Transgenerational effects of stress exposure on offspring phenotypes in apomictic dandelion.

Directory of Open Access Journals (Sweden)

Koen J F Verhoeven

Full Text Available Heritable epigenetic modulation of gene expression is a candidate mechanism to explain parental environmental effects on offspring phenotypes, but current evidence for environment-induced epigenetic changes that persist in offspring generations is scarce. In apomictic dandelions, exposure to various stresses was previously shown to heritably alter DNA methylation patterns. In this study we explore whether these induced changes are accompanied by heritable effects on offspring phenotypes. We observed effects of parental jasmonic acid treatment on offspring specific leaf area and on offspring interaction with a generalist herbivore; and of parental nutrient stress on offspring root-shoot biomass ratio, tissue P-content and leaf morphology. Some of the effects appeared to enhance offspring ability to cope with the same stresses that their parents experienced. Effects differed between apomictic genotypes and were not always consistently observed between different experiments, especially in the case of parental nutrient stress. While this context-dependency of the effects remains to be further clarified, the total set of results provides evidence for the existence of transgenerational effects in apomictic dandelions. Zebularine treatment affected the within-generation response to nutrient stress, pointing at a role of DNA methylation in phenotypic plasticity to nutrient environments. This study shows that stress exposure in apomictic dandelions can cause transgenerational phenotypic effects, in addition to previously demonstrated transgenerational DNA methylation effects.

Transgenerational effects of stress exposure on offspring phenotypes in apomictic dandelion.

Science.gov (United States)

Verhoeven, Koen J F; van Gurp, Thomas P

2012-01-01

Heritable epigenetic modulation of gene expression is a candidate mechanism to explain parental environmental effects on offspring phenotypes, but current evidence for environment-induced epigenetic changes that persist in offspring generations is scarce. In apomictic dandelions, exposure to various stresses was previously shown to heritably alter DNA methylation patterns. In this study we explore whether these induced changes are accompanied by heritable effects on offspring phenotypes. We observed effects of parental jasmonic acid treatment on offspring specific leaf area and on offspring interaction with a generalist herbivore; and of parental nutrient stress on offspring root-shoot biomass ratio, tissue P-content and leaf morphology. Some of the effects appeared to enhance offspring ability to cope with the same stresses that their parents experienced. Effects differed between apomictic genotypes and were not always consistently observed between different experiments, especially in the case of parental nutrient stress. While this context-dependency of the effects remains to be further clarified, the total set of results provides evidence for the existence of transgenerational effects in apomictic dandelions. Zebularine treatment affected the within-generation response to nutrient stress, pointing at a role of DNA methylation in phenotypic plasticity to nutrient environments. This study shows that stress exposure in apomictic dandelions can cause transgenerational phenotypic effects, in addition to previously demonstrated transgenerational DNA methylation effects.

Present status of the radiative neutron capture mechanisms -nonstatistical effects

International Nuclear Information System (INIS)

Brzosko, J.S.

1976-01-01

The present status of our knowledge about neutron radiative capture mechanisms is described. In the first section there are given a review on mathematical description of the neutron capture cross section and possible sources of correlation effects. The point of lecture is the explanation of connections between the intermediate structures and correlation effects. In one of the sections the explanation of the bump in γ-ray spectra is discussed. The typical experimental results are presented. (author)

Understanding mammalian genetic systems: the challenge of phenotyping in the mouse.

Directory of Open Access Journals (Sweden)

Steve D M Brown

2006-08-01

Full Text Available Understanding mammalian genetic systems is predicated on the determination of the relationship between genetic variation and phenotype. Several international programmes are under way to deliver mutations in every gene in the mouse genome. The challenge for mouse geneticists is to develop approaches that will provide comprehensive phenotype datasets for these mouse mutant libraries. Several factors are critical to success in this endeavour. It will be important to catalogue assay and environment and where possible to adopt standardised procedures for phenotyping tests along with common environmental conditions to ensure comparable datasets of phenotypes. Moreover, the scale of the task underlines the need to invest in technological development improving both the speed and cost of phenotyping platforms. In addition, it will be necessary to develop new informatics standards that capture the phenotype assay as well as other factors, genetic and environmental, that impinge upon phenotype outcome.

Structural phenotyping of stem cell-derived cardiomyocytes.

Science.gov (United States)

Pasqualini, Francesco Silvio; Sheehy, Sean Paul; Agarwal, Ashutosh; Aratyn-Schaus, Yvonne; Parker, Kevin Kit

2015-03-10

Structural phenotyping based on classical image feature detection has been adopted to elucidate the molecular mechanisms behind genetically or pharmacologically induced changes in cell morphology. Here, we developed a set of 11 metrics to capture the increasing sarcomere organization that occurs intracellularly during striated muscle cell development. To test our metrics, we analyzed the localization of the contractile protein α-actinin in a variety of primary and stem-cell derived cardiomyocytes. Further, we combined these metrics with data mining algorithms to unbiasedly score the phenotypic maturity of human-induced pluripotent stem cell-derived cardiomyocytes. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

A Novel Drug-Mouse Phenotypic Similarity Method Detects Molecular Determinants of Drug Effects.

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Jeanette Prinz

2016-09-01

Full Text Available The molecular mechanisms that translate drug treatment into beneficial and unwanted effects are largely unknown. We present here a novel approach to detect gene-drug and gene-side effect associations based on the phenotypic similarity of drugs and single gene perturbations in mice that account for the polypharmacological property of drugs. We scored the phenotypic similarity of human side effect profiles of 1,667 small molecules and biologicals to profiles of phenotypic traits of 5,384 mouse genes. The benchmarking with known relationships revealed a strong enrichment of physical and indirect drug-target connections, causative drug target-side effect links as well as gene-drug links involved in pharmacogenetic associations among phenotypically similar gene-drug pairs. The validation by in vitro assays and the experimental verification of an unknown connection between oxandrolone and prokineticin receptor 2 reinforces the ability of this method to provide new molecular insights underlying drug treatment. Thus, this approach may aid in the proposal of novel and personalized treatments.

Calculation of doublet capture rate for muon capture in deuterium within chiral effective field theory

Czech Academy of Sciences Publication Activity Database

Adam, Jiří; Tater, Miloš; Truhlík, Emil; Epelbaum, E.; Machleidt, R.; Ricci, P.

2012-01-01

Roč. 709, 1-2 (2012), s. 93-100 ISSN 0370-2693 R&D Projects: GA MŠk LC06002; GA ČR GAP203/11/0701 Institutional support: RVO:61389005 Keywords : negative muon capture * deuteron * effective field theory * meson exchange currents Subject RIV: BE - Theoretical Physics Impact factor: 4.569, year: 2012

A bioimage informatics platform for high-throughput embryo phenotyping.

Science.gov (United States)

Brown, James M; Horner, Neil R; Lawson, Thomas N; Fiegel, Tanja; Greenaway, Simon; Morgan, Hugh; Ring, Natalie; Santos, Luis; Sneddon, Duncan; Teboul, Lydia; Vibert, Jennifer; Yaikhom, Gagarine; Westerberg, Henrik; Mallon, Ann-Marie

2018-01-01

High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene-phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to prominence in the field of developmental biology for its ability to capture whole embryo morphology and gene expression, as exemplified by the International Mouse Phenotyping Consortium (IMPC). Large volumes of image data are being acquired by multiple institutions around the world that encompass a range of modalities, proprietary software and metadata. To facilitate robust downstream analysis, images and metadata must be standardized to account for these differences. As an open scientific enterprise, making the data readily accessible is essential so that members of biomedical and clinical research communities can study the images for themselves without the need for highly specialized software or technical expertise. In this article, we present a platform of software tools that facilitate the upload, analysis and dissemination of 3D images for the IMPC. Over 750 reconstructions from 80 embryonic lethal and subviable lines have been captured to date, all of which are openly accessible at mousephenotype.org. Although designed for the IMPC, all software is available under an open-source licence for others to use and develop further. Ongoing developments aim to increase throughput and improve the analysis and dissemination of image data. Furthermore, we aim to ensure that images are searchable so that users can locate relevant images associated with genes, phenotypes or human diseases of interest. © The Author 2016. Published by Oxford University Press.

Dielectrophoretic capture and genetic analysis of single neuroblastoma tumor cells

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Erica L Carpenter

2014-07-01

Full Text Available Our understanding of the diversity of cells that escape the primary tumor and seed micrometastases remains rudimentary, and approaches for studying circulating and disseminated tumor cells have been limited by low throughput and sensitivity, reliance on single parameter sorting, and a focus on enumeration rather than phenotypic and genetic characterization. Here we utilize a highly sensitive microfluidic and dielectrophoretic approach for the isolation and genetic analysis of individual tumor cells. We employed fluorescence labeling to isolate 208 single cells from spiking experiments conducted with 11 cell lines, including 8 neuroblastoma cell lines, and achieved a capture sensitivity of 1 tumor cell per 106 white blood cells. Sample fixation or freezing had no detectable effect on cell capture. Point mutations were accurately detected in the whole genome amplification product of captured single tumor cells but not in negative control white blood cells. We applied this approach to capture 144 single tumor cells from 10 bone marrow samples from patients suffering from neuroblastoma. In this pediatric malignancy, high-risk patients often exhibit wide-spread hematogenous metastasis, but access to primary tumor can be difficult or impossible. Here we used flow-based sorting to pre-enrich samples with tumor involvement below 0.02%. For all patients for whom a mutation in the Anaplastic Lymphoma Kinase gene had already been detected in their primary tumor, the same mutation was detected in single cells from their marrow. These findings demonstrate a novel, non-invasive, and adaptable method for the capture and genetic analysis of single tumor cells from cancer patients.

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

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David Goldman

2007-01-01

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

Functionalized metal organic frameworks for effective capture of radioactive organic iodides

KAUST Repository

Li, Baiyan

2017-06-27

Highly efficient capture of radioactive organic iodides (ROIs) from off-gas mixtures remains a substantial challenge for nuclear waste treatment. Current materials utilized for ROI sequestration suffer from low capacity, high cost (e.g. use of noble metals), and poor recyclability. Recently, we have developed a new strategy to tackle this challenge by functionalizing MOF materials with tertiary amines to create molecular traps for the effective capture and removal of ROIs (e.g. radioactive methyl iodide) from nuclear wastes. To further enhance the uptake capacity and performance of CH3I capture by ROI molecular traps, herein, we carry out a systematic study to investigate the effect of different amine molecules on ROI capture. The results demonstrate a record-high CH3I saturation uptake capacity of 80% for MIL-101-Cr-DMEDA at 150 °C, which is 5.3 times that of Ag0@MOR (15 wt%), a leading adsorbent material for capturing ROIs during nuclear fuel reprocessing. Furthermore, the CH3I decontamination factors (DFs) for MIL-101-Cr-DMEDA are as high as 5000 under simulated reprocessing conditions, largely exceeding that of facility regulatory requirements (DF = 3000). In addition, MIL-101-Cr-DMEDA can be recycled without loss of capacity, illustrating yet another advantage compared to known industrial adsorbents, which are typically of a

Effects of inlet/outlet configurations on the electrostatic capture of airborne nanoparticles and viruses

International Nuclear Information System (INIS)

Jang, Jaesung; Akin, Demir; Bashir, Rashid

2008-01-01

Motivated by capture and detection of airborne biological agents in real time with a cantilever biosensor without introducing the agents into liquids, we present the effects of inlet/outlet configurations of a homemade particle collector on the electrostatic capture of airborne 100 nm diameter nanoparticles under swirling gas flows. This particle collector has three different inlet/outlet configurations: forward inlet/outlet (FO), backward inlet/outlet (BO) and straight inlet/outlet (SO) configurations. We also present the electrostatic capture of Vaccinia viruses using the same particle collector and compare these virus measurements with the nanoparticle cases. The most particles were collected in the FO configuration. The numbers of particles captured in the BO and SO configurations were close within their standard deviations. For all the three configurations tested, the number of particles captured in the center electrode C was much smaller than those captured in the other electrodes at a flow rate of 1.1 l min −1 and an applied potential of 2 kV. Using a commercial CFD code FLUENT, we also simulated the effects of the three inlet/outlet configurations on the particle capture in terms of particle trajectories, velocities and travel times. This simulation was in a good agreement with measurements that the FO configuration is the most favorable to particle capture among the tested configurations at a flow rate of 1.1 l min −1 . The effects of particle diameters on the capture will also be discussed. This collector can be used for real-time monitoring of bioaerosols along with cantilever biosensors

Phenotypic effects of salt and heat stress over three generations in Arabidopsis thaliana.

Directory of Open Access Journals (Sweden)

Léonie Suter

Full Text Available Current and predicted environmental change will force many organisms to adapt to novel conditions, especially sessile organisms such as plants. It is therefore important to better understand how plants react to environmental stress and to what extent genotypes differ in such responses. It has been proposed that adaptation to novel conditions could be facilitated by heritable epigenetic changes induced by environmental stress, independent of genetic variation. Here we assessed phenotypic effects of heat and salt stress within and across three generations using four highly inbred Arabidopsis thaliana genotypes (Col, Cvi, Ler and Sha. Salt stress generally decreased fitness, but genotypes were differently affected, suggesting that susceptibility of A. thaliana to salt stress varies among genotypes. Heat stress at an early rosette stage had less detrimental effects but accelerated flowering in three out of four accessions. Additionally, we found three different modes of transgenerational effects on phenotypes, all harboring the potential of being adaptive: heat stress in previous generations induced faster rosette growth in Sha, both under heat and control conditions, resembling a tracking response, while in Cvi, the phenotypic variance of several traits increased, resembling diversified bet-hedging. Salt stress experienced in earlier generations altered plant architecture of Sha under salt but not control conditions, similar to transgenerational phenotypic plasticity. However, transgenerational phenotypic effects depended on the type of stress as well as on genotype, suggesting that such effects may not be a general response leading to adaptation to novel environmental conditions in A. thaliana.

Towards the Biological Understanding of CTC: Capture Technologies, Definitions and Potential to Create Metastasis

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Ana M.C. Barradas

2013-12-01

Full Text Available Circulating Tumor Cells (CTC are rare cells originated from tumors that travel into the blood stream, extravasate to different organs of which only a small fraction will develop into metastasis. The presence of CTC enumerated with the CellSearch system is associated with a relative short survival and their continued presence after the first cycles of therapy indicates a futile therapy in patients with metastatic carcinomas. Detailed characterization of CTC holds the promise to enable the choice of the optimal therapy for the individual patients during the course of the disease. The phenotype, physical and biological properties are however not well understood making it difficult to assess the merit of recent technological advancements to improve upon the capture of CTC or to evaluate their metastatic potential. Here we will discuss the recent advances in the classification of CTC captured by the CellSearch system, the implications of their features and numbers. Latest capture platforms are reviewed and placed in the light of technology improvements needed to detect CTC. Physical properties, phenotype, viability and proliferative potential and means to assess their proliferation and metastatic capacity will be summarized and placed in the context of the latest CTC capture platforms.

Capturing Thoughts, Capturing Minds?

DEFF Research Database (Denmark)

Nielsen, Janni

2004-01-01

Think Aloud is cost effective, promises access to the user's mind and is the applied usability technique. But 'keep talking' is difficult, besides, the multimodal interface is visual not verbal. Eye-tracking seems to get around the verbalisation problem. It captures the visual focus of attention...

Unconscious Attentional Capture Effect Can be Induced by Perceptual Learning

Directory of Open Access Journals (Sweden)

Zhe Qu

2011-05-01

Full Text Available Previous ERP studies have shown that N2pc serves as an index for salient stimuli that capture attention, even if they are task irrelevant. This study aims to investigate whether nonsalient stimuli can capture attention automatically and unconsciously after perceptual learning. Adult subjects were trained with a visual search task for eight to ten sessions. The training task was to detect whether the target (triangle with one particular direction was present or not. After training, an ERP session was performed, in which subjects were required to detect the presence of either the trained triangle (i.e., the target triangle in the training sessions or an untrained triangle. Results showed that, while the untrained triangle did not elicit an N2pc effect, the trained triangle elicited a significant N2pc effect regardless of whether it was perceived correctly or not, even when it was task irrelevant. Moreover, the N2pc effect for the trained triangle was completely retained 3 months later. These results suggest that, after perceptual learning, previously unsalient stimuli become more salient and can capture attention automatically and unconsciously. Once the facilitating process of the unsalient stimulus has been built up in the brain, it can last for a long time.

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

DEFF Research Database (Denmark)

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

2014-01-01

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

Context-dependent control of attention capture: Evidence from proportion congruent effects.

Science.gov (United States)

Crump, Matthew J C; Milliken, Bruce; Leboe-McGowan, Jason; Leboe-McGowan, Launa; Gao, Xiaoqing

2018-06-01

There are several independent demonstrations that attentional phenomena can be controlled in a context-dependent manner by cues associated with differing attentional control demands. The present set of experiments provide converging evidence that attention-capture phenomena can be modulated in a context-dependent fashion. We determined whether methods from the proportion congruent literature (listwide and item- and context-specific proportion congruent designs) that are known to modulate distractor interference effects in Stroop and flanker tasks are capable of modulating attention capture by salient feature singletons. Across experiments we found evidence that attention capture can be modulated by listwide, item-specific, and context-specific manipulations of proportion congruent. We discuss challenges associated with interpreting results from proportion congruent studies but propose that our findings converge with existing work that has demonstrated context-dependent control of attention capture. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

The problem of latent attentional capture: Easy visual search conceals capture by task-irrelevant abrupt onsets.

Science.gov (United States)

Gaspelin, Nicholas; Ruthruff, Eric; Lien, Mei-Ching

2016-08-01

Researchers are sharply divided regarding whether irrelevant abrupt onsets capture spatial attention. Numerous studies report that they do and a roughly equal number report that they do not. This puzzle has inspired numerous attempts at reconciliation, none gaining general acceptance. The authors propose that abrupt onsets routinely capture attention, but the size of observed capture effects depends critically on how long attention dwells on distractor items which, in turn, depends critically on search difficulty. In a series of spatial cuing experiments, the authors show that irrelevant abrupt onsets produce robust capture effects when visual search is difficult, but not when search is easy. Critically, this effect occurs even when search difficulty varies randomly across trials, preventing any strategic adjustments of the attentional set that could modulate probability of capture by the onset cue. The authors argue that easy visual search provides an insensitive test for stimulus-driven capture by abrupt onsets: even though onsets truly capture attention, the effects of capture can be latent. This observation helps to explain previous failures to find capture by onsets, nearly all of which used an easy visual search. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Effect of Surface Modification and Macrophage Phenotype on Particle Internalization

Energy Technology Data Exchange (ETDEWEB)

Wang, Daniel [Iowa State University; Phan, Ngoc [Iowa State University; Isely, Christopher [Iowa State University; Bruene, Lucas [Iowa State University; Bratlie, Kaitlin M [Ames Laboratory

2014-11-10

Material properties play a key role in the cellular internalization of polymeric particles. In the present study, we have investigated the effects of material characteristics such as water contact angle, zeta potential, melting temperature, and alternative activation of complement on particle internalization for pro-inflammatory, pro-angiogenic, and naïve macrophages by using biopolymers (~600 nm), functionalized with 13 different molecules. Understanding how material parameters influence particle internalization for different macrophage phenotypes is important for targeted delivery to specific cell populations. Here, we demonstrate that material parameters affect the alternative pathway of complement activation as well as particle internalization for different macrophage phenotypes. Here, we show that the quantitative structure–activity relationship method (QSAR) previously used to predict physiochemical properties of materials can be applied to targeting different macrophage phenotypes. These findings demonstrated that targeted drug delivery to macrophages could be achieved by exploiting material parameters.

Phenotype Instance Verification and Evaluation Tool (PIVET): A Scaled Phenotype Evidence Generation Framework Using Web-Based Medical Literature

Science.gov (United States)

Ke, Junyuan; Ho, Joyce C; Ghosh, Joydeep; Wallace, Byron C

2018-01-01

Background Researchers are developing methods to automatically extract clinically relevant and useful patient characteristics from raw healthcare datasets. These characteristics, often capturing essential properties of patients with common medical conditions, are called computational phenotypes. Being generated by automated or semiautomated, data-driven methods, such potential phenotypes need to be validated as clinically meaningful (or not) before they are acceptable for use in decision making. Objective The objective of this study was to present Phenotype Instance Verification and Evaluation Tool (PIVET), a framework that uses co-occurrence analysis on an online corpus of publically available medical journal articles to build clinical relevance evidence sets for user-supplied phenotypes. PIVET adopts a conceptual framework similar to the pioneering prototype tool PheKnow-Cloud that was developed for the phenotype validation task. PIVET completely refactors each part of the PheKnow-Cloud pipeline to deliver vast improvements in speed without sacrificing the quality of the insights PheKnow-Cloud achieved. Methods PIVET leverages indexing in NoSQL databases to efficiently generate evidence sets. Specifically, PIVET uses a succinct representation of the phenotypes that corresponds to the index on the corpus database and an optimized co-occurrence algorithm inspired by the Aho-Corasick algorithm. We compare PIVET’s phenotype representation with PheKnow-Cloud’s by using PheKnow-Cloud’s experimental setup. In PIVET’s framework, we also introduce a statistical model trained on domain expert–verified phenotypes to automatically classify phenotypes as clinically relevant or not. Additionally, we show how the classification model can be used to examine user-supplied phenotypes in an online, rather than batch, manner. Results PIVET maintains the discriminative power of PheKnow-Cloud in terms of identifying clinically relevant phenotypes for the same corpus with

Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis.

Science.gov (United States)

Hao, Xiaoke; Li, Chanxiu; Yan, Jingwen; Yao, Xiaohui; Risacher, Shannon L; Saykin, Andrew J; Shen, Li; Zhang, Daoqiang

2017-07-15

Neuroimaging genetics identifies the relationships between genetic variants (i.e., the single nucleotide polymorphisms) and brain imaging data to reveal the associations from genotypes to phenotypes. So far, most existing machine-learning approaches are widely used to detect the effective associations between genetic variants and brain imaging data at one time-point. However, those associations are based on static phenotypes and ignore the temporal dynamics of the phenotypical changes. The phenotypes across multiple time-points may exhibit temporal patterns that can be used to facilitate the understanding of the degenerative process. In this article, we propose a novel temporally constrained group sparse canonical correlation analysis (TGSCCA) framework to identify genetic associations with longitudinal phenotypic markers. The proposed TGSCCA method is able to capture the temporal changes in brain from longitudinal phenotypes by incorporating the fused penalty, which requires that the differences between two consecutive canonical weight vectors from adjacent time-points should be small. A new efficient optimization algorithm is designed to solve the objective function. Furthermore, we demonstrate the effectiveness of our algorithm on both synthetic and real data (i.e., the Alzheimer's Disease Neuroimaging Initiative cohort, including progressive mild cognitive impairment, stable MCI and Normal Control participants). In comparison with conventional SCCA, our proposed method can achieve strong associations and discover phenotypic biomarkers across multiple time-points to guide disease-progressive interpretation. The Matlab code is available at https://sourceforge.net/projects/ibrain-cn/files/ . dqzhang@nuaa.edu.cn or shenli@iu.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Predicting adaptive phenotypes from multilocus genotypes in Sitka spruce (Picea sitchensis) using random forest.

Science.gov (United States)

Holliday, Jason A; Wang, Tongli; Aitken, Sally

2012-09-01

Climate is the primary driver of the distribution of tree species worldwide, and the potential for adaptive evolution will be an important factor determining the response of forests to anthropogenic climate change. Although association mapping has the potential to improve our understanding of the genomic underpinnings of climatically relevant traits, the utility of adaptive polymorphisms uncovered by such studies would be greatly enhanced by the development of integrated models that account for the phenotypic effects of multiple single-nucleotide polymorphisms (SNPs) and their interactions simultaneously. We previously reported the results of association mapping in the widespread conifer Sitka spruce (Picea sitchensis). In the current study we used the recursive partitioning algorithm 'Random Forest' to identify optimized combinations of SNPs to predict adaptive phenotypes. After adjusting for population structure, we were able to explain 37% and 30% of the phenotypic variation, respectively, in two locally adaptive traits--autumn budset timing and cold hardiness. For each trait, the leading five SNPs captured much of the phenotypic variation. To determine the role of epistasis in shaping these phenotypes, we also used a novel approach to quantify the strength and direction of pairwise interactions between SNPs and found such interactions to be common. Our results demonstrate the power of Random Forest to identify subsets of markers that are most important to climatic adaptation, and suggest that interactions among these loci may be widespread.

A data-driven weighting scheme for multivariate phenotypic endpoints recapitulates zebrafish developmental cascades

Energy Technology Data Exchange (ETDEWEB)

Zhang, Guozhu, E-mail: gzhang6@ncsu.edu [Bioinformatics Research Center, North Carolina State University, Raleigh, NC (United States); Roell, Kyle R., E-mail: krroell@ncsu.edu [Bioinformatics Research Center, North Carolina State University, Raleigh, NC (United States); Truong, Lisa, E-mail: lisa.truong@oregonstate.edu [Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR (United States); Tanguay, Robert L., E-mail: robert.tanguay@oregonstate.edu [Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR (United States); Reif, David M., E-mail: dmreif@ncsu.edu [Bioinformatics Research Center, North Carolina State University, Raleigh, NC (United States); Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC (United States)

2017-01-01

Zebrafish have become a key alternative model for studying health effects of environmental stressors, partly due to their genetic similarity to humans, fast generation time, and the efficiency of generating high-dimensional systematic data. Studies aiming to characterize adverse health effects in zebrafish typically include several phenotypic measurements (endpoints). While there is a solid biomedical basis for capturing a comprehensive set of endpoints, making summary judgments regarding health effects requires thoughtful integration across endpoints. Here, we introduce a Bayesian method to quantify the informativeness of 17 distinct zebrafish endpoints as a data-driven weighting scheme for a multi-endpoint summary measure, called weighted Aggregate Entropy (wAggE). We implement wAggE using high-throughput screening (HTS) data from zebrafish exposed to five concentrations of all 1060 ToxCast chemicals. Our results show that our empirical weighting scheme provides better performance in terms of the Receiver Operating Characteristic (ROC) curve for identifying significant morphological effects and improves robustness over traditional curve-fitting approaches. From a biological perspective, our results suggest that developmental cascade effects triggered by chemical exposure can be recapitulated by analyzing the relationships among endpoints. Thus, wAggE offers a powerful approach for analysis of multivariate phenotypes that can reveal underlying etiological processes. - Highlights: • Introduced a data-driven weighting scheme for multiple phenotypic endpoints. • Weighted Aggregate Entropy (wAggE) implies differential importance of endpoints. • Endpoint relationships reveal developmental cascade effects triggered by exposure. • wAggE is generalizable to multi-endpoint data of different shapes and scales.

CHEMICAL EFFECTS IN BIOLOGICAL SYSTEMS – DATA DICTIONARY (CEBS-DD): A COMPENDIUM OF TERMS FOR THE CAPTURE AND INTEGRATION OF BIOLOGICAL STUDY DESIGN DESCRIPTION, CONVENTIONAL PHENOTYPES AND ‘OMICS’ DATA

Science.gov (United States)

A critical component in the design of the Chemical Effects in Biological Systems (CEBS) Knowledgebase is a strategy to capture toxicogenomics study protocols and the toxicity endpoint data (clinical pathology and histopathology). A Study is generally an experiment carried out du...

Parity non-conserving effects in thermal neutron-deuteron radiative capture

International Nuclear Information System (INIS)

Desplanques, B.

1985-01-01

Predictions of parity non-conserving effects in thermal neutron-deuteron radiative capture are presented. The sensitivity of the results to models of the strong interaction as well as the validity of approximations made in previous calculations are discussed

Phenotype Instance Verification and Evaluation Tool (PIVET): A Scaled Phenotype Evidence Generation Framework Using Web-Based Medical Literature.

Science.gov (United States)

Henderson, Jette; Ke, Junyuan; Ho, Joyce C; Ghosh, Joydeep; Wallace, Byron C

2018-05-04

Researchers are developing methods to automatically extract clinically relevant and useful patient characteristics from raw healthcare datasets. These characteristics, often capturing essential properties of patients with common medical conditions, are called computational phenotypes. Being generated by automated or semiautomated, data-driven methods, such potential phenotypes need to be validated as clinically meaningful (or not) before they are acceptable for use in decision making. The objective of this study was to present Phenotype Instance Verification and Evaluation Tool (PIVET), a framework that uses co-occurrence analysis on an online corpus of publically available medical journal articles to build clinical relevance evidence sets for user-supplied phenotypes. PIVET adopts a conceptual framework similar to the pioneering prototype tool PheKnow-Cloud that was developed for the phenotype validation task. PIVET completely refactors each part of the PheKnow-Cloud pipeline to deliver vast improvements in speed without sacrificing the quality of the insights PheKnow-Cloud achieved. PIVET leverages indexing in NoSQL databases to efficiently generate evidence sets. Specifically, PIVET uses a succinct representation of the phenotypes that corresponds to the index on the corpus database and an optimized co-occurrence algorithm inspired by the Aho-Corasick algorithm. We compare PIVET's phenotype representation with PheKnow-Cloud's by using PheKnow-Cloud's experimental setup. In PIVET's framework, we also introduce a statistical model trained on domain expert-verified phenotypes to automatically classify phenotypes as clinically relevant or not. Additionally, we show how the classification model can be used to examine user-supplied phenotypes in an online, rather than batch, manner. PIVET maintains the discriminative power of PheKnow-Cloud in terms of identifying clinically relevant phenotypes for the same corpus with which PheKnow-Cloud was originally developed, but

The Microphenotron: a robotic miniaturized plant phenotyping platform with diverse applications in chemical biology

KAUST Repository

Burrell, Thomas; Fozard, Susan; Holroyd, Geoff H.; French, Andrew P.; Pound, Michael P.; Bigley, Christopher J.; James Taylor, C.; Forde, Brian G.

2017-01-01

of developing shoots and roots; (c) software to control the sequence of robotic movements and integrate these with the image capture process; (d) purpose-made image analysis software for automated extraction of quantitative phenotypic data. Imaging of each plate

Environment Changes Genetic Effects on Respiratory Conditions and Allergic Phenotypes

DEFF Research Database (Denmark)

Song, Yong; Schwager, Michelle J; Backer, Vibeke

2017-01-01

The prevalence of asthma and allergic diseases is disproportionately distributed among different populations, with an increasing trend observed in Western countries. Here we investigated how the environment affected genotype-phenotype association in a genetically homogeneous, but geographically...... separated population. We evaluated 18 single nucleotide polymorphisms (SNPs) corresponding to 8 genes (ADAM33, ALOX5, LT-α, LTC4S, NOS1, ORMDL3, TBXA2R and TNF-α), the lung function and five respiratory/allergic conditions (ever asthma, bronchitis, rhinitis, dermatitis and atopy) in two populations of Inuit......-phenotype associations relating to bronchitis and allergy susceptibility are dependent on the environment and that environmental factors/lifestyles modify genetic predisposition and change the genetic effects on diseases....

The contribution of color to attention capture effects during search for onset targets.

Science.gov (United States)

Goller, Florian; Ditye, Thomas; Ansorge, Ulrich

2016-04-01

The literature on top-down contingent capture is concerned with the question of what constitutes a search set. Is it restricted to single stimulus properties such as color or onsets, or can such sets be more complex? In nine experiments (N = 140), we tested whether cueing effects during search for onset targets were affected by cue color. According to the classic theory of contingent capture (Folk, Remington, & Johnston, Journal of Experimental Psychology: Human Perception and Performance, 18, 1030-1044, 1992), during search for onset targets, cues capture attention on the basis of a match between the cue's onset and top-down control settings directed to the target onsets. However, such cueing effects were based on cues of a color similar to the target color. Therefore, matches of the cue color to the target color could have contributed to the effects. Indeed, here we found cueing effects when the cues and targets were of the same color, but not when they were of different colors (Exps. 1a, 1b, 4a, and 4b). In addition, same-color cueing effects were stronger than different-color cueing effects (Exps. 2a, 2b, 3a, 3b, and the white-target conditions of Exp. 5). In Experiment 5, we also identified efficient search for only one target color as a critical prerequisite for the differences between cueing by color-similar and -dissimilar onset cues. We conclude with a discussion of the contributions of cue-to-set color matches, deallocation of attention, and intertrial priming to what appear to be top-down contingent-capture effects based on abrupt onsets.

A mathematical model of cancer cells with phenotypic plasticity

Directory of Open Access Journals (Sweden)

Da Zhou

2015-12-01

Full Text Available Purpose: The phenotypic plasticity of cancer cells is recently becoming a cutting-edge research area in cancer, which challenges the cellular hierarchy proposed by the conventional cancer stem cell theory. In this study, we establish a mathematical model for describing the phenotypic plasticity of cancer cells, based on which we try to find some salient features that can characterize the dynamic behavior of the phenotypic plasticity especially in comparison to the hierarchical model of cancer cells. Methods: We model cancer as population dynamics composed of different phenotypes of cancer cells. In this model, not only can cancer cells divide (symmetrically and asymmetrically and die, but they can also convert into other cellular phenotypes. According to the Law of Mass Action, the cellular processes can be captured by a system of ordinary differential equations (ODEs. On one hand, we can analyze the long-term stability of the model by applying qualitative method of ODEs. On the other hand, we are also concerned about the short-term behavior of the model by studying its transient dynamics. Meanwhile, we validate our model to the cell-state dynamics in published experimental data.Results: Our results show that the phenotypic plasticity plays important roles in both stabilizing the distribution of different phenotypic mixture and maintaining the cancer stem cells proportion. In particular, the phenotypic plasticity model shows decided advantages over the hierarchical model in predicting the phenotypic equilibrium and cancer stem cells’ overshoot reported in previous biological experiments in cancer cell lines.Conclusion: Since the validity of the phenotypic plasticity paradigm and the conventional cancer stem cell theory is still debated in experimental biology, it is worthy of theoretically searching for good indicators to distinguish the two models through quantitative methods. According to our study, the phenotypic equilibrium and overshoot

Analysis of mammalian gene function through broad based phenotypic screens across a consortium of mouse clinics

Science.gov (United States)

Adams, David J; Adams, Niels C; Adler, Thure; Aguilar-Pimentel, Antonio; Ali-Hadji, Dalila; Amann, Gregory; André, Philippe; Atkins, Sarah; Auburtin, Aurelie; Ayadi, Abdel; Becker, Julien; Becker, Lore; Bedu, Elodie; Bekeredjian, Raffi; Birling, Marie-Christine; Blake, Andrew; Bottomley, Joanna; Bowl, Mike; Brault, Véronique; Busch, Dirk H; Bussell, James N; Calzada-Wack, Julia; Cater, Heather; Champy, Marie-France; Charles, Philippe; Chevalier, Claire; Chiani, Francesco; Codner, Gemma F; Combe, Roy; Cox, Roger; Dalloneau, Emilie; Dierich, André; Di Fenza, Armida; Doe, Brendan; Duchon, Arnaud; Eickelberg, Oliver; Esapa, Chris T; El Fertak, Lahcen; Feigel, Tanja; Emelyanova, Irina; Estabel, Jeanne; Favor, Jack; Flenniken, Ann; Gambadoro, Alessia; Garrett, Lilian; Gates, Hilary; Gerdin, Anna-Karin; Gkoutos, George; Greenaway, Simon; Glasl, Lisa; Goetz, Patrice; Da Cruz, Isabelle Goncalves; Götz, Alexander; Graw, Jochen; Guimond, Alain; Hans, Wolfgang; Hicks, Geoff; Hölter, Sabine M; Höfler, Heinz; Hancock, John M; Hoehndorf, Robert; Hough, Tertius; Houghton, Richard; Hurt, Anja; Ivandic, Boris; Jacobs, Hughes; Jacquot, Sylvie; Jones, Nora; Karp, Natasha A; Katus, Hugo A; Kitchen, Sharon; Klein-Rodewald, Tanja; Klingenspor, Martin; Klopstock, Thomas; Lalanne, Valerie; Leblanc, Sophie; Lengger, Christoph; le Marchand, Elise; Ludwig, Tonia; Lux, Aline; McKerlie, Colin; Maier, Holger; Mandel, Jean-Louis; Marschall, Susan; Mark, Manuel; Melvin, David G; Meziane, Hamid; Micklich, Kateryna; Mittelhauser, Christophe; Monassier, Laurent; Moulaert, David; Muller, Stéphanie; Naton, Beatrix; Neff, Frauke; Nolan, Patrick M; Nutter, Lauryl MJ; Ollert, Markus; Pavlovic, Guillaume; Pellegata, Natalia S; Peter, Emilie; Petit-Demoulière, Benoit; Pickard, Amanda; Podrini, Christine; Potter, Paul; Pouilly, Laurent; Puk, Oliver; Richardson, David; Rousseau, Stephane; Quintanilla-Fend, Leticia; Quwailid, Mohamed M; Racz, Ildiko; Rathkolb, Birgit; Riet, Fabrice; Rossant, Janet; Roux, Michel; Rozman, Jan; Ryder, Ed; Salisbury, Jennifer; Santos, Luis; Schäble, Karl-Heinz; Schiller, Evelyn; Schrewe, Anja; Schulz, Holger; Steinkamp, Ralf; Simon, Michelle; Stewart, Michelle; Stöger, Claudia; Stöger, Tobias; Sun, Minxuan; Sunter, David; Teboul, Lydia; Tilly, Isabelle; Tocchini-Valentini, Glauco P; Tost, Monica; Treise, Irina; Vasseur, Laurent; Velot, Emilie; Vogt-Weisenhorn, Daniela; Wagner, Christelle; Walling, Alison; Weber, Bruno; Wendling, Olivia; Westerberg, Henrik; Willershäuser, Monja; Wolf, Eckhard; Wolter, Anne; Wood, Joe; Wurst, Wolfgang; Yildirim, Ali Önder; Zeh, Ramona; Zimmer, Andreas; Zimprich, Annemarie

2015-01-01

The function of the majority of genes in the mouse and human genomes remains unknown. The mouse ES cell knockout resource provides a basis for characterisation of relationships between gene and phenotype. The EUMODIC consortium developed and validated robust methodologies for broad-based phenotyping of knockouts through a pipeline comprising 20 disease-orientated platforms. We developed novel statistical methods for pipeline design and data analysis aimed at detecting reproducible phenotypes with high power. We acquired phenotype data from 449 mutant alleles, representing 320 unique genes, of which half had no prior functional annotation. We captured data from over 27,000 mice finding that 83% of the mutant lines are phenodeviant, with 65% demonstrating pleiotropy. Surprisingly, we found significant differences in phenotype annotation according to zygosity. Novel phenotypes were uncovered for many genes with unknown function providing a powerful basis for hypothesis generation and further investigation in diverse systems. PMID:26214591

Nanoroughened adhesion-based capture of circulating tumor cells with heterogeneous expression and metastatic characteristics

International Nuclear Information System (INIS)

Chen, Weiqiang; Allen, Steven G.; Reka, Ajaya Kumar; Qian, Weiyi; Han, Shuo; Zhao, Jianing; Bao, Liwei; Keshamouni, Venkateshwar G.; Merajver, Sofia D.; Fu, Jianping

2016-01-01

Circulating tumor cells (CTCs) have shown prognostic relevance in many cancer types. However, the majority of current CTC capture methods rely on positive selection techniques that require a priori knowledge about the surface protein expression of disseminated CTCs, which are known to be a dynamic population. We developed a microfluidic CTC capture chip that incorporated a nanoroughened glass substrate for capturing CTCs from blood samples. Our CTC capture chip utilized the differential adhesion preference of cancer cells to nanoroughened etched glass surfaces as compared to normal blood cells and thus did not depend on the physical size or surface protein expression of CTCs. The microfluidic CTC capture chip was able to achieve a superior capture yield for both epithelial cell adhesion molecule positive (EpCAM+) and EpCAM- cancer cells in blood samples. Additionally, the microfluidic CTC chip captured CTCs undergoing transforming growth factor beta-induced epithelial-to-mesenchymal transition (TGF-β-induced EMT) with dynamically down-regulated EpCAM expression. In a mouse model of human breast cancer using EpCAM positive and negative cell lines, the number of CTCs captured correlated positively with the size of the primary tumor and was independent of their EpCAM expression. Furthermore, in a syngeneic mouse model of lung cancer using cell lines with differential metastasis capability, CTCs were captured from all mice with detectable primary tumors independent of the cell lines’ metastatic ability. The microfluidic CTC capture chip using a novel nanoroughened glass substrate is broadly applicable to capturing heterogeneous CTC populations of clinical interest independent of their surface marker expression and metastatic propensity. We were able to capture CTCs from a non-metastatic lung cancer model, demonstrating the potential of the chip to collect the entirety of CTC populations including subgroups of distinct biological and phenotypical properties. Further

The relationship between action-effect monitoring and attention capture.

Science.gov (United States)

Kumar, Neeraj; Manjaly, Jaison A; Sunny, Meera Mary

2015-02-01

Many recent findings suggest that stimuli that are perceived to be the consequence of one's own actions are processed with priority. According to the preactivation account of intentional binding, predicted consequences are preactivated and hence receive a temporal advantage in processing. The implications of the preactivation account are important for theories of attention capture, as temporal advantage often translates to attention capture. Hence, action might modulate attention capture by feature singletons. Experiment 1 showed that a motion onset and color change captured attention only when it was preceded by an action. Experiment 2 showed that the capture occurs only with predictable, but not with unpredictable, consequences of action. Experiment 3 showed that even when half the display changed color at display transition, they were all prioritized. The results suggest that action modulates attentional control.

Killing effect of carboranyl uridine on boron neutron capture reaction

International Nuclear Information System (INIS)

Takagaki, M.; Oda, Y.; Zhang, Z.

1994-01-01

This paper deals with the killing effect of carboranyl uridine (CU) on thermal neutron capture reaction in cultured glioma cell line (C6). The tumoricidal effect of CU for boron neutron capture therapy in the cultured cell system is presented. To assess the uptake of CU, the number of germ cells was determined by comparing protein concentrations of C6 cells in vitro with that of intracranially transplanted C6 tumor cells in vivo. To assess tumoricidal effects of CU, human glioma cells (T98G), containing 25 ppm natural boron of CU, were irradiated with various doses of thermal neutrons at a constant fluence rate. The uptake and killing effects of mercaptoboron and boric acid were also investigated as controls. Subcellular boron concentrations confirmed the selective affinity to the nucleic acid synthesis. CU was found to have an affinity to nucleic acid synthesis and to be accumulated into nucleus of tumor cells. The irradiation dose which yielded 37% survival rate in the case of CU and control were 3.78+12E nvt and 5.80+12E nvt, respectively. The killing effect of CU was slightly higher than that of B-SH or BA. The effective way of CU injection should be further studied to obtain the uniform CU uptake in tumor cells. (N.K.)

Super-Resolution of Plant Disease Images for the Acceleration of Image-based Phenotyping and Vigor Diagnosis in Agriculture.

Science.gov (United States)

Yamamoto, Kyosuke; Togami, Takashi; Yamaguchi, Norio

2017-11-06

Unmanned aerial vehicles (UAVs or drones) are a very promising branch of technology, and they have been utilized in agriculture-in cooperation with image processing technologies-for phenotyping and vigor diagnosis. One of the problems in the utilization of UAVs for agricultural purposes is the limitation in flight time. It is necessary to fly at a high altitude to capture the maximum number of plants in the limited time available, but this reduces the spatial resolution of the captured images. In this study, we applied a super-resolution method to the low-resolution images of tomato diseases to recover detailed appearances, such as lesions on plant organs. We also conducted disease classification using high-resolution, low-resolution, and super-resolution images to evaluate the effectiveness of super-resolution methods in disease classification. Our results indicated that the super-resolution method outperformed conventional image scaling methods in spatial resolution enhancement of tomato disease images. The results of disease classification showed that the accuracy attained was also better by a large margin with super-resolution images than with low-resolution images. These results indicated that our approach not only recovered the information lost in low-resolution images, but also exerted a beneficial influence on further image analysis. The proposed approach will accelerate image-based phenotyping and vigor diagnosis in the field, because it not only saves time to capture images of a crop in a cultivation field but also secures the accuracy of these images for further analysis.

Transgenerational effects of stress exposure on offspring phenotypes in apomictic dandelion

NARCIS (Netherlands)

Verhoeven, K.J.F.; Van Gurp, T.P.

2012-01-01

Heritable epigenetic modulation of gene expression is a candidate mechanism to explain parental environmental effects on offspring phenotypes, but current evidence for environment-induced epigenetic changes that persist in offspring generations is scarce. In apomictic dandelions, exposure to various

Transgenerational Effects of Stress Exposure on Offspring Phenotypes in Apomictic Dandelion

NARCIS (Netherlands)

Verhoeven, K.J.F.; Gurp, van T.P.

2012-01-01

Heritable epigenetic modulation of gene expression is a candidate mechanism to explain parental environmental effects on offspring phenotypes, but current evidence for environment-induced epigenetic changes that persist in offspring generations is scarce. In apomictic dandelions, exposure to various

Frequency of the cancer-resistant phenotype in SR/CR mice and the effect of litter seriation

DEFF Research Database (Denmark)

Koch, Janne; Boschian, Anna; Hau, Jann

2008-01-01

. The frequency of the SR/CR phenotype in the present study was 30% for the BALB/c strain and 22% for the C57BL/6 strain in the first litters, but the overall frequency was 8% for both strains. A frequency of about 30% was reported in the original US colony. A litter seriation effect on the frequency of the SR....../CR phenotype was recorded. The phenotype frequency in the first-born litters was similar to that recorded in the founder colony in the US. There was no significant difference in the frequency of the SR/CR phenotype between the two genders, but the overall frequency of the SR/CR phenotype was significantly...

A Pipeline for 3D Digital Optical Phenotyping Plant Root System Architecture

Science.gov (United States)

Davis, T. W.; Shaw, N. M.; Schneider, D. J.; Shaff, J. E.; Larson, B. G.; Craft, E. J.; Liu, Z.; Kochian, L. V.; Piñeros, M. A.

2017-12-01

This work presents a new pipeline for digital optical phenotyping the root system architecture of agricultural crops. The pipeline begins with a 3D root-system imaging apparatus for hydroponically grown crop lines of interest. The apparatus acts as a self-containing dark room, which includes an imaging tank, motorized rotating bearing and digital camera. The pipeline continues with the Plant Root Imaging and Data Acquisition (PRIDA) software, which is responsible for image capturing and storage. Once root images have been captured, image post-processing is performed using the Plant Root Imaging Analysis (PRIA) command-line tool, which extracts root pixels from color images. Following the pre-processing binarization of digital root images, 3D trait characterization is performed using the next-generation RootReader3D software. RootReader3D measures global root system architecture traits, such as total root system volume and length, total number of roots, and maximum rooting depth and width. While designed to work together, the four stages of the phenotyping pipeline are modular and stand-alone, which provides flexibility and adaptability for various research endeavors.

Holistic and component plant phenotyping using temporal image sequence.

Science.gov (United States)

Das Choudhury, Sruti; Bashyam, Srinidhi; Qiu, Yumou; Samal, Ashok; Awada, Tala

2018-01-01

Image-based plant phenotyping facilitates the extraction of traits noninvasively by analyzing large number of plants in a relatively short period of time. It has the potential to compute advanced phenotypes by considering the whole plant as a single object (holistic phenotypes) or as individual components, i.e., leaves and the stem (component phenotypes), to investigate the biophysical characteristics of the plants. The emergence timing, total number of leaves present at any point of time and the growth of individual leaves during vegetative stage life cycle of the maize plants are significant phenotypic expressions that best contribute to assess the plant vigor. However, image-based automated solution to this novel problem is yet to be explored. A set of new holistic and component phenotypes are introduced in this paper. To compute the component phenotypes, it is essential to detect the individual leaves and the stem. Thus, the paper introduces a novel method to reliably detect the leaves and the stem of the maize plants by analyzing 2-dimensional visible light image sequences captured from the side using a graph based approach. The total number of leaves are counted and the length of each leaf is measured for all images in the sequence to monitor leaf growth. To evaluate the performance of the proposed algorithm, we introduce University of Nebraska-Lincoln Component Plant Phenotyping Dataset (UNL-CPPD) and provide ground truth to facilitate new algorithm development and uniform comparison. The temporal variation of the component phenotypes regulated by genotypes and environment (i.e., greenhouse) are experimentally demonstrated for the maize plants on UNL-CPPD. Statistical models are applied to analyze the greenhouse environment impact and demonstrate the genetic regulation of the temporal variation of the holistic phenotypes on the public dataset called Panicoid Phenomap-1. The central contribution of the paper is a novel computer vision based algorithm for

Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics.

