeys show considerable craniofacial variation among species, although the evolutionary causes of this diversity are unclear. In light of growing evidence that diet varies considerably among colobine species, we investigated whether colobine craniofacial morphology varies as a function of their diet. We compared craniofacial morphology among five African species: Colobus angolensis, C. guereza, C. polykomos, Piliocolobus badius, and P. verus. Matrix correlation analysis indicated a significant correlation between species-specific morphological distance and dietary distance matrices. The mechanical advantage of the masseter muscle was higher in seed-eaters (C. angolensis and C. polykomos) and lower in those that eat mainly young leaves (C. guereza, P. badius, and P. verus). Canonical correspondence analysis revealed that the durophagous colobines possess relatively wider bigonial breadths, anteroposteriorly shorter faces, shorter postcanine tooth rows, more medially positioned dental batteries, wider bizygomatic arches, and anteroposteriorly longer zygomatic arches. Under the constrained lever model, these morphological features suggest that durophagous colobines have the capacity to generate relatively greater maximum bite forces. However, no consistent relationship was observed between diet and variation in the mandibular corpus and symphysis, implying that robust mandibles are not necessarily adaptations for stress resistance. Factors that may influence mandibular robusticity include allometry of symphyseal curvature and canine tooth support. Finally, linear measures of mandibular robusticity may suffer from error.

Toward understanding the structural heterogeneity and ion pair stability in dicationic ionic liquids.

PubMed

Li, Song; Bañuelos, José Leobardo; Zhang, Pengfei; Feng, Guang; Dai, Sheng; Rother, Gernot; Cummings, Peter T

2014-12-07

The structural and dynamical properties of dicationic ionic liquids (DILs) [Cn(mim)2](Tf2N)2, that is, 3-methylimidazolium dications separated by an alkyl chain and with bis(trifluoromethylsulfonyl)amide as the anion, were investigated by molecular dynamics (MD) simulation in combination with small/wide-angle X-ray scattering (SWAXS) measurements. Enhanced spatial heterogeneity is observed as the DIL chain length is increased, characterized by the changes in the scattering and the increased heterogeneity order parameter (HOP). Temperature variation imposes only slight influences on the local structures of DILs compared to monocationic ionic liquids (MILs). The peaks at 0.9 Å(-1) and 1.4 Å(-1) of the structure function shift towards low Q as the temperature increases, in a similar manner to MILs, and changes in peak positions in response to temperature changes are reflected in HOP variations. However, the prepeak shift with increasing temperature is ∼3 times smaller in DILs compared to MILs, and both MD and SWAXS indicate a DIL-specific prepeak shifting. Furthermore, the high ion pair/ion cage stability in DILs is indicative of high thermal stability and relative insensitivity of structural heterogeneity to temperature variation, which might be caused by the stronger Coulombic interactions in DILs.

Behavior of nanoceria in biologically-relevant environments

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

Kumar, Amit; Das, Soumen; Munusamy, Prabhakaran

2014-09-08

Cerium oxide nanoparticles (CNPs) have gained a considerable attention in biological research due to their anti-oxidant like behaviour and regenerative nature. The current literature on CNPs reports many successful attempts on harnessing the beneficial therapeutic properties in biology. However studies have also shown toxicity effect with some types of CNPs. This review discusses issues associated with the behaviours of CNPs in biological systems and identifies key knowledge gaps. We explore how salient physicochemical properties (size, surface chemistry, surface stabilizers) contribute to the potential positive and negative aspects of nanoceria in biological systems. Based on variations of results reported in themore » literature, important issues need to be addressed. Are we really studying the same particles with slight variations in size and physicochemical properties or do the particles being examined have fundamentally different behaviours? Are the variations observed in the result of differences in the initial properties of the particles or the results of downstream effects that emerge as the particles are prepared for specific studies and they interact with biological or other environmental moieties? How should particles be appropriately prepared for relevant environmental/toxicology/safety studies? It is useful to recognize that nanoparticles encompass some of the same complexities and variability associated with biological components« less