Science.gov (United States)

de Angelis, Martin Hrabě; Nicholson, George; Selloum, Mohammed; White, Jacqui; Morgan, Hugh; Ramirez-Solis, Ramiro; Sorg, Tania; Wells, Sara; Fuchs, Helmut; Fray, Martin; Adams, David J; Adams, Niels C; Adler, Thure; Aguilar-Pimentel, Antonio; Ali-Hadji, Dalila; Amann, Gregory; André, Philippe; Atkins, Sarah; Auburtin, Aurelie; Ayadi, Abdel; Becker, Julien; Becker, Lore; Bedu, Elodie; Bekeredjian, Raffi; Birling, Marie-Christine; Blake, Andrew; Bottomley, Joanna; Bowl, Mike; Brault, Véronique; Busch, Dirk H; Bussell, James N; Calzada-Wack, Julia; Cater, Heather; Champy, Marie-France; Charles, Philippe; Chevalier, Claire; Chiani, Francesco; Codner, Gemma F; Combe, Roy; Cox, Roger; Dalloneau, Emilie; Dierich, André; Di Fenza, Armida; Doe, Brendan; Duchon, Arnaud; Eickelberg, Oliver; Esapa, Chris T; El Fertak, Lahcen; Feigel, Tanja; Emelyanova, Irina; Estabel, Jeanne; Favor, Jack; Flenniken, Ann; Gambadoro, Alessia; Garrett, Lilian; Gates, Hilary; Gerdin, Anna-Karin; Gkoutos, George; Greenaway, Simon; Glasl, Lisa; Goetz, Patrice; Da Cruz, Isabelle Goncalves; Götz, Alexander; Graw, Jochen; Guimond, Alain; Hans, Wolfgang; Hicks, Geoff; Hölter, Sabine M; Höfler, Heinz; Hancock, John M; Hoehndorf, Robert; Hough, Tertius; Houghton, Richard; Hurt, Anja; Ivandic, Boris; Jacobs, Hughes; Jacquot, Sylvie; Jones, Nora; Karp, Natasha A; Katus, Hugo A; Kitchen, Sharon; Klein-Rodewald, Tanja; Klingenspor, Martin; Klopstock, Thomas; Lalanne, Valerie; Leblanc, Sophie; Lengger, Christoph; le Marchand, Elise; Ludwig, Tonia; Lux, Aline; McKerlie, Colin; Maier, Holger; Mandel, Jean-Louis; Marschall, Susan; Mark, Manuel; Melvin, David G; Meziane, Hamid; Micklich, Kateryna; Mittelhauser, Christophe; Monassier, Laurent; Moulaert, David; Muller, Stéphanie; Naton, Beatrix; Neff, Frauke; Nolan, Patrick M; Nutter, Lauryl Mj; Ollert, Markus; Pavlovic, Guillaume; Pellegata, Natalia S; Peter, Emilie; Petit-Demoulière, Benoit; Pickard, Amanda; Podrini, Christine; Potter, Paul; Pouilly, Laurent; Puk, Oliver; Richardson, David; Rousseau, Stephane; Quintanilla-Fend, Leticia; Quwailid, Mohamed M; Racz, Ildiko; Rathkolb, Birgit; Riet, Fabrice; Rossant, Janet; Roux, Michel; Rozman, Jan; Ryder, Ed; Salisbury, Jennifer; Santos, Luis; Schäble, Karl-Heinz; Schiller, Evelyn; Schrewe, Anja; Schulz, Holger; Steinkamp, Ralf; Simon, Michelle; Stewart, Michelle; Stöger, Claudia; Stöger, Tobias; Sun, Minxuan; Sunter, David; Teboul, Lydia; Tilly, Isabelle; Tocchini-Valentini, Glauco P; Tost, Monica; Treise, Irina; Vasseur, Laurent; Velot, Emilie; Vogt-Weisenhorn, Daniela; Wagner, Christelle; Walling, Alison; Weber, Bruno; Wendling, Olivia; Westerberg, Henrik; Willershäuser, Monja; Wolf, Eckhard; Wolter, Anne; Wood, Joe; Wurst, Wolfgang; Yildirim, Ali Önder; Zeh, Ramona; Zimmer, Andreas; Zimprich, Annemarie; Holmes, Chris; Steel, Karen P; Herault, Yann; Gailus-Durner, Valérie; Mallon, Ann-Marie; Brown, Steve Dm

2015-09-01

The function of the majority of genes in the mouse and human genomes remains unknown. The mouse embryonic stem cell knockout resource provides a basis for the characterization of relationships between genes and phenotypes. The EUMODIC consortium developed and validated robust methodologies for the broad-based phenotyping of knockouts through a pipeline comprising 20 disease-oriented platforms. We developed new statistical methods for pipeline design and data analysis aimed at detecting reproducible phenotypes with high power. We acquired phenotype data from 449 mutant alleles, representing 320 unique genes, of which half had no previous functional annotation. We captured data from over 27,000 mice, finding that 83% of the mutant lines are phenodeviant, with 65% demonstrating pleiotropy. Surprisingly, we found significant differences in phenotype annotation according to zygosity. New phenotypes were uncovered for many genes with previously unknown function, providing a powerful basis for hypothesis generation and further investigation in diverse systems.

Computer vision and machine learning for robust phenotyping in genome-wide studies.

Science.gov (United States)

Zhang, Jiaoping; Naik, Hsiang Sing; Assefa, Teshale; Sarkar, Soumik; Reddy, R V Chowda; Singh, Arti; Ganapathysubramanian, Baskar; Singh, Asheesh K

2017-03-08

Traditional evaluation of crop biotic and abiotic stresses are time-consuming and labor-intensive limiting the ability to dissect the genetic basis of quantitative traits. A machine learning (ML)-enabled image-phenotyping pipeline for the genetic studies of abiotic stress iron deficiency chlorosis (IDC) of soybean is reported. IDC classification and severity for an association panel of 461 diverse plant-introduction accessions was evaluated using an end-to-end phenotyping workflow. The workflow consisted of a multi-stage procedure including: (1) optimized protocols for consistent image capture across plant canopies, (2) canopy identification and registration from cluttered backgrounds, (3) extraction of domain expert informed features from the processed images to accurately represent IDC expression, and (4) supervised ML-based classifiers that linked the automatically extracted features with expert-rating equivalent IDC scores. ML-generated phenotypic data were subsequently utilized for the genome-wide association study and genomic prediction. The results illustrate the reliability and advantage of ML-enabled image-phenotyping pipeline by identifying previously reported locus and a novel locus harboring a gene homolog involved in iron acquisition. This study demonstrates a promising path for integrating the phenotyping pipeline into genomic prediction, and provides a systematic framework enabling robust and quicker phenotyping through ground-based systems.

ANISOTROPY EFFECTS IN ELECTRON-CAPTURE BY O6+ FROM ALIGNED NA-ASTERISK(3P)

NARCIS (Netherlands)

SCHLATMANN, AR; WIERSEMA, WP; HOEKSTRA, R; MORGENSTERN, R; OLSON, RE; PASCALE, J

1994-01-01

We report results of one electron capture by highly charged ions colliding with laser excited aligned Na*(3p). The 0 vi(10-->8) photon emission cross section after electron capture by the O6+ projectile is measured in the collision energy range 2-8 keV/amu. Effects of the Na*(3p) orbital alignment

Dynamic plasma screening effects on electron capture process in hydrogenic ion fully stripped ion collisions in dense plasmas

International Nuclear Information System (INIS)

Jung, Y.

1997-01-01

In dense plasmas, dynamic plasma screening effects are investigated on electron capture from hydrogenic ions by past fully stripped ions. The classical Bohr Lindhard model has been applied to obtain the electron capture probability. The interaction potential in dense plasmas is represented in terms of the longitudinal dielectric function. The classical straight-line trajectory approximation is applied to the motion of the projectile ion in order to visualize the electron capture probability as a function of the impact parameter, projectile energy, and plasma parameters. The electron capture probability including the dynamic plasma screening effect is always greater than that including the static plasma screening effect. When the projectile velocity is smaller than the electron thermal velocity, the dynamic polarization screening effect becomes the static plasma screening effect. When the projectile velocity is greater than the plasma electron thermal velocity, the interaction potential is almost unshielded. The difference between the dynamic and static plasma screening effects is more significant for low energy projectiles. It is found that the static screening formula obtained by the Debye Hueckel model overestimates the plasma screening effects on the electron capture processes in dense plasmas. copyright 1997 American Institute of Physics

A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks

Directory of Open Access Journals (Sweden)

Xuezhong Zhou

2018-05-01

Full Text Available The International Classification of Diseases (ICD relies on clinical features and lags behind the current understanding of the molecular specificity of disease pathobiology, necessitating approaches that incorporate growing biomedical data for classifying diseases to meet the needs of precision medicine. Our analysis revealed that the heterogeneous molecular diversity of disease chapters and the blurred boundary between disease categories in ICD should be further investigated. Here, we propose a new classification of diseases (NCD by developing an algorithm that predicts the additional categories of a disease by integrating multiple networks consisting of disease phenotypes and their molecular profiles. With statistical validations from phenotype-genotype associations and interactome networks, we demonstrate that NCD improves disease specificity owing to its overlapping categories and polyhierarchical structure. Furthermore, NCD captures the molecular diversity of diseases and defines clearer boundaries in terms of both phenotypic similarity and molecular associations, establishing a rational strategy to reform disease taxonomy. Keywords: Disease taxonomy, Network medicine, Disease phenotypes, Molecular profiles, Precision medicine

Effects of capturing and collaring on polar bears: findings from long-term research on the southern Beaufort Sea population

Science.gov (United States)

Rode, Karyn D.; Pagano, Anthony M.; Bromaghin, Jeffrey F.; Atwood, Todd C.; Durner, George M.; Simac, Kristin S.; Amstrup, Steven C.

2014-01-01

Context: The potential for research methods to affect wildlife is an increasing concern among both scientists and the public. This topic has a particular urgency for polar bears because additional research is needed to monitor and understand population responses to rapid loss of sea ice habitat.Aims: This study used data collected from polar bears sampled in the Alaska portion of the southern Beaufort Sea to investigate the potential for capture to adversely affect behaviour and vital rates. We evaluated the extent to which capture, collaring and handling may influence activity and movement days to weeks post-capture, and body mass, body condition, reproduction and survival over 6 months or more.Methods: We compared post-capture activity and movement rates, and relationships between prior capture history and body mass, body condition and reproductive success. We also summarised data on capture-related mortality.Key results: Individual-based estimates of activity and movement rates reached near-normal levels within 2–3 days and fully normal levels within 5 days post-capture. Models of activity and movement rates among all bears had poor fit, but suggested potential for prolonged, lower-level rate reductions. Repeated captures was not related to negative effects on body condition, reproduction or cub growth or survival. Capture-related mortality was substantially reduced after 1986, when immobilisation drugs were changed, with only 3 mortalities in 2517 captures from 1987–2013.Conclusions: Polar bears in the southern Beaufort Sea exhibited the greatest reductions in activity and movement rates 3.5 days post-capture. These shorter-term, post-capture effects do not appear to have translated into any long-term effects on body condition, reproduction, or cub survival. Additionally, collaring had no effect on polar bear recovery rates, body condition, reproduction or cub survival.Implications: This study provides empirical evidence that current capture

Protecting embryos from stress: Corticosterone effects and the corticosterone response to capture and confinement during pregnancy in a live-bearing lizard (Hoplodactylus maculatus)

Science.gov (United States)

Cree, A.; Tyrrell, C.L.; Preest, M.R.; Thorburn, D.; Guillette, L.J.

2003-01-01

Hormones in the embryonic environment, including those of the hypothalamo-pituitary-adrenal (HPA) axis, have profound effects on development in eutherian mammals. However, little is known about their effects in reptiles that have independently evolved viviparity. We investigated whether exogenous corticosterone affected embryonic development in the viviparous gecko Hoplodactylus maculatus, and whether pregnant geckos have a corticosterone response to capture and confinement that is suppressed relative to that in non-pregnant (vitellogenic) females and males. Corticosterone implants (5 mg, slow-release) administered to females in mid-pregnancy caused a large elevation of corticosterone in maternal plasma (P<0.001), probable reductions in embryonic growth and development (P=0.069-0.073), developmental abnormalities and eventual abortions. Cool temperature produced similar reductions in embryonic growth and development (P???0.036 cf. warm controls), but pregnancies were eventually successful. Despite the potentially harmful effects of elevated plasma corticosterone, pregnant females did not suppress their corticosterone response to capture and confinement relative to vitellogenic females, and both groups of females had higher responses than males. Future research should address whether lower maternal doses of corticosterone produce non-lethal effects on development that could contribute to phenotypic plasticity. Corticosterone implants also led to increased basking in pregnant females (P<0.001), and basal corticosterone in wild geckos (independent of reproductive condition) was positively correlated with body temperature (P<0.001). Interactions between temperature and corticosterone may have broad significance to other terrestrial ectotherms, and body temperature should be considered as a variable influencing plasma corticosterone concentrations in all future studies on reptiles. ?? 2003 Elsevier Inc. All rights reserved.

Genetic effects of decay by electron capture of radionuclides in yeasts cell

International Nuclear Information System (INIS)

Gracheva, L.M.; Korolev, V.G.

1984-01-01

Regularities of genetic effect on the yeast cell Saccharomyces cerevisiae, incorporated radionuclides decaying according to the scheme of k-capture- 7 Be, 54 Mn, 85 Sr are studied. It is known that this type of decay models the ionization of internal electron shells of atoms which is most probable when a cell is affected by external ionizing radiation. It is shown that the decay of radionuclides connecting with a DNA molecule in a cell according to the scheme of D-capture brings about a strong lethal effect. The relative mutagenic efficiency is much lower than that for gamma-radiation and many radionuclides decaying according to the scheme of B-decay. In the mutation spectrum induced by these radionuclides the increase in the number of mutations of the reading frame shift type is observed

Does imminent threat capture and hold attention?

Science.gov (United States)

Koster, Ernst H W; Crombez, Geert; Van Damme, Stefaan; Verschuere, Bruno; De Houwer, Jan

2004-09-01

According to models of attention and emotion, threat captures and holds attention. In behavioral tasks, robust evidence has been found for attentional holding but not for attentional capture by threat. An important explanation for the absence of attentional capture effects is that the visual stimuli used posed no genuine threat. The present study investigated whether visual cues that signal an aversive white noise can elicit attentional capture and holding effects. Cues presented in an attentional task were simultaneously provided with a threat value through an aversive conditioning procedure. Response latencies showed that threatening cues captured and held attention. These results support recent views on attention to threat, proposing that imminent threat captures attention in everyone. (c) 2004 APA, all rights reserved

Super-Resolution of Plant Disease Images for the Acceleration of Image-based Phenotyping and Vigor Diagnosis in Agriculture

Directory of Open Access Journals (Sweden)

Kyosuke Yamamoto

2017-11-01

Full Text Available Unmanned aerial vehicles (UAVs or drones are a very promising branch of technology, and they have been utilized in agriculture—in cooperation with image processing technologies—for phenotyping and vigor diagnosis. One of the problems in the utilization of UAVs for agricultural purposes is the limitation in flight time. It is necessary to fly at a high altitude to capture the maximum number of plants in the limited time available, but this reduces the spatial resolution of the captured images. In this study, we applied a super-resolution method to the low-resolution images of tomato diseases to recover detailed appearances, such as lesions on plant organs. We also conducted disease classification using high-resolution, low-resolution, and super-resolution images to evaluate the effectiveness of super-resolution methods in disease classification. Our results indicated that the super-resolution method outperformed conventional image scaling methods in spatial resolution enhancement of tomato disease images. The results of disease classification showed that the accuracy attained was also better by a large margin with super-resolution images than with low-resolution images. These results indicated that our approach not only recovered the information lost in low-resolution images, but also exerted a beneficial influence on further image analysis. The proposed approach will accelerate image-based phenotyping and vigor diagnosis in the field, because it not only saves time to capture images of a crop in a cultivation field but also secures the accuracy of these images for further analysis.

Effect of phenotype on health care costs in Crohn's disease: A European study using the Montreal classification.

Science.gov (United States)

Odes, Selwyn; Vardi, Hillel; Friger, Michael; Wolters, Frank; Hoie, Ole; Moum, Bjørn; Bernklev, Tomm; Yona, Hagit; Russel, Maurice; Munkholm, Pia; Langholz, Ebbe; Riis, Lene; Politi, Patrizia; Bondini, Paolo; Tsianos, Epameinondas; Katsanos, Kostas; Clofent, Juan; Vermeire, Severine; Freitas, João; Mouzas, Iannis; Limonard, Charles; O'Morain, Colm; Monteiro, Estela; Fornaciari, Giovanni; Vatn, Morten; Stockbrugger, Reinhold

2007-12-01

Crohn's disease (CD) is a chronic inflammation of the gastrointestinal tract associated with life-long high health care costs. We aimed to determine the effect of disease phenotype on cost. Clinical and economic data of a community-based CD cohort with 10-year follow-up were analyzed retrospectively in relation to Montreal classification phenotypes. In 418 patients, mean total costs of health care for the behavior phenotypes were: nonstricturing-nonpenetrating 1690, stricturing 2081, penetrating 3133 and penetrating-with-perianal-fistula 3356 €/patient-phenotype-year (P<0.001), and mean costs of surgical hospitalization 215, 751, 1293 and 1275 €/patient-phenotype-year respectively (P<0.001). Penetrating-with-perianal-fistula patients incurred significantly greater expenses than penetrating patients for total care, diagnosis and drugs, but not surgical hospitalization. Total costs were similar in the location phenotypes: ileum 1893, colon 1748, ileo-colonic 2010 and upper gastrointestinal tract 1758 €/patient-phenotype-year, but surgical hospitalization costs differed significantly, 558, 209, 492 and 542 €/patient-phenotype-year respectively (P<0.001). By multivariate analysis, the behavior phenotype significantly impacted total, medical and surgical hospitalization costs, whereas the location phenotype affected only surgical costs. Younger age at diagnosis predicted greater surgical expenses. Behavior is the dominant phenotype driving health care cost. Use of the Montreal classification permits detection of cost differences caused by perianal fistula.

IGF-1 Has Plaque-Stabilizing Effects in Atherosclerosis by Altering Vascular Smooth Muscle Cell Phenotype

Science.gov (United States)

von der Thüsen, Jan H.; Borensztajn, Keren S.; Moimas, Silvia; van Heiningen, Sandra; Teeling, Peter; van Berkel, Theo J.C.; Biessen, Erik A.L.

2011-01-01

Insulin-like growth factor-1 (IGF-1) signaling is important for the maintenance of plaque stability in atherosclerosis due to its effects on vascular smooth muscle cell (vSMC) phenotype. To investigate this hypothesis, we studied the effects of the highly inflammatory milieu of the atherosclerotic plaque on IGF-1 signaling and stability-related phenotypic parameters of murine vSMCs in vitro, and the effects of IGF-1 supplementation on plaque phenotype in an atherosclerotic mouse model. M1-polarized, macrophage-conditioned medium inhibited IGF-1 signaling by ablating IGF-1 and increasing IGF-binding protein 3, increased vSMC apoptosis, and decreased proliferation. Expression of α-actin and col3a1 genes was strongly attenuated by macrophage-conditioned medium, whereas expression of matrix-degrading enzymes was increased. Importantly, all of these effects could be corrected by supplementation with IGF-1. In vivo, treatment with the stable IGF-1 analog Long R3 IGF-1 in apolipoprotein E knockout mice reduced stenosis and core size, and doubled cap/core ratio in early atherosclerosis. In advanced plaques, Long R3 IGF-1 increased the vSMC content of the plaque by more than twofold and significantly reduced the rate of intraplaque hemorrhage. We believe that IGF-1 in atherosclerotic plaques may have a role in preventing plaque instability, not only by modulating smooth muscle cell turnover, but also by altering smooth muscle cell phenotype. PMID:21281823

Multilevel effect in uranium-238 and thorium-232 effective neutron capture resonance integrals

International Nuclear Information System (INIS)

Tellier, H.

1981-01-01

Until now, there has been a discrepancy between the computed and the measured values of the /sup 238/U effective capture integral. Recently, several new measurements of the resonance parameters were carried out and the use of a multilevel formalism was suggested to compute the /sup 238/U cross sections. This paper shows that the simultaneous use of recent parameters and the Reich-Moore formalism explain the discrepancy. 31 refs

Candidate gene resequencing to identify rare, pedigree-specific variants influencing healthy aging phenotypes in the long life family study

DEFF Research Database (Denmark)

Druley, Todd E; Wang, Lihua; Lin, Shiow J

2016-01-01

from six pedigrees. OBFC1 (chromosome 10) is involved in telomere maintenance, and falls within a linkage peak recently reported from an analysis of telomere length in LLFS families. Two different algorithms for single gene associations identified three genes with an enrichment of variation......BACKGROUND: The Long Life Family Study (LLFS) is an international study to identify the genetic components of various healthy aging phenotypes. We hypothesized that pedigree-specific rare variants at longevity-associated genes could have a similar functional impact on healthy phenotypes. METHODS......: We performed custom hybridization capture sequencing to identify the functional variants in 464 candidate genes for longevity or the major diseases of aging in 615 pedigrees (4,953 individuals) from the LLFS, using a multiplexed, custom hybridization capture. Variants were analyzed individually...

Quantum effects on the formation of negative hydrogen ion by polarization electron capture in partially ionized dense hydrogen plasmas

International Nuclear Information System (INIS)

Jung, Young-Dae; Kato, Daiji

2009-05-01

The quantum effects on the formation of the negative hydrogen ion (H - ) by the polarization electron capture process are investigated in partially ionized dense hydrogen plasmas. It is shown that the quantum effect strongly suppresses the electron capture radius as well as the cross section for the formation of the negative hydrogen ion. In addition, it has been found that the electron capture position is receded from the center of the projectile with decreasing the quantum effect of the plasma. (author)

The effect of chemically modified alginates on macrophage phenotype and biomolecule transport.

Science.gov (United States)

Bygd, Hannah C; Bratlie, Kaitlin M

2016-07-01

Macrophage (MΦ) reprogramming has received significant attention in applications such as cancer therapeutics and tissue engineering where the host immune response to biomaterials is crucial in determining the success or failure of an implanted device. Polymeric systems can potentially be used to redirect infiltrating M1 MΦs toward a proangiogenic phenotype. This work exploits the concept of MΦ reprogramming in the engineering of materials for improving the longevity of tissue engineering scaffolds. We have investigated the effect of 13 different chemical modifications of alginate on MΦ phenotype. Markers of the M1 response-tumor necrosis factor-α (TNF-α) and inducible nitric oxide synthase-and the M2 response-arginase-were measured and used to determine the ability of the materials to alter MΦ phenotype. It was found that some modifications were able to reduce the pro-inflammatory response of M1 MΦs, others appeared to amplify the M2 phenotype, and the results for two materials suggested they were able to reprogram a MΦ population from M1 to M2. These findings were supplemented by studies done to examine the permselectivity of the materials. Diffusion of TNF-α was completely prevented through some of these materials, while up to 84% was found to diffuse through others. The diffusion of insulin through the materials was statistically consistent. These results suggest that the modification of these materials might alter mass transport in beneficial ways. The ability to control polarization of MΦ phenotypes with immunoprotective materials has the potential to augment the success of tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1707-1719, 2016. © 2016 Wiley Periodicals, Inc.

Imaging techniques for visualizing and phenotyping congenital heart defects in murine models.

Science.gov (United States)

Liu, Xiaoqin; Tobita, Kimimasa; Francis, Richard J B; Lo, Cecilia W

2013-06-01

Mouse model is ideal for investigating the genetic and developmental etiology of congenital heart disease. However, cardiovascular phenotyping for the precise diagnosis of structural heart defects in mice remain challenging. With rapid advances in imaging techniques, there are now high throughput phenotyping tools available for the diagnosis of structural heart defects. In this review, we discuss the efficacy of four different imaging modalities for congenital heart disease diagnosis in fetal/neonatal mice, including noninvasive fetal echocardiography, micro-computed tomography (micro-CT), micro-magnetic resonance imaging (micro-MRI), and episcopic fluorescence image capture (EFIC) histopathology. The experience we have gained in the use of these imaging modalities in a large-scale mouse mutagenesis screen have validated their efficacy for congenital heart defect diagnosis in the tiny hearts of fetal and newborn mice. These cutting edge phenotyping tools will be invaluable for furthering our understanding of the developmental etiology of congenital heart disease. Copyright © 2013 Wiley Periodicals, Inc.

Using Machine Learning to Discover Latent Social Phenotypes in Free-Ranging Macaques

Science.gov (United States)

Madlon-Kay, Seth; Brent, Lauren J. N.; Heller, Katherine A.; Platt, Michael L.

2017-01-01

Investigating the biological bases of social phenotypes is challenging because social behavior is both high-dimensional and richly structured, and biological factors are more likely to influence complex patterns of behavior rather than any single behavior in isolation. The space of all possible patterns of interactions among behaviors is too large to investigate using conventional statistical methods. In order to quantitatively define social phenotypes from natural behavior, we developed a machine learning model to identify and measure patterns of behavior in naturalistic observational data, as well as their relationships to biological, environmental, and demographic sources of variation. We applied this model to extensive observations of natural behavior in free-ranging rhesus macaques, and identified behavioral states that appeared to capture periods of social isolation, competition over food, conflicts among groups, and affiliative coexistence. Phenotypes, represented as the rate of being in each state for a particular animal, were strongly and broadly influenced by dominance rank, sex, and social group membership. We also identified two states for which variation in rates had a substantial genetic component. We discuss how this model can be extended to identify the contributions to social phenotypes of particular genetic pathways. PMID:28754001

Carbon captured from the air

International Nuclear Information System (INIS)

Keith, D.

2008-01-01

This article presented an innovative way to achieve the efficient capture of atmospheric carbon. A team of scientists from the University of Calgary's Institute for Sustainable Energy, Environment and Economy have shown that it is possible to reduce carbon dioxide (CO 2 ) using a simple machine that can capture the trace amount of CO 2 present in ambient air at any place on the planet. The thermodynamics of capturing the small concentrations of CO 2 from the air is only slightly more difficult than capturing much larger concentrations of CO 2 from power plants. The research is significant because it offers a way to capture CO 2 emissions from transportation sources such as vehicles and airplanes, which represent more than half of the greenhouse gases emitted on Earth. The energy efficient and cost effective air capture technology could complement other approaches for reducing emissions from the transportation sector, such as biofuels and electric vehicles. Air capture differs from carbon capture and storage (CCS) technology used at coal-fired power plants where CO 2 is captured and pipelined for permanent storage underground. Air capture can capture the CO 2 that is present in ambient air and store it wherever it is cheapest. The team at the University of Calgary showed that CO 2 could be captured directly from the air with less than 100 kWhrs of electricity per tonne of CO 2 . A custom-built tower was able to capture the equivalent of 20 tonnes per year of CO 2 on a single square meter of scrubbing material. The team devised a way to use a chemical process from the pulp and paper industry to cut the energy cost of air capture in half. Although the technology is only in its early stage, it appears that CO 2 could be captured from the air with an energy demand comparable to that needed for CO 2 capture from conventional power plants, but costs will be higher. The simple, reliable and scalable technology offers an opportunity to build a commercial-scale plant. 1 fig

Exploiting the Capture Effect to Enhance RACH Performance in Cellular-Based M2M Communications

Directory of Open Access Journals (Sweden)

Jonghun Kim

2017-09-01

Full Text Available Cellular-based machine-to-machine (M2M communication is expected to facilitate services for the Internet of Things (IoT. However, because cellular networks are designed for human users, they have some limitations. Random access channel (RACH congestion caused by massive access from M2M devices is one of the biggest factors hindering cellular-based M2M services because the RACH congestion causes random access (RA throughput degradation and connection failures to the devices. In this paper, we show the possibility exploiting the capture effects, which have been known to have a positive impact on the wireless network system, on RA procedure for improving the RA performance of M2M devices. For this purpose, we analyze an RA procedure using a capture model. Through this analysis, we examine the effects of capture on RA performance and propose an Msg3 power-ramping (Msg3 PR scheme to increase the capture probability (thereby increasing the RA success probability even when severe RACH congestion problem occurs. The proposed analysis models are validated using simulations. The results show that the proposed scheme, with proper parameters, further improves the RA throughput and reduces the connection failure probability, by slightly increasing the energy consumption. Finally, we demonstrate the effects of coexistence with other RA-related schemes through simulation results.

Combined effects of aging and inflammation on renin-angiotensin system mediate mitochondrial dysfunction and phenotypic changes in cardiomyopathies.

Science.gov (United States)

Burks, Tyesha N; Marx, Ruth; Powell, Laura; Rucker, Jasma; Bedja, Djahida; Heacock, Elisa; Smith, Barbara J; Foster, D Brian; Kass, David; O'Rourke, Brian; Walston, Jeremy D; Abadir, Peter M

2015-05-20

Although the effects of aging and inflammation on the health of the cardiac muscle are well documented, the combined effects of aging and chronic inflammation on cardiac muscle are largely unknown. The renin-angiotensin system (RAS) has been linked independently to both aging and inflammation, but is understudied in the context of their collective effect. Thus, we investigated localized cardiac angiotensin II type I and type II receptors (AT(1)R, AT(2)R), downstream effectors, and phenotypic outcomes using mouse models of the combination of aging and inflammation and compared it to a model of aging and a model of inflammation. We show molecular distinction in the combined effect of aging and inflammation as compared to each independently. The combination maintained an increased AT(1)R:AT(2)R and expression of Nox2 and exhibited the lowest activity of antioxidants. Despite signaling pathway differences, the combined effect shared phenotypic similarities with aging including oxidative damage, fibrosis, and hypertrophy. These phenotypic similarities have dubbed inflammatory conditions as premature aging, but they are, in fact, molecularly distinct. Moreover, treatment with an AT(1)R blocker, losartan, selectively reversed the signaling changes and ameliorated adverse phenotypic effects in the combination of aging and inflammation as well as each independently.

Capturing the fragile X premutation phenotypes: a collaborative effort across multiple cohorts.

Science.gov (United States)

Hunter, Jessica Ezzell; Sherman, Stephanie; Grigsby, Jim; Kogan, Cary; Cornish, Kim

2012-03-01

To capture the neuropsychological profile among male carriers of the FMR1 premutation allele (55-200 CGG repeats) who do not meet diagnostic criteria for the late-onset fragile X-associated tremor/ataxia syndrome, FXTAS. We have initiated a multicenter collaboration that includes 3 independent cohorts, totaling 100 carriers of the premutation and 216 noncarriers. The initial focus of this collaboration has been on executive function. Four executive function scores are shared among the 3 cohorts (Controlled Oral Word Association Test, Stroop Color-Word Test, and Wechsler backward digit span and letter-number sequencing) whereas additional executive function scores are available for specific cohorts (Behavior Dyscontrol Scale, Hayling Sentence Completion Test Part B, and Wisconsin Card Sorting Test). Raw scores were analyzed by using statistical models that adjust for cohort-specific effects as well as age and education. Carriers scored significantly lower compared to noncarriers on the Stroop Color-Word Test (p = .01), Hayling Sentence Completion Test Part B (p < .01), and Behavioral Dyscontrol Scale (p = .03), with the Hayling displaying a significant age-related decline (p = .01), as assessed by an age and repeat length-group interaction. Follow-up analysis of the collective data did not identify any specific age groups or repeat length ranges (i.e., low premutation = 55-70 repeats, midpremutation = 71-100 repeats, high premutation = 101-199 repeats) that were associated with an increased risk of executive function deficits. Preliminary analyses do not indicate global executive function impairment among male carriers without FXTAS compared to noncarriers. However, impairment in inhibitory capacity may be present among a subset of carriers, though the risk factors for this group do not appear to be related to age or repeat length.

Effects of poor hygiene on cytokine phenotypes in children in the tropics

Directory of Open Access Journals (Sweden)

C. A. Figueiredo

2016-11-01

Full Text Available Abstract We describe immune phenotypes (innate and adaptive cytokines according to environmental exposure using latent class analysis. A total of 310 schoolchildren living in Ecuador were assayed for spontaneous cytokine production as well as mitogen (SEB-stimulated cytokines in whole blood cultures. We collected data on environmental exposures by questionnaire and on intestinal parasites by examination of stool samples. Latent class analysis (LCA was used to group children according to their innate (IL-6, IL-8, IL-10 and TNF-α and adaptive (IL-5, IL-13, IL-17, IFN-γ and IL-10 cytokine profile. We also conducted multiple-group LCA and LCA with covariates to evaluate the effect of predictors on profile membership. We identified both hyporesponsive and Th2-modified immune phenotypes produced by peripheral blood leukocytes (PBLs that were associated with intestinal worms and birth order, providing insights into how poor hygiene mediates immunologic effects on immune-mediated diseases.

Time series modeling of live-cell shape dynamics for image-based phenotypic profiling.

Science.gov (United States)

Gordonov, Simon; Hwang, Mun Kyung; Wells, Alan; Gertler, Frank B; Lauffenburger, Douglas A; Bathe, Mark

2016-01-01

Live-cell imaging can be used to capture spatio-temporal aspects of cellular responses that are not accessible to fixed-cell imaging. As the use of live-cell imaging continues to increase, new computational procedures are needed to characterize and classify the temporal dynamics of individual cells. For this purpose, here we present the general experimental-computational framework SAPHIRE (Stochastic Annotation of Phenotypic Individual-cell Responses) to characterize phenotypic cellular responses from time series imaging datasets. Hidden Markov modeling is used to infer and annotate morphological state and state-switching properties from image-derived cell shape measurements. Time series modeling is performed on each cell individually, making the approach broadly useful for analyzing asynchronous cell populations. Two-color fluorescent cells simultaneously expressing actin and nuclear reporters enabled us to profile temporal changes in cell shape following pharmacological inhibition of cytoskeleton-regulatory signaling pathways. Results are compared with existing approaches conventionally applied to fixed-cell imaging datasets, and indicate that time series modeling captures heterogeneous dynamic cellular responses that can improve drug classification and offer additional important insight into mechanisms of drug action. The software is available at http://saphire-hcs.org.

Observables in muon capture on 23Na and the effective weak couplings ga and gp

International Nuclear Information System (INIS)

Johnson, B.L.; Gorringe, T.P.; Armstrong, D.S.; Bauer, J.; Hasinoff, M.D.; Kovash, M.A.; Measday, D.F.; Moftah, B.A.; Porter, R.; Wright, D.H.

1996-01-01

We report measurements of capture rates and hyperfine dependences in muon capture on 23 Na to various states in Ne and F isotopes. We also report comparisons of the capture rates and hyperfine dependences for six 23 Na → 23 Ne transitions with the 1s-0d shell model with the empirical effective interaction of Brown and Wildenthal and the realistic effective interaction of Kuo and Brown. Fits to the data with the Brown and Wildenthal interaction yield an effective coupling g a = -1.01 ± 0.07 and an effective coupling ratio g p /g a = 6.5 ± 2.4. The value of g a is consistent with values of g a extracted from β + /β - decay and (p,n)/(n,p) charge exchange data, and the value of g p /g a is consistent with the predictions of PCAC and pion-pole dominance. We evaluate the nuclear model dependence of these values of g a and g p /g a and examine the role of the Gamow-Teller and other matrix elements in the 23 Na → 23 Ne transitions. copyright 1996 The American Physical Society

Developmental plasticity in reptiles: Insights into thermal and maternal effects on chameleon phenotypes.

Science.gov (United States)

Andrews, Robin M

2018-04-23

Embryonic environments affect a range of phenotypic traits including sex and reproductive success. I determined (1) how the interaction between incubation temperature and egg size affects sex allocation of Chamaeleo calyptratus and (2) how incubation temperature and maternal parent (clutch) affect water uptake by eggs and body size, growth, and climbing speed of hatchlings and juveniles. Eggs from five clutches were exposed to five temperature treatments with clutches replicated within and among treatments. Temperature affected sex, but only when egg size was included as a factor in analyses. At intermediate (28°C) temperatures, daughters were more likely to be produced from large eggs and sons more likely to be produced from small eggs, while at 25 and 30°C, the pattern of sex allocation was reversed. Temperature and clutch affected water uptake and body size. Nonetheless, the direction of temperature and clutch effects on water uptake by eggs and on the size of hatchlings were not the same and the direction of temperature effects on body sizes of hatchlings and juveniles differed as well. Clutch affected hatchling size but not juvenile size and growth rate. Clutch, but not incubation temperature, affected climbing speed, but the fastest hatchlings were not from the same clutches as the fastest juveniles. The independent effects of incubation temperature and clutch indicate that hatchling phenotypes are influenced largely by conditions experienced during incubation, while juvenile phenotypes are influenced largely by conditions experienced in the rearing environment. © 2018 Wiley Periodicals, Inc.

Model-independent phenotyping of C. elegans locomotion using scale-invariant feature transform.

Directory of Open Access Journals (Sweden)

Yelena Koren

Full Text Available To uncover the genetic basis of behavioral traits in the model organism C. elegans, a common strategy is to study locomotion defects in mutants. Despite efforts to introduce (semi-automated phenotyping strategies, current methods overwhelmingly depend on worm-specific features that must be hand-crafted and as such are not generalizable for phenotyping motility in other animal models. Hence, there is an ongoing need for robust algorithms that can automatically analyze and classify motility phenotypes quantitatively. To this end, we have developed a fully-automated approach to characterize C. elegans' phenotypes that does not require the definition of nematode-specific features. Rather, we make use of the popular computer vision Scale-Invariant Feature Transform (SIFT from which we construct histograms of commonly-observed SIFT features to represent nematode motility. We first evaluated our method on a synthetic dataset simulating a range of nematode crawling gaits. Next, we evaluated our algorithm on two distinct datasets of crawling C. elegans with mutants affecting neuromuscular structure and function. Not only is our algorithm able to detect differences between strains, results capture similarities in locomotory phenotypes that lead to clustering that is consistent with expectations based on genetic relationships. Our proposed approach generalizes directly and should be applicable to other animal models. Such applicability holds promise for computational ethology as more groups collect high-resolution image data of animal behavior.

Krypton and xenon in Apollo 14 samples - Fission and neutron capture effects in gas-rich samples

Science.gov (United States)

Drozd, R.; Hohenberg, C.; Morgan, C.

1975-01-01

Gas-rich Apollo 14 breccias and trench soil are examined for fission xenon from the decay of the extinct isotopes Pu-244 and I-129, and some samples have been found to have an excess fission component which apparently was incorporated after decay elsewhere and was not produced by in situ decay. Two samples have excess Xe-129 resulting from the decay of I-129. The excess is correlated at low temperatures with excess Xe-128 resulting from neutron capture on I-127. This neutron capture effect is accompanied by related low-temperature excesses of Kr-80 and Kr-82 from neutron capture on the bromine isotopes. Surface correlated concentrations of iodine and bromine are calculated from the neutron capture excesses.

Carbon captured from the air

Energy Technology Data Exchange (ETDEWEB)

Keith, D. [Calgary Univ., AB (Canada)

2008-10-15

This article presented an innovative way to achieve the efficient capture of atmospheric carbon. A team of scientists from the University of Calgary's Institute for Sustainable Energy, Environment and Economy have shown that it is possible to reduce carbon dioxide (CO{sub 2}) using a simple machine that can capture the trace amount of CO{sub 2} present in ambient air at any place on the planet. The thermodynamics of capturing the small concentrations of CO{sub 2} from the air is only slightly more difficult than capturing much larger concentrations of CO{sub 2} from power plants. The research is significant because it offers a way to capture CO{sub 2} emissions from transportation sources such as vehicles and airplanes, which represent more than half of the greenhouse gases emitted on Earth. The energy efficient and cost effective air capture technology could complement other approaches for reducing emissions from the transportation sector, such as biofuels and electric vehicles. Air capture differs from carbon capture and storage (CCS) technology used at coal-fired power plants where CO{sub 2} is captured and pipelined for permanent storage underground. Air capture can capture the CO{sub 2} that is present in ambient air and store it wherever it is cheapest. The team at the University of Calgary showed that CO{sub 2} could be captured directly from the air with less than 100 kWhrs of electricity per tonne of CO{sub 2}. A custom-built tower was able to capture the equivalent of 20 tonnes per year of CO{sub 2} on a single square meter of scrubbing material. The team devised a way to use a chemical process from the pulp and paper industry to cut the energy cost of air capture in half. Although the technology is only in its early stage, it appears that CO{sub 2} could be captured from the air with an energy demand comparable to that needed for CO{sub 2} capture from conventional power plants, but costs will be higher. The simple, reliable and scalable technology

EVOLUTION OF PROGENITORS FOR ELECTRON CAPTURE SUPERNOVAE

International Nuclear Information System (INIS)

Takahashi, Koh; Umeda, Hideyuki; Yoshida, Takashi

2013-01-01

We provide progenitor models for electron capture supernovae (ECSNe) with detailed evolutionary calculation. We include minor electron capture nuclei using a large nuclear reaction network with updated reaction rates. For electron capture, the Coulomb correction of rates is treated and the contribution from neutron-rich isotopes is taken into account in each nuclear statistical equilibrium (NSE) composition. We calculate the evolution of the most massive super asymptotic giant branch stars and show that these stars undergo off-center carbon burning and form ONe cores at the center. These cores become heavier up to the critical mass of 1.367 M ☉ and keep contracting even after the initiation of O+Ne deflagration. Inclusion of minor electron capture nuclei causes convective URCA cooling during the contraction phase, but the effect on the progenitor evolution is small. On the other hand, electron capture by neutron-rich isotopes in the NSE region has a more significant effect. We discuss the uniqueness of the critical core mass for ECSNe and the effect of wind mass loss on the plausibility of our models for ECSN progenitors.

Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods.

Science.gov (United States)

Groza, Tudor; Hunter, Jane; Zankl, Andreas

2012-10-15

Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. In order to fully capture the intrinsic value and knowledge expressed within them, we need to take advantage of their inner structure, which implicitly combines qualities and anatomical entities. The first step in this process is the segmentation of the phenotype descriptions into their atomic elements. We present a two-phase hybrid segmentation method that combines a series individual classifiers using different aggregation schemes (set operations and simple majority voting). The approach is tested on a corpus comprised of skeletal phenotype descriptions emerged from the Human Phenotype Ontology. Experimental results show that the best hybrid method achieves an F-Score of 97.05% in the first phase and F-Scores of 97.16% / 94.50% in the second phase. The performance of the initial segmentation of anatomical entities and qualities (phase I) is not affected by the presence / absence of external resources, such as domain dictionaries. From a generic perspective, hybrid methods may not always improve the segmentation accuracy as they are heavily dependent on the goal and data characteristics.

Phenotypic assortment mediates the effect of social selection in a wild beetle population

NARCIS (Netherlands)

Formica, Vincent A.; McGlothlin, Joel W.; Wood, Corlett W.; Augat, Malcolm E.; Butterfield, Rebecca E.; Barnard, Mollie E.; Brodie, Edmund D.

2011-01-01

Social interactions often have major fitness consequences, but little is known about how specific interacting phenotypes affect the strength of natural selection. Social influences on the evolutionary process can be assessed using a multilevel selection approach that partitions the effects of social

Antigen-capturing nanoparticles improve the abscopal effect and cancer immunotherapy

Science.gov (United States)

Min, Yuanzeng; Roche, Kyle C.; Tian, Shaomin; Eblan, Michael J.; McKinnon, Karen P.; Caster, Joseph M.; Chai, Shengjie; Herring, Laura E.; Zhang, Longzhen; Zhang, Tian; Desimone, Joseph M.; Tepper, Joel E.; Vincent, Benjamin G.; Serody, Jonathan S.; Wang, Andrew Z.

2017-09-01

Immunotherapy holds tremendous promise for improving cancer treatment. To administer radiotherapy with immunotherapy has been shown to improve immune responses and can elicit the 'abscopal effect'. Unfortunately, response rates for this strategy remain low. Herein we report an improved cancer immunotherapy approach that utilizes antigen-capturing nanoparticles (AC-NPs). We engineered several AC-NP formulations and demonstrated that the set of protein antigens captured by each AC-NP formulation is dependent on the NP surface properties. We showed that AC-NPs deliver tumour-specific proteins to antigen-presenting cells (APCs) and significantly improve the efficacy of αPD-1 (anti-programmed cell death 1) treatment using the B16F10 melanoma model, generating up to a 20% cure rate compared with 0% without AC-NPs. Mechanistic studies revealed that AC-NPs induced an expansion of CD8+ cytotoxic T cells and increased both CD4+T/Treg and CD8+T/Treg ratios (Treg, regulatory T cells). Our work presents a novel strategy to improve cancer immunotherapy with nanotechnology.

Underestimated effect sizes in GWAS: fundamental limitations of single SNP analysis for dichotomous phenotypes.

Directory of Open Access Journals (Sweden)

Sven Stringer

Full Text Available Complex diseases are often highly heritable. However, for many complex traits only a small proportion of the heritability can be explained by observed genetic variants in traditional genome-wide association (GWA studies. Moreover, for some of those traits few significant SNPs have been identified. Single SNP association methods test for association at a single SNP, ignoring the effect of other SNPs. We show using a simple multi-locus odds model of complex disease that moderate to large effect sizes of causal variants may be estimated as relatively small effect sizes in single SNP association testing. This underestimation effect is most severe for diseases influenced by numerous risk variants. We relate the underestimation effect to the concept of non-collapsibility found in the statistics literature. As described, continuous phenotypes generated with linear genetic models are not affected by this underestimation effect. Since many GWA studies apply single SNP analysis to dichotomous phenotypes, previously reported results potentially underestimate true effect sizes, thereby impeding identification of true effect SNPs. Therefore, when a multi-locus model of disease risk is assumed, a multi SNP analysis may be more appropriate.

Methods for Analyzing Multivariate Phenotypes in Genetic Association Studies

Directory of Open Access Journals (Sweden)

Qiong Yang

2012-01-01

Full Text Available Multivariate phenotypes are frequently encountered in genetic association studies. The purpose of analyzing multivariate phenotypes usually includes discovery of novel genetic variants of pleiotropy effects, that is, affecting multiple phenotypes, and the ultimate goal of uncovering the underlying genetic mechanism. In recent years, there have been new method development and application of existing statistical methods to such phenotypes. In this paper, we provide a review of the available methods for analyzing association between a single marker and a multivariate phenotype consisting of the same type of components (e.g., all continuous or all categorical or different types of components (e.g., some are continuous and others are categorical. We also reviewed causal inference methods designed to test whether the detected association with the multivariate phenotype is truly pleiotropy or the genetic marker exerts its effects on some phenotypes through affecting the others.

Contingent orienting or contingent capture: a size singleton matching the target-distractor size relation cannot capture attention.

Science.gov (United States)

Du, Feng; Yin, Yue; Qi, Yue; Zhang, Kan

2014-08-01

In the present study, we examined whether a peripheral size-singleton distractor that matches the target-distractor size relation can capture attention and disrupt central target identification. Three experiments consistently showed that a size singleton that matches the target-distractor size relation cannot capture attention when it appears outside of the attentional window, even though the same size singleton produces a cuing effect. In addition, a color singleton that matches the target color, instead of a size singleton that matches the target-distractor size relation, captures attention when it is outside of the attentional window. Thus, a size-relation-matched distractor is much weaker than a color-matched distractor in capturing attention and cannot capture attention when the distractor appears outside of the attentional window.

Spice: discovery of phenotype-determining component interplays

Directory of Open Access Journals (Sweden)

Chen Zhengzhang

2012-05-01

Full Text Available Abstract Background A latent behavior of a biological cell is complex. Deriving the underlying simplicity, or the fundamental rules governing this behavior has been the Holy Grail of systems biology. Data-driven prediction of the system components and their component interplays that are responsible for the target system’s phenotype is a key and challenging step in this endeavor. Results The proposed approach, which we call System Phenotype-related Interplaying Components Enumerator (Spice, iteratively enumerates statistically significant system components that are hypothesized (1 to play an important role in defining the specificity of the target system’s phenotype(s; (2 to exhibit a functionally coherent behavior, namely, act in a coordinated manner to perform the phenotype-specific function; and (3 to improve the predictive skill of the system’s phenotype(s when used collectively in the ensemble of predictive models. Spice can be applied to both instance-based data and network-based data. When validated, Spice effectively identified system components related to three target phenotypes: biohydrogen production, motility, and cancer. Manual results curation agreed with the known phenotype-related system components reported in literature. Additionally, using the identified system components as discriminatory features improved the prediction accuracy by 10% on the phenotype-classification task when compared to a number of state-of-the-art methods applied to eight benchmark microarray data sets. Conclusion We formulate a problem—enumeration of phenotype-determining system component interplays—and propose an effective methodology (Spice to address this problem. Spice improved identification of cancer-related groups of genes from various microarray data sets and detected groups of genes associated with microbial biohydrogen production and motility, many of which were reported in literature. Spice also improved the predictive skill of the

Attentional capture under high perceptual load.

Science.gov (United States)

Cosman, Joshua D; Vecera, Shaun P

2010-12-01

Attentional capture by abrupt onsets can be modulated by several factors, including the complexity, or perceptual load, of a scene. We have recently demonstrated that observers are less likely to be captured by abruptly appearing, task-irrelevant stimuli when they perform a search that is high, as opposed to low, in perceptual load (Cosman & Vecera, 2009), consistent with perceptual load theory. However, recent results indicate that onset frequency can influence stimulus-driven capture, with infrequent onsets capturing attention more often than did frequent onsets. Importantly, in our previous task, an abrupt onset was present on every trial, and consequently, attentional capture might have been affected by both onset frequency and perceptual load. In the present experiment, we examined whether onset frequency influences attentional capture under conditions of high perceptual load. When onsets were presented frequently, we replicated our earlier results; attentional capture by onsets was modulated under conditions of high perceptual load. Importantly, however, when onsets were presented infrequently, we observed robust capture effects. These results conflict with a strong form of load theory and, instead, suggest that exposure to the elements of a task (e.g., abrupt onsets) combines with high perceptual load to modulate attentional capture by task-irrelevant information.

High-Throughput Non-destructive Phenotyping of Traits that Contribute to Salinity Tolerance in Arabidopsis thaliana

KAUST Repository

Awlia, Mariam

2016-09-28

Reproducible and efficient high-throughput phenotyping approaches, combined with advances in genome sequencing, are facilitating the discovery of genes affecting plant performance. Salinity tolerance is a desirable trait that can be achieved through breeding, where most have aimed at selecting for plants that perform effective ion exclusion from the shoots. To determine overall plant performance under salt stress, it is helpful to investigate several plant traits collectively in one experimental setup. Hence, we developed a quantitative phenotyping protocol using a high-throughput phenotyping system, with RGB and chlorophyll fluorescence (ChlF) imaging, which captures the growth, morphology, color and photosynthetic performance of Arabidopsis thaliana plants in response to salt stress. We optimized our salt treatment by controlling the soil-water content prior to introducing salt stress. We investigated these traits over time in two accessions in soil at 150, 100, or 50 mM NaCl to find that the plants subjected to 100 mM NaCl showed the most prominent responses in the absence of symptoms of severe stress. In these plants, salt stress induced significant changes in rosette area and morphology, but less prominent changes in rosette coloring and photosystem II efficiency. Clustering of ChlF traits with plant growth of nine accessions maintained at 100 mM NaCl revealed that in the early stage of salt stress, salinity tolerance correlated with non-photochemical quenching processes and during the later stage, plant performance correlated with quantum yield. This integrative approach allows the simultaneous analysis of several phenotypic traits. In combination with various genetic resources, the phenotyping protocol described here is expected to increase our understanding of plant performance and stress responses, ultimately identifying genes that improve plant performance in salt stress conditions.

Radiative electron capture by channeled ions

International Nuclear Information System (INIS)

Pitarke, J.M.; Ritchie, R.H.; Tennessee Univ., Knoxville, TN

1989-01-01

Considerable experimental data have been accumulated relative to the emission of photons accompanying electron capture by swift, highly stripped atoms penetrating crystalline matter under channeling conditions. Recent data suggest that the photon energies may be less than that expected from simple considerations of transitions from the valence band of the solid to hydrogenic states on the moving ion. We have studied theoretically the impact parameter dependence of the radiative electron capture (REC) process, the effect of the ion's wake and the effect of capture from inner shells of the solid on the photon emission probability, using a statistical approach. Numerical comparisons of our results with experiment are made. 13 refs., 6 figs

Effect of culture medium on propagation and phenotype of corneal stroma-derived stem cells.

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Sidney, Laura E; Branch, Matthew J; Dua, Harminder S; Hopkinson, Andrew

2015-12-01

The limbal area of the corneal stroma has been identified as a source of mesenchymal-like stem cells, which have potential for exploitation as a cell therapy. However, the optimal culture conditions are disputed and few direct media comparisons have been performed. In this report, we evaluated several media types to identify the optimal for inducing an in vitro stem cell phenotype. Primary human corneal stroma-derived stem cells (CSSCs) were extracted from corneoscleral rims. Culture in seven different media types was compared: Dulbecco's modified Eagle's medium (DMEM) with 10% fetal bovine serum (FBS); M199 with 20% FBS; DMEM-F12 with 20% serum replacement, basic fibroblast growth factor and leukemia inhibitory factor (SCM); endothelial growth medium (EGM); semi-solid MethoCult; serum-free keratinocyte medium (K-SFM); and StemPro-34. Effects on proliferation, morphology, protein and messenger RNA expression were evaluated. All media supported proliferation of CSSCs with the exception of K-SFM and StemPro-34. Morphology differed between media: DMEM produced large cells, whereas EGM produced very small cells. Culture in M199 produced a typical mesenchymal stromal cell phenotype with high expression of CD105, CD90 and CD73 but not CD34. Culture in SCM produced a phenotype more reminiscent of a progenitor cell type with expression of CD34, ABCG2, SSEA-4 and PAX6. Culture medium can significantly influence CSSC phenotype. SCM produced a cell phenotype closest to that of a pluripotent stem cell, and we consider it to be the most appropriate for development as a clinical-grade medium for the production of CSSC phenotypes suitable for cell therapy. Copyright © 2015 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

Quantitative genetic methods depending on the nature of the phenotypic trait.

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de Villemereuil, Pierre

2018-01-24

A consequence of the assumptions of the infinitesimal model, one of the most important theoretical foundations of quantitative genetics, is that phenotypic traits are predicted to be most often normally distributed (so-called Gaussian traits). But phenotypic traits, especially those interesting for evolutionary biology, might be shaped according to very diverse distributions. Here, I show how quantitative genetics tools have been extended to account for a wider diversity of phenotypic traits using first the threshold model and then more recently using generalized linear mixed models. I explore the assumptions behind these models and how they can be used to study the genetics of non-Gaussian complex traits. I also comment on three recent methodological advances in quantitative genetics that widen our ability to study new kinds of traits: the use of "modular" hierarchical modeling (e.g., to study survival in the context of capture-recapture approaches for wild populations); the use of aster models to study a set of traits with conditional relationships (e.g., life-history traits); and, finally, the study of high-dimensional traits, such as gene expression. © 2018 New York Academy of Sciences.

Similarity-based search of model organism, disease and drug effect phenotypes

KAUST Repository

Hoehndorf, Robert; Gruenberger, Michael; Gkoutos, Georgios V; Schofield, Paul N

2015-01-01

Background: Semantic similarity measures over phenotype ontologies have been demonstrated to provide a powerful approach for the analysis of model organism phenotypes, the discovery of animal models of human disease, novel pathways, gene functions

The phenotypic variance gradient - a novel concept.

Science.gov (United States)

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

2014-11-01

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

Phenotypic plasticity in Drosophila cactophilic species: the effect of competition, density, and breeding sites.

Science.gov (United States)

Fanara, Juan Jose; Werenkraut, Victoria

2017-08-01

Changes in the environmental conditions experienced by naturally occurring populations are frequently accompanied by changes in adaptive traits allowing the organism to cope with environmental unpredictability. Phenotypic plasticity is a major aspect of adaptation and it has been involved in population dynamics of interacting species. In this study, phenotypic plasticity (i.e., environmental sensitivity) of morphological adaptive traits were analyzed in the cactophilic species Drosophila buzzatii and Drosophila koepferae (Diptera: Drosophilidae) considering the effect of crowding conditions (low and high density), type of competition (intraspecific and interspecific competition) and cacti hosts (Opuntia and Columnar cacti). All traits (wing length, wing width, thorax length, wing loading and wing aspect) showed significant variation for each environmental factor considered in both Drosophila species. The phenotypic plasticity pattern observed for each trait was different within and between these cactophilic Drosophila species depending on the environmental factor analyzed suggesting that body size-related traits respond almost independently to environmental heterogeneity. The effects of ecological factors analyzed in this study are discussed in order to elucidate the causal factors investigated (type of competition, crowding conditions and alternative host) affecting the election of the breeding site and/or the range of distribution of these cactophilic species. © 2016 Institute of Zoology, Chinese Academy of Sciences.

Phenotype anchoring in zebrafish reveals a potential role for matrix metalloproteinases (MMPs) in tamoxifen's effects on skin epithelium

Energy Technology Data Exchange (ETDEWEB)

Bugel, Sean M., E-mail: Sean.Bugel@oregonstate.edu; Wehmas, Leah C., E-mail: wehmasl@onid.oregonstate.edu; La Du, Jane K., E-mail: Jane.LaDu@oregonstate.edu; Tanguay, Robert L., E-mail: Robert.Tanguay@oregonstate.edu

2016-04-01

The zebrafish is a powerful alternative model used to link phenotypes with molecular effects to discover drug mode of action. Using a zebrafish embryo-larval toxicity bioassay, we evaluated the effects of tamoxifen — a widely used anti-estrogen chemotherapeutic. Zebrafish exposed to ≥ 10 μM tamoxifen exhibited a unique necrotic caudal fin phenotype that was rapidly induced regardless of developmental life-stage when treatment was applied. To define tamoxifen's bioactivity resulting in this phenotype, targeted gene expression was used to evaluate 100 transcripts involved in tissue remodeling, calcium signaling, cell cycle and cell death, growth factors, angiogenesis and hypoxia. The most robustly misregulated transcripts in the tail were matrix metalloproteinases mmp9 and mmp13a, induced 127 and 1145 fold, respectively. Expression of c-fos, c-jun, and ap1s1 were also moderately elevated (3–7 fold), consistent with AP-1 activity — a transcription factor that regulates MMP expression. Immunohistochemistry confirmed high levels of induction for MMP13a in affected caudal fin skin epithelial tissue. The necrotic caudal fin phenotype was significantly attenuated or prevented by three functionally unique MMP inhibitors: EDTA (metal chelator), GM 6001 (broad MMP inhibitor), and SR 11302 (AP-1 transcription factor inhibitor), suggesting MMP-dependence. SR 11302 also inhibited induction of mmp9, mmp13a, and a putative MMP target, igfbp1a. Overall, our studies suggest that tamoxifen's effect is the result of perturbation of the MMP system in the skin leading to ectopic expression, cytotoxicity, and the necrotic caudal fin phenotype. These studies help advance our understanding of tamoxifen's non-classical mode of action and implicate a possible role for MMPs in tissues such as skin. - Highlights: • Tamoxifen rapidly induced a unique necrotic caudal fin phenotype in zebrafish. • Apoptosis co-localized temporally and spatially in the necrotic tail. �

8 Good Reasons for Reconsidering Lecture Capturing (of which Cost-Effectiveness is One)

DEFF Research Database (Denmark)

Godsk, Mikkel

.g. expressed by Smithers, 2011; Hallett & Faria, 2006; and others). Some of these presuppositions are probably valid in some contexts; however, in other contexts the technology may be a reasonable and cost-effective alternative. This article presents my initial experiences with implementing lecture captures...

Relationship between endophenotype and phenotype in ADHD

Directory of Open Access Journals (Sweden)

Buitelaar Jan K

2008-01-01

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

What Determines State Capture in Poland?

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Stanisław Alwasiak

2013-12-01

Full Text Available Purpose: This study examines the determinants of ex-ante state capture in Poland. Methodology: In order to establish the determinants of ex-ante state capture a logistic regression is estimated. Findings: The study shows that in Poland the majority of legal acts were passed with the aim to satisfy the interest of particular groups. Furthermore, the regression analysis shows that the likelihood of state capture increases during the period of higher economic growth and local elections. The likelihood of state capture, however, declines during presidential elections. The results we attribute to different interests of political parties in the period of local and presidential elections. Finally, we fi nd that the state capture increased over the years in Poland. Additionally, we show that the EU accession did not prevent state capture in Poland. In contrast, the fi nancial crisis of 2007 resulted in a wake-up effect and the likelihood of state capture declined in Poland. Research limitations: In the study we employ proxies for state capture, yet we assume that corruption is a widespread phenomenon in Poland. However, due to its nature corruption is very diffi cult to assess and measure. Originality: The study uses a unique dataset on ex-ante state capture that was identifi ed in the legal acts that have been passed in the period 1990–2011 in Poland.

IGF-1 has plaque-stabilizing effects in atherosclerosis by altering vascular smooth muscle cell phenotype

NARCIS (Netherlands)

von der Thüsen, Jan H.; Borensztajn, Keren S.; Moimas, Silvia; van Heiningen, Sandra; Teeling, Peter; van Berkel, Theo J. C.; Biessen, Erik A. L.

2011-01-01

Insulin-like growth factor-1 (IGF-1) signaling is important for the maintenance of plaque stability in atherosclerosis due to its effects on vascular smooth muscle cell (vSMC) phenotype. To investigate this hypothesis, we studied the effects of the highly inflammatory milieu of the atherosclerotic

Multinucleon effects in muon capture on 3He at high energy transfer

International Nuclear Information System (INIS)

Kuhn, S.E.; Cummings, W.J.; Dodge, G.E.; Hanna, S.S.; King, B.H.; Shin, Y.M.; Congleton, J.G.; Helmer, R.; Schubank, R.B.; Stevenson, N.R.; Wienands, U.; Lee, Y.K.; Mason, G.R.; King, B.E.; Chung, K.S.; Lee, J.M.; Rosenzweig, D.P.

1994-01-01

Energy spectra of both protons and deuterons emitted following the capture of negative muons by 3 He nuclei have been measured for energies above 15 MeV. A limited number of proton-neutron pairs emitted in coincidence were also observed. A simple plane wave impulse approximation (PWIA) model calculation yields fair agreement with the measured proton energy spectra, but underpredicts the measured rate of deuteron production above our energy threshold by a large factor. A more sophisticated PWIA calculation for the two-body breakup channel, based on a realistic three-body wave function for the initial state, is closer to the deuteron data at moderate energies, but still is significantly lower near the kinematic end point. The proton-neutron coincidence data also point to the presence of significant strength involving more than one nucleon in the capture process at high energy transfer. These results indicate that additional terms in the capture matrix element beyond the impulse approximation contribution may be required to explain the experimental data. Specifically, the inclusion of nucleon-nucleon correlations in the initial or final state and meson exchange current contributions could bring calculations into better agreement with our data. A fully microscopic calculation would thus open the possibility for a quantitative test of multinucleon effects in the weak interaction

Thermalization time scales for WIMP capture by the Sun in effective theories

Energy Technology Data Exchange (ETDEWEB)

Widmark, A., E-mail: axel.widmark@fysik.su.se [The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova, SE-106 91 Stockholm (Sweden)

2017-05-01

I study the process of dark matter capture by the Sun, under the assumption of a Weakly Interacting Massive Particle (WIMP), in the framework of non-relativistic effective field theory. Hypothetically, WIMPs from the galactic halo can scatter against atomic nuclei in the solar interior, settle to thermal equilibrium with the solar core and annihilate to produce an observable flux of neutrinos. In particular, I examine the thermalization process using Monte-Carlo integration of WIMP trajectories. I consider WIMPs in a mass range of 10–1000 GeV and WIMP-nucleon interaction operators with different dependence on spin and transferred momentum. I find that the density profiles of captured WIMPs are in accordance with a thermal profile described by the Sun's gravitational potential and core temperature. Depending on the operator that governs the interaction, the majority of the thermalization time is spent in either the solar interior or exterior. If normalizing the WIMP-nuclei interaction strength to a specific capture rate, I find that the thermalization time differs at most by 3 orders of magnitude between operators. In most cases of interest, the thermalization time is many orders of magnitude shorter than the age of the solar system.

Wolbachia wSinvictaA infections in natural populations of the fire ant Solenopsis invicta: testing for phenotypic effects.

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Bouwma, Andrew M; Shoemaker, Dewayne

2011-01-01

Wolbachia are intracellular bacteria that commonly infect many arthropods and some nematodes. In arthropods, these maternally transmitted bacteria often induce a variety of phenotypic effects to enhance their own spread within host populations. Wolbachia phenotypic effects generally either provide benefits to infected host females (cytoplasmic incompatibility, positive fitness effects) or bias host sex ratio in favor of females (male-killing, parthenogenesis, feminization), all of which increase the relative production of infected females in host populations. Wolbachia surveys have found infections to be exceedingly common in ants, but little is known at this juncture as to what phenotypic effects, if any, they induce in this group. Previous studies have demonstrated that individuals from native populations of the invasive fire ant Solenopsis invicta commonly harbor one or more of three Wolbachia variants. One of the variants, wSinvictaA, typically occurs at low prevalence in S. invicta populations, appears to have been transmitted horizontally into S. invicta three or more times, and has been lost repeatedly from host lineages over time. In order to determine the phenotypic effects and likely population dynamics of wSinvictaA infections in these ants, brood production patterns of newly mated fire ant queens were studied during simulated claustral founding and measured wSinvictaA transmission fidelity within mature single-queen families. No clear evidence was found for Wolbachia-induced cytoplasmic incompatibility, significant fitness effects, or male-killing. Maternal transmission was perfect to both virgin queens and males. Possible mechanisms for how this variant could be maintained in host populations are discussed.

Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods

Directory of Open Access Journals (Sweden)

Groza Tudor

2012-10-01

Full Text Available Abstract Background Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. In order to fully capture the intrinsic value and knowledge expressed within them, we need to take advantage of their inner structure, which implicitly combines qualities and anatomical entities. The first step in this process is the segmentation of the phenotype descriptions into their atomic elements. Results We present a two-phase hybrid segmentation method that combines a series individual classifiers using different aggregation schemes (set operations and simple majority voting. The approach is tested on a corpus comprised of skeletal phenotype descriptions emerged from the Human Phenotype Ontology. Experimental results show that the best hybrid method achieves an F-Score of 97.05% in the first phase and F-Scores of 97.16% / 94.50% in the second phase. Conclusions The performance of the initial segmentation of anatomical entities and qualities (phase I is not affected by the presence / absence of external resources, such as domain dictionaries. From a generic perspective, hybrid methods may not always improve the segmentation accuracy as they are heavily dependent on the goal and data characteristics.

Federated Tensor Factorization for Computational Phenotyping

Science.gov (United States)

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

2017-01-01

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

Asynchronous beating of cilia enhances particle capture rate

Science.gov (United States)

Ding, Yang; Kanso, Eva

2014-11-01

Many aquatic micro-organisms use beating cilia to generate feeding currents and capture particles in surrounding fluids. One of the capture strategies is to ``catch up'' with particles when a cilium is beating towards the overall flow direction (effective stroke) and intercept particles on the downstream side of the cilium. Here, we developed a 3D computational model of a cilia band with prescribed motion in a viscous fluid and calculated the trajectories of the particles with different sizes in the fluid. We found an optimal particle diameter that maximizes the capture rate. The flow field and particle motion indicate that the low capture rate of smaller particles is due to the laminar flow in the neighbor of the cilia, whereas larger particles have to move above the cilia tips to get advected downstream which decreases their capture rate. We then analyzed the effect of beating coordination between neighboring cilia on the capture rate. Interestingly, we found that asynchrony of the beating of the cilia can enhance the relative motion between a cilium and the particles near it and hence increase the capture rate.

Packet Capture Solutions: PcapDB Benchmark for High-Bandwidth Capture, Storage, and Searching

Energy Technology Data Exchange (ETDEWEB)

Steinfadt, Shannon Irene [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ferrell, Paul Steven [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-03-21

PcapDB stands alone when looking at the overall field of competitors, from the cost-effective COTS hardware, to the efficient utilization of disk space that enables a longer packet history. A scalable, 100GbE-enabled system that indexes every packet and indexes flow data without complicated load-balancing requirements. The Transport Layer search and indexing approach led to patent-pending flow indexing technology, providing a specialized database system specifically optimized around providing fast flow searches. While there are a plethora of options in network packet capture, there are very few that are able to effectively manage capture rates of more than 10 Gb/s, distributed capture and querying, and a responsive user interface. By far, the primary competitor in the market place is Endace and DeepSee; in addition to meeting the technical requirements we set out in this document, they provide technical support and a fully 'appliance like' system. In terms of cost, however, our experience has been that the yearly maintenance charges alone outstrip the entire hardware cost of solutions like PcapDB. Investment in cyber security research and development is a large part of what has enabled us to build the base of knowlegable workers needed to defend government resources in the rapidly evolving cyber security landscape. We believe projects like Bro, WireCap, and Farm do more than just fill temporary gaps in our capabilities. They give allow us to build the firm foundation needed to tackle the next generation of cyber challenges. PcapDB was built with loftier ambitions than simply solving the packet capture of a single lab site, but instead to provide a robust, scaleable packet capture solution to the DOE complex and beyond.

An effective attentional set for a specific colour does not prevent capture by infrequently presented motion distractors.

Science.gov (United States)

Retell, James D; Becker, Stefanie I; Remington, Roger W

2016-01-01

An organism's survival depends on the ability to rapidly orient attention to unanticipated events in the world. Yet, the conditions needed to elicit such involuntary capture remain in doubt. Especially puzzling are spatial cueing experiments, which have consistently shown that involuntary shifts of attention to highly salient distractors are not determined by stimulus properties, but instead are contingent on attentional control settings induced by task demands. Do we always need to be set for an event to be captured by it, or is there a class of events that draw attention involuntarily even when unconnected to task goals? Recent results suggest that a task-irrelevant event will capture attention on first presentation, suggesting that salient stimuli that violate contextual expectations might automatically capture attention. Here, we investigated the role of contextual expectation by examining whether an irrelevant motion cue that was presented only rarely (∼3-6% of trials) would capture attention when observers had an active set for a specific target colour. The motion cue had no effect when presented frequently, but when rare produced a pattern of interference consistent with attentional capture. The critical dependence on the frequency with which the irrelevant motion singleton was presented is consistent with early theories of involuntary orienting to novel stimuli. We suggest that attention will be captured by salient stimuli that violate expectations, whereas top-down goals appear to modulate capture by stimuli that broadly conform to contextual expectations.

Understanding Motion Capture for Computer Animation

CERN Document Server

Menache, Alberto

2010-01-01

The power of today's motion capture technology has taken animated characters and special effects to amazing new levels of reality. And with the release of blockbusters like Avatar and Tin-Tin, audiences continually expect more from each new release. To live up to these expectations, film and game makers, particularly technical animators and directors, need to be at the forefront of motion capture technology. In this extensively updated edition of Understanding Motion Capture for Computer Animation and Video Games, an industry insider explains the latest research developments in digital design

Phenotype-dependent effects of EpCAM expression on growth and invasion of human breast cancer cell lines

International Nuclear Information System (INIS)

Martowicz, Agnieszka; Spizzo, Gilbert; Gastl, Guenther; Untergasser, Gerold

2012-01-01

The epithelial cell adhesion molecule (EpCAM) has been shown to be overexpressed in breast cancer and stem cells and has emerged as an attractive target for immunotherapy of breast cancer patients. This study analyzes the effects of EpCAM on breast cancer cell lines with epithelial or mesenchymal phenotype. For this purpose, shRNA-mediated knockdown of EpCAM gene expression was performed in EpCAM high breast cancer cell lines with epithelial phenotype (MCF-7, T47D and SkBR3). Moreover, EpCAM low breast carcinoma cell lines with mesenchymal phenotype (MDA-MB-231, Hs578t) and inducible overexpression of EpCAM were used to study effects on proliferation, migration and in vivo growth. In comparison to non-specific silencing controls (n/s-crtl) knockdown of EpCAM (E#2) in EpCAM high cell lines resulted in reduced cell proliferation under serum-reduced culture conditions. Moreover, DNA synthesis under 3D culture conditions in collagen was significantly reduced. Xenografts of MCF-7 and T47D cells with knockdown of EpCAM formed smaller tumors that were less invasive. EpCAM low cell lines with tetracycline-inducible overexpression of EpCAM showed no increased cell proliferation or migration under serum-reduced growth conditions. MDA-MB-231 xenografts with EpCAM overexpression showed reduced invasion into host tissue and more infiltrates of chicken granulocytes. The role of EpCAM in breast cancer strongly depends on the epithelial or mesenchymal phenotype of tumor cells. Cancer cells with epithelial phenotype need EpCAM as a growth- and invasion-promoting factor, whereas tumor cells with a mesenchymal phenotype are independent of EpCAM in invasion processes and tumor progression. These findings might have clinical implications for EpCAM-based targeting strategies in patients with invasive breast cancer

Visual Field Asymmetry in Attentional Capture

Science.gov (United States)

Du, Feng; Abrams, Richard A.

2010-01-01

The present study examined the spatial distribution of involuntary attentional capture over the two visual hemi-fields. A new experiment, and an analysis of three previous experiments showed that distractors in the left visual field that matched a sought-for target in color produced a much larger capture effect than identical distractors in the…

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

Science.gov (United States)

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

2008-01-01

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

Genetic variants and early cigarette smoking and nicotine dependence phenotypes in adolescents.

Directory of Open Access Journals (Sweden)

Jennifer O'Loughlin

Full Text Available While the heritability of cigarette smoking and nicotine dependence (ND is well-documented, the contribution of specific genetic variants to specific phenotypes has not been closely examined. The objectives of this study were to test the associations between 321 tagging single-nucleotide polymorphisms (SNPs that capture common genetic variation in 24 genes, and early smoking and ND phenotypes in novice adolescent smokers, and to assess if genetic predictors differ across these phenotypes.In a prospective study of 1294 adolescents aged 12-13 years recruited from ten Montreal-area secondary schools, 544 participants who had smoked at least once during the 7-8 year follow-up provided DNA. 321 single-nucleotide polymorphisms (SNPs in 24 candidate genes were tested for an association with number of cigarettes smoked in the past 3 months, and with five ND phenotypes (a modified version of the Fagerstrom Tolerance Questionnaire, the ICD-10 and three clusters of ND symptoms representing withdrawal symptoms, use of nicotine for self-medication, and a general ND/craving symptom indicator.The pattern of SNP-gene associations differed across phenotypes. Sixteen SNPs in seven genes (ANKK1, CHRNA7, DDC, DRD2, COMT, OPRM1, SLC6A3 (also known as DAT1 were associated with at least one phenotype with a p-value <0.01 using linear mixed models. After permutation and FDR adjustment, none of the associations remained statistically significant, although the p-values for the association between rs557748 in OPRM1 and the ND/craving and self-medication phenotypes were both 0.076.Because the genetic predictors differ, specific cigarette smoking and ND phenotypes should be distinguished in genetic studies in adolescents. Fifteen of the 16 top-ranked SNPs identified in this study were from loci involved in dopaminergic pathways (ANKK1/DRD2, DDC, COMT, OPRM1, and SLC6A3.Dopaminergic pathways may be salient during early smoking and the development of ND.

Global pharmacogenomics: distribution of CYP3A5 polymorphisms and phenotypes in the Brazilian population.

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Guilherme Suarez-Kurtz

Full Text Available The influence of self-reported "race/color", geographical origin and genetic ancestry on the distribution of three functional CYP3A5 polymorphisms, their imputed haplotypes and inferred phenotypes was examined in 909 healthy, adult Brazilians, self-identified as White, Brown or Black ("race/color" categories of the Brazilian census. The cohort was genotyped for CYP3A5*3 (rs776746, CYP3A5*6 (rs10264272 and CYP3A5*7 (rs41303343, CYP3A5 haplotypes were imputed and CYP3A5 metabolizer phenotypes were inferred according to the number of defective CYP3A5 alleles. Estimates of the individual proportions of Amerindian, African and European ancestry were available for the entire cohort. Multinomial log-linear regression models were applied to infer the statistical association between the distribution of CYP3A5 alleles, haplotypes and phenotypes (response variables, and self-reported Color, geographical region and ancestry (explanatory variables. We found that Color per se or in combination with geographical region associates significantly with the distribution of CYP3A5 variant alleles and CYP3A5 metabolizer phenotypes, whereas geographical region per se influences the frequency distribution of CYP3A5 variant alleles. The odds of having the default CYP3A5*3 allele and the poor metabolizer phenotype increases continuously with the increase of European ancestry and decrease of African ancestry. The opposite trend is observed in relation to CYP3A5*6, CYP3A5*7, the default CYP3A5*1 allele, and both the extensive and intermediate phenotypes. No significant effect of Amerindian ancestry on the distribution of CYP3A5 alleles or phenotypes was observed. In conclusion, this study strongly supports the notion that the intrinsic heterogeneity of the Brazilian population must be acknowledged in the design and interpretation of pharmacogenomic studies, and dealt with as a continuous variable, rather than proportioned in arbitrary categories that do not capture the

Use of the enhanced frog embryo teratogenesis assay-Xenopus (FETAX) to determine chemically-induced phenotypic effects.

Science.gov (United States)

Hu, Lingling; Zhu, Jingmin; Rotchell, Jeanette M; Wu, Lijiao; Gao, Jinjuan; Shi, Huahong

2015-03-01

The frog embryo teratogenesis assay-Xenopus (FETAX) is an established method for the evaluation of the developmental toxicities of chemicals. To develop an enhanced FETAX that is appropriate for common environmental contaminants, we exposed Xenopus tropicalis embryos to eight compounds, including tributyltin, triphenyltin, CdCl2, pyraclostrobin, picoxystrobin, coumoxystrobin, all-trans-retinoic acid and 9-cis-retinoic acid. Multiple malformations were induced in embryos particularly following exposure to tributyltin, triphenyltin and pyraclostrobin at environmentally relevant concentrations. Based on the range of observed malformations, we proposed a phenotypic assessment method with 20 phenotypes and a 0-5 scoring system. This derived index exhibited concentration-dependent relationships for all of the chemicals tested. Furthermore, the phenotype profiles were characteristic of the different tested chemicals. Our results indicate that malformation phenotypes can be quantitatively integrated with the primary endpoints in conventional FETAX assessments to allow for increased sensitivity and measurement of quantitative effects and to provide indicative mechanistic information for each tested chemical. Copyright © 2014 Elsevier B.V. All rights reserved.

Mining for genotype-phenotype relations in Saccharomyces using partial least squares

Directory of Open Access Journals (Sweden)

Sæbø Solve

2011-08-01

Full Text Available Abstract Background Multivariate approaches are important due to their versatility and applications in many fields as it provides decisive advantages over univariate analysis in many ways. Genome wide association studies are rapidly emerging, but approaches in hand pay less attention to multivariate relation between genotype and phenotype. We introduce a methodology based on a BLAST approach for extracting information from genomic sequences and Soft- Thresholding Partial Least Squares (ST-PLS for mapping genotype-phenotype relations. Results Applying this methodology to an extensive data set for the model yeast Saccharomyces cerevisiae, we found that the relationship between genotype-phenotype involves surprisingly few genes in the sense that an overwhelmingly large fraction of the phenotypic variation can be explained by variation in less than 1% of the full gene reference set containing 5791 genes. These phenotype influencing genes were evolving 20% faster than non-influential genes and were unevenly distributed over cellular functions, with strong enrichments in functions such as cellular respiration and transposition. These genes were also enriched with known paralogs, stop codon variations and copy number variations, suggesting that such molecular adjustments have had a disproportionate influence on Saccharomyces yeasts recent adaptation to environmental changes in its ecological niche. Conclusions BLAST and PLS based multivariate approach derived results that adhere to the known yeast phylogeny and gene ontology and thus verify that the methodology extracts a set of fast evolving genes that capture the phylogeny of the yeast strains. The approach is worth pursuing, and future investigations should be made to improve the computations of genotype signals as well as variable selection procedure within the PLS framework.

Bottom-up effects on attention capture and choice

DEFF Research Database (Denmark)

Peschel, Anne; Orquin, Jacob Lund; Mueller Loose, Simone

Attention processes and decision making are accepted to be closely linked together because only information that is attended to can be incorporated in the decision process. Little is known however, to which extent bottom-up processes of attention affect stimulus selection and therefore...... the information available to form a decision. Does changing one visual cue in the stimulus set affect attention towards this cue and what does that mean for the choice outcome? To address this, we conducted a combined eye tracking and choice experiment in a consumer choice setting with visual shelf simulations...... salient. The observed effect on attention also carries over into increased choice likelihood. From these results, we conclude that even small changes in the choice capture attention based on bottom-up processes. Also for eye tracking studies in other domains (e.g. search tasks) this means that stimulus...

Attentional capture by masked colour singletons.

Science.gov (United States)

Ansorge, Ulrich; Horstmann, Gernot; Worschech, Franziska

2010-09-15

We tested under which conditions a colour singleton of which an observer is unaware captures attention. To prevent visual awareness of the colour singleton, we used backward masking. We find that a masked colour singleton cue captures attention if it matches the observer's goal to search for target colours but not if it is task-irrelevant. This is also reflected in event-related potentials to the visible target: the masked goal-matching cue elicits an attentional potential (N2pc) in a target search task. By contrast, a non-matching but equally strong masked colour singleton cue failed to elicit a capture effect and an N2pc. Results are discussed with regard to currently pertaining conceptions of attentional capture by colour singletons. Copyright 2010 Elsevier Ltd. All rights reserved.

Directional selection effects on patterns of phenotypic (co)variation in wild populations.

Science.gov (United States)

Assis, A P A; Patton, J L; Hubbe, A; Marroig, G

2016-11-30

Phenotypic (co)variation is a prerequisite for evolutionary change, and understanding how (co)variation evolves is of crucial importance to the biological sciences. Theoretical models predict that under directional selection, phenotypic (co)variation should evolve in step with the underlying adaptive landscape, increasing the degree of correlation among co-selected traits as well as the amount of genetic variance in the direction of selection. Whether either of these outcomes occurs in natural populations is an open question and thus an important gap in evolutionary theory. Here, we documented changes in the phenotypic (co)variation structure in two separate natural populations in each of two chipmunk species (Tamias alpinus and T. speciosus) undergoing directional selection. In populations where selection was strongest (those of T. alpinus), we observed changes, at least for one population, in phenotypic (co)variation that matched theoretical expectations, namely an increase of both phenotypic integration and (co)variance in the direction of selection and a re-alignment of the major axis of variation with the selection gradient. © 2016 The Author(s).

Toward understanding of the role of reversibility of phenotypic switching in the evolution of resistance to therapy

Science.gov (United States)

Horvath, D.; Brutovsky, B.

2018-06-01

Reversibility of state transitions is intensively studied topic in many scientific disciplines over many years. In cell biology, it plays an important role in epigenetic variation of phenotypes, known as phenotypic plasticity. More interestingly, the cell state reversibility is probably crucial in the adaptation of population phenotypic heterogeneity to environmental fluctuations by evolving bet-hedging strategy, which might confer to cancer cells resistance to therapy. In this article, we propose a formalization of the evolution of highly reversible states in the environments of periodic variability. Two interrelated models of heterogeneous cell populations are proposed and their behavior is studied. The first model captures selection dynamics of the cell clones for the respective levels of phenotypic reversibility. The second model focuses on the interplay between reversibility and drug resistance in the particular case of cancer. Overall, our results show that the threshold dependencies are emergent features of the investigated model with eventual therapeutic relevance. Presented examples demonstrate importance of taking into account cell to cell heterogeneity within a system of clones with different reversibility quantified by appropriately chosen genetic and epigenetic entropy measures.

Effect of the callipyge phenotype and cooking method on tenderness of several major lamb muscles.

Science.gov (United States)

Shackelford, S D; Wheeler, T L; Koohmaraie, M

1997-08-01

We conducted three experiments to determine the effects of the callipyge phenotype on the tenderness of several major lamb muscles and to determine the effect of method of cookery on the tenderness of callipyge lamb at 7 d postmortem. In Exp. 1, chops from normal (n = 23) and callipyge (n = 16) carcasses were open-hearth-broiled. Warner-Bratzler shear force values of longissimus, gluteus medius, semimembranosus, biceps femoris, semitendinosus, adductor, and quadriceps femoris were 123, 44, 28, 26, 19, 16, and 13% greater, respectively, for callipyge (P lamb carcasses (n = 60). Callipyge chops were less tender than normal chops (P cooking method, callipyge samples were less juicy than normal samples (P < .05). These data demonstrate that the callipyge phenotype will likely reduce consumer satisfaction due to reduced tenderness and juiciness; however, reduced tenderness in callipyge leg muscles could be prevented by ovenroasting.

Device of capturing for radioactive corrosion products

International Nuclear Information System (INIS)

Ohara, Atsushi; Fukushima, Kimichika.

1984-01-01

Purpose: To increase the area of contact between the capturing materials for the radioactive corrosion products contained in the coolants and the coolants by producing stirred turbulent flows in the coolant flow channel of LMFBR type reactors. Constitution: Constituent materials for the nuclear fuel elements or the reactor core structures are activated under the neutron irradiation, corroded and transferred into the coolants. While capturing devices made of pure metal nickel are used for the elimination of the corrosion products, since the coolants form laminar flows due to the viscosity thereof near the surface of the capturing materials, the probability that the corrosion products in the coolants flowing through the middle portion of the channel contact the capturing materials is reduced. In this invention, rotating rolls and flow channels in which the balls are rotated are disposed at the upstream of the capturing device to forcively disturb the flow of the liquid sodium, whereby the radioactive corrosion products can effectively be captured. (Kamimura, M.)

Direct neutron capture and related mechanisms

International Nuclear Information System (INIS)

Lynn, J.E.; Raman, S.

1990-01-01

We consider the evidence for the role of direct and related mechanisms in neutron capture at low and medium energies. Firstly, we compare the experimental data on the thermal neutron cross sections for El transitions in light nuclei with careful estimates of direct capture. Over the full range of light nuclei with small cross sections direct capture is found to be the predominant mechanism, in some cases being remarkable accurate, but in a few showing evidence for collective effects. When resonance effects become substantial there is evidence for an important contribution from the closely related valence mechanism, but full agreement with the data in such cases appears to require the introduction of a more generalised valence model. The possibility of direct and valence mechanisms playing a role in M1 capture is studied, and it is concluded that in light nuclei at relatively low gamma ray energies, it does indeed play some role. In heavier nuclei it appears that the evidence, especially from the correlations between E1 and M1 transitions to the same final states, favours the hypothesis that the main transition strength is governed by the M1 giant resonance. 31 refs., 2 tabs

Genotype-Phenotype Aspects of Type 2 Long QT Syndrome

NARCIS (Netherlands)

Shimizu, Wataru; Moss, Arthur J.; Wilde, Arthur A. M.; Towbin, Jeffrey A.; Ackerman, Michael J.; January, Craig T.; Tester, David J.; Zareba, Wojciech; Robinson, Jennifer L.; Qi, Ming; Vincent, G. Michael; Kaufman, Elizabeth S.; Hofman, Nynke; Noda, Takashi; Kamakura, Shiro; Miyamoto, Yoshihiro; Shah, Samit; Amin, Vinit; Goldenberg, Ilan; Andrews, Mark L.; McNitt, Scott

2009-01-01

Objectives The purpose of this study was to investigate the effect of location, coding type, and topology of KCNH2(hERG) mutations on clinical phenotype in type 2 long QT syndrome (LQTS). Background Previous studies were limited by population size in their ability to examine phenotypic effect of

Effect of collective response on electron capture and excitation in collisions of highly charged ions with fullerenes.

Science.gov (United States)

Kadhane, U; Misra, D; Singh, Y P; Tribedi, Lokesh C

2003-03-07

Projectile deexcitation Lyman x-ray emission following electron capture and K excitation has been studied in collisions of bare and Li-like sulphur ions (of energy 110 MeV) with fullerenes (C(60)/C(70)) and different gaseous targets. The intensity ratios of different Lyman x-ray lines in collisions with fullerenes are found to be substantially lower than those for the gas targets, both for capture and excitation. This has been explained in terms of a model based on "solidlike" effect, namely, wakefield induced stark mixing of the excited states populated via electron capture or K excitation: a collective phenomenon of plasmon excitation in the fullerenes under the influence of heavy, highly charged ions.

Gadolinium neutron capture therapy

International Nuclear Information System (INIS)

Akine, Yasuyuki; Tokita, Nobuhiko; Tokuuye, Koichi; Satoh, Michinao; Churei, Hisahiko

1993-01-01

Gadolinium neutron capture therapy makes use of photons and electrons produced by nuclear reactions between gadolinium and lower-energy neutrons which occur within the tumor. The results of our studies have shown that its radiation effect is mostly of low LET and that the electrons are the significant component in the over-all dose. The dose from gadolinium neutron capture reactions does not seem to increase in proportion to the gadolinium concentration, and the Gd-157 concentration of about 100 μg/ml appears most optimal for therapy. Close contact between gadolinium and the cell is not necessarily required for cell inactivation, however, the effect of electrons released from intracellular gadolinium may be significant. Experimental studies on tumor-bearing mice and rabbits have shown that this is a very promising modality though further improvements in gadolinium delivery to tumors are needed. (author)

Climate Strategy with CO2 Capture from the Air

Energy Technology Data Exchange (ETDEWEB)

Keith, D.W. [Department of Chemical and Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB (Canada); Ha-Duong, M. [CNRS-CIRED, Campus du Jardin Tropical, 45 bis, av. de la Belle Gabrielle, 94736 Nogent sur Marne CEDEX (France); Stolaroff, J.K. [Department of Engineering and Public Policy, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213 (United States)

2006-01-15

It is physically possible to capture CO2 directly from the air and immobilize it in geological structures. Air capture differs from conventional mitigation in three key aspects. First, it removes emissions from any part of the economy with equal ease or difficulty, so its cost provides an absolute cap on the cost of mitigation. Second, it permits reduction in concentrations faster than the natural carbon cycle: the effects of irreversibility are thus partly alleviated. Third, because it is weakly coupled to existing energy infrastructure, air capture may offer stronger economies of scale and smaller adjustment costs than the more conventional mitigation technologies. We assess the ultimate physical limits on the amount of energy and land required for air capture and describe two systems that might achieve air capture at prices under 200 and 500 $/tC using current technology. Like geoengineering, air capture limits the cost of a worst-case climate scenario. In an optimal sequential decision framework with uncertainty, existence of air capture decreases the need for near-term precautionary abatement. The long-term effect is the opposite; assuming that marginal costs of mitigation decrease with time while marginal climate change damages increase, then air capture increases long-run abatement. Air capture produces an environmental Kuznets curve, in which concentrations are returned to preindustrial levels.

Effects of Bonding Types and Functional Groups on CO 2 Capture using Novel Multiphase Systems of Liquid-like Nanoparticle Organic Hybrid Materials

KAUST Repository

Lin, Kun-Yi Andrew

2011-08-01

Novel liquid-like nanoparticle organic hybrid materials (NOHMs) which possess unique features including negligible vapor pressure and a high degree of tunability were synthesized and their physical and chemical properties as well as CO 2 capture capacities were investigated. NOHMs can be classified based on the synthesis methods involving different bonding types, the existence of linkers, and the addition of task-specific functional groups including amines for CO 2 capture. As a canopy of polymeric chains was grafted onto the nanoparticle cores, the thermal stability of the resulting NOHMs was improved. In order to isolate the entropy effect during CO 2 capture, NOHMs were first prepared using polymers that do not contain functional groups with strong chemical affinity toward CO 2. However, it was found that even ether groups on the polymeric canopy contributed to CO 2 capture in NOHMs via Lewis acid-base interactions, although this effect was insignificant compared to the effect of task-specific functional groups such as amine. In all cases, a higher partial pressure of CO 2 was more favorable for CO 2 capture, while a higher temperature caused an adverse effect. Multicyclic CO 2 capture tests confirmed superior recyclability of NOHMs and NOHMs also showed a higher selectivity toward CO 2 over N 2O, O 2 and N 2. © 2011 American Chemical Society.

Leveraging 3D chemical similarity, target and phenotypic data in the identification of drug-protein and drug-adverse effect associations.

Science.gov (United States)

Vilar, Santiago; Hripcsak, George

2016-01-01

Drug-target identification is crucial to discover novel applications for existing drugs and provide more insights about mechanisms of biological actions, such as adverse drug effects (ADEs). Computational methods along with the integration of current big data sources provide a useful framework for drug-target and drug-adverse effect discovery. In this article, we propose a method based on the integration of 3D chemical similarity, target and adverse effect data to generate a drug-target-adverse effect predictor along with a simple leveraging system to improve identification of drug-targets and drug-adverse effects. In the first step, we generated a system for multiple drug-target identification based on the application of 3D drug similarity into a large target dataset extracted from the ChEMBL. Next, we developed a target-adverse effect predictor combining targets from ChEMBL with phenotypic information provided by SIDER data source. Both modules were linked to generate a final predictor that establishes hypothesis about new drug-target-adverse effect candidates. Additionally, we showed that leveraging drug-target candidates with phenotypic data is very useful to improve the identification of drug-targets. The integration of phenotypic data into drug-target candidates yielded up to twofold precision improvement. In the opposite direction, leveraging drug-phenotype candidates with target data also yielded a significant enhancement in the performance. The modeling described in the current study is simple and efficient and has applications at large scale in drug repurposing and drug safety through the identification of mechanism of action of biological effects.

Effect of fossil fuels on the parameters of CO2 capture.

Science.gov (United States)

Nagy, Tibor; Mizsey, Peter

2013-08-06

The carbon dioxide capture is a more and more important issue in the design and operation of boilers and/or power stations because of increasing environmental considerations. Such processes, absorber desorber should be able to cope with flue gases from the use of different fossil primary energy sources, in order to guarantee a flexible, stable, and secure energy supply operation. The changing flue gases have significant influence on the optimal operation of the capture process, that is, where the required heating of the desorber is the minimal. Therefore special considerations are devoted to the proper design and control of such boiler and/or power stations equipped with CO2 capture process.

Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes.

Directory of Open Access Journals (Sweden)

Thomas Arbogast

2016-02-01

Full Text Available The 16p11.2 600 kb BP4-BP5 deletion and duplication syndromes have been associated with developmental delay; autism spectrum disorders; and reciprocal effects on the body mass index, head circumference and brain volumes. Here, we explored these relationships using novel engineered mouse models carrying a deletion (Del/+ or a duplication (Dup/+ of the Sult1a1-Spn region homologous to the human 16p11.2 BP4-BP5 locus. On a C57BL/6N inbred genetic background, Del/+ mice exhibited reduced weight and impaired adipogenesis, hyperactivity, repetitive behaviors, and recognition memory deficits. In contrast, Dup/+ mice showed largely opposite phenotypes. On a F1 C57BL/6N × C3B hybrid genetic background, we also observed alterations in social interaction in the Del/+ and the Dup/+ animals, with other robust phenotypes affecting recognition memory and weight. To explore the dosage effect of the 16p11.2 genes on metabolism, Del/+ and Dup/+ models were challenged with high fat and high sugar diet, which revealed opposite energy imbalance. Transcriptomic analysis revealed that the majority of the genes located in the Sult1a1-Spn region were sensitive to dosage with a major effect on several pathways associated with neurocognitive and metabolic phenotypes. Whereas the behavioral consequence of the 16p11 region genetic dosage was similar in mice and humans with activity and memory alterations, the metabolic defects were opposite: adult Del/+ mice are lean in comparison to the human obese phenotype and the Dup/+ mice are overweight in comparison to the human underweight phenotype. Together, these data indicate that the dosage imbalance at the 16p11.2 locus perturbs the expression of modifiers outside the CNV that can modulate the penetrance, expressivity and direction of effects in both humans and mice.

Mobile Motion Capture--MiMiC.

Science.gov (United States)

Harbert, Simeon D; Jaiswal, Tushar; Harley, Linda R; Vaughn, Tyler W; Baranak, Andrew S

2013-01-01

The low cost, simple, robust, mobile, and easy to use Mobile Motion Capture (MiMiC) system is presented and the constraints which guided the design of MiMiC are discussed. The MiMiC Android application allows motion data to be captured from kinematic modules such as Shimmer 2r sensors over Bluetooth. MiMiC is cost effective and can be used for an entire day in a person's daily routine without being intrusive. MiMiC is a flexible motion capture system which can be used for many applications including fall detection, detection of fatigue in industry workers, and analysis of individuals' work patterns in various environments.

Optional carbon capture

Energy Technology Data Exchange (ETDEWEB)

Alderson, T.; Scott, S.; Griffiths, J. [Jacobs Engineering, London (United Kingdom)

2007-07-01

In the case of IGCC power plants, carbon capture can be carried out before combustion. The carbon monoxide in the syngas is catalytically shifted to carbon dioxide and then captured in a standard gas absorption system. However, the insertion of a shift converter into an existing IGCC plant with no shift would mean a near total rebuild of the gasification waste heat recovery, gas treatment system and HRSG, with only the gasifier and gas turbine retaining most of their original features. To reduce the extent, cost and time taken for the revamping, the original plant could incorporate the shift, and the plant would then be operated without capture to advantage, and converted to capture mode of operation when commercially appropriate. This paper examines this concept of placing a shift converter into an IGCC plant before capture is required, and operating the same plant first without and then later with CO{sub 2} capture in a European context. The advantages and disadvantages of this 'capture ready' option are discussed. 6 refs., 2 figs., 4 tabs.

Effects of heat exchanger tubes on hydrodynamics and CO 2 capture of a sorbent-based fluidized bed reactor

Energy Technology Data Exchange (ETDEWEB)

Lai, Canhai; Xu, Zhijie; Li, Tingwen; Lee, Andrew; Dietiker, Jean-François; Lane, William; Sun, Xin

2017-12-01

In virtual design and scale up of pilot-scale carbon capture systems, the coupled reactive multiphase flow problem must be solved to predict the adsorber’s performance and capture efficiency under various operation conditions. This paper focuses on the detailed computational fluid dynamics (CFD) modeling of a pilot-scale fluidized bed adsorber equipped with vertical cooling tubes. Multiphase Flow with Interphase eXchanges (MFiX), an open-source multiphase flow CFD solver, is used for the simulations with custom code to simulate the chemical reactions and filtered models to capture the effect of the unresolved details in the coarser mesh for simulations with reasonable simulations and manageable computational effort. Previously developed two filtered models for horizontal cylinder drag, heat transfer, and reaction kinetics have been modified to derive the 2D filtered models representing vertical cylinders in the coarse-grid CFD simulations. The effects of the heat exchanger configurations (i.e., horizontal or vertical) on the adsorber’s hydrodynamics and CO2 capture performance are then examined. The simulation result subsequently is compared and contrasted with another predicted by a one-dimensional three-region process model.

In vivo evaluation of neutron capture therapy effectivity using calcium phosphate-based nanoparticles as Gd-DTPA delivery agent.

Science.gov (United States)

Dewi, Novriana; Mi, Peng; Yanagie, Hironobu; Sakurai, Yuriko; Morishita, Yasuyuki; Yanagawa, Masashi; Nakagawa, Takayuki; Shinohara, Atsuko; Matsukawa, Takehisa; Yokoyama, Kazuhito; Cabral, Horacio; Suzuki, Minoru; Sakurai, Yoshinori; Tanaka, Hiroki; Ono, Koji; Nishiyama, Nobuhiro; Kataoka, Kazunori; Takahashi, Hiroyuki

2016-04-01

A more immediate impact for therapeutic approaches of current clinical research efforts is of major interest, which might be obtained by developing a noninvasive radiation dose-escalation strategy, and neutron capture therapy represents one such novel approach. Furthermore, some recent researches on neutron capture therapy have focused on using gadolinium as an alternative or complementary for currently used boron, taking into account several advantages that gadolinium offers. Therefore, in this study, we carried out feasibility evaluation for both single and multiple injections of gadolinium-based MRI contrast agent incorporated in calcium phosphate nanoparticles as neutron capture therapy agent. In vivo evaluation was performed on colon carcinoma Col-26 tumor-bearing mice irradiated at nuclear reactor facility of Kyoto University Research Reactor Institute with average neutron fluence of 1.8 × 10(12) n/cm(2). Antitumor effectivity was evaluated based on tumor growth suppression assessed until 27 days after neutron irradiation, followed by histopathological analysis on tumor slice. The experimental results showed that the tumor growth of irradiated mice injected beforehand with Gd-DTPA-incorporating calcium phosphate-based nanoparticles was suppressed up to four times higher compared to the non-treated group, supported by the results of histopathological analysis. The results of antitumor effectivity observed on tumor-bearing mice after neutron irradiation indicated possible effectivity of gadolinium-based neutron capture therapy treatment.

Towards a resolution of the attentional-capture debate.

Science.gov (United States)

Carmel, Tomer; Lamy, Dominique

2015-12-01

The relative contributions of stimulus-driven and goal-directed control of attention have been extensively studied by investigating which irrelevant stimuli capture attention. Although much of this research has focused on color-singleton distractors, the circumstances under which these capture attention remain controversial. In search for a target with a unique known color (known-singleton search), whether singletons in an irrelevant color can be successfully ignored is a hotly debated issue. In search for a target that is not a singleton (feature search), no capture by irrelevant-color singletons is typically observed, but a reverse cueing effect was occasionally reported in the spatial-cueing paradigm. In 3 experiments, we resolve these controversies, by showing that the net spatial effect observed in the spatial-cueing paradigm reflects the sum of 3 separate effects. (a) A same-location benefit, which is determined by the match between the cue and the target colors and indexes contingent attentional capture. (b) A same-location cost, which is also determined by the match between the cue and the target colors, but occurs after selection and indexes processes related to visual working memory; and (c) task-dependent capture by singletons that occurs only when the target is consistently a singleton. Crucially, we show that the same-location cost is strongly determined by cue exposure duration, which explains previous failures to isolate it. The implications of these findings for the attentional capture debate are discussed. (c) 2015 APA, all rights reserved).

CO{sub 2}-capture in coal based IGCC power plants

Energy Technology Data Exchange (ETDEWEB)

Van Aart, F.; Fleuren, W.; Kamphuis, H.; Ploumen, P.; Jelles, S. [KEMA, Arnhem (Netherlands)

2007-07-01

The paper discusses IGCC with carbon capture and storage (CCS), both for retrofit and capture ready plants. The penalties for carbon dioxide capture are given, along with its effect on CAPEX and OPEC costs. 3 refs., 9 figs.

Effect of process parameters on power requirements of vacuum swing adsorption technology for CO2 capture from flue gas

International Nuclear Information System (INIS)

Zhang, Jun; Webley, Paul A.; Xiao, Penny

2008-01-01

This study focuses on the effects of process and operating parameters - feed gas temperature, evacuation pressure and feed concentration - on the performance of carbon dioxide vacuum swing adsorption (CO 2 VSA) processes for CO 2 capture from gas, especially as it affects power consumption. To obtain reliable data on the VSA process, experimental work was conducted on a purposely built three bed CO 2 VSA pilot plant using commercial 13X zeolite. Both 6 step and 9 step cycles were used to determine the influences of temperature, evacuation pressure and feed concentration on process performance (recovery, purity, power and corresponding capture cost). A simple economic model for CO 2 capture was developed and employed herein. Through experiments and analysis, it is found that the feed gas temperature, evacuation pressure and feed concentration have significant effects on power consumption and CO 2 capture cost. Our data demonstrate that the CO 2 VSA process has good recovery (>70%), purity (>90%) and low power cost (4-10 kW/TPDc) when operating with 40 C feed gas provided relatively deep vacuum is used. Enhanced performance is obtained when higher feed gas concentration is fed to the plant, as expected. Our data indicates large potential for application of CO 2 VSA to CO 2 capture from flue gas. (author)

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

KAUST Repository

AlShahrani, Mona; Hoehndorf, Robert

2018-01-01

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

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

KAUST Repository

Alshahrani, Mona

2018-04-30

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

Gravitational capture

International Nuclear Information System (INIS)

Bondi, H.

1979-01-01

In spite of the strength of gravitational focres between celestial bodies, gravitational capture is not a simple concept. The principles of conservation of linear momentum and of conservation of angular momentum, always impose severe constraints, while conservation of energy and the vital distinction between dissipative and non-dissipative systems allows one to rule out capture in a wide variety of cases. In complex systems especially those without dissipation, long dwell time is a more significant concept than permanent capture. (author)

Metformin treatment in different phenotypes of polycystic ovary syndrome.