Choosing a design to fit the situation: how to improve specificity and positive predictive values using Bayesian lot quality assurance sampling

PubMed Central

Olives, Casey; Pagano, Marcello

2013-01-01

Background Lot Quality Assurance Sampling (LQAS) is a provably useful tool for monitoring health programmes. Although LQAS ensures acceptable Producer and Consumer risks, the literature alleges that the method suffers from poor specificity and positive predictive values (PPVs). We suggest that poor LQAS performance is due, in part, to variation in the true underlying distribution. However, until now the role of the underlying distribution in expected performance has not been adequately examined. Methods We present Bayesian-LQAS (B-LQAS), an approach to incorporating prior information into the choice of the LQAS sample size and decision rule, and explore its properties through a numerical study. Additionally, we analyse vaccination coverage data from UNICEF’s State of the World’s Children in 1968–1989 and 2008 to exemplify the performance of LQAS and B-LQAS. Results Results of our numerical study show that the choice of LQAS sample size and decision rule is sensitive to the distribution of prior information, as well as to individual beliefs about the importance of correct classification. Application of the B-LQAS approach to the UNICEF data improves specificity and PPV in both time periods (1968–1989 and 2008) with minimal reductions in sensitivity and negative predictive value. Conclusions LQAS is shown to be a robust tool that is not necessarily prone to poor specificity and PPV as previously alleged. In situations where prior or historical data are available, B-LQAS can lead to improvements in expected performance. PMID:23378151

In vivo verification of proton beam path by using post-treatment PET/CT imaging.

PubMed

Hsi, Wen C; Indelicato, Daniel J; Vargas, Carlos; Duvvuri, Srividya; Li, Zuofeng; Palta, Jatinder

2009-09-01

The purpose of this study is to establish the in vivo verification of proton beam path by using proton-activated positron emission distributions. A total of 50 PET/CT imaging studies were performed on ten prostate cancer patients immediately after daily proton therapy treatment through a single lateral portal. The PET/CT and planning CT were registered by matching the pelvic bones, and the beam path of delivered protons was defined in vivo by the positron emission distribution seen only within the pelvic bones, referred to as the PET-defined beam path. Because of the patient position correction at each fraction, the marker-defined beam path, determined by the centroid of implanted markers seen in the posttreatment (post-Tx) CT, is used for the planned beam path. The angular variation and discordance between the PET- and marker-defined paths were derived to investigate the intrafraction prostate motion. For studies with large discordance, the relative location between the centroid and pelvic bones seen in the post-Tx CT was examined. The PET/CT studies are categorized for distinguishing the prostate motion that occurred before or after beam delivery. The post-PET CT was acquired after PET imaging to investigate prostate motion due to physiological changes during the extended PET acquisition. The less than 2 degrees of angular variation indicates that the patient roll was minimal within the immobilization device. Thirty of the 50 studies with small discordance, referred as good cases, show a consistent alignment between the field edges and the positron emission distributions from the entrance to the distal edge. For those good cases, average displacements are 0.6 and 1.3 mm along the anterior-posterior (D(AP)) and superior-inferior (D(SI)) directions, respectively, with 1.6 mm standard deviations in both directions. For the remaining 20 studies demonstrating a large discordance (more than 6 mm in either D(AP) or D(SI)), 13 studies, referred as motion-after-Tx cases, also show large misalignment between the field edge and the positron emission distribution in lipomatous tissues around the prostate. These motion-after-Tx cases correspond to patients with large changes in volume of rectal gas between the post-Tx and the post-PET CTs. The standard deviations for D(AP) and D(SI) are 5.0 and 3.0 mm, respectively, for these motion-after-Tx cases. The final seven studies, referred to as position-error cases, which had a large discordance but no misalignment, were found to have deviations of 4.6 and 3.6 mm in D(AP) and D(SI), respectively. The position-error cases correspond to a large discrepancy on the relative location between the centroid and pelvic bones seen in post-Tx CT and recorded x-ray radiographs. Systematic analyses of proton-activated positron emission distributions provide patient-specific information on prostate motion (sigmaM) and patient position variability (sigmap) during daily proton beam delivery. The less than 2 mm of displacement variations in the good cases indicates that population-based values of sigmap and sigmaM, used in margin algorithms for treatment planning at the authors' institution are valid for the majority of cases. However, a small fraction of PET/CT studies (approximately 14%) with -4 mm displacement variations may require different margins. Such data are useful in establishing patient-specific planning target volume margins.