Science.gov (United States)

Hosseini, Marzieh Agha; Alleyassin, Ashraf; Sarvi, Fatemeh; Safdarian, Leila; Kokab, Abas; Fanisalek, Mehran

2013-11-01

The aim of this study was to evaluate the effectiveness of Metformin on ovulation and eventual clinical pregnancy in different phenotypes of polycystic ovary syndrome (PCOS). A total of 359 subjects who had proven PCOS according to Rotterdam criteria were prospectively selected. Patients' PCOS phenotypes were determined and recorded. All patients were younger than 35 years. Clinical and biochemical assays in all patients were initially obtained. Then patients were divided into two separate groups. One group received both 1,500 mg of Metformin and 1 mg of folic acid per day and the other group received only 1 mg of folic acid for a total of 2 months. Subsequently, all patients underwent ovulation stimulation with 5 mg of Letrozole per day for 5 days followed by an intra-uterine insemination. Finally, ovulation and pregnancy rates were evaluated for all four PCOS phenotypes. Effect of Metformin therapy was evaluated for each group and each phenotype. The pregnancy rate in Metformin and non-Metformin groups were, respectively, as follows: in phenotype A (39.2 vs. 33.7 %, p = 0.270), phenotype B (43.8 vs. 20 %, p = 0.210), phenotype C (44 vs. 20 %, p = 0.064), and phenotype D (36.5 vs. 28.6 %, p = 0.279). Although there was a little improvement in ovulation and pregnancy rates among patients with B and C phenotypes, there was not a statistically significant difference between the two groups. Based on our study, Metformin therapy does not change the ovulation and pregnancy rate.

Predictable Phenotypes of Antibiotic Resistance Mutations.

Science.gov (United States)

Knopp, M; Andersson, D I

2018-05-15

Antibiotic-resistant bacteria represent a major threat to our ability to treat bacterial infections. Two factors that determine the evolutionary success of antibiotic resistance mutations are their impact on resistance level and the fitness cost. Recent studies suggest that resistance mutations commonly show epistatic interactions, which would complicate predictions of their stability in bacterial populations. We analyzed 13 different chromosomal resistance mutations and 10 host strains of Salmonella enterica and Escherichia coli to address two main questions. (i) Are there epistatic interactions between different chromosomal resistance mutations? (ii) How does the strain background and genetic distance influence the effect of chromosomal resistance mutations on resistance and fitness? Our results show that the effects of combined resistance mutations on resistance and fitness are largely predictable and that epistasis remains rare even when up to four mutations were combined. Furthermore, a majority of the mutations, especially target alteration mutations, demonstrate strain-independent phenotypes across different species. This study extends our understanding of epistasis among resistance mutations and shows that interactions between different resistance mutations are often predictable from the characteristics of the individual mutations. IMPORTANCE The spread of antibiotic-resistant bacteria imposes an urgent threat to public health. The ability to forecast the evolutionary success of resistant mutants would help to combat dissemination of antibiotic resistance. Previous studies have shown that the phenotypic effects (fitness and resistance level) of resistance mutations can vary substantially depending on the genetic context in which they occur. We conducted a broad screen using many different resistance mutations and host strains to identify potential epistatic interactions between various types of resistance mutations and to determine the effect of strain

Capture ready study

Energy Technology Data Exchange (ETDEWEB)

Minchener, A.

2007-07-15

There are a large number of ways in which the capture of carbon as carbon dioxide (CO{sub 2}) can be integrated into fossil fuel power stations, most being applicable for both gas and coal feedstocks. To add to the choice of technology is the question of whether an existing plant should be retrofitted for capture, or whether it is more attractive to build totally new. This miscellany of choices adds considerably to the commercial risk of investing in a large power station. An intermediate stage between the non-capture and full capture state would be advantageous in helping to determine the best way forward and hence reduce those risks. In recent years the term 'carbon capture ready' or 'capture ready' has been coined to describe such an intermediate stage plant and is now widely used. However a detailed and all-encompassing definition of this term has never been published. All fossil fuel consuming plant produce a carbon dioxide gas byproduct. There is a possibility of scrubbing it with an appropriate CO{sub 2} solvent. Hence it could be said that all fossil fuel plant is in a condition for removal of its CO{sub 2} effluent and therefore already in a 'capture ready' state. Evidently, the practical reality of solvent scrubbing could cost more than the rewards offered by such as the ETS (European Trading Scheme). In which case, it can be said that although the possibility exists of capturing CO{sub 2}, it is not a commercially viable option and therefore the plant could not be described as ready for CO{sub 2} capture. The boundary between a capture ready and a non-capture ready condition using this definition cannot be determined in an objective and therefore universally acceptable way and criteria must be found which are less onerous and less potentially contentious to assess. 16 refs., 2 annexes.

Study of the Effectiveness of OCR for Decentralized Data Capture and Conversion. Final Report.

Science.gov (United States)

Liston, David M.; And Others

The ERIC network conversion to an OCR (Optical Character Recognition) mode of data entry was studied to analyze the potential effectiveness of OCR data entry for future EPC/s (Editorial Processing Centers). Study results are also applicable to any other system involving decentralized bibliographic data capture and conversion functions. The report…

Sub-barrier capture with quantum diffusion approach

Directory of Open Access Journals (Sweden)

Scheid W.

2011-10-01

Full Text Available With the quantum diffusion approach the behavior of capture cross sections and mean-square angular momenta of captured systems are revealed in the reactions with deformed and spherical nuclei at sub-barrier energies. With decreasing bombarding energy under the barrier the external turning point of the nucleus-nucleus potential leaves the region of short-range nuclear interaction and action of friction. Because of this change of the regime of interaction, an unexpected enhancement of the capture cross section is found at bombarding energies far below the Coulomb barrier. This effect is shown its worth in the dependence of mean-square angular momentum on the bombarding energy. From the comparison of calculated capture cross sections and experimental capture or fusion cross sections the importance of quasifission near the entrance channel is demonstrated for the actinidebased reactions and reactions with medium-heavy nuclei at extreme sub-barrier energies.

Phenotypic plasticity, costs of phenotypes, and costs of plasticity

DEFF Research Database (Denmark)

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

2008-01-01

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

Contingent Attentional Capture by Conceptually Relevant Images

Science.gov (United States)

Wyble, Brad; Folk, Charles; Potter, Mary C.

2013-01-01

Attentional capture is an unintentional shift of visuospatial attention to the location of a distractor that is either highly salient, or relevant to the current task set. The latter situation is referred to as contingent capture, in that the effect is contingent on a match between characteristics of the stimuli and the task-defined…

Approach to magnetic neutron capture therapy

International Nuclear Information System (INIS)

Kuznetsov, Anatoly A.; Podoynitsyn, Sergey N.; Filippov, Victor I.; Komissarova, Lubov Kh.; Kuznetsov, Oleg A.

2005-01-01

Purpose: The method of magnetic neutron capture therapy can be described as a combination of two methods: magnetic localization of drugs using magnetically targeted carriers and neutron capture therapy itself. Methods and Materials: In this work, we produced and tested two types of particles for such therapy. Composite ultradispersed ferro-carbon (Fe-C) and iron-boron (Fe-B) particles were formed from vapors of respective materials. Results: Two-component ultradispersed particles, containing Fe and C, were tested as magnetic adsorbent of L-boronophenylalanine and borax and were shown that borax sorption could be effective for creation of high concentration of boron atoms in the area of tumor. Kinetics of boron release into the physiologic solution demonstrate that ultradispersed Fe-B (10%) could be applied for an effective magnetic neutron capture therapy. Conclusion: Both types of the particles have high magnetization and magnetic homogeneity, allow to form stable magnetic suspensions, and have low toxicity

Fixation not required: characterizing oculomotor attention capture for looming stimuli.

Science.gov (United States)

Lewis, Joanna E; Neider, Mark B

2015-10-01

A stimulus moving toward us, such as a ball being thrown in our direction or a vehicle braking suddenly in front of ours, often represents a stimulus that requires a rapid response. Using a visual search task in which target and distractor items were systematically associated with a looming object, we explored whether this sort of looming motion captures attention, the nature of such capture using eye movement measures (overt/covert), and the extent to which such capture effects are more closely tied to motion onset or the motion itself. We replicated previous findings indicating that looming motion induces response time benefits and costs during visual search Lin, Franconeri, & Enns(Psychological Science 19(7): 686-693, 2008). These differences in response times were independent of fixation, indicating that these capture effects did not necessitate overt attentional shifts to a looming object for search benefits or costs to occur. Interestingly, we found no differences in capture benefits and costs associated with differences in looming motion type. Combined, our results suggest that capture effects associated with looming motion are more likely subserved by covert attentional mechanisms rather than overt mechanisms, and attention capture for looming motion is likely related to motion itself rather than the onset of motion.

Large Eddy Simulations of Electromagnetic Braking Effects on Argon Bubble Transport and Capture in a Steel Continuous Casting Mold

Science.gov (United States)

Jin, Kai; Vanka, Surya P.; Thomas, Brian G.

2018-06-01

In continuous casting of steel, argon gas is often injected to prevent clogging of the nozzle, but the bubbles affect the flow pattern, and may become entrapped to form defects in the final product. Further, an electromagnetic field is frequently applied to induce a braking effect on the flow field and modify the inclusion transport. In this study, a previously validated GPU-based in-house code CUFLOW is used to investigate the effect of electromagnetic braking on turbulent flow, bubble transport, and capture. Well-resolved large eddy simulations are combined with two-way coupled Lagrangian computations of the bubbles. The drag coefficient on the bubbles is modified to account for the effects of the magnetic field. The distribution of the argon bubbles, capture, and escape rates, are presented and compared with and without the magnetic field. The bubble capture patterns are also compared with results of a previous RANS model as well as with plant measurements.

COMPUTER APPROACHES TO WHEAT HIGH-THROUGHPUT PHENOTYPING

Directory of Open Access Journals (Sweden)

Afonnikov D.

2012-08-01

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

Radiative nucleon capture with quasi-separable potentials

International Nuclear Information System (INIS)

Shubhchintak; Bertulani, C A; Mukhamedzhanov, A M; Kruppa, A T

2016-01-01

We study radiative capture reactions using quasi-separable potentials. This procedure allows an easier treatment of non-local effects that can be extended to three-body problems. Using this technique, we calculate the neutron and proton radiative capture cross sections on 12 C. The results obtained are shown to be in good agreement with the available experimental data. (paper)

Meis1: effects on motor phenotypes and the sensorimotor system in mice

Directory of Open Access Journals (Sweden)

Aaro V. Salminen

2017-08-01

Full Text Available MEIS1 encodes a developmental transcription factor and has been linked to restless legs syndrome (RLS in genome-wide association studies. RLS is a movement disorder leading to severe sleep reduction and has a substantial impact on the quality of life of patients. In genome-wide association studies, MEIS1 has consistently been the gene with the highest effect size and functional studies suggest a disease-relevant downregulation. Therefore, haploinsufficiency of Meis1 could be the system with the most potential for modeling RLS in animals. We used heterozygous Meis1-knockout mice to study the effects of Meis1 haploinsufficiency on mouse behavioral and neurological phenotypes, and to relate the findings to human RLS. We exposed the Meis1-deficient mice to assays of motor, sensorimotor and cognitive ability, and assessed the effect of a dopaminergic receptor 2/3 agonist commonly used in the treatment of RLS. The mutant mice showed a pattern of circadian hyperactivity, which is compatible with human RLS. Moreover, we discovered a replicable prepulse inhibition (PPI deficit in the Meis1-deficient animals. In addition, these mice were hyposensitive to the PPI-reducing effect of the dopaminergic receptor agonist, highlighting a role of Meis1 in the dopaminergic system. Other reported phenotypes include enhanced social recognition at an older age that was not related to alterations in adult olfactory bulb neurogenesis previously shown to be implicated in this behavior. In conclusion, the Meis1-deficient mice fulfill some of the hallmarks of an RLS animal model, and revealed the role of Meis1 in sensorimotor gating and in the dopaminergic systems modulating it.

Short-range phenotypic divergence among genetically distinct parapatric populations of an Australian funnel-web spider.

Science.gov (United States)

Wong, Mark K L; Woodman, James D; Rowell, David M

2017-07-01

Speciation involves divergence at genetic and phenotypic levels. Where substantial genetic differentiation exists among populations, examining variation in multiple phenotypic characters may elucidate the mechanisms by which divergence and speciation unfold. Previous work on the Australian funnel-web spider Atrax sutherlandi Gray (2010; Records of the Australian Museum 62 , 285-392; Mygalomorphae: Hexathelidae: Atracinae) has revealed a marked genetic structure along a 110-kilometer transect, with six genetically distinct, parapatric populations attributable to past glacial cycles. In the present study, we explore variation in three classes of phenotypic characters (metabolic rate, water loss, and morphological traits) within the context of this phylogeographic structuring. Variation in metabolic and water loss rates shows no detectable association with genetic structure; the little variation observed in these rates may be due to the spiders' behavioral adaptations (i.e., burrowing), which buffer the effects of climatic gradients across the landscape. However, of 17 morphological traits measured, 10 show significant variation among genetic populations, in a disjunct manner that is clearly not latitudinal. Moreover, patterns of variation observed for morphological traits serving different organismic functions (e.g., prey capture, burrowing, and locomotion) are dissimilar. In contrast, a previous study of an ecologically similar sympatric spider with little genetic structure indicated a strong latitudinal response in 10 traits over the same range. The congruence of morphological variation with deep phylogeographic structure in Tallaganda's A. sutherlandi populations, as well as the inconsistent patterns of variation across separate functional traits, suggest that the spiders are likely in early stages of speciation, with parapatric populations independently responding to local selective forces.

Effects of capture-related injury on postcapture movement of white-tailed deer.

Science.gov (United States)

Dechen Quinn, Amy C; Williams, David M; Porter, William F; Fitzgerald, Scott D; Hynes, Kevin

2014-04-01

Capture-related injuries or deaths of wildlife study subjects pose concerns to researchers, from considerations for animal welfare to inflated project costs and biased data. Capture myopathy (CM) is an injury that can affect an animal's survival ≤ 30 days postrelease, but is often difficult to detect without close monitoring and immediate necropsy. We evaluated the influence of capture and handling on postcapture movement in an attempt to characterize movement rates of animals suffering from CM. We captured and global positioning system-collared 95 white-tailed deer (Odocoileus virginianus) in central and northern New York during 2006-2008. Six juveniles died within 30 days postrelease, and necropsy reports indicated that two suffered CM (2%). We compared postcapture movement rates for juveniles that survived >30 days with those that died ≤ 30 days postcapture. Survivor movement rates (43.74 m/hr, SD = 3.53, n = 28) were significantly higher than rates for deer that died within 30 days (17.70 m/hr, SD = 1.57, n = 6) (Pheart rate, respiration rate) during handling between survivors and juveniles that died within 30 days postcapture but observed that survivors were in better body condition at capture. These results suggest that deer likely to die within the 30-day CM window can be identified soon after capture, provided that intensive movement data are collected. Further, even if necropsy reports are unavailable, these animals should be censored from analysis because their behavior is not representative of movements of surviving animals.

All I saw was the cake. Hunger effects on attentional capture by visual food cues.

Science.gov (United States)

Piech, Richard M; Pastorino, Michael T; Zald, David H

2010-06-01

While effects of hunger on motivation and food reward value are well-established, far less is known about the effects of hunger on cognitive processes. Here, we deployed the emotional blink of attention paradigm to investigate the impact of visual food cues on attentional capture under conditions of hunger and satiety. Participants were asked to detect targets which appeared in a rapid visual stream after different types of task irrelevant distractors. We observed that food stimuli acquired increased power to capture attention and prevent target detection when participants were hungry. This occurred despite monetary incentives to perform well. Our findings suggest an attentional mechanism through which hunger heightens perception of food cues. As an objective behavioral marker of the attentional sensitivity to food cues, the emotional attentional blink paradigm may provide a useful technique for studying individual differences, and state manipulations in the sensitivity to food cues. Published by Elsevier Ltd.

Genetic Regulation of Phenotypic Plasticity and Canalisation in Yeast Growth.

Directory of Open Access Journals (Sweden)

Anupama Yadav

Full Text Available The ability of a genotype to show diverse phenotypes in different environments is called phenotypic plasticity. Phenotypic plasticity helps populations to evade extinctions in novel environments, facilitates adaptation and fuels evolution. However, most studies focus on understanding the genetic basis of phenotypic regulation in specific environments. As a result, while it's evolutionary relevance is well established, genetic mechanisms regulating phenotypic plasticity and their overlap with the environment specific regulators is not well understood. Saccharomyces cerevisiae is highly sensitive to the environment, which acts as not just external stimulus but also as signalling cue for this unicellular, sessile organism. We used a previously published dataset of a biparental yeast population grown in 34 diverse environments and mapped genetic loci regulating variation in phenotypic plasticity, plasticity QTL, and compared them with environment-specific QTL. Plasticity QTL is one whose one allele exhibits high plasticity whereas the other shows a relatively canalised behaviour. We mapped phenotypic plasticity using two parameters-environmental variance, an environmental order-independent parameter and reaction norm (slope, an environmental order-dependent parameter. Our results show a partial overlap between pleiotropic QTL and plasticity QTL such that while some plasticity QTL are also pleiotropic, others have a significant effect on phenotypic plasticity without being significant in any environment independently. Furthermore, while some plasticity QTL are revealed only in specific environmental orders, we identify large effect plasticity QTL, which are order-independent such that whatever the order of the environments, one allele is always plastic and the other is canalised. Finally, we show that the environments can be divided into two categories based on the phenotypic diversity of the population within them and the two categories have

Physiological reactions to capture in hibernating brown bears.

Science.gov (United States)

Evans, Alina L; Singh, Navinder J; Fuchs, Boris; Blanc, Stéphane; Friebe, Andrea; Laske, Timothy G; Frobert, Ole; Swenson, Jon E; Arnemo, Jon M

2016-01-01

Human disturbance can affect animal life history and even population dynamics. However, the consequences of these disturbances are difficult to measure. This is especially true for hibernating animals, which are highly vulnerable to disturbance, because hibernation is a process of major physiological changes, involving conservation of energy during a resource-depleted time of year. During the winters of 2011-15, we captured 15 subadult brown bears ( Ursus arctos ) and recorded their body temperatures ( n  = 11) and heart rates ( n = 10) before, during and after capture using biologgers. We estimated the time for body temperature and heart rate to normalize after the capture event. We then evaluated the effect of the captures on the pattern and depth of hibernation and the day of den emergence by comparing the body temperature of captured bears with that of undisturbed subadult bears ( n  = 11). Both body temperature and heart rate increased during capture and returned to hibernation levels after 15-20 days. We showed that bears required 2-3 weeks to return to hibernation levels after winter captures, suggesting high metabolic costs during this period. There were also indications that the winter captures resulted in delayed den emergence.

Radiative electron capture

International Nuclear Information System (INIS)

Biggerstaff, J.A.; Appleton, B.R.; Datz, S.; Moak, C.D.; Neelavathi, V.N.; Noggle, T.S.; Ritchie, R.H.; VerBeek, H.

1975-01-01

Some data are presented for radiative electron capture by fast moving ions. The radiative electron capture spectrum is shown for O 8+ in Ag, along with the energy dependence of the capture cross-section. A discrepancy between earlier data, theoretical prediction, and the present data is pointed out. (3 figs) (U.S.)

Evaluating the Effectiveness of Lecture Capture: Lessons Learned from an Undergraduate Political Research Class

Science.gov (United States)

Roberts, James C.

2015-01-01

This article presents the results of a 4-year quasi-experimental study of the effectiveness of lecture capture in an undergraduate political research class. Students self-enrolled in either a traditional in-class lecture-discussion section or a fully online section of a required political research course. The class sessions from the in-class…

Measurements of neutron capture cross sections of wolfram and thulium

International Nuclear Information System (INIS)

Xia Yijun; Wang Chunhao; Yang Jingfu; Yang Zhihua; Luo Xiaobing

1992-01-01

The neutron capture cross sections of wolfram and thulium were measured in the energy range from 10 to 100 KeV using gold as the standard. Kinematically collimated neutrons were produced via the 7 Li(p, n) 7 Be reaction with a 2.5 MV pulsed Van de Graaff accelerator at Sichuan University. The capture events were detected by a pair of Moxon-Rae detectors. Time-of-flight technique was used to improve the signal-background ratio. The present results are compared with data by other authors. The capture cross section were calculated from 10 to 100 KeV for two nuclides by the Hauser-Feshbach statistical theory with width fluctuation correction. The nonstatistical effects such as potential capture and radiative capture in elastic and inelastic channels of a compound nucleus were included in the calculations. The calculated results show that the nonstatistical contribution to the capture cross sections is negligible compared with that of the statistical effects

Myosin content of individual human muscle fibers isolated by laser capture microdissection.

Science.gov (United States)

Stuart, Charles A; Stone, William L; Howell, Mary E A; Brannon, Marianne F; Hall, H Kenton; Gibson, Andrew L; Stone, Michael H

2016-03-01

Muscle fiber composition correlates with insulin resistance, and exercise training can increase slow-twitch (type I) fibers and, thereby, mitigate diabetes risk. Human skeletal muscle is made up of three distinct fiber types, but muscle contains many more isoforms of myosin heavy and light chains, which are coded by 15 and 11 different genes, respectively. Laser capture microdissection techniques allow assessment of mRNA and protein content in individual fibers. We found that specific human fiber types contain different mixtures of myosin heavy and light chains. Fast-twitch (type IIx) fibers consistently contained myosin heavy chains 1, 2, and 4 and myosin light chain 1. Type I fibers always contained myosin heavy chains 6 and 7 (MYH6 and MYH7) and myosin light chain 3 (MYL3), whereas MYH6, MYH7, and MYL3 were nearly absent from type IIx fibers. In contrast to cardiomyocytes, where MYH6 (also known as α-myosin heavy chain) is seen solely in fast-twitch cells, only slow-twitch fibers of skeletal muscle contained MYH6. Classical fast myosin heavy chains (MHC1, MHC2, and MHC4) were present in variable proportions in all fiber types, but significant MYH6 and MYH7 expression indicated slow-twitch phenotype, and the absence of these two isoforms determined a fast-twitch phenotype. The mixed myosin heavy and light chain content of type IIa fibers was consistent with its role as a transition between fast and slow phenotypes. These new observations suggest that the presence or absence of MYH6 and MYH7 proteins dictates the slow- or fast-twitch phenotype in skeletal muscle. Copyright © 2016 the American Physiological Society.

Potassium Capture by Kaolin, Part 1: KOH

DEFF Research Database (Denmark)

Wang, Guoliang; Jensen, Peter Arendt; Wu, Hao

2018-01-01

-capture level. The effect of reaction temperature,K-concentration in the flue gas, and, thereby, molar ratio of K/(Al+Si) in reactants, gas residence time, and solid particle size on K-capture reaction was systematically investigated. Corresponding equilibrium calculations were conducted with FactSage 7.......0. The experimental results showed that kaolin reached almost full conversion to K-aluminosilicates under suspension-fired conditions at 1100–1450 °C for a residence time of 1.2 s and a particle size of D50 = 5.47 μm. The amount of potassium captured by kaolin generally followed the equilibrium at temperatures above...

Auditory Attentional Capture: Effects of Singleton Distractor Sounds

Science.gov (United States)

Dalton, Polly; Lavie, Nilli

2004-01-01

The phenomenon of attentional capture by a unique yet irrelevant singleton distractor has typically been studied in visual search. In this article, the authors examine whether a similar phenomenon occurs in the auditory domain. Participants searched sequences of sounds for targets defined by frequency, intensity, or duration. The presence of a…

The ion capturing effect of 5° SiOx alignment films in liquid crystal devices

Science.gov (United States)

Huang, Yi; Bos, Philip J.; Bhowmik, Achintya

2010-09-01

We show that SiOx, deposited at 5° to the interior surface of a liquid crystal cell allows for a surprisingly substantial reduction in the ion concentration of liquid crystal devices. We have investigated this effect and found that this type of film, due to its surface morphology, captures ions from the liquid crystal material. Ion adsorption on 5° SiOx film obeys the Langmuir isotherm. Experimental results shown allow estimation of the ion capturing capacity of these films to be more than an order of 10 000/μm2. These types of materials are useful for new types of very low power liquid crystal devices such as e-books.

Modeling the effects of space structure and combination therapies on phenotypic heterogeneity and drug resistance in solid tumors.

Science.gov (United States)

Lorz, Alexander; Lorenzi, Tommaso; Clairambault, Jean; Escargueil, Alexandre; Perthame, Benoît

2015-01-01

Histopathological evidence supports the idea that the emergence of phenotypic heterogeneity and resistance to cytotoxic drugs can be considered as a process of selection in tumor cell populations. In this framework, can we explain intra-tumor heterogeneity in terms of selection driven by the local cell environment? Can we overcome the emergence of resistance and favor the eradication of cancer cells by using combination therapies? Bearing these questions in mind, we develop a model describing cell dynamics inside a tumor spheroid under the effects of cytotoxic and cytostatic drugs. Cancer cells are assumed to be structured as a population by two real variables standing for space position and the expression level of a phenotype of resistance to cytotoxic drugs. The model takes explicitly into account the dynamics of resources and anticancer drugs as well as their interactions with the cell population under treatment. We analyze the effects of space structure and combination therapies on phenotypic heterogeneity and chemotherapeutic resistance. Furthermore, we study the efficacy of combined therapy protocols based on constant infusion and bang-bang delivery of cytotoxic and cytostatic drugs.

Individual Differences in Recovery Time From Attentional Capture

Science.gov (United States)

Fukuda, Keisuke; Vogel, Edward K.

2015-01-01

Working memory capacity reflects a core ability of the individual that affects performance on many cognitive tasks. Recent work has suggested that an important covariate of memory capacity is attentional control, and specifically that low-capacity individuals are more susceptible to attentional capture by distractors than high-capacity individuals are, with the latter being able to resist capture. Here, we tested an alternative account according to which all individuals are equally susceptible to attentional capture, but high-capacity individuals recover more quickly than low-capacity individuals. Using psychophysical and electrophysiological methods, we measured recovery time from attentional capture. In two experiments, we found that high- and low-capacity individuals showed equivalent attentional capture effects in the initial moments following capture, but that low-capacity individuals took much longer to recover than high-capacity individuals did. These results suggest that the poor attentional control associated with low capacity is due to slow disengagement from distractors. PMID:21310945

Capture of exogenous attention modulates the attentional blink

DEFF Research Database (Denmark)

Nielsen, Simon; Andersen, Tobias

2011-01-01

When two targets (T1 & T2) are presented in rapid succession, observers often fail to report T2 if they attend to T1. Bottleneck theories propose that this attentional blink (AB) is due to T1 occupying a slow processing stage when T2 is presented. Accordingly, if increasing T1 difficulty increases...... T1 processing time, this should cause a greater AB. Attention capture hypotheses suggest that T1 captures attention, which cannot be reallocated to T2 in time. Accordingly, if increasing T1 difficulty, decreases saliency, this should cause a smaller AB. Studies examining how T1 difficulty affects...... with T1 contrast energy. Our results indicate that T1 capture modulates the AB. We suggest that this effect has confounded previous studies on the effect of T1 difficulty. In an electrophysiological version of the study we will further examine the implied relation between attention capture and the AB....

Deep machine learning provides state-of-the-art performance in image-based plant phenotyping.

Science.gov (United States)

Pound, Michael P; Atkinson, Jonathan A; Townsend, Alexandra J; Wilson, Michael H; Griffiths, Marcus; Jackson, Aaron S; Bulat, Adrian; Tzimiropoulos, Georgios; Wells, Darren M; Murchie, Erik H; Pridmore, Tony P; French, Andrew P

2017-10-01

In plant phenotyping, it has become important to be able to measure many features on large image sets in order to aid genetic discovery. The size of the datasets, now often captured robotically, often precludes manual inspection, hence the motivation for finding a fully automated approach. Deep learning is an emerging field that promises unparalleled results on many data analysis problems. Building on artificial neural networks, deep approaches have many more hidden layers in the network, and hence have greater discriminative and predictive power. We demonstrate the use of such approaches as part of a plant phenotyping pipeline. We show the success offered by such techniques when applied to the challenging problem of image-based plant phenotyping and demonstrate state-of-the-art results (>97% accuracy) for root and shoot feature identification and localization. We use fully automated trait identification using deep learning to identify quantitative trait loci in root architecture datasets. The majority (12 out of 14) of manually identified quantitative trait loci were also discovered using our automated approach based on deep learning detection to locate plant features. We have shown deep learning-based phenotyping to have very good detection and localization accuracy in validation and testing image sets. We have shown that such features can be used to derive meaningful biological traits, which in turn can be used in quantitative trait loci discovery pipelines. This process can be completely automated. We predict a paradigm shift in image-based phenotyping bought about by such deep learning approaches, given sufficient training sets. © The Authors 2017. Published by Oxford University Press.

Partial radiative capture of resonance neutrons; Capture radiative partielle des neutrons de resonance

Energy Technology Data Exchange (ETDEWEB)

Samour, C [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1969-07-01

The radiative capture of resonance neutrons has been studied near the Saclay linac between 0.5 and 700 eV with time-of-flight method and a Ge(Li) detector. {sup 195}Pt + n and {sup 183}W + n allow the study of the distribution of partial radiative widths and their eventual correlation and also the variation of < {gamma}{sub {gamma}{sub i}} > with E{sub {gamma}}. The mean values of Ml and El transition intensities are compared in several tin isotopes. Interference effects, either between resonances or between direct capture and resonant capture are found in {sup 195}Pt + n, {sup 197}Au + n and {sup 59}Co + n. The excited level schemes of a great deal of nuclei are obtained and compared with theoretical predictions. This study has been completed by an analysis of thermal spectrum. (author) [French] La capture radiative des neutrons de resonance a ete etudiee pres de l'accelerateur lineaire de Saclay entre 0,5 et 700 eV a l'aide de la methode du temps-de-vol et d'un detecteur Ge(Li). Les noyaux {sup 195}Pt + n et {sup 183}W + n permettent l'analyse de la distribution de resonance en resonance des largeurs radiatives partielles {gamma}{sub {gamma}{sub i}} et de leur eventuelle correlation, ainsi que l'etude de la variation de < {gamma}{sub {gamma}{sub i}} > en fonction de E{sub {gamma}}. Les intensites moyennes des transitions Ml et El sont comparees pour quelques isotopes de l'etain. Des effets d'interference, soit entre resonances, soit entre capture directe et capture resonnante sont mis en evidence dans {sup 195}Pt + n, {sup 197}Au + n et {sup 59}Co + n. Enfin les schemas des etats excites d'un grand nombre de noyaux sont obtenus et compares avec les predictions theoriques. Cette etude a ete completee par une analyse des spectres thermiques. (auteur)

Partial radiative capture of resonance neutrons; Capture radiative partielle des neutrons de resonance

Energy Technology Data Exchange (ETDEWEB)

Samour, C. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1969-07-01

The radiative capture of resonance neutrons has been studied near the Saclay linac between 0.5 and 700 eV with time-of-flight method and a Ge(Li) detector. {sup 195}Pt + n and {sup 183}W + n allow the study of the distribution of partial radiative widths and their eventual correlation and also the variation of < {gamma}{sub {gamma}{sub i}} > with E{sub {gamma}}. The mean values of Ml and El transition intensities are compared in several tin isotopes. Interference effects, either between resonances or between direct capture and resonant capture are found in {sup 195}Pt + n, {sup 197}Au + n and {sup 59}Co + n. The excited level schemes of a great deal of nuclei are obtained and compared with theoretical predictions. This study has been completed by an analysis of thermal spectrum. (author) [French] La capture radiative des neutrons de resonance a ete etudiee pres de l'accelerateur lineaire de Saclay entre 0,5 et 700 eV a l'aide de la methode du temps-de-vol et d'un detecteur Ge(Li). Les noyaux {sup 195}Pt + n et {sup 183}W + n permettent l'analyse de la distribution de resonance en resonance des largeurs radiatives partielles {gamma}{sub {gamma}{sub i}} et de leur eventuelle correlation, ainsi que l'etude de la variation de < {gamma}{sub {gamma}{sub i}} > en fonction de E{sub {gamma}}. Les intensites moyennes des transitions Ml et El sont comparees pour quelques isotopes de l'etain. Des effets d'interference, soit entre resonances, soit entre capture directe et capture resonnante sont mis en evidence dans {sup 195}Pt + n, {sup 197}Au + n et {sup 59}Co + n. Enfin les schemas des etats excites d'un grand nombre de noyaux sont obtenus et compares avec les predictions theoriques. Cette etude a ete completee par une analyse des spectres thermiques. (auteur)

Neutron Capture Gamma-Ray Spectroscopy. Proceedings of the International Symposium on Neutron Capture Gamma-Ray Spectroscopy

Energy Technology Data Exchange (ETDEWEB)

NONE

1969-11-15

Experimental capabilities in the field of neutron capture gamma-ray spectroscopy have expanded greatly in the last few years; this has been due in large part to the advent of high-quality Ge(Li) detectors, improvements in electronic data processing, and improvements in bent-crystal spectrometers. Previously unsuspected phenomena, such as the '5. 5-MeV1 anomaly, have appeared and new research tools, such as neutron guide tubes, have been brought into use. Equally exciting developments have occurred in the theory of neutron capture. Complex spectra have yielded to analysis after account had been taken of such effects as vibration, rotation and Coriolis forces, and the theoretical prediction of capture spectra seems to be a future possibility. In view of the International Atomic Energy Agency's close interest in this subject and the need for an international exchange of ideas to analyse and study the latest developments, the organizers of the Symposium felt that work on neutron capture gamma-ray spectroscopy had achieved such valuable and significant results that the time had come for this information to be presented, examined and discussed internationally.

Neutron Capture Gamma-Ray Spectroscopy. Proceedings of the International Symposium on Neutron Capture Gamma-Ray Spectroscopy

International Nuclear Information System (INIS)

1969-01-01

Experimental capabilities in the field of neutron capture gamma-ray spectroscopy have expanded greatly in the last few years; this has been due in large part to the advent of high-quality Ge(Li) detectors, improvements in electronic data processing, and improvements in bent-crystal spectrometers. Previously unsuspected phenomena, such as the '5. 5-MeV1 anomaly, have appeared and new research tools, such as neutron guide tubes, have been brought into use. Equally exciting developments have occurred in the theory of neutron capture. Complex spectra have yielded to analysis after account had been taken of such effects as vibration, rotation and Coriolis forces, and the theoretical prediction of capture spectra seems to be a future possibility. In view of the International Atomic Energy Agency's close interest in this subject and the need for an international exchange of ideas to analyse and study the latest developments, the organizers of the Symposium felt that work on neutron capture gamma-ray spectroscopy had achieved such valuable and significant results that the time had come for this information to be presented, examined and discussed internationally

Effects of activated fibroblasts on phenotype modulation, EGFR signalling and cell cycle regulation in OSCC cells

Energy Technology Data Exchange (ETDEWEB)

Berndt, Alexander, E-mail: alexander.berndt@med.uni-jena.de [Center for Molecular Biomedicine, Institute of Pathology, Jena University Hospital, 07740 Jena (Germany); Büttner, Robert, E-mail: Robert-Buettner@gmx.net [Institute of Biochemistry and Biophysics, Friedrich Schiller University Jena, 07740 Jena (Germany); Gühne, Stefanie, E-mail: stefanie_guehne@gmx.net [Center for Molecular Biomedicine, Institute of Pathology, Jena University Hospital, 07740 Jena (Germany); Gleinig, Anna, E-mail: annagleinig@yahoo.com [Center for Molecular Biomedicine, Institute of Pathology, Jena University Hospital, 07740 Jena (Germany); Richter, Petra, E-mail: P.Richter@med.uni-jena.de [Center for Molecular Biomedicine, Institute of Pathology, Jena University Hospital, 07740 Jena (Germany); Chen, Yuan, E-mail: Yuan.Chen@med.uni-jena.de [Center for Molecular Biomedicine, Institute of Pathology, Jena University Hospital, 07740 Jena (Germany); Franz, Marcus, E-mail: Marcus.Franz@med.uni-jena.de [Clinic of Internal Medicine I, Jena University Hospital, 07740 Jena (Germany); Liebmann, Claus, E-mail: Claus.Liebmann@uni-jena.de [Institute of Biochemistry and Biophysics, Friedrich Schiller University Jena, 07740 Jena (Germany)

2014-04-01

Crosstalk between carcinoma associated fibroblasts (CAFs) and oral squamous cell carcinoma (OSCC) cells is suggested to mediate phenotype transition of cancer cells as a prerequisite for tumour progression, to predict patients’ outcome, and to influence the efficacy of EGFR inhibitor therapies. Here we investigate the influence of activated fibroblasts as a model for CAFs on phenotype and EGFR signalling in OSCC cells in vitro. For this, immortalised hTERT-BJ1 fibroblasts were activated with TGFβ1 and PDGFAB to generate a myofibroblast or proliferative phenotype, respectively. Conditioned media (FCM{sub TGF}, FCM{sub PDGF}) were used to stimulate PE/CA-PJ15 OSCC cells. Results were compared to the effect of conditioned media of non-stimulated fibroblasts (FCM{sub B}). FCM{sub TGF} stimulation leads to an up-regulation of vimentin in the OSCC cells and an enhancement of invasive behaviour, indicating EMT-like effects. Similarly, FCM{sub TGF}≫FCM{sub PDGF} induced up-regulation of EGFR, but not of ErbB2/ErbB3. In addition, we detected an increase in basal activities of ERK, PI3K/Akt and Stat3 (FCM{sub TGF}>FCM{sub PDGF}) accompanied by protein interaction of vimentin with pERK. These effects are correlated with an increased proliferation. In summary, our results suggest that the activated myofibroblast phenotype provides soluble factors which are able to induce EMT-like phenomena and to increase EGFR signalling as well as cell proliferation in OSCC cells. Our results indicate a possible influence of activated myofibroblasts on EGFR-inhibitor therapy. Therefore, CAFs may serve as promising novel targets for combined therapy strategies. - Highlights: • A cell culture model for cancer associated fibroblasts is described. • The mutual interaction with OSCC cells leads to up-regulation of EGFR in tumour cells. • mCAF induces EGFR downstream signalling with increased proliferation in OSCC. • Erk activation is associated with protein interaction with vimentin

Effects of activated fibroblasts on phenotype modulation, EGFR signalling and cell cycle regulation in OSCC cells

International Nuclear Information System (INIS)

Berndt, Alexander; Büttner, Robert; Gühne, Stefanie; Gleinig, Anna; Richter, Petra; Chen, Yuan; Franz, Marcus; Liebmann, Claus

2014-01-01

Crosstalk between carcinoma associated fibroblasts (CAFs) and oral squamous cell carcinoma (OSCC) cells is suggested to mediate phenotype transition of cancer cells as a prerequisite for tumour progression, to predict patients’ outcome, and to influence the efficacy of EGFR inhibitor therapies. Here we investigate the influence of activated fibroblasts as a model for CAFs on phenotype and EGFR signalling in OSCC cells in vitro. For this, immortalised hTERT-BJ1 fibroblasts were activated with TGFβ1 and PDGFAB to generate a myofibroblast or proliferative phenotype, respectively. Conditioned media (FCM TGF , FCM PDGF ) were used to stimulate PE/CA-PJ15 OSCC cells. Results were compared to the effect of conditioned media of non-stimulated fibroblasts (FCM B ). FCM TGF stimulation leads to an up-regulation of vimentin in the OSCC cells and an enhancement of invasive behaviour, indicating EMT-like effects. Similarly, FCM TGF ≫FCM PDGF induced up-regulation of EGFR, but not of ErbB2/ErbB3. In addition, we detected an increase in basal activities of ERK, PI3K/Akt and Stat3 (FCM TGF >FCM PDGF ) accompanied by protein interaction of vimentin with pERK. These effects are correlated with an increased proliferation. In summary, our results suggest that the activated myofibroblast phenotype provides soluble factors which are able to induce EMT-like phenomena and to increase EGFR signalling as well as cell proliferation in OSCC cells. Our results indicate a possible influence of activated myofibroblasts on EGFR-inhibitor therapy. Therefore, CAFs may serve as promising novel targets for combined therapy strategies. - Highlights: • A cell culture model for cancer associated fibroblasts is described. • The mutual interaction with OSCC cells leads to up-regulation of EGFR in tumour cells. • mCAF induces EGFR downstream signalling with increased proliferation in OSCC. • Erk activation is associated with protein interaction with vimentin as sign of EMT. • Results qualify

The Time Course of Attentional and Oculomotor Capture Reveals a Common Cause

Science.gov (United States)

Hunt, Amelia R.; von Muhlenen, Adrian; Kingstone, Alan

2007-01-01

Eye movements are often misdirected toward a distractor when it appears abruptly, an effect known as oculomotor capture. Fundamental differences between eye movements and attention have led to questions about the relationship of oculomotor capture to the more general effect of sudden onsets on performance, known as attentional capture. This study…

Entrained Flow Reactor Study of K-Capture by Solid Additives

DEFF Research Database (Denmark)

Wang, Guoliang; Jensen, Peter Arendt; Wu, Hao

2016-01-01

are collected from the cyclone and filter. The K-capture reaction is evaluated by determining the fraction of water-insoluble K in the products. The results showed that KCl can effectively be captured by kaolin and coal fly ash, forming water-insoluble K-aluminosilicates. The amount of K, captured per gram...

Function and Phenotype prediction through Data and Knowledge Fusion

KAUST Repository

Vespoor, Karen

2016-01-27

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

Widespread differential maternal and paternal genome effects on fetal bone phenotype at mid-gestation.

Science.gov (United States)

Xiang, Ruidong; Lee, Alice M C; Eindorf, Tanja; Javadmanesh, Ali; Ghanipoor-Samami, Mani; Gugger, Madeleine; Fitzsimmons, Carolyn J; Kruk, Zbigniew A; Pitchford, Wayne S; Leviton, Alison J; Thomsen, Dana A; Beckman, Ian; Anderson, Gail I; Burns, Brian M; Rutley, David L; Xian, Cory J; Hiendleder, Stefan

2014-11-01

Parent-of-origin-dependent (epi)genetic factors are important determinants of prenatal development that program adult phenotype. However, data on magnitude and specificity of maternal and paternal genome effects on fetal bone are lacking. We used an outbred bovine model to dissect and quantify effects of parental genomes, fetal sex, and nongenetic maternal effects on the fetal skeleton and analyzed phenotypic and molecular relationships between fetal muscle and bone. Analysis of 51 bone morphometric and weight parameters from 72 fetuses recovered at day 153 gestation (54% term) identified six principal components (PC1-6) that explained 80% of the variation in skeletal parameters. Parental genomes accounted for most of the variation in bone wet weight (PC1, 72.1%), limb ossification (PC2, 99.8%), flat bone size (PC4, 99.7%), and axial skeletal growth (PC5, 96.9%). Limb length showed lesser effects of parental genomes (PC3, 40.8%) and a significant nongenetic maternal effect (gestational weight gain, 29%). Fetal sex affected bone wet weight (PC1, p maternal genome effects on bone wet weight (74.1%, p paternal genome controlled limb ossification (95.1%, p maternal genome effects on growth plate height (98.6%, p maternal genome effects on fetal serum 25-hydroxyvitamin D (96.9%, p paternal genome effects on alkaline phosphatase (90.0%, p maternally controlled bone wet weight and paternally controlled limb ossification, respectively. Bone wet weight and flat bone size correlated positively with muscle weight (r = 0.84 and 0.77, p maternally expressed H19 regulates growth factors by miRNA interference, this suggests muscle-bone interaction via epigenetic factors. © 2014 American Society for Bone and Mineral Research.

Management of radioactive waste gases from PET radiopharmaceutical synthesis using cost effective capture systems integrated with a cyclotron safety system.

Science.gov (United States)

Stimson, D H R; Pringle, A J; Maillet, D; King, A R; Nevin, S T; Venkatachalam, T K; Reutens, D C; Bhalla, R

2016-09-01

The emphasis on the reduction of gaseous radioactive effluent associated with PET radiochemistry laboratories has increased. Various radioactive gas capture strategies have been employed historically including expensive automated compression systems. We have implemented a new cost-effective strategy employing gas capture bags with electronic feedback that are integrated with the cyclotron safety system. Our strategy is suitable for multiple automated 18 F radiosynthesis modules and individual automated 11 C radiosynthesis modules. We describe novel gas capture systems that minimize the risk of human error and are routinely used in our facility.

CO2 Capture and Reuse

International Nuclear Information System (INIS)

Thambimuthu, K.; Gupta, M.; Davison, J.

2003-01-01

producing streams for use as a feedstock or by product for subsequent utilization in industrial processes, this paper will also review existing methods of CO2 utilization and the future scope for utilization as a sink that could prevent the release of anthropogenic CO2 emissions into the atmosphere. In order to be effective as a sink, the process or product that uses CO2 must take cognisance of the type of energy use, energy penalties and net greenhouse gas emissions associated with the 'capture' and 'fixation' of carbon, as well as significantly prolonging the period between CO2 production from fossil fuels and the stage of its final discharge into the atmosphere from any degradation or release of the 'fixed' carbon. Hence, the manufacturing of various chemicals, materials or products using CO2 as a raw material will be reviewed and evaluated in terms of these criteria as well as their chemical/thermodynamic stability relative to CO2

Computational evaluation of metal-organic frameworks for carbon dioxide capture

Science.gov (United States)

Yu, Jiamei

Metal-organic frameworks (MOFs), a new class of porous solids comprised of metal-containing nodes linked by organic ligands, have become promising materials for gas separations. In particular, their flexible chemistry makes them attractive for CO2 capture from flue gas streams in post-combustion plants. Although numerous efforts have been exerted on the investigation of MOFs for CO2 capture, the exploration of the effects from coexisting components present in very dilute proportions in flue gases is limited because of the experimental difficulty to determine the coadsorption of CO2 with trace components. In this regard, molecular simulations show superiority. In this study, molecular simulations are used to estimate the influence of impurities: water, O2, and SO2 on post-combustion CO2 capture in MOFs. Firstly, two MOFs with coordinatively unsaturated metal sites (CUMs), HKUST-1 and Mg-MOF-74 are explored. Increase of CO 2 adsorption is observed for hydrated HKUST-1; on the contrary, the opposite water adsorption behavior is observed in hydrated Mg-MOF-74, leading to decrease of CO2 adsorption. Further, water effects on CO 2 capture in M-HKUST1 (M = Mg, Zn, Co, Ni) are evaluated to test whether comparing the binding energy could be a general method to evaluate water effects in MOFs with CUMs. It is found that the method works well for Zn-, Co-, and Ni-HKUST1 but partially for Mg-HKUST1. In addition, the effects of O2 and SO2 on CO2 capture in MOFs are also investigated for the first time, showing that the effects of O2 may be negligible but SO2 has negative effects in the CO 2 capture process in HKUST-1 systems. Secondly, the influences of water on CO2 capture in three UiO-66 MOFs with functional groups, --NH2, --OH and --Br are explored, respectively. For UiO-66-NH2 and -OH, the presence of water lowers CO2 adsorption significantly; in contrast, water shows much smaller effects in UiO-66-Br. Moreover, the presence of SO 2 decreases water adsorption but enhances CO

Boron neutron capture therapy (BNCT) using fast neutrons: Effects in two human tumor cell lines

International Nuclear Information System (INIS)

Sauerwein, W.; Ziegler, W.; Szypniewski, H.; Streffer, C.

1990-01-01

The results demonstrate that the effect of fast neutrons on cell survival in cell culture can be enhanced by boron neutron capture reaction. Even with lower enhancement ratios, the concept of NCT assisted fast neutron therapy may successfully be applied for tumor treatment with the Essen cyclotron. (orig.)

Confusion noise from LISA capture sources

International Nuclear Information System (INIS)

Barack, Leor; Cutler, Curt

2004-01-01

Captures of compact objects (COs) by massive black holes (MBHs) in galactic nuclei will be an important source for LISA, the proposed space-based gravitational wave (GW) detector. However, a large fraction of captures will not be individually resolvable - either because they are too distant, have unfavorable orientation, or have too many years to go before final plunge - and so will constitute a source of 'confusion noise', obscuring other types of sources. In this paper we estimate the shape and overall magnitude of the GW background energy spectrum generated by CO captures. This energy spectrum immediately translates to a spectral density S h capt (f) for the amplitude of capture-generated GWs registered by LISA. The overall magnitude of S h capt (f) is linear in the CO capture rates, which are rather uncertain; therefore we present results for a plausible range of rates. S h capt (f) includes the contributions from both resolvable and unresolvable captures, and thus represents an upper limit on the confusion noise level. We then estimate what fraction of S h capt (f) is due to unresolvable sources and hence constitutes confusion noise. We find that almost all of the contribution to S h capt (f) coming from white dwarf and neutron star captures, and at least ∼30% of the contribution from black hole captures, is from sources that cannot be individually resolved. Nevertheless, we show that the impact of capture confusion noise on the total LISA noise curve ranges from insignificant to modest, depending on the rates. Capture rates at the high end of estimated ranges would raise LISA's overall (effective) noise level [fS h eff (f)] 1/2 by at most a factor ∼2 in the frequency range 1-10 mHz, where LISA is most sensitive. While this slightly elevated noise level would somewhat decrease LISA's sensitivity to other classes of sources, we argue that, overall, this would be a pleasant problem for LISA to have: It would also imply that detection rates for CO captures

Audiovisual Capture with Ambiguous Audiovisual Stimuli

Directory of Open Access Journals (Sweden)

Jean-Michel Hupé

2011-10-01

Full Text Available Audiovisual capture happens when information across modalities get fused into a coherent percept. Ambiguous multi-modal stimuli have the potential to be powerful tools to observe such effects. We used such stimuli made of temporally synchronized and spatially co-localized visual flashes and auditory tones. The flashes produced bistable apparent motion and the tones produced ambiguous streaming. We measured strong interferences between perceptual decisions in each modality, a case of audiovisual capture. However, does this mean that audiovisual capture occurs before bistable decision? We argue that this is not the case, as the interference had a slow temporal dynamics and was modulated by audiovisual congruence, suggestive of high-level factors such as attention or intention. We propose a framework to integrate bistability and audiovisual capture, which distinguishes between “what” competes and “how” it competes (Hupé et al., 2008. The audiovisual interactions may be the result of contextual influences on neural representations (“what” competes, quite independent from the causal mechanisms of perceptual switches (“how” it competes. This framework predicts that audiovisual capture can bias bistability especially if modalities are congruent (Sato et al., 2007, but that is fundamentally distinct in nature from the bistable competition mechanism.

Electrofishing capture probability of smallmouth bass in streams

Science.gov (United States)

Dauwalter, D.C.; Fisher, W.L.

2007-01-01

Abundance estimation is an integral part of understanding the ecology and advancing the management of fish populations and communities. Mark-recapture and removal methods are commonly used to estimate the abundance of stream fishes. Alternatively, abundance can be estimated by dividing the number of individuals sampled by the probability of capture. We conducted a mark-recapture study and used multiple repeated-measures logistic regression to determine the influence of fish size, sampling procedures, and stream habitat variables on the cumulative capture probability for smallmouth bass Micropterus dolomieu in two eastern Oklahoma streams. The predicted capture probability was used to adjust the number of individuals sampled to obtain abundance estimates. The observed capture probabilities were higher for larger fish and decreased with successive electrofishing passes for larger fish only. Model selection suggested that the number of electrofishing passes, fish length, and mean thalweg depth affected capture probabilities the most; there was little evidence for any effect of electrofishing power density and woody debris density on capture probability. Leave-one-out cross validation showed that the cumulative capture probability model predicts smallmouth abundance accurately. ?? Copyright by the American Fisheries Society 2007.

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

Directory of Open Access Journals (Sweden)

Yook Karen

2011-01-01

Full Text Available Abstract Background Caenorhabditis elegans gene-based phenotype information dates back to the 1970's, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in order to understand nervous system function. Since then C. elegans has become an important genetic model system for the study of basic biological and biomedical principles, largely through the use of phenotype analysis. Because of the growth of C. elegans as a genetically tractable model organism and the development of large-scale analyses, there has been a significant increase of phenotype data that needs to be managed and made accessible to the research community. To do so, a standardized vocabulary is necessary to integrate phenotype data from diverse sources, permit integration with other data types and render the data in a computable form. Results We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO. The WPO is currently comprised of 1,880 phenotype terms, 74% of which have been used in the annotation of phenotypes associated with greater than 18,000 C. elegans genes. The scope of the WPO is not exclusively limited to C. elegans biology, rather it is devised to also incorporate phenotypes observed in related nematode species. We have enriched the value of the WPO by integrating it with other ontologies, thereby increasing the accessibility of worm phenotypes to non-nematode biologists. We are actively developing the WPO to continue to fulfill the evolving needs of the scientific community and hope to engage researchers in this crucial endeavor. Conclusions We provide a phenotype ontology (WPO that will help to facilitate data retrieval, and cross-species comparisons within the nematode community. In the larger scientific community, the WPO will permit data integration, and

How good is your phenotyping? Methods for quality assessment

OpenAIRE

Nicole L Washington; Melissa A Haendel; Sebastian Köhler; Suzanna E Lewis; Peter Robinson; Damian Smedley

2014-01-01

Semantic phenotyping has been shown to be an effective means to aid variant prioritization and characterization by comparison to both known Mendelian diseases and across species with animal models (Robinson et al 2013). This process, whereby symptoms and characteristic phenotypic findings are curated with species-specific ontology terms, has generated a baseline set of disease phenotype descriptions for more than 7,000 Mendelian diseases (Kohler et al 2014a) as well as many thousands of descr...

Effect of SO 2 on CO 2 Capture Using Liquid-like Nanoparticle Organic Hybrid Materials

KAUST Repository

Lin, Kun-Yi Andrew

2013-08-15

Liquid-like nanoparticle organic hybrid materials (NOHMs), consisting of silica nanoparticles with a grafted polymeric canopy, were synthesized. Previous work on NOHMs has revealed that CO2 capture behaviors in these hybrid materials can be tuned by modifying the structure of the polymeric canopy. Because SO2, which is another acidic gas found in flue gas, would also interact with NOHMs, this study was designed to investigate its effect on CO2 capture in NOHMs. In particular, CO2 capture capacities as well as swelling and CO2 packing behaviors of NOHMs were analyzed using thermogravimetric analyses and Raman and attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopies before and after exposure of NOHMs to SO2. It was found that the SO2 absorption in NOHMs was only prominent at high SO2 levels (i.e., 3010 ppm; Ptot = 0.4 MPa) far exceeding the typical SO2 concentration in flue gas. As expected, the competitive absorption between SO2 and CO2 for the same absorption sites (i.e., ether and amine groups) resulted in a decreased CO2 capture capacity of NOHMs. The swelling of NOHMs was not notably affected by the presence of SO 2 within the given concentration range (Ptot = 0-0.68 MPa). On the other hand, SO2, owing to its Lewis acidic nature, interacted with the ether groups of the polymeric canopy and, thus, changed the CO2 packing behaviors in NOHMs. © 2013 American Chemical Society.

Effect of SO 2 on CO 2 Capture Using Liquid-like Nanoparticle Organic Hybrid Materials

KAUST Repository

Lin, Kun-Yi Andrew; Petit, Camille; Park, Ah-Hyung Alissa

2013-01-01

Liquid-like nanoparticle organic hybrid materials (NOHMs), consisting of silica nanoparticles with a grafted polymeric canopy, were synthesized. Previous work on NOHMs has revealed that CO2 capture behaviors in these hybrid materials can be tuned by modifying the structure of the polymeric canopy. Because SO2, which is another acidic gas found in flue gas, would also interact with NOHMs, this study was designed to investigate its effect on CO2 capture in NOHMs. In particular, CO2 capture capacities as well as swelling and CO2 packing behaviors of NOHMs were analyzed using thermogravimetric analyses and Raman and attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopies before and after exposure of NOHMs to SO2. It was found that the SO2 absorption in NOHMs was only prominent at high SO2 levels (i.e., 3010 ppm; Ptot = 0.4 MPa) far exceeding the typical SO2 concentration in flue gas. As expected, the competitive absorption between SO2 and CO2 for the same absorption sites (i.e., ether and amine groups) resulted in a decreased CO2 capture capacity of NOHMs. The swelling of NOHMs was not notably affected by the presence of SO 2 within the given concentration range (Ptot = 0-0.68 MPa). On the other hand, SO2, owing to its Lewis acidic nature, interacted with the ether groups of the polymeric canopy and, thus, changed the CO2 packing behaviors in NOHMs. © 2013 American Chemical Society.

Chemical processes in neutron capture therapy

International Nuclear Information System (INIS)

Brown, B.J.

1975-01-01

Research into the radiation chemical effects of neutron capture therapy are described. In the use of neutron capture therapy for the treatment of brain tumours, compounds containing an activatable nuclide are selectively concentrated within tumour tissue and irradiated with neutrons. Target compounds for use in therapy must accumulate selectively in high concentrations in the tumour and must be non toxic to the patient. The most suitable of these are the boron hydrides. Radiation dosages, resulting from neutron capture in normal tissue constituents are tabulated. As part of the program to study the radiation-induced chemical processes undergone by boron target compounds, the radiolytic degredation of boron hydride and phenyl boric acid system was investigated. No direct dependence between the yield of the transient radiolytic species and the concentration of the B-compound was observed. (author)

Partial radiative capture of resonance neutrons

International Nuclear Information System (INIS)

Samour, C.

1969-01-01

The radiative capture of resonance neutrons has been studied near the Saclay linac between 0.5 and 700 eV with time-of-flight method and a Ge(Li) detector. 195 Pt + n and 183 W + n allow the study of the distribution of partial radiative widths and their eventual correlation and also the variation of γ i > with E γ . The mean values of Ml and El transition intensities are compared in several tin isotopes. Interference effects, either between resonances or between direct capture and resonant capture are found in 195 Pt + n, 197 Au + n and 59 Co + n. The excited level schemes of a great deal of nuclei are obtained and compared with theoretical predictions. This study has been completed by an analysis of thermal spectrum. (author) [fr

Simulation of the capture process in the Fermilab Booster

International Nuclear Information System (INIS)

Stahl, S.; Ankenbrandt, C.

1987-01-01

A progress report on efforts to understand and improve adiabatic capture in the Fermilab Booster by experiment and simulation is presented. In particular, a new Rf voltage program for capture which ameliorates transverse space-charge effects is described and simulated

The effect of waaL genes deletion from Yersinia enterocolitica O:3 genome on bacteria LPS’ phenotype

Directory of Open Access Journals (Sweden)

Shevchenko J. I.

2014-11-01

Full Text Available Aim. To estimate WaaL ligase contribution in the lipopolysaccharide (LPS phenotype profile formation of Y. enterocolitica O:3 (YeO3 bacteria. Methods. The waaL-knock-out mutants were created by an allelic exchange strategy. The LPS phenotypes of created mutants were visualized by silver-stained DOC-PAGE and immunoblotting with specific outer core (core oligosaccharide, hexasaccharide, OC and O-polysaccharide (OPS or O-Ag monoclonal antibodies. Results. Deletion of waaLOS gene from YeO3 genome has a marked effect on OC ligation in either single or double mutants. The waaLPS deletion has an opposite effect on the OPS ligation – barely detected increasing of OPS bands. Conclusions. The LPS ligases of YeO3 exhibit relaxed donor substrate specificity. Under given conditions the effect of WaaLOS ligase is more significant for OC and OPS ligation onto lipid A than that of WaaLPS.

Genetic and Computational Approaches for Studying Plant Development and Abiotic Stress Responses Using Image-Based Phenotyping

Science.gov (United States)

Campbell, M. T.; Walia, H.; Grondin, A.; Knecht, A.

2017-12-01

The development of abiotic stress tolerant crops (i.e. drought, salinity, or heat stress) requires the discovery of DNA sequence variants associated with stress tolerance-related traits. However, many traits underlying adaptation to abiotic stress involve a suite of physiological pathways that may be induced at different times throughout the duration of stress. Conventional single-point phenotyping approaches fail to fully capture these temporal responses, and thus downstream genetic analysis may only identify a subset of the genetic variants that are important for adaptation to sub-optimal environments. Although genomic resources for crops have advanced tremendously, the collection of phenotypic data for morphological and physiological traits is laborious and remains a significant bottleneck in bridging the phenotype-genotype gap. In recent years, the availability of automated, image-based phenotyping platforms has provided researchers with an opportunity to collect morphological and physiological traits non-destructively in a highly controlled environment. Moreover, these platforms allow abiotic stress responses to be recorded throughout the duration of the experiment, and have facilitated the use of function-valued traits for genetic analyses in major crops. We will present our approaches for addressing abiotic stress tolerance in cereals. This talk will focus on novel open-source software to process and extract biological meaningful data from images generated from these phenomics platforms. In addition, we will discuss the statistical approaches to model longitudinal phenotypes and dissect the genetic basis of dynamic responses to these abiotic stresses throughout development.

Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia

DEFF Research Database (Denmark)

Wesolowska, Agata; Dalgaard, M. D.; Borst, L.

2011-01-01

designed a cost-effective, high-throughput capture assay of â¼25â000 clinically relevant SNPs, and demonstrated that multiple samples can be tagged and pooled before genome capture in targeted enrichment with a sufficient sequencing depth for genotyping. This multiplexed, targeted sequencing method allows...... exploration of the impact of pharmacogenetics on efficacy and toxicity in childhood ALL treatment, which will be of importance for personalized chemotherapy.Leukemia advance online publication, 18 March 2011; doi:10.1038/leu.2011.32....

Novel R pipeline for analyzing Biolog Phenotypic MicroArray data.

Directory of Open Access Journals (Sweden)

Minna Vehkala

Full Text Available Data produced by Biolog Phenotype MicroArrays are longitudinal measurements of cells' respiration on distinct substrates. We introduce a three-step pipeline to analyze phenotypic microarray data with novel procedures for grouping, normalization and effect identification. Grouping and normalization are standard problems in the analysis of phenotype microarrays defined as categorizing bacterial responses into active and non-active, and removing systematic errors from the experimental data, respectively. We expand existing solutions by introducing an important assumption that active and non-active bacteria manifest completely different metabolism and thus should be treated separately. Effect identification, in turn, provides new insights into detecting differing respiration patterns between experimental conditions, e.g. between different combinations of strains and temperatures, as not only the main effects but also their interactions can be evaluated. In the effect identification, the multilevel data are effectively processed by a hierarchical model in the Bayesian framework. The pipeline is tested on a data set of 12 phenotypic plates with bacterium Yersinia enterocolitica. Our pipeline is implemented in R language on the top of opm R package and is freely available for research purposes.

Effects of phenotypes in heterocyclic aromatic amine (HCA) metabolism-related genes on the association of HCA intake with the risk of colorectal adenomas.

Science.gov (United States)

Barbir, Aline; Linseisen, Jakob; Hermann, Silke; Kaaks, Rudolf; Teucher, Birgit; Eichholzer, Monika; Rohrmann, Sabine

2012-09-01

Heterocyclic aromatic amines (HCA), formed by high-temperature cooking of meat, are well-known risk factors for colorectal cancer (CRC). Enzymes metabolizing HCAs may influence the risk of CRC depending on the enzyme activity level. We aimed to assess effect modification by polymorphisms in the HCA-metabolizing genes on the association of HCA intake with colorectal adenoma (CRA) risk, which are precursors of CRC. A case-control study nested in the EPIC-Heidelberg cohort was conducted. Between 1994 and 2005, 413 adenoma cases were identified and 796 controls were matched to cases. Genotypes were determined and used to predict phenotypes (i.e., enzyme activities). Odds ratios (OR) and corresponding 95 % confidence intervals (CI) were calculated by logistic regression analysis. CRA risk was positively associated with PhIP, MeIQx, and DiMeIQx (p trend = 0.006, 0.022, and 0.045, respectively) intake. SULT1A1 phenotypes modified the effect of MeIQx on CRA risk (p (Interaction) > 0.01) such that the association of MeIQx intake with CRA was stronger for slow than for normal phenotypes. Other modifying effects by phenotypes did not reach statistical significance. HCA intake is positively associated with CRA risk, regardless of phenotypes involved in the metabolizing process. Due to the number of comparisons made in the analysis, the modifying effect of SULT1A1 on the association of HCA intake with CRA risk may be due to chance.

How within-group behavioural variation and task efficiency enhance fitness in a social group.

Science.gov (United States)

Pruitt, Jonathan N; Riechert, Susan E

2011-04-22

How task specialization, individual task performance and within-group behavioural variation affects fitness is a longstanding and unresolved problem in our understanding of animal societies. In the temperate social spider, Anelosimus studiosus, colony members exhibit a behavioural polymorphism; females either exhibit an aggressive 'asocial' or docile 'social' phenotype. We assessed individual prey-capture success for both phenotypes, and the role of phenotypic composition on group-level prey-capture success for three prey size classes. We then estimated the effect of group phenotypic composition on fitness in a common garden, as inferred from individual egg-case masses. On average, asocial females were more successful than social females at capturing large prey, and colony-level prey-capture success was positively associated with the frequency of the asocial phenotype. Asocial colony members were also more likely to engage in prey-capture behaviour in group-foraging situations. Interestingly, our fitness estimates indicate females of both phenotypes experience increased fitness when occupying colonies containing unlike individuals. These results imply a reciprocal fitness benefit of within-colony behavioural variation, and perhaps division of labour in a spider society.

Towards Automated Large-Scale 3D Phenotyping of Vineyards under Field Conditions

Directory of Open Access Journals (Sweden)

Johann Christian Rose

2016-12-01

Full Text Available In viticulture, phenotypic data are traditionally collected directly in the field via visual and manual means by an experienced person. This approach is time consuming, subjective and prone to human errors. In recent years, research therefore has focused strongly on developing automated and non-invasive sensor-based methods to increase data acquisition speed, enhance measurement accuracy and objectivity and to reduce labor costs. While many 2D methods based on image processing have been proposed for field phenotyping, only a few 3D solutions are found in the literature. A track-driven vehicle consisting of a camera system, a real-time-kinematic GPS system for positioning, as well as hardware for vehicle control, image storage and acquisition is used to visually capture a whole vine row canopy with georeferenced RGB images. In the first post-processing step, these images were used within a multi-view-stereo software to reconstruct a textured 3D point cloud of the whole grapevine row. A classification algorithm is then used in the second step to automatically classify the raw point cloud data into the semantic plant components, grape bunches and canopy. In the third step, phenotypic data for the semantic objects is gathered using the classification results obtaining the quantity of grape bunches, berries and the berry diameter.

Individual differences in working memory capacity predict learned control over attentional capture.

Science.gov (United States)

Robison, Matthew K; Unsworth, Nash

2017-11-01

Although individual differences in working memory capacity (WMC) typically predict susceptibility to attentional capture in various paradigms (e.g., Stroop, antisaccade, flankers), it sometimes fails to correlate with the magnitude of attentional capture effects in visual search (e.g., Stokes, 2016), which is 1 of the most frequently studied tasks to study capture (Theeuwes, 2010). But some studies have shown that search modes can mitigate the effects of attentional capture (Leber & Egeth, 2006). Therefore, the present study examined whether or not the relationship between WMC and attentional capture changes as a function of the search modes available. In Experiment 1, WMC was unrelated to attentional capture, but only 1 search mode (singleton-detection) could be employed. In Experiment 2, greater WMC predicted smaller attentional capture effects, but only when multiple search modes (feature-search and singleton-detection) could be employed. Importantly this relationship was entirely independent of variation in attention control, which suggests that this effect is driven by WMC-related long-term memory differences (Cosman & Vecera, 2013a, 2013b). The present set of findings help to further our understanding of the nuanced ways in which memory and attention interact. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Causal Mechanism Graph - A new notation for capturing cause-effect knowledge in software dependability

International Nuclear Information System (INIS)

Huang, Fuqun; Smidts, Carol

2017-01-01

Understanding cause-effect relations between concepts in software dependability engineering is fundamental to various research or industrial activities. Cognitive maps are traditionally used to elicit and represent such knowledge; however they seem incapable of accurately representing complex causal mechanisms in dependability engineering. This paper proposes a new notation called Causal Mechanism Graph (CMG) to elicit and represent the cause-effect domain knowledge embedded in experts’ minds or described in the literature. CMG contains a new set of symbols elicited from domain experts to capture the recurring interaction mechanisms between multiple concepts in software dependability engineering. Furthermore, compared to major existing graphic methods, CMG is particularly robust and suitable for mental knowledge elicitation: it allows one to represent the full range of cause-effect knowledge, accurately or fuzzily as one sees fit depending on the depth of knowledge he/she has. This feature combined with excellent reliability and validity poses CMG as a promising method that has the potential to be used in various areas, such as software dependability requirement elicitation, software dependability assessment and dependability risk control. - Highlights: • A new notation CMG for capturing cause-effect conceptual knowledge in software dependability. • CMG is particularly robust and suitable for mental knowledge representation. • CMG is a visual representation that bridges mental knowledge, natural and mathematical language. • CMG possesses excellent representation capability, validity and inter-coder reliability. • CMG is a fundamental method for various areas in dependability engineering.

Asthma phenotypes in childhood.

Science.gov (United States)

Reddy, Monica B; Covar, Ronina A

2016-04-01

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

Simulation of the capture process in the Fermilab Booster

International Nuclear Information System (INIS)

Stahl, S.; Ankenbrandt, C.

1987-09-01

A progress report on efforts to understand and improve adiabatic capture in the Fermilab Booster by experiment and simulation is presented. In particular, a new RF voltage program for capture which ameliorates transverse space-charge effects is described and simulated. 7 refs., 4 figs

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

NARCIS (Netherlands)

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

2014-01-01

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

Capture by colour: evidence for dimension-specific singleton capture.

Science.gov (United States)

Harris, Anthony M; Becker, Stefanie I; Remington, Roger W

2015-10-01

Previous work on attentional capture has shown the attentional system to be quite flexible in the stimulus properties it can be set to respond to. Several different attentional "modes" have been identified. Feature search mode allows attention to be set for specific features of a target (e.g., red). Singleton detection mode sets attention to respond to any discrepant item ("singleton") in the display. Relational search sets attention for the relative properties of the target in relation to the distractors (e.g., redder, larger). Recently, a new attentional mode was proposed that sets attention to respond to any singleton within a particular feature dimension (e.g., colour; Folk & Anderson, 2010). We tested this proposal against the predictions of previously established attentional modes. In a spatial cueing paradigm, participants searched for a colour target that was randomly either red or green. The nature of the attentional control setting was probed by presenting an irrelevant singleton cue prior to the target display and assessing whether it attracted attention. In all experiments, the cues were red, green, blue, or a white stimulus rapidly rotated (motion cue). The results of three experiments support the existence of a "colour singleton set," finding that all colour cues captured attention strongly, while motion cues captured attention only weakly or not at all. Notably, we also found that capture by motion cues in search for colour targets was moderated by their frequency; rare motion cues captured attention (weakly), while frequent motion cues did not.

Materials For Gas Capture, Methods Of Making Materials For Gas Capture, And Methods Of Capturing Gas

KAUST Repository

Polshettiwar, Vivek

2013-06-20

In accordance with the purpose(s) of the present disclosure, as embodied and broadly described herein, embodiments of the present disclosure, in one aspect, relate to materials that can be used for gas (e.g., CO.sub.2) capture, methods of making materials, methods of capturing gas (e.g., CO.sub.2), and the like, and the like.

Determination of cost-effective operating condition for CO{sub 2} capturing using 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid

Energy Technology Data Exchange (ETDEWEB)

Ali, Emad; Alnashef, Inas; Ajbar, Abdelhamid; Mulyono, Sarwono; Hadj-Kali, Mohamed Kamel [King Saud University, Riyadh (Saudi Arabia); Hizaddin, Hanee Farzana [University of Malaya, Kuala Lumpur (Malaysia)

2013-11-15

1-Butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) ionic liquid (IL) is considered for CO{sub 2} capturing in a typical absorption/stripper process. The use of ionic liquids is considered to be cost-effective because it requires less energy for solvent recovery compared to other conventional processes. A mathematical model was developed for the process based on Peng-Robinson (PR) equation of state (EoS). The model was validated with experimental data for CO{sub 2} solubility in [BMIM][BF4]. The model is utilized to study the sorbent effect and energy demand for selected operating pressure at specific CO{sub 2} capturing rates. The energy demand is expressed by the vapor-liquid equilibrium temperature necessary to remove the captured CO{sub 2} from the spent solvent in the regeneration step. It is found that low recovery temperature can be achieved at specific pressure combination for the absorber/stripper units. In fact, the temperature requirement is less than that required by the typical monoethanolamine (MEA) solvent. The effect of the CO{sub 2} loading in the sorbent stream on the process performance is also examined.

The influence of anisotropy on capture zone analysis

International Nuclear Information System (INIS)

Hansen, K.

1995-01-01

Approximately 50,000 gallons of various grades of gasoline and aviation fuel were leaked into silty clay overburden overlying phyllite of the Wissahickon Formation. Pumping tests and measurements of water table recovery from recovery and production wells suggested that elliptical cones of depression were caused by anisotropic groundwater flow in steeply dipping fractures trending between N60 degree E and N75 degree E which were formed by weathered metamorphic foliation. Fracture trace analysis, outcrop measurements, borehole camera surveys, straddle packer testing, and test excavations supported this conceptual model for hydraulic conductivity. Using both quantitative and semi-quantitative methods, the magnitude of anisotropy was calculated from both pumping tests and water table recovery data. Calculated anisotropies showed variations related to the particular method of analysis. Simulations of capture zones using numerical techniques indicated that anisotropic conditions had produced actual capture zones influenced by groundwater flow not orthogonal to equipotential lines. Capture zone shapes were significantly distorted along the primary axis of anisotropy within the range of variation in anisotropy (n) measured by the different analysis methods. Using the mean value of anisotropy from this site (n = 14), actual recovery well capture areas were subsequently corrected for anisotropic effects. The use of capture areas corrected for the mean value of anisotropy enabled more effective placement of subsequent recovery wells. The relatively consistent foliation of rocks in the Wissahickon Formation suggested that capture zone correction should be considered when developing recovery strategies in aquifer systems where anisotropic conditions are likely

Effects of the number of people on efficient capture and sample collection: A lion case study

Directory of Open Access Journals (Sweden)

Sam M. Ferreira

2013-05-01

Full Text Available Certain carnivore research projects and approaches depend on successful capture of individuals of interest. The number of people present at a capture site may determine success of a capture. In this study 36 lion capture cases in the Kruger National Park were used to evaluate whether the number of people present at a capture site influenced lion response rates and whether the number of people at a sampling site influenced the time it took to process the collected samples. The analyses suggest that when nine or fewer people were present, lions appeared faster at a call-up locality compared with when there were more than nine people. The number of people, however, did not influence the time it took to process the lions. It is proposed that efficient lion capturing should spatially separate capture and processing sites and minimise the number of people at a capture site.

Effects of the number of people on efficient capture and sample collection: a lion case study.

Science.gov (United States)

Ferreira, Sam M; Maruping, Nkabeng T; Schoultz, Darius; Smit, Travis R

2013-05-24

Certain carnivore research projects and approaches depend on successful capture of individuals of interest. The number of people present at a capture site may determine success of a capture. In this study 36 lion capture cases in the Kruger National Park were used to evaluate whether the number of people present at a capture site influenced lion response rates and whether the number of people at a sampling site influenced the time it took to process the collected samples. The analyses suggest that when nine or fewer people were present, lions appeared faster at a call-up locality compared with when there were more than nine people. The number of people, however, did not influence the time it took to process the lions. It is proposed that efficient lion capturing should spatially separate capture and processing sites and minimise the number of people at a capture site.

Computational materials chemistry for carbon capture using porous materials

International Nuclear Information System (INIS)

Sharma, Abhishek; Malani, Ateeque; Huang, Runhong; Babarao, Ravichandar

2017-01-01

Control over carbon dioxide (CO 2 ) release is extremely important to decrease its hazardous effects on the environment such as global warming, ocean acidification, etc. For CO 2 capture and storage at industrial point sources, nanoporous materials offer an energetically viable and economically feasible approach compared to chemisorption in amines. There is a growing need to design and synthesize new nanoporous materials with enhanced capability for carbon capture. Computational materials chemistry offers tools to screen and design cost-effective materials for CO 2 separation and storage, and it is less time consuming compared to trial and error experimental synthesis. It also provides a guide to synthesize new materials with better properties for real world applications. In this review, we briefly highlight the various carbon capture technologies and the need of computational materials design for carbon capture. This review discusses the commonly used computational chemistry-based simulation methods for structural characterization and prediction of thermodynamic properties of adsorbed gases in porous materials. Finally, simulation studies reported on various potential porous materials, such as zeolites, porous carbon, metal organic frameworks (MOFs) and covalent organic frameworks (COFs), for CO 2 capture are discussed. (topical review)

Interatomic Coulombic electron capture

International Nuclear Information System (INIS)

Gokhberg, K.; Cederbaum, L. S.

2010-01-01

In a previous publication [K. Gokhberg and L. S. Cederbaum, J. Phys. B 42, 231001 (2009)] we presented the interatomic Coulombic electron capture process--an efficient electron capture mechanism by atoms and ions in the presence of an environment. In the present work we derive and discuss the mechanism in detail. We demonstrate thereby that this mechanism belongs to a family of interatomic electron capture processes driven by electron correlation. In these processes the excess energy released in the capture event is transferred to the environment and used to ionize (or to excite) it. This family includes the processes where the capture is into the lowest or into an excited unoccupied orbital of an atom or ion and proceeds in step with the ionization (or excitation) of the environment, as well as the process where an intermediate autoionizing excited resonance state is formed in the capturing center which subsequently deexcites to a stable state transferring its excess energy to the environment. Detailed derivation of the asymptotic cross sections of these processes is presented. The derived expressions make clear that the environment assisted capture processes can be important for many systems. Illustrative examples are presented for a number of model systems for which the data needed to construct the various capture cross sections are available in the literature.

Preclinical studies on gadolinium neutron capture therapy

International Nuclear Information System (INIS)

Akine, Yasuyuki

1994-01-01

Gadolinium neutron capture therapy is based on radiations (photons and electrons) produced in the tumor by a nuclear reaction between gadolinium and lower-energy neutrons. Studies with Chinese hamster cells have shown that the radiation effect resulting from gadolinium neutron capture reactions is mostly of low LET and that released electrons are the significant component in the over-all dose. Biological dosimetry revealed that the dose does not seem to increase in proportion to the gadolinium concentration, leading to a conclusion that there is a range of gadolinium concentrations most efficient for gadolinium neutron capture therapy. The in vivo studies with transplantable tumors in mice and rabbits have revealed that close contact between gadolinium and the cell is not necessarily required for cell inactivation and that gadolinium delivery selective to tumors is crucial. The results show that the potential of gadolinium neutron capture therapy as a therapeutic modality appears very promising. (author)

Phenotypic equilibrium as probabilistic convergence in multi-phenotype cell population dynamics.

Directory of Open Access Journals (Sweden)

Da-Quan Jiang

Full Text Available We consider the cell population dynamics with n different phenotypes. Both the Markovian branching process model (stochastic model and the ordinary differential equation (ODE system model (deterministic model are presented, and exploited to investigate the dynamics of the phenotypic proportions. We will prove that in both models, these proportions will tend to constants regardless of initial population states ("phenotypic equilibrium" under weak conditions, which explains the experimental phenomenon in Gupta et al.'s paper. We also prove that Gupta et al.'s explanation is the ODE model under a special assumption. As an application, we will give sufficient and necessary conditions under which the proportion of one phenotype tends to 0 (die out or 1 (dominate. We also extend our results to non-Markovian cases.

CAPTURE OF PLANETESIMALS BY GAS DRAG FROM CIRCUMPLANETARY DISKS

International Nuclear Information System (INIS)

Fujita, Tetsuya; Ohtsuki, Keiji; Suetsugu, Ryo; Tanigawa, Takayuki

2013-01-01

Growing giant planets have circumplanetary disks around them in the late stage of their formation if their mass is sufficiently large. We examine capture of relatively large planetesimals that are decoupled from the gas inflow, due to gas drag from a circumplanetary disk of a growing giant planet. Assuming that the structure of the circumplanetary disk is axisymmetric, and solving the three-body problem including gas drag, we perform analytic and numerical calculations for capture of planetesimals. When planetesimal random velocity is small, planetesimals approaching in the retrograde direction are more easily captured, owing to their larger velocity relative to the gas. Planetesimals with large orbital inclinations interact with the disk for a short period of time and show lower capture rates. The effect of ablation on capture rates seems insignificant, although mass loss due to ablation would be significant in the case of high random velocity. We also examine the effect of non-uniform radial distribution of planetesimals in the protoplanetary disk due to gap opening by the planet. When the random velocity of planetesimals is small, the planetesimal capture rate decreases rapidly as the half width of the gap in the planetesimal disk increases from two planetary Hill radii to three planetary Hill radii; planetesimals with low random velocities cannot approach the planet in the case of a sufficiently wide gap. Our results show that the radial distribution and random velocity of planetesimals in the protoplanetary disk are essentially important for the understanding of capture of planetesimals by circumplanetary disks

Knowledge-based analysis of phenotypes

KAUST Repository

Hoendorf, Robert

2016-01-27

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

The potential indirect effects among plants via shared hummingbird pollinators are structured by phenotypic similarity.

Science.gov (United States)

Bergamo, Pedro Joaquim; Wolowski, Marina; Maruyama, Pietro Kiyoshi; Vizentin-Bugoni, Jeferson; Carvalheiro, Luísa G; Sazima, Marlies

2017-07-01

Plant species within communities may overlap in pollinators' use and influence visitation patterns of shared pollinators, potentially engaging in indirect interactions (e.g., facilitation or competition). While several studies have explored the mechanisms regulating insect-pollination networks, there is a lack of studies on bird-pollination systems, particularly in species-rich tropical areas. Here, we evaluated if phenotypic similarity, resource availability (floral abundance), evolutionary relatedness and flowering phenology affect the potential for indirect effects via shared pollinators in hummingbird-pollinated plant species within four communities in the Brazilian Atlantic forest. Among the evaluated factors, phenotypic similarity (corolla length and anther height) was the most important variable, while resource availability (floral abundance) had a secondary importance. On the other hand, evolutionary relatedness and flowering phenology were less important, which altogether highlights the relevance of convergent evolution and that the contribution of a plant to the diet of the pollinators of another plant is independent of the level of temporal overlap in flowering in this tropical system. Interestingly, our findings contrast with results from multiple insect-pollinated plant communities, mostly from temperate regions, in which floral abundance was the most important driver, followed by evolutionary relatedness and phenotypic similarity. We propose that these contrasting results are due to high level of specialization inherent to tropical hummingbird-pollination systems. Moreover, our results demonstrated that factors defining linkage rules of plant-hummingbird networks also determinate plant-plant potential indirect effects. Future studies are needed to test if these findings can be generalized to other highly specialized systems. Overall, our results have important implications for the understanding of ecological processes due resource sharing in

The Phenotypic Effects of Royal Jelly on Wild-Type D. melanogaster Are Strain-Specific

OpenAIRE

Morgan, Stefanie L.; Seggio, Joseph A.; Nascimento, Nara F.; Huh, Dana D.; Hicks, Jasmin A.; Sharp, Katherine A.; Axelrod, Jeffrey D.; Wang, Kevin C.

2016-01-01

The role for royal jelly (RJ) in promoting caste differentiation of honeybee larvae into queens rather than workers is well characterized. A recent study demonstrated that this poorly understood complex nutrition drives strikingly similar phenotypic effects in Drosophila melanogaster, such as increased body size and reduced developmental time, making possible the use of D. melanogaster as a model system for the genetic analysis of the cellular mechanisms underlying RJ and caste differentiatio...

Recent enlightening strategies for co2 capture: a review

Science.gov (United States)

Yuan, Peng; Qiu, Ziyang; Liu, Jia

2017-05-01

The global climate change has seriously affected the survival and prosperity of mankind, where greenhouse effect owing to atmospheric carbon dioxide (CO2) enrichment is a great cause. Accordingly, a series of down-to-earth measures need to be implemented urgently to control the output of CO2. As CO2 capture appears as a core issue in developing low-carbon economy, this review provides a comprehensive introduction of recent CO2 capture technologies used in power plants or other industries. Strategies for CO2 capture, e.g. pre-combustion, post-combustion and oxyfuel combustion, are covered in this article. Another enlightening technology for CO2 capture based on fluidized beds is intensively discussed.

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

Directory of Open Access Journals (Sweden)

Juliana Maria de Paula

2017-08-01

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

Targeted next-generation sequencing reveals novel USH2A mutations associated with diverse disease phenotypes: implications for clinical and molecular diagnosis.

Science.gov (United States)

Chen, Xue; Sheng, Xunlun; Liu, Xiaoxing; Li, Huiping; Liu, Yani; Rong, Weining; Ha, Shaoping; Liu, Wenzhou; Kang, Xiaoli; Zhao, Kanxing; Zhao, Chen

2014-01-01

USH2A mutations have been implicated in the disease etiology of several inherited diseases, including Usher syndrome type 2 (USH2), nonsyndromic retinitis pigmentosa (RP), and nonsyndromic deafness. The complex genetic and phenotypic spectrums relevant to USH2A defects make it difficult to manage patients with such mutations. In the present study, we aim to determine the genetic etiology and to characterize the correlated clinical phenotypes for three Chinese pedigrees with nonsyndromic RP, one with RP sine pigmento (RPSP), and one with USH2. Family histories and clinical details for all included patients were reviewed. Ophthalmic examinations included best corrected visual acuities, visual field measurements, funduscopy, and electroretinography. Targeted next-generation sequencing (NGS) was applied using two sequence capture arrays to reveal the disease causative mutations for each family. Genotype-phenotype correlations were also annotated. Seven USH2A mutations, including four missense substitutions (p.P2762A, p.G3320C, p.R3719H, and p.G4763R), two splice site variants (c.8223+1G>A and c.8559-2T>C), and a nonsense mutation (p.Y3745*), were identified as disease causative in the five investigated families, of which three reported to have consanguineous marriage. Among all seven mutations, six were novel, and one was recurrent. Two homozygous missense mutations (p.P2762A and p.G3320C) were found in one individual family suggesting a potential double hit effect. Significant phenotypic divergences were revealed among the five families. Three families of the five families were affected with early, moderated, or late onset RP, one with RPSP, and the other one with USH2. Our study expands the genotypic and phenotypic variability relevant to USH2A mutations, which would help with a clear insight into the complex genetic and phenotypic spectrums relevant to USH2A defects, and is complementary for a better management of patients with such mutations. We have also

Effects of paternal phenotype and environmental variability on age and size at maturity in a male dimorphic mite

Science.gov (United States)

Smallegange, Isabel M.

2011-04-01

Investigating how the environment affects age and size at maturity of individuals is crucial to understanding how changes in the environment affect population dynamics through the biology of a species. Paternal phenotype, maternal, and offspring environment may crucially influence these traits, but to my knowledge, their combined effects have not yet been tested. Here, I found that in bulb mites ( Rhizoglyphus robini), maternal nutrition, offspring nutrition, and paternal phenotype (males are fighters, able to kill other mites, or benign scramblers) interactively affected offspring age and size at maturity. The largest effect occurred when both maternal and offspring nutrition was poor: in that case offspring from fighter sires required a significantly longer development time than offspring from scrambler sires. Investigating parental effects on the relationship between age and size at maturity revealed no paternal effects, and only for females was its shape influenced by maternal nutrition. Overall, this reaction norm was nonlinear. These non-genetic intergenerational effects may play a complex, yet unexplored role in influencing population fluctuations—possibly explaining why results from field studies often do not match theoretical predictions on maternal effects on population dynamics.

The evolution of multivariate maternal effects.

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Bram Kuijper

2014-04-01

Full Text Available There is a growing interest in predicting the social and ecological contexts that favor the evolution of maternal effects. Most predictions focus, however, on maternal effects that affect only a single character, whereas the evolution of maternal effects is poorly understood in the presence of suites of interacting traits. To overcome this, we simulate the evolution of multivariate maternal effects (captured by the matrix M in a fluctuating environment. We find that the rate of environmental fluctuations has a substantial effect on the properties of M: in slowly changing environments, offspring are selected to have a multivariate phenotype roughly similar to the maternal phenotype, so that M is characterized by positive dominant eigenvalues; by contrast, rapidly changing environments favor Ms with dominant eigenvalues that are negative, as offspring favor a phenotype which substantially differs from the maternal phenotype. Moreover, when fluctuating selection on one maternal character is temporally delayed relative to selection on other traits, we find a striking pattern of cross-trait maternal effects in which maternal characters influence not only the same character in offspring, but also other offspring characters. Additionally, when selection on one character contains more stochastic noise relative to selection on other traits, large cross-trait maternal effects evolve from those maternal traits that experience the smallest amounts of noise. The presence of these cross-trait maternal effects shows that individual maternal effects cannot be studied in isolation, and that their study in a multivariate context may provide important insights about the nature of past selection. Our results call for more studies that measure multivariate maternal effects in wild populations.

The evolution of multivariate maternal effects.

Science.gov (United States)

Kuijper, Bram; Johnstone, Rufus A; Townley, Stuart

2014-04-01

There is a growing interest in predicting the social and ecological contexts that favor the evolution of maternal effects. Most predictions focus, however, on maternal effects that affect only a single character, whereas the evolution of maternal effects is poorly understood in the presence of suites of interacting traits. To overcome this, we simulate the evolution of multivariate maternal effects (captured by the matrix M) in a fluctuating environment. We find that the rate of environmental fluctuations has a substantial effect on the properties of M: in slowly changing environments, offspring are selected to have a multivariate phenotype roughly similar to the maternal phenotype, so that M is characterized by positive dominant eigenvalues; by contrast, rapidly changing environments favor Ms with dominant eigenvalues that are negative, as offspring favor a phenotype which substantially differs from the maternal phenotype. Moreover, when fluctuating selection on one maternal character is temporally delayed relative to selection on other traits, we find a striking pattern of cross-trait maternal effects in which maternal characters influence not only the same character in offspring, but also other offspring characters. Additionally, when selection on one character contains more stochastic noise relative to selection on other traits, large cross-trait maternal effects evolve from those maternal traits that experience the smallest amounts of noise. The presence of these cross-trait maternal effects shows that individual maternal effects cannot be studied in isolation, and that their study in a multivariate context may provide important insights about the nature of past selection. Our results call for more studies that measure multivariate maternal effects in wild populations.

Feature-based attention is functionally distinct from relation-based attention: The double dissociation between color-based capture and color-relation-based capture of attention.

Science.gov (United States)

Du, Feng; Jiao, Jun

2016-04-01

The present study used a spatial blink task and a cuing task to examine the boundary between feature-based capture and relation-based capture. Feature-based capture occurs when distractors match the target feature such as target color. The occurrence of relation-based capture is contingent upon the feature relation between target and distractor (e.g., color relation). The results show that color distractors that match the target-nontarget color relation do not consistently capture attention when they appear outside of the attentional window, but distractors appearing outside the attentional window that match the target color consistently capture attention. In contrast, color distractors that best match the target-nontarget color relation but not the target color, are more likely to capture attention when they appear within the attentional window. Consistently, color cues that match the target-nontarget color relation produce a cuing effect when they appear within the attentional window, while target-color matched cues do not. Such a double dissociation between color-based capture and color-relation-based capture indicates functionally distinct mechanisms for these 2 types of attentional selection. This also indicates that the spatial blink task and the uninformative cuing task are measuring distinctive aspects of involuntary attention. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Deep Phenotyping: Deep Learning For Temporal Phenotype/Genotype Classification

OpenAIRE

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

2017-01-01

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

Multi-scale modeling of carbon capture systems

Energy Technology Data Exchange (ETDEWEB)

Kress, Joel David [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-03-03

The development and scale up of cost effective carbon capture processes is of paramount importance to enable the widespread deployment of these technologies to significantly reduce greenhouse gas emissions. The U.S. Department of Energy initiated the Carbon Capture Simulation Initiative (CCSI) in 2011 with the goal of developing a computational toolset that would enable industry to more effectively identify, design, scale up, operate, and optimize promising concepts. The first half of the presentation will introduce the CCSI Toolset consisting of basic data submodels, steady-state and dynamic process models, process optimization and uncertainty quantification tools, an advanced dynamic process control framework, and high-resolution filtered computationalfluid- dynamics (CFD) submodels. The second half of the presentation will describe a high-fidelity model of a mesoporous silica supported, polyethylenimine (PEI)-impregnated solid sorbent for CO₂ capture. The sorbent model includes a detailed treatment of transport and amine-CO₂- H₂O interactions based on quantum chemistry calculations. Using a Bayesian approach for uncertainty quantification, we calibrate the sorbent model to Thermogravimetric (TGA) data.

The Larson Blue coat color phenotype in Holsteins: Characteristics and effects on body temperature regulation and production in lactating cows in a hot climate.

Science.gov (United States)

Dikmen, S; Dahl, G E; Cole, J B; Null, D J; Hansen, P J

2017-03-01

Here we report a previously undescribed coat color phenotype in Holstein cattle. Larson Blue Holsteins, located on a dairy in south Florida, exhibit a coloration pattern that is similar to that of black and white or red and white Holsteins except that, instead of being black or red, darker regions of the body vary in color from gray to taupe. The Larson Blue phenotype was readily apparent in young calves. The phenotype is not due to inheritance of known mutations causing coat color variation in cattle, including dominant red, Telstar, silver color dilutor, or Dun color. Three variants with moderate effects on the () gene were identified in 2 Larson blue cows. Despite being lighter in color, there was no difference in daily variation in vaginal temperature between Larson Blue and other Holsteins when recorded during the summer for cows housed in free-stall barns with shade, fans, and sprinklers. Similarly, there was no effect of the Larson Blue phenotype on seasonal variation in milk yield. Therefore, the phenotype confers no advantage in terms of response to heat stress when cattle are housed in facilities with extensive cooling.

The Human Phenotype Ontology in 2017

International Nuclear Information System (INIS)

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

2016-01-01

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

Microdosimetry for Boron Neutron Capture Therapy

International Nuclear Information System (INIS)

Maughan, R.L.; Kota, C.

2000-01-01

The specific aims of the research proposal were as follows: (1) To design and construct small volume tissue equivalent proportional counters for the dosimetry and microdosimetry of high intensity thermal and epithermal neutron beams used in BNCT, and of modified fast neutron beams designed for boron neutron capture enhanced fast neutron therapy (BNCEFNT). (2) To develop analytical methods for estimating the biological effectiveness of the absorbed dose in BNCT and BNCEFNT based on the measured microdosimetric spectra. (3) To develop an analytical framework for comparing the biological effectiveness of different epithermal neutron beams used in BNCT and BNCEFNT, based on correlated sets of measured microdosimetric spectra and radiobiological data. Specific aims (1) and (2) were achieved in their entirety and are comprehensively documented in Jay Burmeister's Ph.D. dissertation entitled ''Specification of physical and biologically effective absorbed dose in radiation therapies utilizing the boron neutron capture reaction'' (Wayne State University, 1999). Specific aim (3) proved difficult to accomplish because of a lack of sufficient radiobiological data

Genetic variants influencing phenotypic variance heterogeneity.

Science.gov (United States)

Ek, Weronica E; Rask-Andersen, Mathias; Karlsson, Torgny; Enroth, Stefan; Gyllensten, Ulf; Johansson, Åsa

2018-03-01

Most genetic studies identify genetic variants associated with disease risk or with the mean value of a quantitative trait. More rarely, genetic variants associated with variance heterogeneity are considered. In this study, we have identified such variance single-nucleotide polymorphisms (vSNPs) and examined if these represent biological gene × gene or gene × environment interactions or statistical artifacts caused by multiple linked genetic variants influencing the same phenotype. We have performed a genome-wide study, to identify vSNPs associated with variance heterogeneity in DNA methylation levels. Genotype data from over 10 million single-nucleotide polymorphisms (SNPs), and DNA methylation levels at over 430 000 CpG sites, were analyzed in 729 individuals. We identified vSNPs for 7195 CpG sites (P mean DNA methylation levels. We further showed that variance heterogeneity between genotypes mainly represents additional, often rare, SNPs in linkage disequilibrium (LD) with the respective vSNP and for some vSNPs, multiple low frequency variants co-segregating with one of the vSNP alleles. Therefore, our results suggest that variance heterogeneity of DNA methylation mainly represents phenotypic effects by multiple SNPs, rather than biological interactions. Such effects may also be important for interpreting variance heterogeneity of more complex clinical phenotypes.

Formation of double galaxies by tidal capture

International Nuclear Information System (INIS)

Alladin, S.M.; Potdar, A.; Sastry, K.S.

1975-01-01

The conditions under which double galaxies may be formed by tidal capture are considered. Estimates for the increase in the internal energy of colliding galaxies due to tidal effects are used to determine the magnitudes Vsub(cap) and Vsub(dis) of the maximum relative velocities at infinite separation required for tidal capture and tidal disruption respectively. A double galaxy will be formed by tidal capture without tidal disruption of a component if Vsub(cap)>Vsub(i) and Vsub(cap)>Vsub(dis) where Vsub(i) is the initial relative speed of the two galaxies at infinite separation. If the two galaxies are of the same dimension, formulation of double galaxies by tidal capture is possible in a close collision either if the two galaxies do not differ much in mass and density distribution or if the more massive galaxy is less centrally concentrated than the other. If it is assumed as statistics suggest, that the mass of a galaxy is proportional to the square of its radius, it follows that the probability of the formation of double galaxies by tidal capture increases with the increase in mass of the galaxies and tidal distribution does not occur in a single collision for any distance of closest approach of the two galaxies. (Auth.)

Effect of liver disease on dextromethorphan oxidation capacity and phenotype: a study in 107 patients.

OpenAIRE

Larrey, D; Babany, G; Tinel, M; Freneaux, E; Amouyal, G; Habersetzer, F; Letteron, P; Pessayre, D

1989-01-01

1. The O-demethylation of dextromethorphan to dextrorphan exhibits a genetically-controlled polymorphism, co-segregating with that of debrisoquine hydroxylation. Dextromethorphan has been proposed as a test compound to assess drug oxidation polymorphism. 2. We studied the effects of liver disease of varying severity on dextromethorphan oxidation capacity. Phenotyping was performed using the urinary dextromethorphan/dextrorphan metabolic ratio after oral administration of 40 mg dextromethorpha...

Low energy, low cost, efficient CO{sub 2} capture

Energy Technology Data Exchange (ETDEWEB)

Michael C. Trachtenberg; Lihong Bao; David A. Smith; Remy Dumortier [Carbozyme, Inc., Monmouth Junction, NJ (United States)

2006-07-01

This paper discusses the development and some characteristics of a new, enzyme-based, contained liquid membrane contactor to capture CO{sub 2}. The enzyme carbonic anhydrase catalyzes the removal of CO{sub 2} while the membrane contactor increases the surface area to allow the reduction of the size of the system. The modular system design is easily scaled to any required size reducing the investment costs. The system captures CO{sub 2} at a low energy and low cost promising to be a cost effective technology for CO{sub 2} capture. 5 refs., 7 figs.

Are there any agricultural effects on the capture rates of male euglossine bees (Apidae: Euglossini?

Directory of Open Access Journals (Sweden)

Juan Carlos Sandino

2004-03-01

Full Text Available During 30 days male euglossine bees were bait-sampled at 12 sites, in the central Pacific coast of Colombia (ten days and four sites at each of three adjacent habitats: farmlands, highly disturbed forest and less disturbed forest and 487 individuals were captured. Most captured individuals belonged to six species, five widely distributed through the American tropics and an endemic species. Two of the frequently captured species presented no different abundances between habitats, while the other four (67.97% of all the captured individuals, all of them big sized or long-tongued, were more frequently captured at the farmlands. A cluster analysis of the data matrix for the 23 captured species and the 12 sampling sites, grouped together the farmland sites, apart from the forest sites. It is proposed that male euglossine bees from generalist, long-tongued or big sized species, forage frequently at the farmlands, where fragrance or nectar resources may be clumped, less diverse, and present an access restricted by deep corollas or by microclimatic conditions of high temperature and low humidity

Induction of appropriate Th-cell phenotypes: cellular decision-making in heterogeneous environments.

Science.gov (United States)

van den Ham, H-J; Andeweg, A C; de Boer, R J

2013-11-01

Helper T (Th)-cell differentiation is a key event in the development of the adaptive immune response. By the production of a range of cytokines, Th cells determine the type of immune response that is raised against an invading pathogen. Th cells can adopt many different phenotypes, and Th-cell phenotype decision-making is crucial in mounting effective host responses. This review discusses the different Th-cell phenotypes that have been identified and how Th cells adopt a particular phenotype. The regulation of Th-cell phenotypes has been studied extensively using mathematical models, which have explored the role of regulatory mechanisms such as autocrine cytokine signalling and cross-inhibition between self-activating transcription factors. At the single cell level, Th responses tend to be heterogeneous, but corrections can be made soon after T-cell activation. Although pathogens and the innate immune system provide signals that direct the induction of Th-cell phenotypes, these instructive mechanisms could be easily subverted by pathogens. We discuss that a model of success-driven feedback would select the most appropriate phenotype for clearing a pathogen. Given the heterogeneity in the induction phase of the Th response, such a success-driven feedback loop would allow the selection of effective Th-cell phenotypes while terminating incorrect responses. © 2013 John Wiley & Sons Ltd.

Current status of fast-neutron-capture calculations

International Nuclear Information System (INIS)

Gardner, D.G.