Impact of inter-seasonal solar variability on the association of lower troposphere and cold point tropopause in the tropics: Observations using RO data from COSMIC

NASA Astrophysics Data System (ADS)

Kumar, V.; Dhaka, S. K.; Ho, Shu-Peng; Singh, Narendra; Singh, Vir; Reddy, K. K.; Chun, H.-Y.

2017-12-01

Association of lower tropospheric variations with the cold point tropopause (CPT) is examined on inter-seasonal basis over the tropical region (30°N-30°S) during 2007-2010 using COSMIC/FORMOST-3 Radio Occultation (RO) data. Temperature analyses for this association are shown over different regions of the globe having contrast topography namely over Western Pacific sector, Indian sector, and African sector. Correlation coefficient (r), taken as a measurement of association, show specific longitudinal differences between the lower troposphere (from 1 km to 5 km height) and the CPT. The northern and southern hemispheres show contrast coupling of temperature variation between lower tropospheric region and the CPT. Land and ocean effects are found to contribute in a different way to the correlation coefficient. Analyses show symmetrical structure of 'r' on both sides of the equator over the African region, as data include mostly land region on both side of equator. Data represent positive correlation (r 0.5) over 15°-20° latitudes on either side of the equator over the African region, suggesting strong hold of the inter-seasonal variation of solar diabatic heating influence over the tropic of Cancer and tropic of Capricorn. On the other hand, there is a contrast behaviour over the Indian region, 'r' is nearly negative ( - 1.0) each year in the southern hemisphere (SH) and positive ( 0.4) in the northern hemisphere (NH) with a maxima near tropic of Cancer. Western Pacific region is found to display a linear increase in 'r' from negative ( - 1.0) in SH to positive ( 0.8) in NH. In general, 'r' (positive) maximizes over the land region around 15°-20° latitudes, suggesting a control of in phase inter-seasonal solar heating on the coupling of boundary layer/lower troposphere and CPT region, whereas it turns negative over water body. Analyses suggest that variabilities in CPT over different regions of globe show significant inter-seasonal association with the lower troposphere. Thus CPT variabilities are not only governed by QBO, ENSO, gravity waves and Kelvin wave system as reported in earlier studies but also considerably affected by inter-seasonal changes taking place in the lower troposphere.

Comparative cytogenetics of some marsupial species (Didelphimorphia, Didelphidae) from the Amazon basin

PubMed Central

Silva, Carlos Eduardo Faresin e; de Andrade, Rodrigo Amaral; de Souza, Érica Martinha Silva; Eler, Eduardo Schmidt; da Silva, Maria Nazareth Ferreira; Feldberg, Eliana