1982-01-01

This work is primarily concerned with the calculation of neutron capture cross sections and capture gamma-ray spectra, in the framework of the Hauser-Feshbach statistical model and for neutrons from the resonance region up to several MeV. An argument is made that, for applied purposes such as constructing evaluated cross-section libraries, nonstatistical capture mechanisms may be completely neglected at low energies and adequately approximated at high energies in a simple way. The use of gamma-ray strength functions to obtain radiation widths is emphasized. Using the reaction 89 Y + n as an example, the problems encountered in trying to construct a case that could be run equivalently on two different nuclear reaction codes are illustrated, and the effects produced by certain parameter variations are discussed

Analysis of transcription factor mRNAs in identified oxytocin and vasopressin magnocellular neurons isolated by laser capture microdissection.

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Madison Humerick

Full Text Available The oxytocin (Oxt and vasopressin (Avp magnocellular neurons (MCNs in the hypothalamus are the only neuronal phenotypes that are present in the supraoptic nucleus (SON, and are characterized by their robust and selective expression of either the Oxt or Avp genes. In this paper, we take advantage of the differential expression of these neuropeptide genes to identify and isolate these two individual phenotypes from the rat SON by laser capture microdissection (LCM, and to analyze the differential expression of several of their transcription factor mRNAs by qRT-PCR. We identify these neuronal phenotypes by stereotaxically injecting recombinant Adeno-Associated Viral (rAAV vectors which contain cell-type specific Oxt or Avp promoters that drive expression of EGFP selectively in either the Oxt or Avp MCNs into the SON. The fluorescent MCNs are then dissected by LCM using a novel Cap Road Map protocol described in this paper, and the purified MCNs are extracted for their RNAs. qRT-PCR of these RNAs show that some transcription factors (RORA and c-jun are differentially expressed in the Oxt and Avp MCNs.

GGCX-Associated Phenotypes: An Overview in Search of Genotype-Phenotype Correlations

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Eva Y. G. De Vilder

2017-01-01

Full Text Available Gamma-carboxylation, performed by gamma-glutamyl carboxylase (GGCX, is an enzymatic process essential for activating vitamin K-dependent proteins (VKDP with important functions in various biological processes. Mutations in the encoding GGCX gene are associated with multiple phenotypes, amongst which vitamin K-dependent coagulation factor deficiency (VKCFD1 is best known. Other patients have skin, eye, heart or bone manifestations. As genotype–phenotype correlations were never described, literature was systematically reviewed in search of patients with at least one GGCX mutation with a phenotypic description, resulting in a case series of 47 patients. Though this number was too low for statistically valid correlations—a frequent problem in orphan diseases—we demonstrate the crucial role of the horizontally transferred transmembrane domain in developing cardiac and bone manifestations. Moreover, natural history suggests ageing as the principal determinant to develop skin and eye symptoms. VKCFD1 symptoms seemed more severe in patients with both mutations in the same protein domain, though this could not be linked to a more perturbed coagulation factor function. Finally, distinct GGCX functional domains might be dedicated to carboxylation of very specific VKDP. In conclusion, this systematic review suggests that there indeed may be genotype–phenotype correlations for GGCX-related phenotypes, which can guide patient counseling and management.

Interoperability between phenotype and anatomy ontologies.

Science.gov (United States)

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

2010-12-15

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

Do Local Elites Capture Natural Disaster Reconstruction Funds?

OpenAIRE

Yoshito Takasaki

2009-01-01

This paper examines the allocation of natural disaster reconstruction funds among cyclone victims in rural Fiji. During post-emergency periods, when good information about cyclone damage is available, do local elites, a powerful minority, capture housing construction materials? With effective targeting in both receipt and the amount received, local elites do not capture larger benefits. More severely affected victims are not early recipients, though, because the supply of reconstruction funds...

Efficacy of Exome-Targeted Capture Sequencing to Detect Mutations in Known Cerebellar Ataxia Genes.

Science.gov (United States)

Coutelier, Marie; Hammer, Monia B; Stevanin, Giovanni; Monin, Marie-Lorraine; Davoine, Claire-Sophie; Mochel, Fanny; Labauge, Pierre; Ewenczyk, Claire; Ding, Jinhui; Gibbs, J Raphael; Hannequin, Didier; Melki, Judith; Toutain, Annick; Laugel, Vincent; Forlani, Sylvie; Charles, Perrine; Broussolle, Emmanuel; Thobois, Stéphane; Afenjar, Alexandra; Anheim, Mathieu; Calvas, Patrick; Castelnovo, Giovanni; de Broucker, Thomas; Vidailhet, Marie; Moulignier, Antoine; Ghnassia, Robert T; Tallaksen, Chantal; Mignot, Cyril; Goizet, Cyril; Le Ber, Isabelle; Ollagnon-Roman, Elisabeth; Pouget, Jean; Brice, Alexis; Singleton, Andrew; Durr, Alexandra

2018-05-01

Molecular diagnosis is difficult to achieve in disease groups with a highly heterogeneous genetic background, such as cerebellar ataxia (CA). In many patients, candidate gene sequencing or focused resequencing arrays do not allow investigators to reach a genetic conclusion. To assess the efficacy of exome-targeted capture sequencing to detect mutations in genes broadly linked to CA in a large cohort of undiagnosed patients and to investigate their prevalence. Three hundred nineteen index patients with CA and without a history of dominant transmission were included in the this cohort study by the Spastic Paraplegia and Ataxia Network. Centralized storage was in the DNA and cell bank of the Brain and Spine Institute, Salpetriere Hospital, Paris, France. Patients were classified into 6 clinical groups, with the largest being those with spastic ataxia (ie, CA with pyramidal signs [n = 100]). Sequencing was performed from January 1, 2014, through December 31, 2016. Detected variants were classified as very probably or definitely causative, possibly causative, or of unknown significance based on genetic evidence and genotype-phenotype considerations. Identification of variants in genes broadly linked to CA, classified in pathogenicity groups. The 319 included patients had equal sex distribution (160 female [50.2%] and 159 male patients [49.8%]; mean [SD] age at onset, 27.9 [18.6] years). The age at onset was younger than 25 years for 131 of 298 patients (44.0%) with complete clinical information. Consanguinity was present in 101 of 298 (33.9%). Very probable or definite diagnoses were achieved for 72 patients (22.6%), with an additional 19 (6.0%) harboring possibly pathogenic variants. The most frequently mutated genes were SPG7 (n = 14), SACS (n = 8), SETX (n = 7), SYNE1 (n = 6), and CACNA1A (n = 6). The highest diagnostic rate was obtained for patients with an autosomal recessive CA with oculomotor apraxia-like phenotype (6 of 17 [35.3%]) or

Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods.

Science.gov (United States)

Notaro, Marco; Schubach, Max; Robinson, Peter N; Valentini, Giorgio

2017-10-12

The prediction of human gene-abnormal phenotype associations is a fundamental step toward the discovery of novel genes associated with human disorders, especially when no genes are known to be associated with a specific disease. In this context the Human Phenotype Ontology (HPO) provides a standard categorization of the abnormalities associated with human diseases. While the problem of the prediction of gene-disease associations has been widely investigated, the related problem of gene-phenotypic feature (i.e., HPO term) associations has been largely overlooked, even if for most human genes no HPO term associations are known and despite the increasing application of the HPO to relevant medical problems. Moreover most of the methods proposed in literature are not able to capture the hierarchical relationships between HPO terms, thus resulting in inconsistent and relatively inaccurate predictions. We present two hierarchical ensemble methods that we formally prove to provide biologically consistent predictions according to the hierarchical structure of the HPO. The modular structure of the proposed methods, that consists in a "flat" learning first step and a hierarchical combination of the predictions in the second step, allows the predictions of virtually any flat learning method to be enhanced. The experimental results show that hierarchical ensemble methods are able to predict novel associations between genes and abnormal phenotypes with results that are competitive with state-of-the-art algorithms and with a significant reduction of the computational complexity. Hierarchical ensembles are efficient computational methods that guarantee biologically meaningful predictions that obey the true path rule, and can be used as a tool to improve and make consistent the HPO terms predictions starting from virtually any flat learning method. The implementation of the proposed methods is available as an R package from the CRAN repository.

Evaluation of bias associated with capture maps derived from nonlinear groundwater flow models

Science.gov (United States)

Nadler, Cara; Allander, Kip K.; Pohll, Greg; Morway, Eric D.; Naranjo, Ramon C.; Huntington, Justin

2018-01-01

The impact of groundwater withdrawal on surface water is a concern of water users and water managers, particularly in the arid western United States. Capture maps are useful tools to spatially assess the impact of groundwater pumping on water sources (e.g., streamflow depletion) and are being used more frequently for conjunctive management of surface water and groundwater. Capture maps have been derived using linear groundwater flow models and rely on the principle of superposition to demonstrate the effects of pumping in various locations on resources of interest. However, nonlinear models are often necessary to simulate head-dependent boundary conditions and unconfined aquifers. Capture maps developed using nonlinear models with the principle of superposition may over- or underestimate capture magnitude and spatial extent. This paper presents new methods for generating capture difference maps, which assess spatial effects of model nonlinearity on capture fraction sensitivity to pumping rate, and for calculating the bias associated with capture maps. The sensitivity of capture map bias to selected parameters related to model design and conceptualization for the arid western United States is explored. This study finds that the simulation of stream continuity, pumping rates, stream incision, well proximity to capture sources, aquifer hydraulic conductivity, and groundwater evapotranspiration extinction depth substantially affect capture map bias. Capture difference maps demonstrate that regions with large capture fraction differences are indicative of greater potential capture map bias. Understanding both spatial and temporal bias in capture maps derived from nonlinear groundwater flow models improves their utility and defensibility as conjunctive-use management tools.

Rethinking the evolution of specialization: A model for the evolution of phenotypic heterogeneity.

Science.gov (United States)

Rubin, Ilan N; Doebeli, Michael

2017-12-21

Phenotypic heterogeneity refers to genetically identical individuals that express different phenotypes, even when in the same environment. Traditionally, "bet-hedging" in fluctuating environments is offered as the explanation for the evolution of phenotypic heterogeneity. However, there are an increasing number of examples of microbial populations that display phenotypic heterogeneity in stable environments. Here we present an evolutionary model of phenotypic heterogeneity of microbial metabolism and a resultant theory for the evolution of phenotypic versus genetic specialization. We use two-dimensional adaptive dynamics to track the evolution of the population phenotype distribution of the expression of two metabolic processes with a concave trade-off. Rather than assume a Gaussian phenotype distribution, we use a Beta distribution that is capable of describing genotypes that manifest as individuals with two distinct phenotypes. Doing so, we find that environmental variation is not a necessary condition for the evolution of phenotypic heterogeneity, which can evolve as a form of specialization in a stable environment. There are two competing pressures driving the evolution of specialization: directional selection toward the evolution of phenotypic heterogeneity and disruptive selection toward genetically determined specialists. Because of the lack of a singular point in the two-dimensional adaptive dynamics and the fact that directional selection is a first order process, while disruptive selection is of second order, the evolution of phenotypic heterogeneity dominates and often precludes speciation. We find that branching, and therefore genetic specialization, occurs mainly under two conditions: the presence of a cost to maintaining a high phenotypic variance or when the effect of mutations is large. A cost to high phenotypic variance dampens the strength of selection toward phenotypic heterogeneity and, when sufficiently large, introduces a singular point into

Congestive heart failure effects on atrial fibroblast phenotype: differences between freshly-isolated and cultured cells.

Directory of Open Access Journals (Sweden)

Kristin Dawson

Full Text Available Fibroblasts are important in the atrial fibrillation (AF substrate resulting from congestive heart failure (CHF. We previously noted changes in in vivo indices of fibroblast function in a CHF dog model, but could not detect changes in isolated cells. This study assessed CHF-induced changes in the phenotype of fibroblasts freshly isolated from control versus CHF dogs, and examined effects of cell culture on these differences.Left-atrial fibroblasts were isolated from control and CHF dogs (ventricular tachypacing 240 bpm × 2 weeks. Freshly-isolated fibroblasts were compared to fibroblasts in primary culture. Extracellular-matrix (ECM gene-expression was assessed by qPCR, protein by Western blot, fibroblast morphology with immunocytochemistry, and K(+-current with patch-clamp. Freshly-isolated CHF fibroblasts had increased expression-levels of collagen-1 (10-fold, collagen-3 (5-fold, and fibronectin-1 (3-fold vs. control, along with increased cell diameter (13.4 ± 0.4 µm vs control 8.4 ± 0.3 µm and cell spreading (shape factor 0.81 ± 0.02 vs. control 0.87 ± 0.02, consistent with an activated phenotype. Freshly-isolated control fibroblasts displayed robust tetraethylammonium (TEA-sensitive K(+-currents that were strongly downregulated in CHF. The TEA-sensitive K(+-current differences between control and CHF fibroblasts were attenuated after 2-day culture and eliminated after 7 days. Similarly, cell-culture eliminated the ECM protein-expression and shape differences between control and CHF fibroblasts.Freshly-isolated CHF and control atrial fibroblasts display distinct ECM-gene and morphological differences consistent with in vivo pathology. Culture for as little as 48 hours activates fibroblasts and obscures the effects of CHF. These results demonstrate potentially-important atrial-fibroblast phenotype changes in CHF and emphasize the need for caution in relating properties of cultured fibroblasts to in vivo systems.

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

Science.gov (United States)

Borges, Renee M

2009-10-01

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

Optimising the application of multiple-capture traps for invasive species management using spatial simulation.

Science.gov (United States)

Warburton, Bruce; Gormley, Andrew M

2015-01-01

Internationally, invasive vertebrate species pose a significant threat to biodiversity, agricultural production and human health. To manage these species a wide range of tools, including traps, are used. In New Zealand, brushtail possums (Trichosurus vulpecula), stoats (Mustela ermine), and ship rats (Rattus rattus) are invasive and there is an ongoing demand for cost-effective non-toxic methods for controlling these pests. Recently, traps with multiple-capture capability have been developed which, because they do not require regular operator-checking, are purported to be more cost-effective than traditional single-capture traps. However, when pest populations are being maintained at low densities (as is typical of orchestrated pest management programmes) it remains uncertain if it is more cost-effective to use fewer multiple-capture traps or more single-capture traps. To address this uncertainty, we used an individual-based spatially explicit modelling approach to determine the likely maximum animal-captures per trap, given stated pest densities and defined times traps are left between checks. In the simulation, single- or multiple-capture traps were spaced according to best practice pest-control guidelines. For possums with maintenance densities set at the lowest level (i.e. 0.5/ha), 98% of all simulated possums were captured with only a single capacity trap set at each site. When possum density was increased to moderate levels of 3/ha, having a capacity of three captures per trap caught 97% of all simulated possums. Results were similar for stoats, although only two potential captures per site were sufficient to capture 99% of simulated stoats. For rats, which were simulated at their typically higher densities, even a six-capture capacity per trap site only resulted in 80% kill. Depending on target species, prevailing density and extent of immigration, the most cost-effective strategy for pest control in New Zealand might be to deploy several single-capture

Cognition and gait show a selective pattern of association dominated by phenotype in incident Parkinson’s disease

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Sue eLord

2014-10-01

Full Text Available Reports outlining the association between gait and cognition in Parkinson’s disease (PD are limited because of methodological issues and a bias towards studying advanced disease. This study examines the association between gait and cognition in 121 early PD who were characterized according to motor phenotype, and 184 healthy older adults. Quantitative gait was captured using a 7m GAITrite walkway whilst walking for two minutes under single task conditions and described by five domains (pace, rhythm, variability, asymmetry and postural control. Cognitive outcomes were summarized by six domains (attention, working memory, visual memory, executive function, visuospatial function and global cognition. Partial correlations and multivariate linear regression were used to determine independent associations for all participants and for PD tremor-dominant (TD and postural instability and gait disorder (PIGD phenotypes, controlling for age, sex, and premorbid intelligence using the National Adult Reading Test (NART. Cognitive and gait outcomes were significantly worse for PD. Gait, but not cognitive outcomes, were selectively worse for the PIGD phenotype. Significant associations emerged for two gait domains for controls (pace and postural control and four gait domains for PD (pace, rhythm, variability, and postural control.The strongest correlation was for pace and attention for PD and controls. Associations were not significant for participants with the TD phenotype. In early PD the cognitive correlates of gait are predominantly with fronto-executive functions, and are determined by the PIGD PD phenotype. These associations provide a basis for understanding the complex role of cognition in Parkinsonian gait.

Root phenotyping: from component trait in the lab to breeding.

Science.gov (United States)

Kuijken, René C P; van Eeuwijk, Fred A; Marcelis, Leo F M; Bouwmeester, Harro J

2015-09-01

In the last decade cheaper and faster sequencing methods have resulted in an enormous increase in genomic data. High throughput genotyping, genotyping by sequencing and genomic breeding are becoming a standard in plant breeding. As a result, the collection of phenotypic data is increasingly becoming a limiting factor in plant breeding. Genetic studies on root traits are being hampered by the complexity of these traits and the inaccessibility of the rhizosphere. With an increasing interest in phenotyping, breeders and scientists try to overcome these limitations, resulting in impressive developments in automated phenotyping platforms. Recently, many such platforms have been thoroughly described, yet their efficiency to increase genetic gain often remains undiscussed. This efficiency depends on the heritability of the phenotyped traits as well as the correlation of these traits with agronomically relevant breeding targets. This review provides an overview of the latest developments in root phenotyping and describes the environmental and genetic factors influencing root phenotype and heritability. It also intends to give direction to future phenotyping and breeding strategies for optimizing root system functioning. A quantitative framework to determine the efficiency of phenotyping platforms for genetic gain is described. By increasing heritability, managing effects caused by interactions between genotype and environment and by quantifying the genetic relation between traits phenotyped in platforms and ultimate breeding targets, phenotyping platforms can be utilized to their maximum potential. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Mobility and Cooperation to Thwart Node Capture Attacks in MANETs

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Mauro Conti

2009-01-01

Full Text Available The nature of mobile ad hoc networks (MANETs, often unattended, makes this type of networks subject to some unique security issues. In particular, one of the most vexing problem for MANETs security is the node capture attack: an adversary can capture a node from the network eventually acquiring all the cryptographic material stored in it. Further, the captured node can be reprogrammed by the adversary and redeployed in the network in order to perform malicious activities. In this paper, we address the node capture attack in MANETs. We start from the intuition that mobility, in conjunction with a reduced amount of local cooperation, helps computing effectively and with a limited resource usage network global security properties. Then, we develop this intuition and use it to design a mechanism to detect the node capture attack. We support our proposal with a wide set of experiments showing that mobile networks can leverage mobility to compute global security properties, like node capture detection, with a small overhead.

Discrimination of meniscal cell phenotypes using gene expression profiles

Directory of Open Access Journals (Sweden)

M Son

2012-03-01

Full Text Available The lack of quantitative and objective metrics to assess cartilage and meniscus cell phenotypes contributes to the challenges in fibrocartilage tissue engineering. Although functional assessment of the final resulting tissue is essential, initial characterization of cell sources and quantitative description of their progression towards the natural, desired cell phenotype would provide an effective tool in optimizing cell-based tissue engineering strategies. The purpose of this study was to identify quantifiable characteristics of meniscal cells and thereby find phenotypical markers that could effectively categorize cells based on their tissue of origin (cartilage, inner, middle, and outer meniscus. The combination of gene expression ratios collagen VI/collagen II, ADAMTS-5/collagen II, and collagen I/collagen II was the most effective indicator of variation among different tissue regions. We additionally demonstrate a possible application of these quantifiable metrics in evaluating the use of serially passaged chondrocytes as a possible cell source in fibrocartilage engineering. Comparing the ratios of the passaged chondrocytes and the native meniscal cells may provide direction to optimize towards the desired cell phenotype. We have thus shown that measurable markers defining the characteristics of the native meniscus can establish a standard by which different tissue engineering strategies can be objectively assessed. Such metrics could additionally be useful in exploring the different stages of meniscal degradation in osteoarthritis and provide some insight in the disease progression.

Phenotypic plasticity in response to the social environment: effects of density and sex ratio on mating behaviour following ecotype divergence.

Directory of Open Access Journals (Sweden)

Kristina Karlsson

Full Text Available The ability to express phenotypically plastic responses to environmental cues might be adaptive in changing environments. We studied phenotypic plasticity in mating behaviour as a response to population density and adult sex ratio in a freshwater isopod (Asellus aquaticus. A. aquaticus has recently diverged into two distinct ecotypes, inhabiting different lake habitats (reed Phragmites australis and stonewort Chara tomentosa, respectively. In field surveys, we found that these habitats differ markedly in isopod population densities and adult sex ratios. These spatially and temporally demographic differences are likely to affect mating behaviour. We performed behavioural experiments using animals from both the ancestral ecotype ("reed" isopods and from the novel ecotype ("stonewort" isopods population. We found that neither ecotype adjusted their behaviour in response to population density. However, the reed ecotype had a higher intrinsic mating propensity across densities. In contrast to the effects of density, we found ecotype differences in plasticity in response to sex ratio. The stonewort ecotype show pronounced phenotypic plasticity in mating propensity to adult sex ratio, whereas the reed ecotype showed a more canalised behaviour with respect to this demographic factor. We suggest that the lower overall mating propensity and the phenotypic plasticity in response to sex ratio have evolved in the novel stonewort ecotype following invasion of the novel habitat. Plasticity in mating behaviour may in turn have effects on the direction and intensity of sexual selection in the stonewort habitat, which may fuel further ecotype divergence.

Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.

Science.gov (United States)

Gasc, Cyrielle; Peyretaillade, Eric; Peyret, Pierre

2016-06-02

The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Sex hormone binding globulin phenotypes

DEFF Research Database (Denmark)

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

1994-01-01

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

The Pleiotropic Phenotype of Apc Mutations in the Mouse: Allele Specificity and Effects of the Genetic Background

Science.gov (United States)

Halberg, Richard B.; Chen, Xiaodi; Amos-Landgraf, James M.; White, Alanna; Rasmussen, Kristin; Clipson, Linda; Pasch, Cheri; Sullivan, Ruth; Pitot, Henry C.; Dove, William F.

2008-01-01

Familial adenomatous polyposis (FAP) is a human cancer syndrome characterized by the development of hundreds to thousands of colonic polyps and extracolonic lesions including desmoid fibromas, osteomas, epidermoid cysts, and congenital hypertrophy of the pigmented retinal epithelium. Afflicted individuals are heterozygous for mutations in the APC gene. Detailed investigations of mice heterozygous for mutations in the ortholog Apc have shown that other genetic factors strongly influence the phenotype. Here we report qualitative and quantitative modifications of the phenotype of Apc mutants as a function of three genetic variables: Apc allele, p53 allele, and genetic background. We have found major differences between the Apc alleles Min and 1638N in multiplicity and regionality of intestinal tumors, as well as in incidence of extracolonic lesions. By contrast, Min mice homozygous for either of two different knockout alleles of p53 show similar phenotypic effects. These studies illustrate the classic principle that functional genetics is enriched by assessing penetrance and expressivity with allelic series. The mouse permits study of an allelic gene series on multiple genetic backgrounds, thereby leading to a better understanding of gene action in a range of biological processes. PMID:18723878

Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis.

Science.gov (United States)

Lee, Jessica J Y; Gottlieb, Michael M; Lever, Jake; Jones, Steven J M; Blau, Nenad; van Karnebeek, Clara D M; Wasserman, Wyeth W

2018-05-01

Phenomics is the comprehensive study of phenotypes at every level of biology: from metabolites to organisms. With high throughput technologies increasing the scope of biological discoveries, the field of phenomics has been developing rapid and precise methods to collect, catalog, and analyze phenotypes. Such methods have allowed phenotypic data to be widely used in medical applications, from assisting clinical diagnoses to prioritizing genomic diagnoses. To channel the benefits of phenomics into the field of inborn errors of metabolism (IEM), we have recently launched IEMbase, an expert-curated knowledgebase of IEM and their disease-characterizing phenotypes. While our efforts with IEMbase have realized benefits, taking full advantage of phenomics requires a comprehensive curation of IEM phenotypes in core phenomics projects, which is dependent upon contributions from the IEM clinical and research community. Here, we assess the inclusion of IEM biochemical phenotypes in a core phenomics project, the Human Phenotype Ontology. We then demonstrate the utility of biochemical phenotypes using a text-based phenomics method to predict gene-disease relationships, showing that the prediction of IEM genes is significantly better using biochemical rather than clinical profiles. The findings herein provide a motivating goal for the IEM community to expand the computationally accessible descriptions of biochemical phenotypes associated with IEM in phenomics resources.

The effect of uniform capture molecule orientation on biosensor sensitivity : dependence on analyte properties

NARCIS (Netherlands)

Trilling, A.K.; Harmsen, M.M.; Ruigrok, V.J.; Zuilhof, H.; Beekwilder, J.

2013-01-01

Uniform orientation of capture molecules on biosensors has been reported to increase sensitivity. Here it is investigated which analyte properties contribute to sensitivity by orientation. Orientation of capture molecules on biosensors was investigated using variable domains of llama heavy-chain

Studies of electron correlation effects in multicharged ion atom collisions involving double capture

International Nuclear Information System (INIS)

Stolterfoht, N.; Sommer, K.; Griffin, D.C.; Havener, C.C.; Huq, M.S.; Phaneuf, R.A.; Swenson, J.K.; Meyer, F.W.

1988-01-01

We review measurements of L-Coster Kronig and Auger electron production in slow, multicharged collision systems to study electron correlation effects in the process of double electron capture. The n/sup /minus/3/ law was confirmed for the production of the Coster-Kronig configurations 1s 2 2pn/ell/ (n ≥ 6) in O 6+ + He collisions. Enhancement of high angular momentum /ell/ in specific 1s 2 2pn/ell/ configurations was observed by means of high-resolution measurements of the Coster-Kronig lines. The importance of electron correlation effects in couplings of potential energy curves leading to the 1s 2 2pn/ell/ configurations is verified by means of Landau-Zener model calculations. 32 refs., 4 figs

Small Particles Intact Capture Experiment (SPICE)

Science.gov (United States)

Nishioka, Ken-Ji; Carle, G. C.; Bunch, T. E.; Mendez, David J.; Ryder, J. T.

1994-01-01

The Small Particles Intact Capture Experiment (SPICE) will develop technologies and engineering techniques necessary to capture nearly intact, uncontaminated cosmic and interplanetary dust particles (IDP's). Successful capture of such particles will benefit the exobiology and planetary science communities by providing particulate samples that may have survived unaltered since the formation of the solar system. Characterization of these particles may contribute fundamental data to our knowledge of how these particles could have formed into our planet Earth and, perhaps, contributed to the beginnings of life. The term 'uncontaminated' means that captured cosmic and IDP particles are free of organic contamination from the capture process and the term 'nearly intact capture' means that their chemical and elemental components are not materially altered during capture. The key to capturing cosmic and IDP particles that are organic-contamination free and nearly intact is the capture medium. Initial screening of capture media included organic foams, multiple thin foil layers, and aerogel (a silica gel); but, with the exception of aerogel, the requirements of no contamination or nearly intact capture were not met. To ensure no contamination of particles in the capture process, high-purity aerogel was chosen. High-purity aerogel results in high clarity (visual clearness), a useful quality in detection and recovery of embedded captured particles from the aerogel. P. Tsou at the Jet Propulsion Laboratory (JPL) originally described the use of aerogel for this purpose and reported laboratory test results. He has flown aerogel as a 'GAS-can Lid' payload on STS-47 and is evaluating the results. The Timeband Capture Cell Experiment (TICCE), a Eureca 1 experiment, is also flying aerogel and is scheduled for recovery in late April.

Childhood asthma-predictive phenotype.

Science.gov (United States)

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

2014-01-01

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

Laser capture microdissection: Arcturus(XT) infrared capture and UV cutting methods.

Science.gov (United States)

Gallagher, Rosa I; Blakely, Steven R; Liotta, Lance A; Espina, Virginia

2012-01-01

Laser capture microdissection (LCM) is a technique that allows the precise procurement of enriched cell populations from a heterogeneous tissue under direct microscopic visualization. LCM can be used to harvest the cells of interest directly or can be used to isolate specific cells by ablating the unwanted cells, resulting in histologically enriched cell populations. The fundamental components of laser microdissection technology are (a) visualization of the cells of interest via microscopy, (b) transfer of laser energy to a thermolabile polymer with either the formation of a polymer-cell composite (capture method) or transfer of laser energy via an ultraviolet laser to photovolatize a region of tissue (cutting method), and (c) removal of cells of interest from the heterogeneous tissue section. Laser energy supplied by LCM instruments can be infrared (810 nm) or ultraviolet (355 nm). Infrared lasers melt thermolabile polymers for cell capture, whereas ultraviolet lasers ablate cells for either removal of unwanted cells or excision of a defined area of cells. LCM technology is applicable to an array of applications including mass spectrometry, DNA genotyping and loss-of-heterozygosity analysis, RNA transcript profiling, cDNA library generation, proteomics discovery, and signal kinase pathway profiling. This chapter describes the unique features of the Arcturus(XT) laser capture microdissection instrument, which incorporates both infrared capture and ultraviolet cutting technology in one instrument, using a proteomic downstream assay as a model.

Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection

Directory of Open Access Journals (Sweden)

Zhang Yanxin

2012-11-01

Full Text Available Abstract Background Sesame (Sesamum indicum L. is one of the four major oil crops in China. A sesame core collection (CC was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC. Results Results from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525. The Shannon-Weaver diversity index (I and Nei genetic diversity index (h were higher (I = 0.9537, h = 0.5490 when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218. A mini-core collection (MC containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%, low variance difference percentage (VD, 22.58%, large variable rate of coefficient of variance (VR, 114.86%, and large coincidence rate of range (CR, 95.76%. For molecular data, the diversity indices and the polymorphism information content (PIC for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven. Conclusions This study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and

Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection

Science.gov (United States)

2012-01-01

Background Sesame (Sesamum indicum L.) is one of the four major oil crops in China. A sesame core collection (CC) was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC). Results Results from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525). The Shannon-Weaver diversity index (I) and Nei genetic diversity index (h) were higher (I = 0.9537, h = 0.5490) when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218). A mini-core collection (MC) containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%), low variance difference percentage (VD, 22.58%), large variable rate of coefficient of variance (VR, 114.86%), and large coincidence rate of range (CR, 95.76%). For molecular data, the diversity indices and the polymorphism information content (PIC) for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven. Conclusions This study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and large VR% and CR

Can we "apply" the findings of Forster and Lavie (2008)? On the generalizability of attentional capture effects under varying levels of perceptual load.

Science.gov (United States)

Lleras, Alejandro; Chu, Hengqing; Buetti, Simona

2017-06-01

Perceptual Load theory states that the degree of perceptual load on a display determines the amount of leftover attentional resources that the system can use to process distracting information. An important corollary of this theory is that the amount of perceptual load determines the vulnerability of the attention system to being captured by completely irrelevant stimuli, predicting larger amounts of capture with low perceptual load than with high perceptual load. This prediction was first confirmed by Forster and Lavie (2008). Here, we report 6 experiments that followed up on those earlier results, where we find that in many cases, the opposite pattern is obtained: attentional capture increased with increasing perceptual load. Given the lack of generalizability of the theory to new experimental contexts with fairly minor methodological differences, we conclude that Perceptual Load may not be a useful framework for understanding attentional capture. The theoretical and applied importance of these findings is discussed. In particular, we caution against using this theory in applied tasks and settings because best-use recommendations stemming from this theory regarding strategies to decrease distractibility may in fact produce the opposite effect: an increase in distractibility (with distractibility being indexed by the magnitude of the capture effect). (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Thermochemistry of a Biomimetic and Rubisco-Inspired CO2 Capture System from Air

Directory of Open Access Journals (Sweden)

Andrew Muelleman

2016-07-01

Full Text Available In theoretical studies of chemical reactions the reaction thermochemistry is usually reported for the stoichiometric reaction at standard conditions (ΔG°, ΔH°, ΔS°. We describe the computation of the equilibrium concentrations of the CO2-adducts for the general capture reaction CO2 + Capture System ⇆ CO2-adduct (GCR and the rubisco-type capture reaction CO2 + Capture System ⇆ CO2-adduct + H2O (RCR with consideration of the reaction CO2(g ⇆ CO2(aq via Henry’s law. The resulting equations are evaluated and graphically illustrated as a function of atmospheric CO2 concentration and as a function of temperature. The equations were applied to the thermochemistry of small molecule rubisco-model reactions and series of additional model reactions to illustrate the range of the Gibbs free enthalpy for the effective reversible capture and of the reaction entropy for economic CO2 release at elevated temperature. A favorable capture of free enthalpy is of course a design necessity, but not all exergonic reactions are suitable CO2 capture systems. Successful CO2 capture systems must allow for effective release as well, and this feature is controlled by the reaction entropy. The principle of using a two-pronged capture system to ensure a large negative capture entropy is explained and highlighted in the graphical abstract. It is hoped that the presentation of the numerical examples provides useful guidelines for the design of more efficient capture systems.

A “Forward Genomics” Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species

Directory of Open Access Journals (Sweden)

Michael Hiller

2012-10-01

Full Text Available Genotype-phenotype mapping is hampered by countless genomic changes between species. We introduce a computational “forward genomics” strategy that—given only an independently lost phenotype and whole genomes—matches genomic and phenotypic loss patterns to associate specific genomic regions with this phenotype. We conducted genome-wide screens for two metabolic phenotypes. First, our approach correctly matches the inactivated Gulo gene exactly with the species that lost the ability to synthesize vitamin C. Second, we attribute naturally low biliary phospholipid levels in guinea pigs and horses to the inactivated phospholipid transporter Abcb4. Human ABCB4 mutations also result in low phospholipid levels but lead to severe liver disease, suggesting compensatory mechanisms in guinea pig and horse. Our simulation studies, counts of independent changes in existing phenotype surveys, and the forthcoming availability of many new genomes all suggest that forward genomics can be applied to many phenotypes, including those relevant for human evolution and disease.

Study on keV-neutron capture cross sections and capture γ-ray spectra of 117,119Sn

International Nuclear Information System (INIS)

Nishiyama, J.; Igashira, M.; Ohsaki, T.; Kim, G.N.; Chung, W.C.; Ro, T.I.

2006-01-01

The capture cross sections and capture γ-ray spectra of 117,119 Sn were measured in an incident neutron energy region from 10 to 100 keV and at 570 keV, using a 1.5-ns pulsed neutron source by the 7 Li(p,n) 7 Be reaction and a large anti-Compton NaI(Tl) γ-ray spectrometer. A pulse-height weighting technique was applied to observed capture γ-ray pulse-height spectra to derive capture yields. The capture cross sections of 117,119 Sn were obtained with the error of about 5% by using the standard capture cross sections of 197 Au. The present cross sections were compared with previous experimental data and the evaluated values in JENDL-3.3 and ENDF/B-VI. The capture γ-ray spectra of 117,119 Sn were derived by unfolding the observed capture γ-ray pulse-height spectra. The calculations of capture cross sections and capture γ-ray spectra of 117,119 Sn were performed with the EMPIRE-II code. The calculated results were compared with the present experimental ones. (author)

Wheat shovelomics I: A field phenotyping approach for characterising the structure and function of root systems in tillering species

OpenAIRE

Bennett, Malcolm; York, Larry; Foulkes, M; Slack, Shaunagh

2018-01-01

Wheat represents a major crop, yet the current rate of yield improvement is insufficient to meet its projected global food demand. Breeding root systems more efficient for water and nitrogen capture represents a promising avenue for accelerating yield gains. Root crown phenotyping, or shovelomics, relies on excavation of the upper portions of root systems in the field and measuring root properties such as numbers, angles, densities and lengths. We report a new shovelomics method that images t...

Space, energy and anisotropy effects on 238U effective capture cross sections in the resonance region

International Nuclear Information System (INIS)

Meftah, B.; Karam, R.A.

1984-01-01

Agreement between calculations and measurements within prescribed limits of error is always the test of engineering design analysis. Large and puzzling discrepancies do exist between several measured and calculated important integral reactor parameters. A thorough and exhaustive investigation of the methods used in reactor analysis revealed that in the generation of effective resonance cross sections no anisotropy effects are considered in the resonances. This is true in the integral transport and fundamental-mode codes. The neglect of anisotropy introduces errors at two levels: (1) the effective group cross sections such as σsub(c), σsub(f) and σsub(s); and (2) the diffusion coefficients and P 1 and higher components of the scattering cross sections. The study showed that the inclusion of linear scattering anisotropy increases, in general, the cell effective capture cross section of 238 U in both ZPR-6/5 and TRX-3 reactors. The increase was up to 2% in TRX-3 and 0.5% in ZPR-6/5. The effect on the multiplication factor was -0.003% Δk/k for ZPR-6/5 and -0.05% Δk/k for TRX-3. (author)

Framing and bias in CO2 capture and storage communication films: Reflections from a CO2 capture and storage research group.

Science.gov (United States)

Maynard, Carly M; Shackley, Simon

2017-03-01

There has been a growing trend towards incorporating short, educational films as part of research funding and project proposals. Researchers and developers in CO 2 capture and storage are using films to communicate outcomes, but such films can be influenced by experiences and values of the producers. We document the content and presentation of seven online CO 2 capture and storage films to determine how framing occurs and its influence on the tone of films. The core frame presents CO 2 capture and storage as a potential solution to an imminent crisis in climatic warming and lack of a sustainable energy supply. Three subsidiary frames represent CO 2 capture and storage as (1) the only option, (2) a partial option or (3) a scientific curiosity. The results demonstrate that an understanding of the nuanced explicit and implicit messages portrayed by films is essential both for effective framing according to one's intention and for wider public understanding of a field.

Effects of ACTH, capture, and short term confinement on glucocorticoid concentrations in harlequin ducks (Histrionicus histrionicus)

Science.gov (United States)

Nilsson, P.B.; Hollmén, Tuula E.; Atkinson, S.; Mashburn, K.L.; Tuomi, P.A.; Esler, Daniel N.; Mulcahy, D.M.; Rizzolo, D.J.

2008-01-01

Little is known about baseline concentrations of adrenal hormones and hormonal responses to stress in sea ducks, although significant population declines documented in several species suggest that sea ducks are exposed to increased levels of environmental stress. Such declines have been observed in geographically distinct harlequin duck populations. We performed an adrenocorticotropic hormone (ACTH) challenge to evaluate adrenal function and characterize corticosterone concentrations in captive harlequin ducks and investigated the effects of capture, surgery, and short term confinement on corticosterone concentrations in wild harlequin ducks. Harlequin ducks responded to the ACTH challenge with an average three-fold increase in serum corticosterone concentration approximately 90 min post injection, and a four- to five-fold increase in fecal glucocorticoid concentration 2 to 4 h post injection. Serum corticosterone concentrations in wild harlequin ducks increased within min of capture and elevated levels were found for several hours post capture, indicating that surgery and confinement maintain elevated corticosterone concentrations in this species. Mean corticosterone concentrations in wild harlequin ducks held in temporary captivity were similar to the maximum response levels during the ACTH challenge in captive birds. However, large variation among individuals was observed in responses of wild birds, and we found additional evidence suggesting that corticosterone responses varied between hatch year and after hatch year birds.

Mutations and phenotype in isolated glycerol kinase deficiency

Energy Technology Data Exchange (ETDEWEB)

Walker, A.P.; Muscatelli, F.; Stafford, A.N.; Monaco, A.P. [Inst. of Molecular Medicine, Oxford (United Kingdom)] [and others

1996-06-01

We demonstrate that isolated glycerol kinase (GK) deficiency in three families results from mutation of the Xp21 GK gene. GK mutations were detected in four patients with widely differing phenotypes. Patient 1 had a splice-site mutation causing premature termination. His general health was good despite absent GK activity, indicating that isolated GK deficiency can be silent. Patient 2 had GK deficiency and a severe phenotype involving psychomotor retardation and growth delay, bone dysplasia, and seizures, similar to the severe phenotype of one of the first described cases of GK deficiency. His younger brother, patient 3, also had GK deficiency, but so far his development has been normal. GK exon 17 was deleted in both brothers, implicating additional factors in causation of the severe phenotype of patient 2. Patient 4 had both GK deficiency with mental retardation and a GK missense mutation (D440V). Possible explanations for the phenotypic variation of these four patients include ascertainment bias; metabolic or environmental stress as a precipitating factor in revealing GK-related changes, as has previously been described in juvenile GK deficiency; and interactions with functional polymorphisms in other genes that alter the effect of GK deficiency on normal development. 36 refs., 4 figs., 1 tab.

Prevalence of sexual dimorphism in mammalian phenotypic traits

Science.gov (United States)

Karp, Natasha A.; Mason, Jeremy; Beaudet, Arthur L.; Benjamini, Yoav; Bower, Lynette; Braun, Robert E.; Brown, Steve D.M.; Chesler, Elissa J.; Dickinson, Mary E.; Flenniken, Ann M.; Fuchs, Helmut; Angelis, Martin Hrabe de; Gao, Xiang; Guo, Shiying; Greenaway, Simon; Heller, Ruth; Herault, Yann; Justice, Monica J.; Kurbatova, Natalja; Lelliott, Christopher J.; Lloyd, K.C. Kent; Mallon, Ann-Marie; Mank, Judith E.; Masuya, Hiroshi; McKerlie, Colin; Meehan, Terrence F.; Mott, Richard F.; Murray, Stephen A.; Parkinson, Helen; Ramirez-Solis, Ramiro; Santos, Luis; Seavitt, John R.; Smedley, Damian; Sorg, Tania; Speak, Anneliese O.; Steel, Karen P.; Svenson, Karen L.; Obata, Yuichi; Suzuki, Tomohiro; Tamura, Masaru; Kaneda, Hideki; Furuse, Tamio; Kobayashi, Kimio; Miura, Ikuo; Yamada, Ikuko; Tanaka, Nobuhiko; Yoshiki, Atsushi; Ayabe, Shinya; Clary, David A.; Tolentino, Heather A.; Schuchbauer, Michael A.; Tolentino, Todd; Aprile, Joseph Anthony; Pedroia, Sheryl M.; Kelsey, Lois; Vukobradovic, Igor; Berberovic, Zorana; Owen, Celeste; Qu, Dawei; Guo, Ruolin; Newbigging, Susan; Morikawa, Lily; Law, Napoleon; Shang, Xueyuan; Feugas, Patricia; Wang, Yanchun; Eskandarian, Mohammad; Zhu, Yingchun; Nutter, Lauryl M. J.; Penton, Patricia; Laurin, Valerie; Clarke, Shannon; Lan, Qing; Sohel, Khondoker; Miller, David; Clark, Greg; Hunter, Jane; Cabezas, Jorge; Bubshait, Mohammed; Carroll, Tracy; Tondat, Sandra; MacMaster, Suzanne; Pereira, Monica; Gertsenstein, Marina; Danisment, Ozge; Jacob, Elsa; Creighton, Amie; Sleep, Gillian; Clark, James; Teboul, Lydia; Fray, Martin; Caulder, Adam; Loeffler, Jorik; Codner, Gemma; Cleak, James; Johnson, Sara; Szoke-Kovacs, Zsombor; Radage, Adam; Maritati, Marina; Mianne, Joffrey; Gardiner, Wendy; Allen, Susan; Cater, Heather; Stewart, Michelle; Keskivali-Bond, Piia; Sinclair, Caroline; Brown, Ellen; Doe, Brendan; Wardle-Jones, Hannah; Grau, Evelyn; Griggs, Nicola; Woods, Mike; Kundi, Helen; Griffiths, Mark N. D.; Kipp, Christian; Melvin, David G.; Raj, Navis P. S.; Holroyd, Simon A.; Gannon, David J.; Alcantara, Rafael; Galli, Antonella; Hooks, Yvette E.; Tudor, Catherine L.; Green, Angela L.; Kussy, Fiona L.; Tuck, Elizabeth J.; Siragher, Emma J.; Maguire, Simon A.; Lafont, David T.; Vancollie, Valerie E.; Pearson, Selina A.; Gates, Amy S.; Sanderson, Mark; Shannon, Carl; Anthony, Lauren F. E.; Sumowski, Maksymilian T.; McLaren, Robbie S. B.; Swiatkowska, Agnieszka; Isherwood, Christopher M.; Cambridge, Emma L; Wilson, Heather M.; Caetano, Susana S.; Mazzeo, Cecilia Icoresi; Dabrowska, Monika H.; Lillistone, Charlotte; Estabel, Jeanne; Maguire, Anna Karin B.; Roberson, Laura-Anne; Pavlovic, Guillaume; Birling, Marie-Christine; Marie, Wattenhofer-Donze; Jacquot, Sylvie; Ayadi, Abdel; Ali-Hadji, Dalila; Charles, Philippe; André, Philippe; Le Marchand, Elise; El Amri, Amal; Vasseur, Laurent; Aguilar-Pimentel, Antonio; Becker, Lore; Treise, Irina; Moreth, Kristin; Stoeger, Tobias; Amarie, Oana V.; Neff, Frauke; Wurst, Wolfgang; Bekeredjian, Raffi; Ollert, Markus; Klopstock, Thomas; Calzada-Wack, Julia; Marschall, Susan; Brommage, Robert; Steinkamp, Ralph; Lengger, Christoph; Östereicher, Manuela A.; Maier, Holger; Stoeger, Claudia; Leuchtenberger, Stefanie; Yildrim, AliÖ; Garrett, Lillian; Hölter, Sabine M; Zimprich, Annemarie; Seisenberger, Claudia; Bürger, Antje; Graw, Jochen; Eickelberg, Oliver; Zimmer, Andreas; Wolf, Eckhard; Busch, Dirk H; Klingenspor, Martin; Schmidt-Weber, Carsten; Gailus-Durner, Valérie; Beckers, Johannes; Rathkolb, Birgit; Rozman, Jan; Wakana, Shigeharu; West, David; Wells, Sara; Westerberg, Henrik; Yaacoby, Shay; White, Jacqueline K.

2017-01-01

The role of sex in biomedical studies has often been overlooked, despite evidence of sexually dimorphic effects in some biological studies. Here, we used high-throughput phenotype data from 14,250 wildtype and 40,192 mutant mice (representing 2,186 knockout lines), analysed for up to 234 traits, and found a large proportion of mammalian traits both in wildtype and mutants are influenced by sex. This result has implications for interpreting disease phenotypes in animal models and humans. PMID:28650954

Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology.

Science.gov (United States)

Masino, Aaron J; Dechene, Elizabeth T; Dulik, Matthew C; Wilkens, Alisha; Spinner, Nancy B; Krantz, Ian D; Pennington, Jeffrey W; Robinson, Peter N; White, Peter S

2014-07-21

Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging variants that must be individually assessed to establish clear association with patient phenotype. To assist interpretation, we implemented an algorithm that ranks a given set of genes relative to patient phenotype. The algorithm orders genes by the semantic similarity computed between phenotypic descriptors associated with each gene and those describing the patient. Phenotypic descriptor terms are taken from the Human Phenotype Ontology (HPO) and semantic similarity is derived from each term's information content. Model validation was performed via simulation and with clinical data. We simulated 33 Mendelian diseases with 100 patients per disease. We modeled clinical conditions by adding noise and imprecision, i.e. phenotypic terms unrelated to the disease and terms less specific than the actual disease terms. We ranked the causative gene against all 2488 HPO annotated genes. The median causative gene rank was 1 for the optimal and noise cases, 12 for the imprecision case, and 60 for the imprecision with noise case. Additionally, we examined a clinical cohort of subjects with hearing impairment. The disease gene median rank was 22. However, when also considering the patient's exome data and filtering non-exomic and common variants, the median rank improved to 3. Semantic similarity can rank a causative gene highly within a gene list relative to patient phenotype characteristics, provided that imprecision is mitigated. The clinical case results suggest that phenotype rank combined with variant analysis provides significant improvement over the individual approaches. We expect that this combined prioritization approach may increase accuracy and decrease effort for

The novelty-seeking phenotype modulates the long-lasting effects of intermittent ethanol administration during adolescence.

Directory of Open Access Journals (Sweden)

Sandra Montagud-Romero

Full Text Available The aim of the present study was to investigate if a novelty-seeking phenotype mediates the long-lasting consequences of intermittent EtOH intoxication during adolescence. The hole board test was employed to classify adolescent mice as High- or Low-Novelty Seekers. Subsequently, animals were administered ethanol (1.25 or 2.5 g/kg on two consecutive days at 48-h intervals over a 14-day period. Anxiety levels--measured using the elevated plus maze- spontaneous motor activity and social interaction test were studied 3 weeks later. A different set of mice underwent the same procedure, but received only the 2.5 g/kg dose of ethanol. Three weeks later, in order to induce CPP, the same animals were administered 1 or 6 mg/kg of cocaine or 1 or 2.5 mg/kg MDMA. The results revealed a decrease in aggressive behaviors and an anxiolytic profile in HNS mice and longer latency to explore the novel object by LNS mice. Ethanol exposure enhanced the reinforcing effects of cocaine and MDMA in both groups when CPP was induced with a sub-threshold dose of the drugs. The extinguished cocaine-induced CPP (1 and 6 mg/kg was reinstated after a priming dose in HNS animals only. Our results confirm that intermittent EtOH administration during adolescence induces long-lasting effects that are manifested in adult life, and that there is an association between these effects and the novelty-seeking phenotype.

Experimental study on pion capture by hydrogen bound in molecules

International Nuclear Information System (INIS)

Horvath, D.; Aniol, K.A.; Entezami, F.; Measday, D.F.; Noble, A.J.; Stanislaus, S.; Virtue, C.J.

1988-08-01

An experiment was performed at TRIUMF to study the formation of pionic hydrogen atoms and molecules in solids, particularly in groups of organic molecules of slightly different structure in order to help further clarify the problem. The nuclear capture of pions by hydrogen was measured using the charge exchange of stopped pions. The coincident photons emitted by the decaying π 0 mesons were detected by TRIUMF's two large NaI spectrometers. New experimental results were obtained for the capture probability of stopped π - mesons in the nuclei of hydrogen atoms, chemically bound in molecules of some simple hydrides, acid anhydrides, and sugar isomers. A linear relation was found between pion capture in hydrogen and melting point in sugar isomers. The pion capture probability in acid anhydrides is fairly well described by a simple atomic capture model in which the capture probability on the hydrogen dramatically increases as the hydrogen atom is separated from the strongly electronegative C 2 O 3 group. Both effects are consistent with a correlation between pion capture and electron density on hydrogen atoms. (Author) (38 refs., 4 tabs., 7 figs.)