2017-01-01

Abstract We investigated the karyotype of 18 didelphid species captured at 13 localities in the Brazilian Amazon, after conventional staining, C-banding, Ag-NOR and fluorescent in situ hybridization (FISH) using the 18S rDNA probe. Variations were found in the X chromosome, heterochromatin distribution and the 18S rDNA sequence. The main variation observed was in the position of the centromere in the X chromosome of Caluromys philander Linnaeus, 1758 and Marmosa murina Linnaeus, 1758. For both species, the X chromosome showed a geographical segregation in the pattern of variation between eastern and western Brazil, with a possible contact area in the central Amazon. C-banding on the X chromosome revealed two patterns for the species of Marmosops Matschie, 1916, apparently without geographic or specific relationships. The nucleolus organizer region (NOR) of all species was confirmed with the 18S rDNA probe, except on the Y chromosome of Monodelphis touan Shaw, 1800. The distribution of this marker varied only in the genus Marmosa Gray, 1821 [M. murina Thomas, 1905 and M. demerarae Thomas, 1905]. Considering that simple NORs are seen as a plesiomorphic character, we conclude that the species Marmosa spp. and Didelphis marsupialis Linnaeus, 1758 evolved independently to the multiple condition. By increasing the sample, using chromosomal banding, and FISH, we verified that marsupials present intra- and interspecific chromosomal variations, which suggests the occurrence of frequent chromosomal rearrangements in the evolution of this group. This observation contrasts with the chromosomal conservatism expected for didelphids. PMID:29114362

Schooling and variation in the COMT gene: the devil is in the details.

PubMed

Campbell, Daniel; Bick, Johanna; Yrigollen, Carolyn M; Lee, Maria; Joseph, Antony; Chang, Joseph T; Grigorenko, Elena L

2013-10-01

Schooling is considered one of the major contributors to the development of intelligence within societies and individuals. Genetic variation might modulate the impact of schooling and explain, at least partially, the presence of individual differences in classrooms. We studied a sample of 1,502 children (mean age = 11.7 years) from Zambia. Approximately 57% of these children were enrolled in school, and the rest were not. To quantify genetic variation, we investigated a number of common polymorphisms in the catechol-O-methyltransferase (COMT) gene that controls the production of the protein thought to account for >60% of the dopamine degradation in the prefrontal cortex. Haplotype analyses generated results ranging from the presence to absence of significant interactions between a number of COMT haplotypes and indicators of schooling (i.e., in- vs. out-of-school and grade completed) in the prediction of nonverbal intelligence, depending on the parameter specification. However, an investigation of the distribution of corresponding p-values suggested that these positive results were false. Convincing evidence that the variation in the COMT gene is associated with individual differences in nonverbal intelligence either directly or through interactions with schooling was not found. p-values produced by the method of testing for haplotype effects employed here may be sensitive to parameter settings, invalid under default settings, and should be checked for validity through simulation. © 2013 The Authors. Journal of Child Psychology and Psychiatry © 2013 Association for Child and Adolescent Mental Health.

Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors

PubMed Central

2013-01-01

Background Rice blast caused by the fungus Magnaporthe oryzae is an important disease in virtually every rice growing region of the world, which leads to significant annual decreases of grain quality and yield. To prevent disease, resistance genes in rice have been cloned and introduced into susceptible cultivars. However, introduced resistance can often be broken within few years of release, often due to mutation of cognate avirulence genes in fungal field populations. Results To better understand the pattern of mutation of M. oryzae field isolates under natural selection forces, we used a next generation sequencing approach to analyze the genomes of two field isolates FJ81278 and HN19311, as well as the transcriptome of FJ81278. By comparing the de novo genome assemblies of the two isolates against the finished reference strain 70–15, we identified extensive polymorphisms including unique genes, SNPs (single nucleotide polymorphism) and indels, structural variations, copy number variations, and loci under strong positive selection. The 1.75 MB of isolate-specific genome content carrying 118 novel genes from FJ81278, and 0.83 MB from HN19311 were also identified. By analyzing secreted proteins carrying polymorphisms, in total 256 candidate virulence effectors were found and 6 were chosen for functional characterization. Conclusions We provide results from genome comparison analysis showing extensive genome variation, and generated a list of M. oryzae candidate virulence effectors for functional characterization. PMID:24341723

Spatial Normalization of Reverse Phase Protein Array Data

PubMed Central

Kaushik, Poorvi; Molinelli, Evan J.; Miller, Martin L.; Wang, Weiqing; Korkut, Anil; Liu, Wenbin; Ju, Zhenlin; Lu, Yiling; Mills, Gordon; Sander, Chris

2014-01-01

Reverse phase protein arrays (RPPA) are an efficient, high-throughput, cost-effective method for the quantification of specific proteins in complex biological samples. The quality of RPPA data may be affected by various sources of error. One of these, spatial variation, is caused by uneven exposure of different parts of an RPPA slide to the reagents used in protein detection. We present a method for the determination and correction of systematic spatial variation in RPPA slides using positive control spots printed on each slide. The method uses a simple bi-linear interpolation technique to obtain a surface representing the spatial variation occurring across the dimensions of a slide. This surface is used to calculate correction factors that can normalize the relative protein concentrations of the samples on each slide. The adoption of the method results in increased agreement between technical and biological replicates of various tumor and cell-line derived samples. Further, in data from a study of the melanoma cell-line SKMEL-133, several slides that had previously been rejected because they had a coefficient of variation (CV) greater than 15%, are rescued by reduction of CV below this threshold in each case. The method is implemented in the R statistical programing language. It is compatible with MicroVigene and SuperCurve, packages commonly used in RPPA data analysis. The method is made available, along with suggestions for implementation, at http://bitbucket.org/rppa_preprocess/rppa_preprocess/src. PMID:25501559

Rapid Detection of Positive Selection in Genes and Genomes Through Variation Clusters

PubMed Central

Wagner, Andreas

2007-01-01

Positive selection in genes and genomes can point to the evolutionary basis for differences among species and among races within a species. The detection of positive selection can also help identify functionally important protein regions and thus guide protein engineering. Many existing tests for positive selection are excessively conservative, vulnerable to artifacts caused by demographic population history, or computationally very intensive. I here propose a simple and rapid test that is complementary to existing tests and that overcomes some of these problems. It relies on the null hypothesis that neutrally evolving DNA regions should show a Poisson distribution of nucleotide substitutions. The test detects significant deviations from this expectation in the form of variation clusters, highly localized groups of amino acid changes in a coding region. In applying this test to several thousand human–chimpanzee gene orthologs, I show that such variation clusters are not generally caused by relaxed selection. They occur in well-defined domains of a protein's tertiary structure and show a large excess of amino acid replacement over silent substitutions. I also identify multiple new human–chimpanzee orthologs subject to positive selection, among them genes that are involved in reproductive functions, immune defense, and the nervous system. PMID:17603100

Statistical study of cold-dense plasma sheet: spatial distribution and semi-annual variation

NASA Astrophysics Data System (ADS)

Shi, Q.; Bai, S.; Tian, A.; Nowada, M.; Degeling, A. W.; Zhou, X. Z.; Zong, Q.; Rae, J.; Fu, S.; Zhang, H.; Pu, Z.; Fazakerley, A. N.

2017-12-01

The cold-dense plasma sheet (CDPS), which plays an important role in the solar wind-magnetosphere coupling during geomagnetic quiet times, is often observed in the magnetosphere, and also be considered as an important particle source for the ring current during geomagnetic storms. However, the long term variation of CDPS occurrences has not been investigated. Using 21 years of Geotail data (1996-2016), we found 677 CDPS events and investigated the long term variation of CDPS occurrence. The spatial distribution of CDPS is also investigated using the in situ observation of Geotail. Since the solar wind entry is easier to occur under stronger northward IMF conditions, we investigated the IMF conditions using 49 years of IMF data (1968-2016) from OMNI data set. We found that both the CDPS occurrence and positive IMF Bz have semi-annual variations, and the variation of positive IMF Bz is consistent with the Russell-McPherron (R-M) effect. Therefore we consider that the semi-annual variation of CDPS occurrence is related to the R-M effect.