Simulation of a bubbling fluidized bed process for capturing CO2 from flue gas

International Nuclear Information System (INIS)

Choi, Jeong-Hoo; Yi, Chang-Keun; Jo, Sung-Ho; Ryu, Ho-Jung; Park, Young-Cheol

2014-01-01

We simulated a bubbling bed process capturing CO 2 from flue gas. It applied for a laboratory scale process to investigate effects of operating parameters on capture efficiency. The adsorber temperature had a stronger effect than the regenerator temperature. The effect of regenerator temperature was minor for high adsorber temperature. The effect of regenerator temperature decreased to level off for the temperature >250 .deg. C. The capture efficiency was rather dominated by the adsorption reaction than the regeneration reaction. The effect of gas velocity was as appreciable as that of adsorber temperature. The capture efficiency increased with the solids circulation rate since it was ruled by the molar ratio of K to CO 2 for solids circulation smaller than the minimum required one (G s, min ). However, it leveled off for solids circulation rate >G s, min . As the ratio of adsorber solids inventory to the total solids inventory (x w1 ) increased, the capture efficiency increased until x w1 =0.705, but decreased for x w1 >0.705 because the regeneration time decreased too small. It revealed that the regeneration reaction was faster than the adsorption reaction. Increase of total solids inventory is a good way to get further increase in capture efficiency

Laser capture microdissection-based in vivo genomic profiling of wound keratinocytes identifies similarities and differences to squamous cell carcinoma

DEFF Research Database (Denmark)

Pedersen, Tanja Xenia; Leethanakul, Chidchanop; Patel, Vyomesh

2003-01-01

keratinocytes from incisional mouse skin wounds and adjacent normal skin keratinocytes. Changes in gene expression were determined by comparative cDNA array analyses, and the approach was validated by in situ hybridization. The analyses identified 48 candidate genes not previously associated with wound...... reepithelialization. Furthermore, the analyses revealed that the phenotypic resemblance of wound keratinocytes to squamous cell carcinoma is mimicked at the level of gene expression, but notable differences between the two tissue-remodeling processes were also observed. The combination of laser capture...

Contingent capture can occur at specific feature values: behavioral and electrophysiological evidence.

Science.gov (United States)

Jiao, Jun; Zhao, Guang; Wang, Qi; Zhang, Kan; Li, Hong; Sun, Hong-Jin; Liu, Qiang

2013-02-01

The notion that attentional top-down control can be tuned to a stimulus feature is widely accepted. Although previous studies suggested that the stimulus-driven attentional capture could be contingent on top-down attentional control settings, it was uncertain whether contingent capture can occur at a specific feature value. Three experiments were conducted to address this issue using both behavioral and ERPs measures. Participants were required to respond to one color singleton in the search display (target) but refrain from responding to the search display containing another color singleton (nontarget). When target and nontarget belonged to different color categories (Experiment 1), only the target-color cue and within category irrelevant-color cue elicited the significant cue validity effect (i.e. RTs were shorter when the target was presented at the same location as the preceding cue rather than at a different location); they also lead to a robust N2pc effect, indicative of attention-capture. In addition, these two cue types had similar attention-capturing capacity. However, when target and nontarget belonged to the same color category (Experiments 2 and 3), only the target-color cue elicited the significant cue validity effect and the robust N2pc effect. The same within category irrelevant-color cue no longer elicited the cue validity effect, and the N2pc effect was also attenuated. Present findings suggest that contingent capture can occur at a specific feature value. Copyright © 2012 Elsevier B.V. All rights reserved.

Mechanistic phenotypes: an aggregative phenotyping strategy to identify disease mechanisms using GWAS data.

Directory of Open Access Journals (Sweden)

Jonathan D Mosley

Full Text Available A single mutation can alter cellular and global homeostatic mechanisms and give rise to multiple clinical diseases. We hypothesized that these disease mechanisms could be identified using low minor allele frequency (MAF<0.1 non-synonymous SNPs (nsSNPs associated with "mechanistic phenotypes", comprised of collections of related diagnoses. We studied two mechanistic phenotypes: (1 thrombosis, evaluated in a population of 1,655 African Americans; and (2 four groupings of cancer diagnoses, evaluated in 3,009 white European Americans. We tested associations between nsSNPs represented on GWAS platforms and mechanistic phenotypes ascertained from electronic medical records (EMRs, and sought enrichment in functional ontologies across the top-ranked associations. We used a two-step analytic approach whereby nsSNPs were first sorted by the strength of their association with a phenotype. We tested associations using two reverse genetic models and standard additive and recessive models. In the second step, we employed a hypothesis-free ontological enrichment analysis using the sorted nsSNPs to identify functional mechanisms underlying the diagnoses comprising the mechanistic phenotypes. The thrombosis phenotype was solely associated with ontologies related to blood coagulation (Fisher's p = 0.0001, FDR p = 0.03, driven by the F5, P2RY12 and F2RL2 genes. For the cancer phenotypes, the reverse genetics models were enriched in DNA repair functions (p = 2×10-5, FDR p = 0.03 (POLG/FANCI, SLX4/FANCP, XRCC1, BRCA1, FANCA, CHD1L while the additive model showed enrichment related to chromatid segregation (p = 4×10-6, FDR p = 0.005 (KIF25, PINX1. We were able to replicate nsSNP associations for POLG/FANCI, BRCA1, FANCA and CHD1L in independent data sets. Mechanism-oriented phenotyping using collections of EMR-derived diagnoses can elucidate fundamental disease mechanisms.

Supernovae and nuclear structure: Electron capture and the nuclear incompressibility

International Nuclear Information System (INIS)

Cooperstein, J.

1985-01-01

The author considers the effects of electron capture and the high density equation of state on supernovae. Electron captures on nuclei with 60 s it is helpful for supernovae to have a soft equation of state. Present knowledge of the nuclear matter parameters is considered and implications for supernovae are drawn. (orig.)

PhenoLines: Phenotype Comparison Visualizations for Disease Subtyping via Topic Models.

Science.gov (United States)

Glueck, Michael; Naeini, Mahdi Pakdaman; Doshi-Velez, Finale; Chevalier, Fanny; Khan, Azam; Wigdor, Daniel; Brudno, Michael

2018-01-01

PhenoLines is a visual analysis tool for the interpretation of disease subtypes, derived from the application of topic models to clinical data. Topic models enable one to mine cross-sectional patient comorbidity data (e.g., electronic health records) and construct disease subtypes-each with its own temporally evolving prevalence and co-occurrence of phenotypes-without requiring aligned longitudinal phenotype data for all patients. However, the dimensionality of topic models makes interpretation challenging, and de facto analyses provide little intuition regarding phenotype relevance or phenotype interrelationships. PhenoLines enables one to compare phenotype prevalence within and across disease subtype topics, thus supporting subtype characterization, a task that involves identifying a proposed subtype's dominant phenotypes, ages of effect, and clinical validity. We contribute a data transformation workflow that employs the Human Phenotype Ontology to hierarchically organize phenotypes and aggregate the evolving probabilities produced by topic models. We introduce a novel measure of phenotype relevance that can be used to simplify the resulting topology. The design of PhenoLines was motivated by formative interviews with machine learning and clinical experts. We describe the collaborative design process, distill high-level tasks, and report on initial evaluations with machine learning experts and a medical domain expert. These results suggest that PhenoLines demonstrates promising approaches to support the characterization and optimization of topic models.

Marker-Free Human Motion Capture

DEFF Research Database (Denmark)

Grest, Daniel

Human Motion Capture is a widely used technique to obtain motion data for animation of virtual characters. Commercial optical motion capture systems are marker-based. This book is about marker-free motion capture and its possibilities to acquire motion from a single viewing direction. The focus...

Impact of QTL minor allele frequency on genomic evaluation using real genotype data and simulated phenotypes in Japanese Black cattle.

Science.gov (United States)

Uemoto, Yoshinobu; Sasaki, Shinji; Kojima, Takatoshi; Sugimoto, Yoshikazu; Watanabe, Toshio

2015-11-19

Genetic variance that is not captured by single nucleotide polymorphisms (SNPs) is due to imperfect linkage disequilibrium (LD) between SNPs and quantitative trait loci (QTLs), and the extent of LD between SNPs and QTLs depends on different minor allele frequencies (MAF) between them. To evaluate the impact of MAF of QTLs on genomic evaluation, we performed a simulation study using real cattle genotype data. In total, 1368 Japanese Black cattle and 592,034 SNPs (Illumina BovineHD BeadChip) were used. We simulated phenotypes using real genotypes under different scenarios, varying the MAF categories, QTL heritability, number of QTLs, and distribution of QTL effect. After generating true breeding values and phenotypes, QTL heritability was estimated and the prediction accuracy of genomic estimated breeding value (GEBV) was assessed under different SNP densities, prediction models, and population size by a reference-test validation design. The extent of LD between SNPs and QTLs in this population was higher in the QTLs with high MAF than in those with low MAF. The effect of MAF of QTLs depended on the genetic architecture, evaluation strategy, and population size in genomic evaluation. In genetic architecture, genomic evaluation was affected by the MAF of QTLs combined with the QTL heritability and the distribution of QTL effect. The number of QTL was not affected on genomic evaluation if the number of QTL was more than 50. In the evaluation strategy, we showed that different SNP densities and prediction models affect the heritability estimation and genomic prediction and that this depends on the MAF of QTLs. In addition, accurate QTL heritability and GEBV were obtained using denser SNP information and the prediction model accounted for the SNPs with low and high MAFs. In population size, a large sample size is needed to increase the accuracy of GEBV. The MAF of QTL had an impact on heritability estimation and prediction accuracy. Most genetic variance can be captured

Pain relief with lidocaine 5% patch in localized peripheral neuropathic pain in relation to pain phenotype

DEFF Research Database (Denmark)

Torgaard Demant, Dyveke; Lund, Karen; Finnerup, Nanna B

2015-01-01

In neuropathic pain with irritable nociceptor phenotype, up-regulation of sodium channels on nociceptors is supposed to be an important pain mechanism that may be targeted by topical sodium channel blockade. This randomised, double-blind, phenotype-panel, cross-over study with 4-week treatment pe...... had an effect on peripheral neuropathic pain, and it may be most efficacious in patients with irritable nociceptor phenotype. The lack of significant phenotype differences may be caused by too low statistical power.......In neuropathic pain with irritable nociceptor phenotype, up-regulation of sodium channels on nociceptors is supposed to be an important pain mechanism that may be targeted by topical sodium channel blockade. This randomised, double-blind, phenotype-panel, cross-over study with 4-week treatment...... periods of lidocaine 5% patch and placebo was performed to search for phenotype differences in effect. The primary efficacy measure was the total pain intensity on an 11-point numeric rating scale (NRS), and the primary objective was to compare the effect of lidocaine in patients with and without...

Fibroblast-matrix interplay: Nintedanib and pirfenidone modulate the effect of IPF fibroblast-conditioned matrix on normal fibroblast phenotype.

Science.gov (United States)

Epstein Shochet, Gali; Wollin, Lutz; Shitrit, David

2018-03-12

Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis. Activated fibroblasts are the key effector cells in fibrosis, producing excessive amounts of collagen and extracellular matrix (ECM) proteins. Whether the ECM conditioned by IPF fibroblasts determines the phenotype of naïve fibroblasts is difficult to explore. IPF-derived primary fibroblasts were cultured on Matrigel and then cleared using ammonium hydroxide, creating an IPF-conditioned matrix (CM). Normal fibroblast CM served as control. Normal fibroblasts were cultured on both types of CM, and cell count, cell distribution and markers of myofibroblast differentiation; transforming growth factor beta (TGFβ) signalling; and ECM expression were assessed. The effects of the anti-fibrotic drugs nintedanib and pirfenidone at physiologically relevant concentrations were also explored. Normal fibroblasts cultured on IPF-CM arranged in large aggregates as a result of increased proliferation and migration. Moreover, increased levels of pSmad3, pSTAT3 (phospho signal transducer and activator of transcription 3), alpha smooth muscle actin (αSMA) and Collagen1a were found, suggesting a differentiation towards a myofibroblast-like phenotype. SB505124 (10 μmol/L) partially reversed these alterations, suggesting a TGFβ contribution. Furthermore, nintedanib at 100 nmol/L and, to a lesser extent, pirfenidone at 100 μmol/L prevented the IPF-CM-induced fibroblast phenotype alterations, suggesting an attenuation of the ECM-fibroblast interplay. IPF fibroblasts alter the ECM, thus creating a CM that further propagates an IPF-like phenotype in normal fibroblasts. This assay demonstrated differences in drug activities for approved IPF drugs at clinically relevant concentrations. Thus, the matrix-fibroblast phenotype interplay might be a relevant assay to explore drug candidates for IPF treatment. © 2018 Asian Pacific Society of Respirology.

Video capture virtual reality as a flexible and effective rehabilitation tool

Directory of Open Access Journals (Sweden)

Katz Noomi

2004-12-01

Full Text Available Abstract Video capture virtual reality (VR uses a video camera and software to track movement in a single plane without the need to place markers on specific bodily locations. The user's image is thereby embedded within a simulated environment such that it is possible to interact with animated graphics in a completely natural manner. Although this technology first became available more than 25 years ago, it is only within the past five years that it has been applied in rehabilitation. The objective of this article is to describe the way this technology works, to review its assets relative to other VR platforms, and to provide an overview of some of the major studies that have evaluated the use of video capture technologies for rehabilitation.

Phenotypic Approaches to Drought in Cassava: Review

Directory of Open Access Journals (Sweden)

Emmanuel eOkogbenin

2013-05-01

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

Studies of electron correlation effects in multicharged ion atom collisions involving double capture

Energy Technology Data Exchange (ETDEWEB)

Stolterfoht, N.; Sommer, K.; Griffin, D.C.; Havener, C.C.; Huq, M.S.; Phaneuf, R.A.; Swenson, J.K.; Meyer, F.W.

1988-01-01

We review measurements of L-Coster Kronig and Auger electron production in slow, multicharged collision systems to study electron correlation effects in the process of double electron capture. The n/sup /minus/3/ law was confirmed for the production of the Coster-Kronig configurations 1s/sup 2/2pn/ell/ (n greater than or equal to 6) in O/sup 6 +/ + He collisions. Enhancement of high angular momentum /ell/ in specific 1s/sup 2/2pn/ell/ configurations was observed by means of high-resolution measurements of the Coster-Kronig lines. The importance of electron correlation effects in couplings of potential energy curves leading to the 1s/sup 2/2pn/ell/ configurations is verified by means of Landau-Zener model calculations. 32 refs., 4 figs.

Stimulus-driven capture and contingent capture

NARCIS (Netherlands)

Theeuwes, J.; Olivers, C.N.L.; Belopolsky, A.V.

2010-01-01

Whether or not certain physical events can capture attention has been one of the most debated issues in the study of attention. This discussion is concerned with how goal-directed and stimulus-driven processes interact in perception and cognition. On one extreme of the spectrum is the idea that

Ocean acidification challenges copepod phenotypic plasticity

Science.gov (United States)

Vehmaa, Anu; Almén, Anna-Karin; Brutemark, Andreas; Paul, Allanah; Riebesell, Ulf; Furuhagen, Sara; Engström-Öst, Jonna

2016-11-01

Ocean acidification is challenging phenotypic plasticity of individuals and populations. Calanoid copepods (zooplankton) are shown to be fairly plastic against altered pH conditions, and laboratory studies indicate that transgenerational effects are one mechanism behind this plasticity. We studied phenotypic plasticity of the copepod Acartia sp. in the course of a pelagic, large-volume mesocosm study that was conducted to investigate ecosystem and biogeochemical responses to ocean acidification. We measured copepod egg production rate, egg-hatching success, adult female size and adult female antioxidant capacity (ORAC) as a function of acidification (fCO2 ˜ 365-1231 µatm) and as a function of quantity and quality of their diet. We used an egg transplant experiment to reveal whether transgenerational effects can alleviate the possible negative effects of ocean acidification on offspring development. We found significant negative effects of ocean acidification on adult female size. In addition, we found signs of a possible threshold at high fCO2, above which adaptive maternal effects cannot alleviate the negative effects of acidification on egg-hatching and nauplii development. We did not find support for the hypothesis that insufficient food quantity (total particulate carbon < 55 µm) or quality (C : N) weakens the transgenerational effects. However, females with high-ORAC-produced eggs with high hatching success. Overall, these results indicate that Acartia sp. could be affected by projected near-future CO2 levels.

Evaluation of XHVRB for Capturing Explosive Shock Desensitization

Science.gov (United States)

Tuttle, Leah; Schmitt, Robert; Kittell, Dave; Harstad, Eric

2017-06-01

Explosive shock desensitization phenomena have been recognized for some time. It has been demonstrated that pressure-based reactive flow models do not adequately capture the basic nature of the explosive behavior. Historically, replacing the local pressure with a shock captured pressure has dramatically improved the numerical modeling approaches. Models based upon shock pressure or functions of entropy have recently been developed. A pseudo-entropy based formulation using the History Variable Reactive Burn model, as proposed by Starkenberg, was implemented into the Eulerian shock physics code CTH. Improvements in the shock capturing algorithm were made. The model is demonstrated to reproduce single shock behavior consistent with published pop plot data. It is also demonstrated to capture a desensitization effect based on available literature data, and to qualitatively capture dead zones from desensitization in 2D corner turning experiments. This models shows promise for use in modeling and simulation problems that are relevant to the desensitization phenomena. Issues are identified with the current implementation and future work is proposed for improving and expanding model capabilities. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Physiological ramifications for loggerhead turtles captured in pelagic longlines.

Science.gov (United States)

Williard, Amanda; Parga, Mariluz; Sagarminaga, Ricardo; Swimmer, Yonat

2015-10-01

Bycatch of endangered loggerhead turtles in longline fisheries results in high rates of post-release mortality that may negatively impact populations. The factors contributing to post-release mortality have not been well studied, but traumatic injuries and physiological disturbances experienced as a result of capture are thought to play a role. The goal of our study was to gauge the physiological status of loggerhead turtles immediately upon removal from longline gear in order to refine our understanding of the impacts of capture and the potential for post-release mortality. We analysed blood samples collected from longline- and hand-captured loggerhead turtles, and discovered that capture in longline gear results in blood loss, induction of the systemic stress response, and a moderate increase in lactate. The method by which turtles are landed and released, particularly if released with the hook or line still attached, may exacerbate stress and lead to chronic injuries, sublethal effects or delayed mortality. Our study is the first, to the best of our knowledge, to document the physiological impacts of capture in longline gear, and our findings underscore the importance of best practices gear removal to promote post-release survival in longline-captured turtles. © 2015 The Author(s).

The macroevolutionary consequences of phenotypic integration: from development to deep time.

Science.gov (United States)

Goswami, A; Smaers, J B; Soligo, C; Polly, P D

2014-08-19

Phenotypic integration is a pervasive characteristic of organisms. Numerous analyses have demonstrated that patterns of phenotypic integration are conserved across large clades, but that significant variation also exists. For example, heterochronic shifts related to different mammalian reproductive strategies are reflected in postcranial skeletal integration and in coordination of bone ossification. Phenotypic integration and modularity have been hypothesized to shape morphological evolution, and we extended simulations to confirm that trait integration can influence both the trajectory and magnitude of response to selection. We further demonstrate that phenotypic integration can produce both more and less disparate organisms than would be expected under random walk models by repartitioning variance in preferred directions. This effect can also be expected to favour homoplasy and convergent evolution. New empirical analyses of the carnivoran cranium show that rates of evolution, in contrast, are not strongly influenced by phenotypic integration and show little relationship to morphological disparity, suggesting that phenotypic integration may shape the direction of evolutionary change, but not necessarily the speed of it. Nonetheless, phenotypic integration is problematic for morphological clocks and should be incorporated more widely into models that seek to accurately reconstruct both trait and organismal evolution.

Clusters of conserved beta cell marker genes for assessment of beta cell phenotype

DEFF Research Database (Denmark)

Martens, Geert A; Jiang, Lei; Hellemans, Karine H

2011-01-01

The aim of this study was to establish a gene expression blueprint of pancreatic beta cells conserved from rodents to humans and to evaluate its applicability to assess shifts in the beta cell differentiated state. Genome-wide mRNA expression profiles of isolated beta cells were compared to those...... of a large panel of other tissue and cell types, and transcripts with beta cell-abundant and -selective expression were identified. Iteration of this analysis in mouse, rat and human tissues generated a panel of conserved beta cell biomarkers. This panel was then used to compare isolated versus laser capture...... microdissected beta cells, monitor adaptations of the beta cell phenotype to fasting, and retrieve possible conserved transcriptional regulators....

More Energy-Efficient CO2 Capture from IGCC GE Flue Gases

Directory of Open Access Journals (Sweden)

Rakpong Peampermpool

2017-03-01

Full Text Available Carbon dioxide (CO2 emissions are one of the main reasons for the increase in greenhouse gasses in the earth’s atmosphere and carbon capture and sequestration (CCS is known as an effective method to reduce CO2 emissions on a larger scale, such as for fossil energy utilization systems. In this paper, the feasibility of capturing CO2 using cryogenic liquefaction and improving the capture rate by expansion will be discussed. The main aim was to design an energy-saving scheme for an IGCC (integrated gasification combined cycle power plant with CO2 cryogenic liquefaction capture. The experimental results provided by the authors, using the feed gas specification of a 740 MW IGCC General Electric (GE combustion power plant, demonstrated that using an orifice for further expanding the vent gas after cryogenic capture from 57 bar to 24 bar gave an experimentally observed capture rate up to 65%. The energy-saving scheme can improve the overall CO2 capture rate, and hence save energy. The capture process has also been simulated using Aspen HYSYS simulation software to evaluate its energy penalty. The results show that a 92% overall capture rate can be achieved by using an orifice.

Incentives for early adoption of carbon capture technology

International Nuclear Information System (INIS)

Comello, Stephen; Reichelstein, Stefan

2014-01-01

We analyze a policy proposal for regulating the next generation of baseload electricity generation facilities in the United States. The cornerstone of this regulation is a (hypothetical) EPA mandate for an emission standard of 80 kg of CO 2 per MWh of electricity generated. The mandate would go into effect at the end of 2027 for all power generating facilities that come into operation after 2017. Fossil-fuel power plants could meet the standard by capturing between 80 and 90% of their current CO 2 emissions. While the initial cost of complying with this standard is relatively high for first-of-a-kind facilities, learning effects are projected to reduce this cost substantially by the end of 2027, provided new facilities consistently adopt carbon capture technology in the intervening years. We identify a combination of investment- and production tax credits that provide the required incentives for new facilities to be willing to comply with the standard ahead of the mandate. Due to the anticipated learning effects, the incremental cost associated with the stricter emission limit is projected to about 1.2¢ per kWh of electricity in the long run. - Highlights: • Study the cost effects of a CO 2 emission standard for natural gas power plants. • The standard requires the deployment of carbon capture technology. • Future compliance costs are reduced through learning effects. • Identify tax incentives that induce early technology adoption. • Early adoption results in relatively modest electricity cost increases

Resource capture by single leaves

Energy Technology Data Exchange (ETDEWEB)

Long, S.P.

1992-05-01

Leaves show a variety of strategies for maximizing CO{sub 2} and light capture. These are more meaningfully explained if they are considered in the context of maximizing capture relative to the utilization of water, nutrients and carbohydrates reserves. There is considerable variation between crops in their efficiency of CO{sub 2} and light capture at the leaf level. Understanding of these mechanisms indicate some ways in which efficiency of resource capture could be level cannot be meaningfully considered without simultaneous understanding of implications at the canopy level. 36 refs., 5 figs., 1 tab.

Biological indicators of stress in pacu (Piaractus mesopotamicus after capture

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JS. Abreu

Full Text Available The effects of capture (chasing, netting and air exposure on cortisol, glucose, chloride, sodium, potassium and calcium concentrations, osmolality, hematocrit, hemoglobin concentration, red blood cells count (RBC and mean corpuscular volume (MCV were investigated in pacu (Piaractus mesopotamicus. A total of 132 fish (49.7 ± 11.7 g were subjected to capture and 3 minutes air exposure and capture and 5 minutes air exposure. Nine fish at each treatment were sampled at 5, 15, 30, 60 minutes and 24 hours after the procedure. Nine undisturbed fish were sacrificed before the handling and used as controls. Capture resulted in a rise in blood cortisol and glucose 30 and 5 minutes, respectively, after both air exposures. Both indicators returned to resting levels 24 hours after capture. In both fish groups, plasma chloride decreased 60 minutes after capture, not recovering the resting levels within 24 hours after, and serum sodium rose at 15 and 30 minutes and recovered the resting levels 24 hours later. There were no significant changes neither in potassium, calcium and osmolality nor in hematocrit, hemoglobin, RBC and MCV as a consequence of capture. The sequential stressors imposed to pacu during capture activated the brain-pituitary-interrenal axis (cortisol and glucose responses but the activation of the brain-sympathetic-chromaffin cell axis was apparently moderate (ionic and hematological responses.

A New Motion Capture System For Automated Gait Analysis Based On Multi Video Sequence Analysis

DEFF Research Database (Denmark)

Jensen, Karsten; Juhl, Jens

There is an increasing demand for assessing foot mal positions and an interest in monitoring the effect of treatment. In the last decades several different motion capture systems has been used. This abstract describes a new low cost motion capture system.......There is an increasing demand for assessing foot mal positions and an interest in monitoring the effect of treatment. In the last decades several different motion capture systems has been used. This abstract describes a new low cost motion capture system....

Annual Report: Carbon Capture (30 September 2012)

Energy Technology Data Exchange (ETDEWEB)

Luebke, David; Morreale, Bryan; Richards, George; Syamlal, Madhava

2014-04-16

Capture of carbon dioxide (CO{sub 2}) is a critical component in reducing greenhouse gas emissions from fossil fuel-based processes. The Carbon Capture research to be performed is aimed at accelerating the development of efficient, cost-effective technologies which meet the post-combustion programmatic goal of capture of 90% of the CO{sub 2} produced from an existing coal-fired power plant with less than a 35% increase in the cost of electricity (COE), and the pre-combustion goal of 90% CO{sub 2} capture with less than a 10% increase in COE. The specific objective of this work is to develop innovative materials and approaches for the economic and efficient capture of CO{sub 2} from coal-based processes, and ultimately assess the performance of promising technologies at conditions representative of field application (i.e., slip stream evaluation). The Carbon Capture research includes seven core technical research areas: post-combustion solvents, sorbents, and membranes; pre-combustion solvents, sorbents, and membranes; and oxygen (O{sub 2}) production. The goal of each of these tasks is to develop advanced materials and processes that are able to reduce the energy penalty and cost of CO{sub 2} (or O{sub 2}) separation over conventional technologies. In the first year of development, materials will be examined by molecular modeling, and then synthesized and experimentally characterized at lab scale. In the second year, they will be tested further under ideal conditions. In the third year, they will be tested under realistic conditions. The most promising materials will be tested at the National Carbon Capture Center (NCCC) using actual flue or fuel gas. Systems analyses will be used to determine whether or not materials developed are likely to meet the Department of Energy (DOE) COE targets. Materials which perform well and appear likely to improve in performance will be licensed for further development outside of the National Energy Technology Laboratory (NETL

Lecture Capturing: Its Effects on Students' Absenteeism, Performance, and Impressions in a Traditional Marketing Research Course

Science.gov (United States)

Dommeyer, Curt J.

2017-01-01

A quasiexperiment was conducted among marketing research students to determine the effects of lecture capturing (LC). One group of students (the LC group) was allowed access to video recordings of the class lectures whereas another group of students in a parallel class (the control group) was not given access to the recordings. When both groups…

Attentional Capture and Inhibition of Saccades after Irrelevant and Relevant Cues

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Heinz-Werner Priess

2014-01-01

Full Text Available Attentional capture is usually stronger for task-relevant than irrelevant stimuli, whereas irrelevant stimuli can trigger equal or even stronger amounts of inhibition than relevant stimuli. Capture and inhibition, however, are typically assessed in separate trials, leaving it open whether or not inhibition of irrelevant stimuli is a consequence of preceding attentional capture by the same stimuli or whether inhibition is the only response to these stimuli. Here, we tested the relationship between capture and inhibition in a setup allowing for estimates of the capture and inhibition based on the very same trials. We recorded saccadic inhibition after relevant and irrelevant stimuli. At the same time, we recorded the N2pc, an event-related potential, reflecting initial capture of attention. We found attentional capture not only for, relevant but importantly also for irrelevant stimuli, although the N2pc was stronger for relevant than irrelevant stimuli. In addition, inhibition of saccades was the same for relevant and irrelevant stimuli. We conclude with a discussion of the mechanisms that are responsible for these effects.

Clinical phenotypes of asthma

NARCIS (Netherlands)

Bel, Elisabeth H.

2004-01-01

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

An attempt to explain the uranium 238 effective capture integral discrepancy

International Nuclear Information System (INIS)

Tellier, Henry; Grandotto-Biettoli, Marc; Vanuxeem, Jacqueline

1979-02-01

Up to now, there was a discrepancy between the computed value and the measured value of the uranium 238 effective capture integral. The former has been always greater than the latter. For this reason, the reactor physicists have used an adjustment of the computed value. Nowadays the accuracy of the cross sections knowledge is increased and the reactors computation codes are almost exact. Such an adjustment is no more justified. Recently several new measurements of the resonance parameters were carried out and the use of a multilevel formalism was suggested to compute the uranium 238 cross sections. It is shown in this work that the simultaneous use of recent parameters and Reich and Moore formalism explain the discrepancy. For the thermal neutron reactors, two thirds of this discrepancy are explained by the neutron data and the last third by the multilevel formalism [fr

Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin/TOR and associated phenotypes in Drosophila melanogaster

Directory of Open Access Journals (Sweden)

Harshman Lawrence G

2009-03-01

Full Text Available Abstract Background A molecular process based genotype-to-phenotype map will ultimately enable us to predict how genetic variation among individuals results in phenotypic alterations. Building such a map is, however, far from straightforward. It requires understanding how molecular variation re-shapes developmental and metabolic networks, and how the functional state of these networks modifies phenotypes in genotype specific way. We focus on the latter problem by describing genetic variation in transcript levels of genes in the InR/TOR pathway among 72 Drosophila melanogaster genotypes. Results We observe tight co-variance in transcript levels of genes not known to influence each other through direct transcriptional control. We summarize transcriptome variation with factor analyses, and observe strong co-variance of gene expression within the dFOXO-branch and within the TOR-branch of the pathway. Finally, we investigate whether major axes of transcriptome variation shape phenotypes expected to be influenced through the InR/TOR pathway. We find limited evidence that transcript levels of individual upstream genes in the InR/TOR pathway predict fly phenotypes in expected ways. However, there is no evidence that these effects are mediated through the major axes of downstream transcriptome variation. Conclusion In summary, our results question the assertion of the 'sparse' nature of genetic networks, while validating and extending candidate gene approaches in the analyses of complex traits.

Measurement of keV-neutron capture cross sections and capture gamma-ray spectra of Er isotopes

International Nuclear Information System (INIS)

Harun-Ar-Rashid, A.K.M.; Igashira, Masayuki; Ohsaki, Toshiro

2000-01-01

Neutron capture cross sections and capture γ-ray spectra of 166,167, 168 Er were measured in the energy region of 10 to 550 keV. The measurements were performed with a pulsed 7 Li(p,n) 7 Be neutron source and a large anti-Compton NaI(Tl) γ-ray spectrometer. A pulse-height weighting technique and the standard capture cross sections of gold were used to derive the capture cross sections. The errors of the derived cross sections were about 5%. The present results were compared with other measurements and evaluations. The observed capture γ-ray pulse-height spectra were unfolded to obtain the corresponding γ-ray spectra. An anomalous shoulder was observed around 3 MeV in each of the capture γ-ray spectra. (author)

Targeted next-generation sequencing reveals novel USH2A mutations associated with diverse disease phenotypes: implications for clinical and molecular diagnosis.

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Xue Chen

Full Text Available USH2A mutations have been implicated in the disease etiology of several inherited diseases, including Usher syndrome type 2 (USH2, nonsyndromic retinitis pigmentosa (RP, and nonsyndromic deafness. The complex genetic and phenotypic spectrums relevant to USH2A defects make it difficult to manage patients with such mutations. In the present study, we aim to determine the genetic etiology and to characterize the correlated clinical phenotypes for three Chinese pedigrees with nonsyndromic RP, one with RP sine pigmento (RPSP, and one with USH2. Family histories and clinical details for all included patients were reviewed. Ophthalmic examinations included best corrected visual acuities, visual field measurements, funduscopy, and electroretinography. Targeted next-generation sequencing (NGS was applied using two sequence capture arrays to reveal the disease causative mutations for each family. Genotype-phenotype correlations were also annotated. Seven USH2A mutations, including four missense substitutions (p.P2762A, p.G3320C, p.R3719H, and p.G4763R, two splice site variants (c.8223+1G>A and c.8559-2T>C, and a nonsense mutation (p.Y3745*, were identified as disease causative in the five investigated families, of which three reported to have consanguineous marriage. Among all seven mutations, six were novel, and one was recurrent. Two homozygous missense mutations (p.P2762A and p.G3320C were found in one individual family suggesting a potential double hit effect. Significant phenotypic divergences were revealed among the five families. Three families of the five families were affected with early, moderated, or late onset RP, one with RPSP, and the other one with USH2. Our study expands the genotypic and phenotypic variability relevant to USH2A mutations, which would help with a clear insight into the complex genetic and phenotypic spectrums relevant to USH2A defects, and is complementary for a better management of patients with such mutations. We have

Influence of wetting layer wave functions on carrier capture in quantum dots

DEFF Research Database (Denmark)

Markussen, Troels; Kristensen, Philip; Tromborg, Bjarne

2005-01-01

This work numerically solves the effective mass Schrodinger equation and shows that the capture times are strongly influenced by details of the continuum states not accounted for by the approximate wave functions. Results show that calculations of capture time for phonon mediated carrier capture...... from a wetting layer into a quantum dot depend critically on the approximations used for the wetting layer wave functions....

The role of environment and core-margin effects on range-wide phenotypic variation in a montane grasshopper.

Science.gov (United States)

Noguerales, V; García-Navas, V; Cordero, P J; Ortego, J

2016-11-01

The integration of genetic information with ecological and phenotypic data constitutes an effective approach to gain insight into the mechanisms determining interpopulation variability and the evolutionary processes underlying local adaptation and incipient speciation. Here, we use the Pyrenean Morales grasshopper (Chorthippus saulcyi moralesi) as study system to (i) analyse the relative role of genetic drift and selection in range-wide patterns of phenotypic differentiation and (ii) identify the potential selective agents (environment, elevation) responsible for variation. We also test the hypothesis that (iii) the development of dispersal-related traits is associated with different parameters related to population persistence/turnover, including habitat suitability stability over the last 120 000 years, distance to the species distribution core and population genetic variability. Our results indicate that selection shaped phenotypic differentiation across all the studied morphological traits (body size, forewing length and shape). Subsequent analyses revealed that among-population differentiation in forewing length was significantly explained by a temperature gradient, suggesting an adaptive response to thermoregulation or flight performance under contrasting temperature regimes. We found support for our hypothesis predicting a positive association between the distance to the species distribution core and the development of dispersal-related morphology, which suggests an increased dispersal capability in populations located at range edges that, in turn, exhibit lower levels of genetic variability. Overall, our results indicate that range-wide patterns of phenotypic variation are partially explained by adaptation in response to local environmental conditions and differences in habitat persistence between core and peripheral populations. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary

Techniques for capturing bighorn sheep lambs

Science.gov (United States)

Smith, Joshua B.; Walsh, Daniel P.; Goldstein, Elise J.; Parsons, Zachary D.; Karsch, Rebekah C.; Stiver, Julie R.; Cain, James W.; Raedeke, Kenneth J.; Jenks, Jonathan A.

2014-01-01

Low lamb recruitment is a major challenge facing managers attempting to mitigate the decline of bighorn sheep (Ovis canadensis), and investigations into the underlying mechanisms are limited because of the inability to readily capture and monitor bighorn sheep lambs. We evaluated 4 capture techniques for bighorn sheep lambs: 1) hand-capture of lambs from radiocollared adult females fitted with vaginal implant transmitters (VITs), 2) hand-capture of lambs of intensively monitored radiocollared adult females, 3) helicopter net-gunning, and 4) hand-capture of lambs from helicopters. During 2010–2012, we successfully captured 90% of lambs from females that retained VITs to ≤1 day of parturition, although we noted differences in capture rates between an area of high road density in the Black Hills (92–100%) of South Dakota, USA, and less accessible areas of New Mexico (71%), USA. Retention of VITs was 78% with pre-partum expulsion the main cause of failure. We were less likely to capture lambs from females that expelled VITs ≥1 day of parturition (range = 80–83%) or females that were collared without VITs (range = 60–78%). We used helicopter net-gunning at several sites in 1999, 2001–2002, and 2011, and it proved a useful technique; however, at one site, attempts to capture lambs led to lamb predation by golden eagles (Aquila chrysaetos). We attempted helicopter hand-captures at one site in 1999, and they also were successful in certain circumstances and avoided risk of physical trauma from net-gunning; however, application was limited. In areas of low accessibility or if personnel lack the ability to monitor females and/or VITs for extended periods, helicopter capture may provide a viable option for lamb capture.

Motion Capturing Emotions

Directory of Open Access Journals (Sweden)

Wood Karen

2017-12-01

Full Text Available The paper explores the activities conducted as part of WhoLoDancE: Whole Body Interaction Learning for Dance Education which is an EU-funded Horizon 2020 project. In particular, we discuss the motion capture sessions that took place at Motek, Amsterdam as well as the dancers’ experience of being captured and watching themselves or others as varying visual representations through the HoloLens. HoloLens is Microsoft’s first holographic computer that you wear as you would a pair of glasses. The study embraced four dance genres: Ballet, Contemporary, Flamenco and Greek Folk dance. We are specifically interested in the kinesthetic and emotional engagement with the moving body and what new corporeal awareness may be experienced. Positioning the moving, dancing body as fundamental to technological advancements, we discuss the importance of considering the dancer’s experience in the real and virtual space. Some of the artists involved in the project have offered their experiences, which are included, and they form the basis of the discussion. In addition, we discuss the affect of immersive environments, how these environments expand reality and what effect (emotionally and otherwise that has on the body. The research reveals insights into relationships between emotion, movement and technology and what new sensorial knowledge this evokes for the dancer.

Effect of chitosan and coagulation factors on the wound repair phenotype of bioengineered blood clots.

Science.gov (United States)

Hoemann, Caroline D; Marchand, Catherine; Rivard, Georges-Etienne; El-Gabalawy, Hani; Poubelle, Patrice E

2017-11-01

Controlling the blood clot phenotype in a surgically prepared wound is an evolving concept in scaffold-guided tissue engineering. Here, we investigated the effect of added chitosan (80% or 95% Degree of Deacetylation, DDA) or coagulation factors (recombinant human Factor VIIa, Tissue Factor, thrombin) on inflammatory factors released by blood clots. We tested the hypothesis that 80% DDA chitosan specifically enhances leukotriene B 4 (LTB 4 ) production. Human or rabbit whole blood was combined with isotonic chitosan solutions, coagulation factors, or lipopolysaccharide, cultured in vitro at 37°C, and after 4hours the serum was assayed for LTB 4 or inflammatory factors. Only 80% DDA chitosan clots produced around 15-fold more LTB 4 over other clots including 95% DDA chitosan clots. All serum contained high levels of PDGF-BB and CXCL8. Normal clots produced very low type I cytokines compared to lipopolysaccharide clots, with even lower IL-6 and IL-12 and more CCL3/CCL4 produced by chitosan clots. Coagulation factors had no detectable effect on clot phenotype. Conclusion In blood clots from healthy individuals, 80% DDA chitosan has a unique influence of inducing more LTB 4 , a potent neutrophil chemoattractant, with similar production of PDGF-BB and CXCL8, and lower type I cytokines, compared to whole blood clots. Copyright © 2017 Elsevier B.V. All rights reserved.

Persistence of Value-Driven Attentional Capture

Science.gov (United States)

Anderson, Brian A.; Yantis, Steven

2013-01-01

Stimuli that have previously been associated with the delivery of reward involuntarily capture attention when presented as unrewarded and task-irrelevant distractors in a subsequent visual search task. It is unknown how long such effects of reward learning on attention persist. One possibility is that value-driven attentional biases are plastic…

Quantifying small molecule phenotypic effects using mitochondrial morpho-functional fingerprinting and machine learning

Science.gov (United States)

Blanchet, Lionel; Smeitink, Jan A. M.; van Emst-de Vries, Sjenet E.; Vogels, Caroline; Pellegrini, Mina; Jonckheere, An I.; Rodenburg, Richard J. T.; Buydens, Lutgarde M. C.; Beyrath, Julien; Willems, Peter H. G. M.; Koopman, Werner J. H.

2015-01-01

In primary fibroblasts from Leigh Syndrome (LS) patients, isolated mitochondrial complex I deficiency is associated with increased reactive oxygen species levels and mitochondrial morpho-functional changes. Empirical evidence suggests these aberrations constitute linked therapeutic targets for small chemical molecules. However, the latter generally induce multiple subtle effects, meaning that in vitro potency analysis or single-parameter high-throughput cell screening are of limited use to identify these molecules. We combine automated image quantification and artificial intelligence to discriminate between primary fibroblasts of a healthy individual and a LS patient based upon their mitochondrial morpho-functional phenotype. We then evaluate the effects of newly developed Trolox variants in LS patient cells. This revealed that Trolox ornithylamide hydrochloride best counterbalanced mitochondrial morpho-functional aberrations, effectively scavenged ROS and increased the maximal activity of mitochondrial complexes I, IV and citrate synthase. Our results suggest that Trolox-derived antioxidants are promising candidates in therapy development for human mitochondrial disorders.

UAV-Based Thermal Imaging for High-Throughput Field Phenotyping of Black Poplar Response to Drought

Directory of Open Access Journals (Sweden)

Riccardo Ludovisi

2017-09-01

Full Text Available Poplars are fast-growing, high-yielding forest tree species, whose cultivation as second-generation biofuel crops is of increasing interest and can efficiently meet emission reduction goals. Yet, breeding elite poplar trees for drought resistance remains a major challenge. Worldwide breeding programs are largely focused on intra/interspecific hybridization, whereby Populus nigra L. is a fundamental parental pool. While high-throughput genotyping has resulted in unprecedented capabilities to rapidly decode complex genetic architecture of plant stress resistance, linking genomics to phenomics is hindered by technically challenging phenotyping. Relying on unmanned aerial vehicle (UAV-based remote sensing and imaging techniques, high-throughput field phenotyping (HTFP aims at enabling highly precise and efficient, non-destructive screening of genotype performance in large populations. To efficiently support forest-tree breeding programs, ground-truthing observations should be complemented with standardized HTFP. In this study, we develop a high-resolution (leaf level HTFP approach to investigate the response to drought of a full-sib F2 partially inbred population (termed here ‘POP6’, whose F1 was obtained from an intraspecific P. nigra controlled cross between genotypes with highly divergent phenotypes. We assessed the effects of two water treatments (well-watered and moderate drought on a population of 4603 trees (503 genotypes hosted in two adjacent experimental plots (1.67 ha by conducting low-elevation (25 m flights with an aerial drone and capturing 7836 thermal infrared (TIR images. TIR images were undistorted, georeferenced, and orthorectified to obtain radiometric mosaics. Canopy temperature (Tc was extracted using two independent semi-automated segmentation techniques, eCognition- and Matlab-based, to avoid the mixed-pixel problem. Overall, results showed that the UAV platform-based thermal imaging enables to effectively assess genotype

UAV-Based Thermal Imaging for High-Throughput Field Phenotyping of Black Poplar Response to Drought.

Science.gov (United States)

Ludovisi, Riccardo; Tauro, Flavia; Salvati, Riccardo; Khoury, Sacha; Mugnozza Scarascia, Giuseppe; Harfouche, Antoine

2017-01-01

Poplars are fast-growing, high-yielding forest tree species, whose cultivation as second-generation biofuel crops is of increasing interest and can efficiently meet emission reduction goals. Yet, breeding elite poplar trees for drought resistance remains a major challenge. Worldwide breeding programs are largely focused on intra/interspecific hybridization, whereby Populus nigra L. is a fundamental parental pool. While high-throughput genotyping has resulted in unprecedented capabilities to rapidly decode complex genetic architecture of plant stress resistance, linking genomics to phenomics is hindered by technically challenging phenotyping. Relying on unmanned aerial vehicle (UAV)-based remote sensing and imaging techniques, high-throughput field phenotyping (HTFP) aims at enabling highly precise and efficient, non-destructive screening of genotype performance in large populations. To efficiently support forest-tree breeding programs, ground-truthing observations should be complemented with standardized HTFP. In this study, we develop a high-resolution (leaf level) HTFP approach to investigate the response to drought of a full-sib F 2 partially inbred population (termed here 'POP6'), whose F 1 was obtained from an intraspecific P. nigra controlled cross between genotypes with highly divergent phenotypes. We assessed the effects of two water treatments (well-watered and moderate drought) on a population of 4603 trees (503 genotypes) hosted in two adjacent experimental plots (1.67 ha) by conducting low-elevation (25 m) flights with an aerial drone and capturing 7836 thermal infrared (TIR) images. TIR images were undistorted, georeferenced, and orthorectified to obtain radiometric mosaics. Canopy temperature ( T c ) was extracted using two independent semi-automated segmentation techniques, eCognition- and Matlab-based, to avoid the mixed-pixel problem. Overall, results showed that the UAV platform-based thermal imaging enables to effectively assess genotype

A comparison of the COG and MCNP codes in computational neutron capture therapy modeling, Part II: gadolinium neutron capture therapy models and therapeutic effects.

Science.gov (United States)

Wangerin, K; Culbertson, C N; Jevremovic, T

2005-08-01

The goal of this study was to evaluate the COG Monte Carlo radiation transport code, developed and tested by Lawrence Livermore National Laboratory, for gadolinium neutron capture therapy (GdNCT) related modeling. The validity of COG NCT model has been established for this model, and here the calculation was extended to analyze the effect of various gadolinium concentrations on dose distribution and cell-kill effect of the GdNCT modality and to determine the optimum therapeutic conditions for treating brain cancers. The computational results were compared with the widely used MCNP code. The differences between the COG and MCNP predictions were generally small and suggest that the COG code can be applied to similar research problems in NCT. Results for this study also showed that a concentration of 100 ppm gadolinium in the tumor was most beneficial when using an epithermal neutron beam.

Nominal effective radiation doses delivered during clinical trials of boron neutron capture therapy

International Nuclear Information System (INIS)

Capala, J.; Diaz, A.Z.; Chanana, A.D.

1997-01-01

Boron neutron capture therapy (BNCT) is a binary system that, in theory, should selectively deliver lethal, high linear energy transfer (LET) radiation to tumor cells dispersed within normal tissues. It is based on the nuclear reaction 10-B(n, α)7-Li, which occurs when the stable nucleus of boron-10 captures a thermal neutron. Due to the relatively high cross-section of the 10-B nucleus for thermal neutron capture and short ranges of the products of this reaction, tumor cells in the volume exposed to thermal neutrons and containing sufficiently high concentration of 10-B would receive a much higher radiation dose than the normal cells contained within the exposed volume. Nevertheless, radiation dose deposited in normal tissue by gamma and fast neutron contamination of the neutron beam, as well as neutron capture in nitrogen, 14-N(n,p)14-C, hydrogen, 1-H(n,γ)2-H, and in boron present in blood and normal cells, limits the dose that can be delivered to tumor cells. It is, therefore, imperative for the success of the BNCT the dosed delivered to normal tissues be accurately determined in order to optimize the irradiation geometry and to limit the volume of normal tissue exposed to thermal neutrons. These are the major objectives of BNCT treatment planning

Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype.

Science.gov (United States)

Chang, Peter L; Kopania, Emily; Keeble, Sara; Sarver, Brice A J; Larson, Erica; Orth, Annie; Belkhir, Khalid; Boursot, Pierre; Bonhomme, François; Good, Jeffrey M; Dean, Matthew D

2017-10-01

The house mouse is a powerful model to dissect the genetic basis of phenotypic variation, and serves as a model to study human diseases. Despite a wealth of discoveries, most classical laboratory strains have captured only a small fraction of genetic variation known to segregate in their wild progenitors, and existing strains are often related to each other in complex ways. Inbred strains of mice independently derived from natural populations have the potential to increase power in genetic studies with the addition of novel genetic variation. Here, we perform exome-enrichment and high-throughput sequencing (~8× coverage) of 26 wild-derived strains known in the mouse research community as the "Montpellier strains." We identified 1.46 million SNPs in our dataset, approximately 19% of which have not been detected from other inbred strains. This novel genetic variation is expected to contribute to phenotypic variation, as they include 18,496 nonsynonymous variants and 262 early stop codons. Simulations demonstrate that the higher density of genetic variation in the Montpellier strains provides increased power for quantitative genetic studies. Inasmuch as the power to connect genotype to phenotype depends on genetic variation, it is important to incorporate these additional genetic strains into future research programs.

A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis.

Directory of Open Access Journals (Sweden)

Alexander D Malkin

2015-10-01

Full Text Available Neutrophils play a central role in eliminating bacterial pathogens, but may also contribute to end-organ damage in sepsis. Interleukin-8 (IL-8, a key modulator of neutrophil function, signals through neutrophil specific surface receptors CXCR-1 and CXCR-2. In this study a mechanistic computational model was used to evaluate and deploy an extracorporeal sepsis treatment which modulates CXCR-1/2 levels. First, a simplified mechanistic computational model of IL-8 mediated activation of CXCR-1/2 receptors was developed, containing 16 ODEs and 43 parameters. Receptor level dynamics and systemic parameters were coupled with multiple neutrophil phenotypes to generate dynamic populations of activated neutrophils which reduce pathogen load, and/or primed neutrophils which cause adverse tissue damage when misdirected. The mathematical model was calibrated using experimental data from baboons administered a two-hour infusion of E coli and followed for a maximum of 28 days. Ensembles of parameters were generated using a Bayesian parallel tempering approach to produce model fits that could recreate experimental outcomes. Stepwise logistic regression identified seven model parameters as key determinants of mortality. Sensitivity analysis showed that parameters controlling the level of killer cell neutrophils affected the overall systemic damage of individuals. To evaluate rescue strategies and provide probabilistic predictions of their impact on mortality, time of onset, duration, and capture efficacy of an extracorporeal device that modulated neutrophil phenotype were explored. Our findings suggest that interventions aiming to modulate phenotypic composition are time sensitive. When introduced between 3-6 hours of infection for a 72 hour duration, the survivor population increased from 31% to 40-80%. Treatment efficacy quickly diminishes if not introduced within 15 hours of infection. Significant harm is possible with treatment durations ranging from 5

Motivationally Significant Stimuli Show Visual Prior Entry: Evidence for Attentional Capture

Science.gov (United States)

West, Greg L.; Anderson, Adam A. K.; Pratt, Jay

2009-01-01

Previous studies that have found attentional capture effects for stimuli of motivational significance do not directly measure initial attentional deployment, leaving it unclear to what extent these items produce attentional capture. Visual prior entry, as measured by temporal order judgments (TOJs), rests on the premise that allocated attention…

Effects of species-specific leaf characteristics and reduced water availability on fine particle capture efficiency of trees

International Nuclear Information System (INIS)

Räsänen, Janne V.; Holopainen, Toini; Joutsensaari, Jorma; Ndam, Collins; Pasanen, Pertti; Rinnan, Åsmund; Kivimäenpää, Minna

2013-01-01

Trees can improve air quality by capturing particles in their foliage. We determined the particle capture efficiencies of coniferous Pinus sylvestris and three broadleaved species: Betula pendula, Betula pubescens and Tilia vulgaris in a wind tunnel using NaCl particles. The importance of leaf surface structure, physiology and moderate soil drought on the particle capture efficiencies of the trees were determined. The results confirm earlier findings of more efficient particle capture by conifers compared to broadleaved plants. The particle capture efficiency of P. sylvestris (0.21%) was significantly higher than those of B. pubescens, T. vulgaris and B. pendula (0.083%, 0.047%, 0.043%, respectively). The small leaf size of P. sylvestris was the major characteristic that increased particle capture. Among the broadleaved species, low leaf wettability, low stomatal density and leaf hairiness increased particle capture. Moderate soil drought tended to increase particle capture efficiency of P. sylvestris. -- Highlights: • Coniferous Scots pine was the most efficient particle collector. • Decreasing single leaf size increases particle deposition of the total leaf area. • Hairiness of the leaf increases particle deposition. -- Trees can improve air quality by removing PM 2.5 pollutants carried on the wind at a velocity of 3 m s −1 , the efficiency of which depends on species leaf characteristics and physical factors

Functionalized metal organic frameworks for effective capture of radioactive organic iodides

KAUST Repository

Li, Baiyan; Dong, Xinglong; Wang, Hao; Ma, Dingxuan; Tan, Kui; Shi, Zhan; Chabal, Yves J.; Han, Yu; Li, Jing

2017-01-01

Highly efficient capture of radioactive organic iodides (ROIs) from off-gas mixtures remains a substantial challenge for nuclear waste treatment. Current materials utilized for ROI sequestration suffer from low capacity, high cost (e.g. use of noble

Exploratory investigations of hypervelocity intact capture spectroscopy

Science.gov (United States)

Tsou, P.; Griffiths, D. J.