Substrate Specificity of Cysteine Proteases Beyond the S2 Pocket: Mutagenesis and Molecular Dynamics Investigation of Fasciola hepatica Cathepsins L

PubMed Central

Corvo, Ileana; Ferraro, Florencia; Merlino, Alicia; Zuberbühler, Kathrin; O'Donoghue, Anthony J.; Pastro, Lucía; Pi-Denis, Natalia; Basika, Tatiana; Roche, Leda; McKerrow, James H.; Craik, Charles S.; Caffrey, Conor R.; Tort, José F.

2018-01-01

Cysteine proteases are widespread in all life kingdoms, being central to diverse physiological processes based on a broad range of substrate specificity. Paralogous Fasciola hepatica cathepsin L proteases are essential to parasite invasion, tissue migration and reproduction. In spite of similarities in their overall sequence and structure, these enzymes often exhibit different substrate specificity. These preferences are principally determined by the amino acid composition of the active site's S2 subsite (pocket) of the enzyme that interacts with the substrate P2 residue (Schetcher and Berger nomenclature). Although secreted FhCL1 accommodates aliphatic residues in the S2 pocket, FhCL2 is also efficient in cleaving proline in that position. To understand these differences, we engineered the FhCL1 S2 subsite at three amino acid positions to render it identical to that present in FhCL2. The substitutions did not produce the expected increment in proline accommodation in P2. Rather, they decreased the enzyme's catalytic efficiency toward synthetic peptides. Nonetheless, a change in the P3 specificity was associated with the mutation of Leu67 to Tyr, a hinge residue between the S2 and S3 subsites that contributes to the accommodation of Gly in S3. Molecular dynamic simulations highlighted changes in the spatial distribution and secondary structure of the S2 and S3 pockets of the mutant FhCL1 enzymes. The reduced affinity and catalytic efficiency of the mutant enzymes may be due to a narrowing of the active site cleft that hinders the accommodation of substrates. Because the variations in the enzymatic activity measured could not be exclusively allocated to those residues lining the active site, other more external positions might modulate enzyme conformation, and, therefore, catalytic activity. PMID:29725596

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

Mittauer, Kathryn E.; Deraniyagala, Rohan; Li, Jonathan G.

Purpose: Recent knowledge on the effects of cardiac toxicity warrants greater precision for left-sided breast radiotherapy. Different breath-hold (BH) maneuvers (abdominal vs thoracic breathing) can lead to chest wall positional variations, even though the patient’s tidal volume remains consistent. This study aims to investigate the feasibility of using optical tracking for real-time quality control of active breathing coordinator (ABC)-assisted deep inspiration BH (DIBH). Methods: An in-house optical tracking system (OTS) was used to monitor ABC-assisted DIBH. The stability and localization accuracy of the OTS were assessed with a ball-bearing phantom. Seven patients with left-sided breast cancer were included. A free-breathingmore » (FB) computed tomography (CT) scan and an ABC-assisted BH CT scan were acquired for each patient. The OTS tracked an infrared (IR) marker affixed over the patient’s xiphoid process to measure the positional variation of each individual BH. Using the BH within which the CT scan was performed as the reference, the authors quantified intra- and interfraction BH variations for each patient. To estimate the dosimetric impact of BH variations, the authors studied the positional correlation between the marker and the left breast using the FB CT and BH CT scans. The positional variations of 860 BHs as measured by the OTS were retrospectively incorporated into the original treatment plans to evaluate their dosimetric impact on breast and cardiac organs [heart and left anterior descending (LAD) artery]. Results: The stability and localization accuracy of the OTS was within 0.2 mm along each direction. The mean intrafraction variation among treatment BHs was less than 2.8 mm in all directions. Up to 12.6 mm anteroposterior undershoot, where the patient’s chest wall displacement of a BH is less than that of a reference BH, was observed with averages of 4.4, 3.6, and 0.1 mm in the anteroposterior, craniocaudal, and mediolateral directions, respectively. A high positional correlation between the marker and the breast was found in the anteroposterior and craniocaudal directions with respective Pearson correlation values of 0.95 and 0.93, but no mediolateral correlation was found. Dosimetric impact of BH variations on breast coverage was negligible. However, the mean heart dose, mean LAD dose, and max LAD dose were estimated to increase from 1.4/7.4/18.6 Gy (planned) to 2.1/15.7/31.0 Gy (delivered), respectively. Conclusions: In ABC-assisted DIBH, large positional variation can occur in some patients, due to their different BH maneuvers. The authors’ study has shown that OTS can be a valuable tool for real-time quality control of ABC-assisted DIBH.« less

Polymorphisms in Inc Proteins and Differential Expression of inc Genes among Chlamydia trachomatis Strains Correlate with Invasiveness and Tropism of Lymphogranuloma Venereum Isolates

PubMed Central

Almeida, Filipe; Borges, Vítor; Ferreira, Rita; Borrego, Maria José; Gomes, João Paulo

2012-01-01

Chlamydia trachomatis is a human bacterial pathogen that multiplies only within an intracellular membrane-bound vacuole, the inclusion. C. trachomatis includes ocular and urogenital strains, usually causing infections restricted to epithelial cells of the conjunctiva and genital mucosa, respectively, and lymphogranuloma venereum (LGV) strains, which can infect macrophages and spread into lymph nodes. However, C. trachomatis genomes display >98% identity at the DNA level. In this work, we studied whether C. trachomatis Inc proteins, which have a bilobed hydrophobic domain that may mediate their insertion in the inclusion membrane, could be a factor determining these different types of infection and tropisms. Analyses of polymorphisms and phylogeny of 48 Inc proteins from 51 strains encompassing the three disease groups showed significant amino acid differences that were mainly due to variations between Inc proteins from LGV and ocular or urogenital isolates. Studies of the evolutionary dynamics of inc genes suggested that 10 of them are likely under positive selection and indicated that most nonsilent mutations are LGV specific. Additionally, real-time quantitative PCR analyses in prototype and clinical strains covering the three disease groups identified three inc genes with LGV-specific expression. We determined the transcriptional start sites of these genes and found LGV-specific nucleotides within their promoters. Thus, subtle variations in the amino acids of a subset of Inc proteins and in the expression of inc genes may contribute to the unique tropism and invasiveness of C. trachomatis LGV strains. PMID:23042990

Solvent effects in time-dependent self-consistent field methods. II. Variational formulations and analytical gradients

DOE PAGES

Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.

2015-08-06

This study describes variational energy expressions and analytical excited state energy gradients for time-dependent self-consistent field methods with polarizable solvent effects. Linear response, vertical excitation, and state-specific solventmodels are examined. Enforcing a variational ground stateenergy expression in the state-specific model is found to reduce it to the vertical excitation model. Variational excited state energy expressions are then provided for the linear response and vertical excitation models and analytical gradients are formulated. Using semiempiricalmodel chemistry, the variational expressions are verified by numerical and analytical differentiation with respect to a static external electric field. Lastly, analytical gradients are further tested by performingmore » microcanonical excited state molecular dynamics with p-nitroaniline.« less

Cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor L.; Brow, Mary Ann D.; Dahlberg, James E.

2007-12-11

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Invasive cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

1999-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Invasive cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

2002-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow; Mary Ann D.; Dahlberg, James E.

2010-11-09

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

2000-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Nucleic acid detection assays

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann; Dahlberg, James E.

2005-04-05

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Developmental Change and Time-Specific Variation in Global and Specific Aspects of Self-Concept in Adolescence and Association with Depressive Symptoms

PubMed Central

Kuzucu, Yasar; Bontempo, Daniel E.; Hofer, Scott M.; Stallings, Michael C.; Piccinin, Andrea M.

2014-01-01

Previous research has demonstrated that adolescents make differential self-evaluations in multiple domains that include physical appearance, academic competence, and peer acceptance. We report growth curve analyses over a seven year period from age 9 to age 16 on the six domains of the Harter Self-Perception Profile for Children. In general, we find little change in self-concept, on average, but do find substantial individual differences in level, rate of change, and time-specific variation in these self- evaluations. The results suggest that sex differences and adoptive status were related to only certain aspects of the participants’ self-concept. Depressive symptoms were found to have significant effects on individual differences in rate of change and on time-specific variation in general self-concept, as well as on some of the specific domains of self-concept. PMID:25143664

Bistability of the lac operon during growth of Escherichia coli on lactose and lactose+glucose.

PubMed

Narang, Atul; Pilyugin, Sergei S

2008-05-01

The lac operon of Escherichia coli can exhibit bistability. Early studies showed that bistability occurs during growth on TMG/succinate and lactose+glucose, but not during growth on lactose. More recently, studies with lacGFP-transfected cells show bistability during growth on TMG/succinate, but not during growth on lactose and lactose+glucose. In the literature, these results are invariably attributed to variations in the destabilizing effect of the positive feedback generated by induction. Specifically, during growth on TMG/succinate, lac induction generates strong positive feedback because the permease stimulates the accumulation of intracellular TMG, which in turn, promotes the synthesis of even more permease. This positive feedback is attenuated during growth on lactose because hydrolysis of intracellular lactose by beta-galactosidase suppresses the stimulatory effect of the permease. It is attenuated even more during growth on lactose + glucose because glucose inhibits the uptake of lactose. But it is clear that the stabilizing effect of dilution also changes dramatically as a function of the medium composition. For instance, during growth on TMG/succinate, the dilution rate of lac permease is proportional to its activity, e, because the specific growth rate is independent of e (it is completely determined by the concentration of succinate). However, during growth on lactose, the dilution rate of the permease is proportional to e2 because the specific growth rate is proportional to the specific lactose uptake rate, which in turn, proportional to e. We show that: (a) This dependence on e2 creates such a strong stabilizing effect that bistability is virtually impossible during growth on lactose, even in the face of the intense positive feedback generated by induction. (b) This stabilizing effect is weakened during growth on lactose+glucose because the specific growth rate on glucose is independent of e, so that the dilution rate once again contains a term that is proportional to e. These results imply that the lac operon is much more prone to bistability if the medium contains carbon sources that cannot be metabolized by the lac enzymes, e.g., succinate during growth on TMG/succinate and glucose during growth on lactose+glucose. We discuss the experimental data in the light of these results.

Components of variation of surface hoof strain with time.

PubMed

Thomason, J J; Bignell, W W; Sears, W

2001-04-01

The relative contribution of a number of random and fixed variables to variation in surface strain magnitudes on the hoof capsule was assessed for healthy feet under normal conditions. Principal strains were recorded in vivo from 5 rosette gauges glued around the circumference of the right forefeet of 4 horses on 4 occasions over a 9 month period. Recordings were made at every other trimming and reshoeing. During each session, gauges were positioned with a template for repeatability. Strains were recorded at the trot and canter (at consistent speeds), for straight motion and turns, and before and after the hoof was trimmed and reset. Up to 30 strides were recorded for each combination of these variables. ANOVAs were performed on midstance strains of 7008 strides to determine the relative contributions to strain variation of individual horse, test day, gait and direction combined as one factor, gauge position on the hoof, trimming, interstride variability and the interactions among these factors. The ANOVA model explained 87% of the variation, of which approximately 84% was due to fixed effects and 16% to random effects. Circumferential position of the gauges and several of the interactions including this term were by far the greatest contributors to strain variation. Differences among gauge positions, individuals and gait + direction are consistent with previous work. This study has added the relative effects, which are small but significant, of trimming on a regular basis and of time. The change in strain magnitudes with trimming was different for each horse, which leads to the possibility that over- and underuse may have to be quantified on an individual basis.