1993-01-01

The ability to capture hypervelocity projectiles intact opens a new technique available for hypervelocity research. A determination of the reactions taking place between the projectile and the capture medium during the process of intact capture is extremely important to an understanding of the intact capture phenomenon, to improving the capture technique, and to developing a theory describing the phenomenon. The intact capture of hypervelocity projectiles by underdense media generates spectra, characteristic of the material species of projectile and capture medium involved. Initial exploratory results into real-time characterization of hypervelocity intact capture techniques by spectroscopy include ultra-violet and visible spectra obtained by use of reflecting gratings, transmitting gratings, and prisms, and recorded by photographic and electronic means. Spectrometry proved to be a valuable real-time diagnostic tool for hypervelocity intact capture events, offering understanding of the interactions of the projectile and the capture medium during the initial period and providing information not obtainable by other characterizations. Preliminary results and analyses of spectra produced by the intact capture of hypervelocity aluminum spheres in polyethylene (PE), polystyrene (PS), and polyurethane (PU) foams are presented. Included are tentative emission species identifications, as well as gray body temperatures produced in the intact capture process.

Cyclic-AMP metabolism in synaptic growth, strength and precision: Neural and behavioral phenotype-specific counterbalancing effects between dnc PDE and rut AC mutations

Science.gov (United States)

Ueda, Atsushi; Wu, Chun-Fang

2012-01-01

Two classic learning mutants in Drosophila, rutabaga (rut) and dunce (dnc), are defective in cAMP synthesis and degradation, respectively, exhibiting a variety of neuronal and behavioral defects. We ask how the opposing effects of these mutations on cAMP levels modify subsets of phenotypes, and whether any specific phenotypes could be ameliorated by biochemical counter balancing effects in dnc rut double mutants. Our study at larval neuromuscular junctions (NMJs) demonstrate that dnc mutations caused severe defects in nerve terminal morphology, characterized by unusually large synaptic boutons and aberrant innervation patterns. Interestingly, a counterbalancing effect led to rescue of the aberrant innervation patterns but the enlarged boutons in dnc rut double mutant remained as extreme as those in dnc. In contrast to dnc, rut mutations strongly affect synaptic transmission. Focal loose-patch recording data accumulated over 4 years suggest that synaptic currents in rut boutons were characterized by unusually large temporal dispersion and a seasonal variation in the amount of transmitter release, with diminished synaptic currents in summer months. Experiments with different rearing temperatures revealed that high temperature (29–30 °C) decreased synaptic transmission in rut, but did not alter dnc and WT. Importantly, the large temporal dispersion and abnormal temperature dependence of synaptic transmission, characteristic of rut, still persisted in dnc rut double mutants. To interpret these results in a proper perspective, we reviewed previously documented differential effects of dnc and rut mutations and their genetic interactions in double mutants on a variety of physiological and behavioral phenotypes. The cases of rescue in double mutants are associated with gradual developmental and maintenance processes whereas many behavioral and physiological manifestations on faster time scales could not be rescued. We discuss factors that could contribute to the

Phenotypic and genetic effects of contrasting ethanol environments on physiological and developmental traits in Drosophila melanogaster.

Directory of Open Access Journals (Sweden)

Luis E Castañeda

Full Text Available A central problem in evolutionary physiology is to understand the relationship between energy metabolism and fitness-related traits. Most attempts to do so have been based on phenotypic correlations that are not informative for the evolutionary potential of natural populations. Here, we explored the effect of contrasting ethanol environments on physiological and developmental traits, their genetic (covariances and genetic architecture in Drosophila melanogaster. Phenotypic and genetic parameters were estimated in two populations (San Fernando and Valdivia, Chile, using a half-sib family design where broods were split into ethanol-free and ethanol-supplemented conditions. Our findings show that metabolic rate, body mass and development times were sensitive (i.e., phenotypic plasticity to ethanol conditions and dependent on population origin. Significant heritabilities were found for all traits, while significant genetic correlations were only found between larval and total development time and between development time and metabolic rate for flies of the San Fernando population developed in ethanol-free conditions. Posterior analyses indicated that the G matrices differed between ethanol conditions for the San Fernando population (mainly explained by differences in genetic (covariances of developmental traits, whereas the Valdivia population exhibited similar G matrices between ethanol conditions. Our findings suggest that ethanol-free environment increases the energy available to reduce development time. Therefore, our results indicate that environmental ethanol could modify the process of energy allocation, which could have consequences on the evolutionary response of natural populations of D. melanogaster.

Phenotypic and Genetic Effects of Contrasting Ethanol Environments on Physiological and Developmental Traits in Drosophila melanogaster

Science.gov (United States)

Castañeda, Luis E.; Nespolo, Roberto F.

2013-01-01

A central problem in evolutionary physiology is to understand the relationship between energy metabolism and fitness-related traits. Most attempts to do so have been based on phenotypic correlations that are not informative for the evolutionary potential of natural populations. Here, we explored the effect of contrasting ethanol environments on physiological and developmental traits, their genetic (co)variances and genetic architecture in Drosophila melanogaster. Phenotypic and genetic parameters were estimated in two populations (San Fernando and Valdivia, Chile), using a half-sib family design where broods were split into ethanol-free and ethanol-supplemented conditions. Our findings show that metabolic rate, body mass and development times were sensitive (i.e., phenotypic plasticity) to ethanol conditions and dependent on population origin. Significant heritabilities were found for all traits, while significant genetic correlations were only found between larval and total development time and between development time and metabolic rate for flies of the San Fernando population developed in ethanol-free conditions. Posterior analyses indicated that the G matrices differed between ethanol conditions for the San Fernando population (mainly explained by differences in genetic (co)variances of developmental traits), whereas the Valdivia population exhibited similar G matrices between ethanol conditions. Our findings suggest that ethanol-free environment increases the energy available to reduce development time. Therefore, our results indicate that environmental ethanol could modify the process of energy allocation, which could have consequences on the evolutionary response of natural populations of D. melanogaster. PMID:23505567

Knowledge Capture and Management for Space Flight Systems

Science.gov (United States)

Goodman, John L.

2005-01-01

The incorporation of knowledge capture and knowledge management strategies early in the development phase of an exploration program is necessary for safe and successful missions of human and robotic exploration vehicles over the life of a program. Following the transition from the development to the flight phase, loss of underlying theory and rationale governing design and requirements occur through a number of mechanisms. This degrades the quality of engineering work resulting in increased life cycle costs and risk to mission success and safety of flight. Due to budget constraints, concerned personnel in legacy programs often have to improvise methods for knowledge capture and management using existing, but often sub-optimal, information technology and archival resources. Application of advanced information technology to perform knowledge capture and management would be most effective if program wide requirements are defined at the beginning of a program.

A dynamic mathematical model for packed columns in carbon capture plants

DEFF Research Database (Denmark)

Gaspar, Jozsef; Jørgensen, John Bagterp; Fosbøl, Philip Loldrup

2015-01-01

simulation using monoethanolamine (MEA) and piperazine (PZ) as solvent. MEA is considered as the base-case solvent in the carbon capture business. The effect of changes in the flue gas flow rate and changes in the available steam are investigated to determine their influence on the performance of the capture...

Ocean acidification challenges copepod phenotypic plasticity

Directory of Open Access Journals (Sweden)

A. Vehmaa

2016-11-01

Full Text Available Ocean acidification is challenging phenotypic plasticity of individuals and populations. Calanoid copepods (zooplankton are shown to be fairly plastic against altered pH conditions, and laboratory studies indicate that transgenerational effects are one mechanism behind this plasticity. We studied phenotypic plasticity of the copepod Acartia sp. in the course of a pelagic, large-volume mesocosm study that was conducted to investigate ecosystem and biogeochemical responses to ocean acidification. We measured copepod egg production rate, egg-hatching success, adult female size and adult female antioxidant capacity (ORAC as a function of acidification (fCO2  ∼  365–1231 µatm and as a function of quantity and quality of their diet. We used an egg transplant experiment to reveal whether transgenerational effects can alleviate the possible negative effects of ocean acidification on offspring development. We found significant negative effects of ocean acidification on adult female size. In addition, we found signs of a possible threshold at high fCO2, above which adaptive maternal effects cannot alleviate the negative effects of acidification on egg-hatching and nauplii development. We did not find support for the hypothesis that insufficient food quantity (total particulate carbon < 55 µm or quality (C : N weakens the transgenerational effects. However, females with high-ORAC-produced eggs with high hatching success. Overall, these results indicate that Acartia sp. could be affected by projected near-future CO2 levels.

Method for high temperature mercury capture from gas streams

Science.gov (United States)

Granite, Evan J [Wexford, PA; Pennline, Henry W [Bethel Park, PA

2006-04-25

A process to facilitate mercury extraction from high temperature flue/fuel gas via the use of metal sorbents which capture mercury at ambient and high temperatures. The spent sorbents can be regenerated after exposure to mercury. The metal sorbents can be used as pure metals (or combinations of metals) or dispersed on an inert support to increase surface area per gram of metal sorbent. Iridium and ruthenium are effective for mercury removal from flue and smelter gases. Palladium and platinum are effective for mercury removal from fuel gas (syngas). An iridium-platinum alloy is suitable for metal capture in many industrial effluent gas streams including highly corrosive gas streams.

Etude des erreurs d'estimation des populations par la méthode des captures successives (DeLURY, 2 captures et des captures-recaptures (PETERSEN

Directory of Open Access Journals (Sweden)

LAURENT M.

1978-01-01

Full Text Available L'estimation des populations naturelles par capture-recapture et par captures successives est souvent entachée d'erreur car, dans de nombreux cas, l'hypothèse fondamentale d'égalité des probabilités de captures pour tous les individus dans le temps et dans l'espace n'est pas respectée. Dans le cas des populations de poissons envisagés ici, les captures ont lieu par la pêche électrique. On a pu chiffrer l'ordre de grandeur des erreurs systématiques faites sur l'estimation des peuplements, en fonction des conditions particulières, biotiques et abiotiques, des différents milieux inventoriés.

Rapid suppression of testosterone secretion after capture in male American alligators (Alligator mississippiensis).

Science.gov (United States)

Lance, Valentine A; Elsey, Ruth M; Butterstein, George; Trosclair, Phillip L

2004-01-15

All reptiles studied to date show an increase in circulating corticosterone following capture. This rise in corticosterone has also been shown in a number of instances to result in a decline in reproductive steroids within hours after capture. As a result of these observations it has been considered imperative to collect blood samples as soon as possible after capture to get reliable measures of reproductive hormones. It has been claimed, however, that there is no effect of capture stress on reproductive steroids in juvenile alligators held for 2 h following capture. As we generally reject blood samples that are not collected within 15 min of capture we decided to reinvestigate the effect of short-term capture (2 h) on corticosterone and testosterone in male alligators. Four groups of alligators, ranging in size from 74 to 212 cm total length were captured in a 2-week period in May, the time of year when testosterone levels are highest. Two groups were captured during the day (eight bled at capture and again at 2 h, eight bled at 2 h only) and two at night (10 bled at capture and again at 2 h, 10 bled at 2 h only). Testosterone and corticosterone in alligators bled immediately on capture and at 2 h were not significantly different in the AM and PM samples so the results were combined (Initial bleed: corticosterone, 0.95 +/- 0.09 ng/ml, n=18; testosterone, 6.06 +/- 2.09 ng/ml, n=18. Two-hour bleed: corticosterone 15.68 +/- 1.91, n=18; testosterone, 2.75 +/- 0.79, n=18). Both the increase in corticosterone and the decline in testosterone at 2 h were significant (palligators sampled only once at 2 h were not significantly different from the 2-h values in alligators sampled twice (corticosterone 15.04 +/- 1.29, n=18; testosterone, 1.85 +/- 0.62, n=18). These results clearly demonstrate that short-term capture stress results in a significant decline in testosterone in male alligators.

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

Science.gov (United States)

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

2017-12-10

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

De-anonymizing Genomic Databases Using Phenotypic Traits

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Humbert Mathias

2015-06-01

Full Text Available People increasingly have their genomes sequenced and some of them share their genomic data online. They do so for various purposes, including to find relatives and to help advance genomic research. An individual’s genome carries very sensitive, private information such as its owner’s susceptibility to diseases, which could be used for discrimination. Therefore, genomic databases are often anonymized. However, an individual’s genotype is also linked to visible phenotypic traits, such as eye or hair color, which can be used to re-identify users in anonymized public genomic databases, thus raising severe privacy issues. For instance, an adversary can identify a target’s genome using known her phenotypic traits and subsequently infer her susceptibility to Alzheimer’s disease. In this paper, we quantify, based on various phenotypic traits, the extent of this threat in several scenarios by implementing de-anonymization attacks on a genomic database of OpenSNP users sequenced by 23andMe. Our experimental results show that the proportion of correct matches reaches 23% with a supervised approach in a database of 50 participants. Our approach outperforms the baseline by a factor of four, in terms of the proportion of correct matches, in most scenarios. We also evaluate the adversary’s ability to predict individuals’ predisposition to Alzheimer’s disease, and we observe that the inference error can be halved compared to the baseline. We also analyze the effect of the number of known phenotypic traits on the success rate of the attack. As progress is made in genomic research, especially for genotype-phenotype associations, the threat presented in this paper will become more serious.

Effects of environmental and clinical interferents on the host capture efficiency of immobilized bacteriophages.

Science.gov (United States)

Dixon, Daniel V; Hosseinidoust, Zeinab; Tufenkji, Nathalie

2014-03-25

Bacteriophage-functionalized surfaces are a new class of advanced functional material and have been demonstrated to be applicable for use as antimicrobial surfaces in medical applications (e.g., indwelling medical devices or wound dressings) or as biosensors for bacterial capture and detection. However, the complex composition of many real life samples (e.g., blood, natural waters, etc.) can potentially interfere with the interaction of phage and its bacterial host, leading to a decline in the efficiency of the phage-functionalized surface. In this study, the bacterial capture efficiency of two model phage-functionalized surfaces was assessed in the presence of potential environmental and biomedical interferents. The two phage-bacteria systems used in this study are PRD1 with Salmonella Typhimurium and T4 with Escherichia coli. The potential interferents tested included humic and fulvic acids, natural groundwater, colloidal latex microspheres, host extracellular polymeric substances (EPS), albumin, fibrinogen, and human serum. EPS and human serum decreased the host capture efficiency for immobilized PRD1 and T4, and also impaired the infectivity of the nonimmobilized (planktonic) phage. Interestingly, humic and fulvic acids reduced the capture efficiency of T4-functionalized surfaces, even though they did not lead to inactivation of the suspended virions. Neither humic nor fulvic acids affected the capture efficiency of PRD1. These findings demonstrate the inadequacy of traditional phage selection methods (i.e., infectivity of suspended phage toward its host in clean buffer) for designing advanced functional materials and further highlight the importance of taking into account the environmental conditions in which the immobilized phage is expected to function.

Adiabatic capture and debunching

International Nuclear Information System (INIS)

Ng, K.Y.

2012-01-01

In the study of beam preparation for the g-2 experiment, adiabatic debunching and adiabatic capture are revisited. The voltage programs for these adiabbatic processes are derived and their properties discussed. Comparison is made with some other form of adiabatic capture program. The muon g-2 experiment at Fermilab calls for intense proton bunches for the creation of muons. A booster batch of 84 bunches is injected into the Recycler Ring, where it is debunched and captured into 4 intense bunches with the 2.5-MHz rf. The experiment requires short bunches with total width less than 100 ns. The transport line from the Recycler to the muon-production target has a low momentum aperture of ∼ ±22 MeV. Thus each of the 4 intense proton bunches required to have an emittance less than ∼ 3.46 eVs. The incoming booster bunches have total emittance ∼ 8.4 eVs, or each one with an emittance ∼ 0.1 eVs. However, there is always emittance increase when the 84 booster bunches are debunched. There will be even larger emittance increase during adiabatic capture into the buckets of the 2.5-MHz rf. In addition, the incoming booster bunches may have emittances larger than 0.1 eVs. In this article, we will concentrate on the analysis of the adiabatic capture process with the intention of preserving the beam emittance as much as possible. At this moment, beam preparation experiment is being performed at the Main Injector. Since the Main Injector and the Recycler Ring have roughly the same lattice properties, we are referring to adiabatic capture in the Main Injector instead in our discussions.

Crop 3D-a LiDAR based platform for 3D high-throughput crop phenotyping.

Science.gov (United States)

Guo, Qinghua; Wu, Fangfang; Pang, Shuxin; Zhao, Xiaoqian; Chen, Linhai; Liu, Jin; Xue, Baolin; Xu, Guangcai; Li, Le; Jing, Haichun; Chu, Chengcai

2018-03-01

With the growing population and the reducing arable land, breeding has been considered as an effective way to solve the food crisis. As an important part in breeding, high-throughput phenotyping can accelerate the breeding process effectively. Light detection and ranging (LiDAR) is an active remote sensing technology that is capable of acquiring three-dimensional (3D) data accurately, and has a great potential in crop phenotyping. Given that crop phenotyping based on LiDAR technology is not common in China, we developed a high-throughput crop phenotyping platform, named Crop 3D, which integrated LiDAR sensor, high-resolution camera, thermal camera and hyperspectral imager. Compared with traditional crop phenotyping techniques, Crop 3D can acquire multi-source phenotypic data in the whole crop growing period and extract plant height, plant width, leaf length, leaf width, leaf area, leaf inclination angle and other parameters for plant biology and genomics analysis. In this paper, we described the designs, functions and testing results of the Crop 3D platform, and briefly discussed the potential applications and future development of the platform in phenotyping. We concluded that platforms integrating LiDAR and traditional remote sensing techniques might be the future trend of crop high-throughput phenotyping.

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

Science.gov (United States)

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

2017-11-01

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

Elucidating the genotype-phenotype map by automatic enumeration and analysis of the phenotypic repertoire.

Science.gov (United States)

Lomnitz, Jason G; Savageau, Michael A

The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process. The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters. Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed. Starting with a system's relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy.

Aquatic prey capture in snakes: the link between morphology, behavior and hydrodynamics

Science.gov (United States)

Segall, Marion; Herrel, Anthony; Godoy-Diana, Ramiro; Funevol Team; Pmmh Team

2017-11-01

Natural selection favors animals that are the most successful in their fitness-related behaviors, such as foraging. Secondary adaptations pose the problem of re-adapting an already 'hypothetically optimized' phenotype to new constraints. When animals forage underwater, they face strong physical constraints, particularly when capturing a prey. The capture requires the predator to be fast and to generate a high acceleration to catch the prey. This involves two main constraints due to the surrounding fluid: drag and added mass. Both of these constraints are related to the shape of the animal. We experimentally explore the relationship between shape and performance in the context of an aquatic strike. As a model, we use 3D-printed snake heads of different shapes and frontal strike kinematics based on in vivo observations. By using direct force measurements, we compare the drag and added mass generated by aquatic and non-aquatic snake models during a strike. Our results show that drag is optimized in aquatic snakes. Added mass appears less important than drag for snakes during an aquatic strike. The flow features associated to the hydrodynamic forces measured allows us to propose a mechanism rendering the shape of the head of aquatic snakes well adapted to catch prey underwater. Region Ile de France and the doctoral school Frontieres du Vivant (FdV) - Programme Bettencourt.

The Generic Data Capture Facility

Science.gov (United States)

Connell, Edward B.; Barnes, William P.; Stallings, William H.

1987-01-01

The Generic Data Capture Facility, which can provide data capture support for a variety of different types of spacecraft while enabling operations costs to be carefully controlled, is discussed. The data capture functions, data protection, isolation of users from data acquisition problems, data reconstruction, and quality and accounting are addressed. The TDM and packet data formats utilized by the system are described, and the development of generic facilities is considered.

Negative meson capture in hydrogen

International Nuclear Information System (INIS)

Baird, T.J.

1977-01-01

The processes of deexcitation and capture of negative mesons and hadrons in atomic hydrogen are investigated. Only slow collisions in which the projectile-atom relative velocity is less than one atomic unit are considered, and the motion of the incident particle is treated classically. For each classical trajectory the probability of ionizing the hydrogen atom is determined, together with the energy spectrum of the emitted electron. Ionization probabilities are calculated using the time-dependent formulation of the perturbed stationary state method. Exact two-center electronic wave functions are used for both bound and continuum states. The total ionization cross section and electron energy spectrum have been calculated for negative muons, kaons and antiprotons at incident relative velocities between 0.04 and 1.0 atomic units. The electron energy spectrum has a sharp peak for electron kinetic energies on the order of 10 -3 Rydbergs. The ionization process thus favors the emission of very slow electrons. The cross section for ionization with capture of the incident particle was calculated for relative kinetic energies greater than 1.0 Rydberg. Since ionization was found to occur with the emission of electrons of nearly zero kinetic energy, the fraction of ionizing collisions which result in capture decreases very rapidly with projectile kinetic energy. The energy distributions of slowed down muons and hadrons were also computed. These distributions were used together with the capture cross section to determine the distribution of kinetic energies at which capture takes place. It was found that most captures occur for kinetic energies slightly less than 1.0 Rydbergs with relatively little capture at thermal energies. The captured particles therefore tend to go into very large and loosely found orbits with binding energies less than 0.1 Rydbergs

Nitrosamine degradation by UV light in post-combustion CO2 capture: effect of solvent matrix

NARCIS (Netherlands)

Miguel Mercader, F. de; Voice, A.K.; Trap, H.C.; Goetheer, E.L.V.

2013-01-01

Potential production and emission of nitrosamines during post-combustion CO2 capture has drawn some attention due to their toxicity and potential carcinogenicity. One of the possible ways to reduce the concentration of nitrosamines is irradiation of the liquid streams of the capture plant with UV

Radiation-induced senescence-like phenotype in proliferating and plateau-phase vascular endothelial cells

International Nuclear Information System (INIS)

Igarashi, Kaori; Sakimoto, Ippei; Kataoka, Keiko; Ohta, Keisuke; Miura, Masahiko

2007-01-01

The effects of ionizing radiation (IR) on tumor angiogenesis still remain largely unknown. In this study, we found that IR (8 Gy) induces a high-frequency (80-90%) senescence-like phenotype in vascular endothelial cells (ECs) undergoing exponential growth. This finding allowed us to characterize the IR-induced senescence-like (IRSL) phenotype by examining the gene expression profiles and in vitro angiogenic activities of these ECs. The expression levels of genes associated with cell cycle progression and DNA replication were remarkably reduced in the IRSL ECs. Additionally, the in vitro invasion and migration activities of these cells through Matrigel were significantly suppressed. We also found that confluent ECs exhibited a high-frequency IRSL phenotype when they were replated immediately after irradiation, whereas incubation in plateau-phase conditions reduced the induction of this phenotype and enhanced colony formation. The kinetics of DNA double-strand break repair, which showed a faster time course in confluent ECs than in growing ECs, may contribute to the protective mechanism associated with the IRSL phenotype. These results imply that the IRSL phenotype may be important for determining the angiogenic activity of ECs following irradiation. The present study should contribute to the understanding of the effects of IR on tumor angiogenesis

The importance of environment on respiratory genotype/phenotype relationships in the Inuit

DEFF Research Database (Denmark)

Candelaria, P V; Backer, V; Khoo, S-K

2010-01-01

Genetic and environmental influences and their interactions are central to asthma pathogenesis. This study aimed to investigate the effects of different macro-environments on asthma genotype-phenotype associations in two geographically separated populations with common ancestry.......Genetic and environmental influences and their interactions are central to asthma pathogenesis. This study aimed to investigate the effects of different macro-environments on asthma genotype-phenotype associations in two geographically separated populations with common ancestry....

Effects of trap type, placement and ash distribution on emerald ash borer captures in a low density site

Science.gov (United States)

Deborah G. McCullough; Nathan W. Siegert; Therese M. Poland; Steven J. Pierce; Su Zie. Ahn

2011-01-01

Effective methods for early detection of newly established, low density emerald ash borer (Agrilus planipennis Fairmaire) infestations are critically needed in North America. We assessed adult A. planipennis captures on four types of traps in a 16-ha site in central Michigan. The site was divided into 16 blocks, each comprised of...

S-ketamine influences strategic allocation of attention but not exogenous capture of attention.

Science.gov (United States)

Fuchs, Isabella; Ansorge, Ulrich; Huber-Huber, Christoph; Höflich, Anna; Lanzenberger, Rupert

2015-09-01

We investigated whether s-ketamine differentially affects strategic allocation of attention. In Experiment 1, (1) a less visible cue was weakly masked by the onsets of competing placeholders or (2) a better visible cue was not masked because it was presented in isolation. Both types of cue appeared more often opposite of the target (75%) than at target position (25%). With this setup, we tested for strategic attention shifts to the opposite side of the cues and for exogenous attentional capture toward the cue's side in a short cue-target interval, as well as for (reverse) cueing effects in a long cue-target interval after s-ketamine and after placebo treatment in a double-blind within-participant design. We found reduced strategic attention shifts after cues presented without placeholders for the s-ketamine compared to the placebo treatment in the short interval, indicating an early effect on the strategic allocation of attention. No differences between the two treatments were found for exogenous attentional capture by less visible cues, suggesting that s-ketamine does not affect exogenous attentional capture in the presence of competing distractors. Experiment 2 confirmed that the competing onsets of the placeholders prevented the strategic cueing effect. Taken together, the results indicate that s-ketamine affects strategic attentional capture, but not exogenous attentional capture. The findings point to a more prominent role of s-ketamine during top-down controlled forms of attention that require suppression of automatic capture than during automatic capture itself. Copyright © 2015 Elsevier Inc. All rights reserved.

CAPTURED India Country Evaluation

NARCIS (Netherlands)

O'Donoghue, R.; Brouwers, J.H.A.M.

2012-01-01

This report provides the findings of the India Country Evaluation and is produced as part of the overall CAPTURED End Evaluation. After five years of support by the CAPTURED project the End Evaluation has assessed that results are commendable. I-AIM was able to design an approach in which health

Carbon Capture and Storage

NARCIS (Netherlands)

Benson, S.M.; Bennaceur, K.; Cook, P.; Davison, J.; Coninck, H. de; Farhat, K.; Ramirez, C.A.; Simbeck, D.; Surles, T.; Verma, P.; Wright, I.

2012-01-01

Emissions of carbon dioxide, the most important long-lived anthropogenic greenhouse gas, can be reduced by Carbon Capture and Storage (CCS). CCS involves the integration of four elements: CO 2 capture, compression of the CO2 from a gas to a liquid or a denser gas, transportation of pressurized CO 2

Incremental learning for automated knowledge capture

Energy Technology Data Exchange (ETDEWEB)

Benz, Zachary O. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Basilico, Justin Derrick [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Davis, Warren Leon [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Dixon, Kevin R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Jones, Brian S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Martin, Nathaniel [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Wendt, Jeremy Daniel [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2013-12-01

People responding to high-consequence national-security situations need tools to help them make the right decision quickly. The dynamic, time-critical, and ever-changing nature of these situations, especially those involving an adversary, require models of decision support that can dynamically react as a situation unfolds and changes. Automated knowledge capture is a key part of creating individualized models of decision making in many situations because it has been demonstrated as a very robust way to populate computational models of cognition. However, existing automated knowledge capture techniques only populate a knowledge model with data prior to its use, after which the knowledge model is static and unchanging. In contrast, humans, including our national-security adversaries, continually learn, adapt, and create new knowledge as they make decisions and witness their effect. This artificial dichotomy between creation and use exists because the majority of automated knowledge capture techniques are based on traditional batch machine-learning and statistical algorithms. These algorithms are primarily designed to optimize the accuracy of their predictions and only secondarily, if at all, concerned with issues such as speed, memory use, or ability to be incrementally updated. Thus, when new data arrives, batch algorithms used for automated knowledge capture currently require significant recomputation, frequently from scratch, which makes them ill suited for use in dynamic, timecritical, high-consequence decision making environments. In this work we seek to explore and expand upon the capabilities of dynamic, incremental models that can adapt to an ever-changing feature space.

New genes as drivers of phenotypic evolution

Science.gov (United States)

Chen, Sidi; Krinsky, Benjamin H.; Long, Manyuan

2014-01-01

During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution. PMID:23949544

Capturing the Daylight Dividend

Energy Technology Data Exchange (ETDEWEB)

Peter Boyce; Claudia Hunter; Owen Howlett

2006-04-30

Capturing the Daylight Dividend conducted activities to build market demand for daylight as a means of improving indoor environmental quality, overcoming technological barriers to effective daylighting, and informing and assisting state and regional market transformation and resource acquisition program implementation efforts. The program clarified the benefits of daylight by examining whole building systems energy interactions between windows, lighting, heating, and air conditioning in daylit buildings, and daylighting's effect on the human circadian system and productivity. The project undertook work to advance photosensors, dimming systems, and ballasts, and provided technical training in specifying and operating daylighting controls in buildings. Future daylighting work is recommended in metric development, technology development, testing, training, education, and outreach.

Motion Capturing Emotions

OpenAIRE

Wood Karen; Cisneros Rosemary E.; Whatley Sarah

2017-01-01

The paper explores the activities conducted as part of WhoLoDancE: Whole Body Interaction Learning for Dance Education which is an EU-funded Horizon 2020 project. In particular, we discuss the motion capture sessions that took place at Motek, Amsterdam as well as the dancers’ experience of being captured and watching themselves or others as varying visual representations through the HoloLens. HoloLens is Microsoft’s first holographic computer that you wear as you would a pair of glasses. The ...

Obesity-Associated Hypertension: the Upcoming Phenotype in African-American Women.

Science.gov (United States)

Samson, Rohan; Qi, Andrea; Jaiswal, Abhishek; Le Jemtel, Thierry H; Oparil, Suzanne

2017-05-01

The present obesity epidemic particularly affects African-American women. Whether the obesity epidemic will alter the hypertension phenotype in African-American women is entertained. The prevalence of morbid obesity is steadily increasing in African-American women, who are prone to developing hypertension (HTN) even in the absence of obesity. The obesity-associated hypertension phenotype is characterized by marked sympathetic nervous system activation and resistance/refractoriness to antihypertensive therapy. Weight loss achieved through lifestyle interventions and pharmacotherapy has a modest and rarely sustained antihypertensive effect. In contrast, bariatric surgery has a sustained antihypertensive effect, as evidenced by normalization of hypertension or lessening of antihypertensive therapy. The prevalence of HTN and its obesity-associated phenotype is likely to increase in African-American women over the next decades. Obese African-American women may be increasingly referred for bariatric surgery when hypertension remains uncontrolled despite lifestyle interventions and pharmacological therapy for weight loss and blood pressure (BP) control.

Delineation of C12orf65-related phenotypes: a genotype-phenotype relationship.

Science.gov (United States)

Spiegel, Ronen; Mandel, Hanna; Saada, Ann; Lerer, Issy; Burger, Ayala; Shaag, Avraham; Shalev, Stavit A; Jabaly-Habib, Haneen; Goldsher, Dorit; Gomori, John M; Lossos, Alex; Elpeleg, Orly; Meiner, Vardiella

2014-08-01

C12orf65 participates in the process of mitochondrial translation and has been shown to be associated with a spectrum of phenotypes, including early onset optic atrophy, progressive encephalomyopathy, peripheral neuropathy, and spastic paraparesis.We used whole-genome homozygosity mapping as well as exome sequencing and targeted gene sequencing to identify novel C12orf65 disease-causing mutations in seven affected individuals originating from two consanguineous families. In four family members affected with childhood-onset optic atrophy accompanied by slowly progressive peripheral neuropathy and spastic paraparesis, we identified a homozygous frame shift mutation c.413_417 delAACAA, which predicts a truncated protein lacking the C-terminal portion. In the second family, we studied three affected individuals who presented with early onset optic atrophy, peripheral neuropathy, and spastic gait in addition to moderate intellectual disability. Muscle biopsy in two of the patients revealed decreased activities of the mitochondrial respiratory chain complexes I and IV. In these patients, we identified a homozygous splice mutation, g.21043 T>A (c.282+2 T>A) which leads to skipping of exon 2. Our study broadens the phenotypic spectrum of C12orf65 defects and highlights the triad of optic atrophy, axonal neuropathy and spastic paraparesis as its key clinical features. In addition, a clear genotype-phenotype correlation is anticipated in which deleterious mutations which disrupt the GGQ-containing domain in the first coding exon are expected to result in a more severe phenotype, whereas down-stream C-terminal mutations may result in a more favorable phenotype, typically lacking cognitive impairment.

CO2 capture by Li-functionalized silicene

KAUST Repository

Zhu, Jiajie; Chroneos, Alexander; Schwingenschlö gl, Udo

2016-01-01

CO2 capture and storage technology is of key importance to reduce the greenhouse effect. By its large surface area and sp3 hybridization, Li-functionalized silicene is demonstrated to be a promising CO2 absorbent that is stable up to at least 500 K

Machine-learning phenotypic classification of bicuspid aortopathy.

Science.gov (United States)

Wojnarski, Charles M; Roselli, Eric E; Idrees, Jay J; Zhu, Yuanjia; Carnes, Theresa A; Lowry, Ashley M; Collier, Patrick H; Griffin, Brian; Ehrlinger, John; Blackstone, Eugene H; Svensson, Lars G; Lytle, Bruce W

2018-02-01

Bicuspid aortic valves (BAV) are associated with incompletely characterized aortopathy. Our objectives were to identify distinct patterns of aortopathy using machine-learning methods and characterize their association with valve morphology and patient characteristics. We analyzed preoperative 3-dimensional computed tomography reconstructions for 656 patients with BAV undergoing ascending aorta surgery between January 2002 and January 2014. Unsupervised partitioning around medoids was used to cluster aortic dimensions. Group differences were identified using polytomous random forest analysis. Three distinct aneurysm phenotypes were identified: root (n = 83; 13%), with predominant dilatation at sinuses of Valsalva; ascending (n = 364; 55%), with supracoronary enlargement rarely extending past the brachiocephalic artery; and arch (n = 209; 32%), with aortic arch dilatation. The arch phenotype had the greatest association with right-noncoronary cusp fusion: 29%, versus 13% for ascending and 15% for root phenotypes (P < .0001). Severe valve regurgitation was most prevalent in root phenotype (57%), followed by ascending (34%) and arch phenotypes (25%; P < .0001). Aortic stenosis was most prevalent in arch phenotype (62%), followed by ascending (50%) and root phenotypes (28%; P < .0001). Patient age increased as the extent of aneurysm became more distal (root, 49 years; ascending, 53 years; arch, 57 years; P < .0001), and root phenotype was associated with greater male predominance compared with ascending and arch phenotypes (94%, 76%, and 70%, respectively; P < .0001). Phenotypes were visually recognizable with 94% accuracy. Three distinct phenotypes of bicuspid valve-associated aortopathy were identified using machine-learning methodology. Patient characteristics and valvular dysfunction vary by phenotype, suggesting that the location of aortic pathology may be related to the underlying pathophysiology of this disease. Copyright © 2017 The American

Human thiopurine methyltransferase pharmacogenetics: effect of phenotype on sensitivity of cultured lymphocytes to 6-mercaptopurine

International Nuclear Information System (INIS)

Van Loon, J.; Weinshilboum, R.

1986-01-01

Thiopurine methyltransferase (EC 2.1.1.67, TPMT) catalyzes the S-methylation of thiopurine drugs such as 6-mercaptopurine (6-MP). TPMT activity in human lymphocytes and other tissues is controlled by a common genetic polymorphism. These experiments were designed to study the relationship between TPMT phenotype and the effect of 6-MP on 3 H-thymidine ( 3 H-TdR) incorporation into phytohemaglutinin (PHA) stimulated human peripheral blood lymphocytes. Lymphocytes were obtained from the blood of nine subjects, three subjects with each TPMT phenotype. 6-MP dose response curves were performed at optimal (10 μg/ml) and suboptimal (1 μg/ml) concentrations of PHA. ED50 values for 6-MP with lymphocytes from subjects who genetically lacked TPMT activity were higher than ED50 values for lymphocytes from subjects with genetically intermediate or high TPMT activity. However, ED50 values decreased as level of stimulation increased. Therefore, the effects of 6-MP were studied at a series of PHA concentrations that ranged from 0.1 μg/ml to 10 μg/ml. Lymphocytes from subjects who lacked TPMT activity had significantly higher K/sub ii/ values (1.37 +/- 0.340 μM; mean +/- SEM) for inhibition of 3 H-TdR incorporation by 6-MP than did lymphocytes from subjects with intermediate or high TPMT activity (0.529 +/- 0.068 μM and 0.327 +/- 0.064 μM, respectively, P < .05 for both comparisons)

Human thiopurine methyltransferase pharmacogenetics: effect of phenotype on sensitivity of cultured lymphocytes to 6-mercaptopurine

Energy Technology Data Exchange (ETDEWEB)

Van Loon, J.; Weinshilboum, R.

1986-03-05

Thiopurine methyltransferase (EC 2.1.1.67, TPMT) catalyzes the S-methylation of thiopurine drugs such as 6-mercaptopurine (6-MP). TPMT activity in human lymphocytes and other tissues is controlled by a common genetic polymorphism. These experiments were designed to study the relationship between TPMT phenotype and the effect of 6-MP on /sup 3/H-thymidine (/sup 3/H-TdR) incorporation into phytohemaglutinin (PHA) stimulated human peripheral blood lymphocytes. Lymphocytes were obtained from the blood of nine subjects, three subjects with each TPMT phenotype. 6-MP dose response curves were performed at optimal (10 ..mu..g/ml) and suboptimal (1 ..mu..g/ml) concentrations of PHA. ED50 values for 6-MP with lymphocytes from subjects who genetically lacked TPMT activity were higher than ED50 values for lymphocytes from subjects with genetically intermediate or high TPMT activity. However, ED50 values decreased as level of stimulation increased. Therefore, the effects of 6-MP were studied at a series of PHA concentrations that ranged from 0.1 ..mu..g/ml to 10 ..mu..g/ml. Lymphocytes from subjects who lacked TPMT activity had significantly higher K/sub ii/ values (1.37 +/- 0.340 ..mu..M; mean +/- SEM) for inhibition of /sup 3/H-TdR incorporation by 6-MP than did lymphocytes from subjects with intermediate or high TPMT activity (0.529 +/- 0.068 ..mu..M and 0.327 +/- 0.064 ..mu..M, respectively, P < .05 for both comparisons).

A link between thrifty phenotype and maternal care across two generations of intercrossed mice.

Directory of Open Access Journals (Sweden)

Bruno Sauce

Full Text Available Maternal effects are causal influences from mother to offspring beyond genetic information, and have lifelong consequences for multiple traits. Previously, we reported that mice whose mothers did not nurse properly had low birth weight followed by rapid fat accumulation and disturbed development of some organs. That pattern resembles metabolic syndromes known collectively as the thrifty phenotype, which is believed to be an adaptation to a stressful environment which prepares offspring for reduced nutrient supply. The potential link between maternal care, stress reactivity, and the thrifty phenotype, however, has been poorly explored in the human and animal literature: only a couple of studies even mention (much less, test these concepts under a cohesive framework. Here, we explored this link using mice of the parental inbred strains SM/J and LG/J-who differ dramatically in their maternal care-and the intercrossed generations F1 and F2. We measured individual differences in 15 phenotypes and used structural equation modeling to test our hypotheses. We found a remarkable relationship between thrifty phenotype and lower quality of maternal behaviors, including nest building, pup retrieval, grooming/licking, and nursing. To our knowledge, this is the first study to show, in any mammal, a clear connection between the natural variation in thrifty phenotype and maternal care. Both traits in the mother also had a substantial effect on survival rate in the F3 offspring. To our surprise, however, stress reactivity seemed to play no role in our models. Furthermore, the strain of maternal grandmother, but not of paternal grandmother, affected the variation of maternal care in F2 mice, and this effect was mediated by thrifty phenotype in F2. Since F1 animals were all genetically identical, this finding suggests that maternal effects pass down both maternal care and thrifty phenotype in these mice across generations via epigenetic transmission.

Deep Learning for Plant Phenotyping

OpenAIRE

Mori, Matteo

2016-01-01

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

A survey of the Carbon Capture

International Nuclear Information System (INIS)

Jokrllova, J.; Cik, G.; Takacova, A.; Smolinska, M.

2014-01-01

The concentration of carbon dioxide, one of the most important representatives of greenhouse gases in the atmosphere continues to rise. Fossil fuels burned in thermal power plants currently represent 80% of total energy production around the world and are the largest point sources of CO 2 , accounting for approximately 40% of total CO 2 emissions. There are several options for reducing CO 2 emissions: reducing demand, improving production efficiency and carbon capture and storage (CCS, carbon capture and storage). Capture and storage of carbon dioxide is generally a three-step process: 1 st Capture and compression of combustion products, 2 nd transport (mostly pipeline) and 3 rd utilization (eg. production of urea, beverage industry, production of dry ice, etc.). Technologies for CO 2 capturing used in power plants burning fossil fuels can be divided into four groups, each of which requires a completely different approach to CO 2 capture.

Robust and sensitive analysis of mouse knockout phenotypes.

Directory of Open Access Journals (Sweden)

Natasha A Karp

Full Text Available A significant challenge of in-vivo studies is the identification of phenotypes with a method that is robust and reliable. The challenge arises from practical issues that lead to experimental designs which are not ideal. Breeding issues, particularly in the presence of fertility or fecundity problems, frequently lead to data being collected in multiple batches. This problem is acute in high throughput phenotyping programs. In addition, in a high throughput environment operational issues lead to controls not being measured on the same day as knockouts. We highlight how application of traditional methods, such as a Student's t-Test or a 2-way ANOVA, in these situations give flawed results and should not be used. We explore the use of mixed models using worked examples from Sanger Mouse Genome Project focusing on Dual-Energy X-Ray Absorptiometry data for the analysis of mouse knockout data and compare to a reference range approach. We show that mixed model analysis is more sensitive and less prone to artefacts allowing the discovery of subtle quantitative phenotypes essential for correlating a gene's function to human disease. We demonstrate how a mixed model approach has the additional advantage of being able to include covariates, such as body weight, to separate effect of genotype from these covariates. This is a particular issue in knockout studies, where body weight is a common phenotype and will enhance the precision of assigning phenotypes and the subsequent selection of lines for secondary phenotyping. The use of mixed models with in-vivo studies has value not only in improving the quality and sensitivity of the data analysis but also ethically as a method suitable for small batches which reduces the breeding burden of a colony. This will reduce the use of animals, increase throughput, and decrease cost whilst improving the quality and depth of knowledge gained.

The Nature of Stable Insomnia Phenotypes

Science.gov (United States)

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

2015-01-01

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

US Spacesuit Knowledge Capture

Science.gov (United States)

Chullen, Cinda; Thomas, Ken; McMann, Joe; Dolan, Kristi; Bitterly, Rose; Lewis, Cathleen

2011-01-01

The ability to learn from both the mistakes and successes of the past is vital to assuring success in the future. Due to the close physical interaction between spacesuit systems and human beings as users, spacesuit technology and usage lends itself rather uniquely to the benefits realized from the skillful organization of historical information; its dissemination; the collection and identification of artifacts; and the education of those in the field. The National Aeronautics and Space Administration (NASA), other organizations and individuals have been performing United States (U.S.) Spacesuit Knowledge Capture since the beginning of space exploration. Avenues used to capture the knowledge have included publication of reports; conference presentations; specialized seminars; and classes usually given by veterans in the field. More recently the effort has been more concentrated and formalized whereby a new avenue of spacesuit knowledge capture has been added to the archives in which videotaping occurs engaging both current and retired specialists in the field presenting technical scope specifically for education and preservation of knowledge. With video archiving, all these avenues of learning can now be brought to life with the real experts presenting their wealth of knowledge on screen for future learners to enjoy. Scope and topics of U.S. spacesuit knowledge capture have included lessons learned in spacesuit technology, experience from the Gemini, Apollo, Skylab and Shuttle programs, hardware certification, design, development and other program components, spacesuit evolution and experience, failure analysis and resolution, and aspects of program management. Concurrently, U.S. spacesuit knowledge capture activities have progressed to a level where NASA, the National Air and Space Museum (NASM), Hamilton Sundstrand (HS) and the spacesuit community are now working together to provide a comprehensive closed-looped spacesuit knowledge capture system which includes

Implementing targeted region capture sequencing for the clinical detection of Alagille syndrome: An efficient and cost‑effective method.

Science.gov (United States)

Huang, Tianhong; Yang, Guilin; Dang, Xiao; Ao, Feijian; Li, Jiankang; He, Yizhou; Tang, Qiyuan; He, Qing

2017-11-01

Alagille syndrome (AGS) is a highly variable, autosomal dominant disease that affects multiple structures including the liver, heart, eyes, bones and face. Targeted region capture sequencing focuses on a panel of known pathogenic genes and provides a rapid, cost‑effective and accurate method for molecular diagnosis. In a Chinese family, this method was used on the proband and Sanger sequencing was applied to validate the candidate mutation. A de novo heterozygous mutation (c.3254_3255insT p.Leu1085PhefsX24) of the jagged 1 gene was identified as the potential disease‑causing gene mutation. In conclusion, the present study suggested that target region capture sequencing is an efficient, reliable and accurate approach for the clinical diagnosis of AGS. Furthermore, these results expand on the understanding of the pathogenesis of AGS.

Continuum capture in the three-body problem

International Nuclear Information System (INIS)

Sellin, I.A.

1980-01-01

The three-body problem, especially the problem of electron capture to the continuum in heavy particle collisions is reviewed. Major topics covered include: second born-induced asymmetry in electron capture to the continuum; historical context, links to other tests of atomic scattering theory; experiments characterizing the velocity distribution of ECC electrons; other atomic physics tests of high velocity Born expansions; atom capture; capture by positrons; and pion capture to the continuum

Parity non-conservation in the capture of polarized thermal neutrons

DEFF Research Database (Denmark)

Warming, Inge Elisabeth

1969-01-01

The asymmetry in the intensity of γ-radiation following the capture of polarized thermal neutrons in 113Cd has been measured with Ge(Li) detectors. The result, A = (−0.6±1.8)×10−4, like that previously reported [1], gives no evidence for a non-zero effect.......The asymmetry in the intensity of γ-radiation following the capture of polarized thermal neutrons in 113Cd has been measured with Ge(Li) detectors. The result, A = (−0.6±1.8)×10−4, like that previously reported [1], gives no evidence for a non-zero effect....

Elucidating the genotype–phenotype map by automatic enumeration and analysis of the phenotypic repertoire

Science.gov (United States)

Lomnitz, Jason G; Savageau, Michael A

2015-01-01

Background: The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process. Methods: The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters. Results: Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed. Conclusions: Starting with a system’s relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy. PMID:26998346

The nature of stable insomnia phenotypes.

Science.gov (United States)

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

2015-01-01

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

Capture of irregular satellites at Jupiter

International Nuclear Information System (INIS)

Nesvorný, David; Vokrouhlický, David; Deienno, Rogerio

2014-01-01

The irregular satellites of outer planets are thought to have been captured from heliocentric orbits. The exact nature of the capture process, however, remains uncertain. We examine the possibility that irregular satellites were captured from the planetesimal disk during the early solar system instability when encounters between the outer planets occurred. Nesvorný et al. already showed that the irregular satellites of Saturn, Uranus, and Neptune were plausibly captured during planetary encounters. Here we find that the current instability models present favorable conditions for capture of irregular satellites at Jupiter as well, mainly because Jupiter undergoes a phase of close encounters with an ice giant. We show that the orbital distribution of bodies captured during planetary encounters provides a good match to the observed distribution of irregular satellites at Jupiter. The capture efficiency for each particle in the original transplanetary disk is found to be (1.3-3.6) × 10 –8 . This is roughly enough to explain the observed population of jovian irregular moons. We also confirm Nesvorný et al.'s results for the irregular satellites of Saturn, Uranus, and Neptune.

Age-Differential Effects of Job Characteristics on Job Attraction: A Policy-Capturing Study.

Science.gov (United States)

Zacher, Hannes; Dirkers, Bodil T; Korek, Sabine; Hughes, Brenda

2017-01-01

Based on an integration of job design and lifespan developmental theories, Truxillo et al. (2012) proposed that job characteristics interact with employee age in predicting important work outcomes. Using an experimental policy-capturing design, we investigated age-differential effects of four core job characteristics (i.e., job autonomy, task variety, task significance, and feedback from the job) on job attraction (i.e., individuals' rating of job attractiveness). Eighty-two employees between 19 and 65 years ( M age = 41, SD = 14) indicated their job attraction for each of 40 hypothetical job descriptions in which the four job characteristics were systematically manipulated (in total, participants provided 3,280 ratings). Results of multilevel analyses showed that the positive effects of task variety, task significance, and feedback from the job were stronger for younger compared to older employees, whereas we did not find significant age-differential effects of job autonomy on job attraction. These findings are only partially consistent with propositions of Truxillo et al.'s (2012) lifespan perspective on job design.

Privacy-preserving screen capture: towards closing the loop for health IT usability.

Science.gov (United States)

Cooley, Joseph; Smith, Sean

2013-08-01

As information technology permeates healthcare (particularly provider-facing systems), maximizing system effectiveness requires the ability to document and analyze tricky or troublesome usage scenarios. However, real-world health IT systems are typically replete with privacy-sensitive data regarding patients, diagnoses, clinicians, and EMR user interface details; instrumentation for screen capture (capturing and recording the scenario depicted on the screen) needs to respect these privacy constraints. Furthermore, real-world health IT systems are typically composed of modules from many sources, mission-critical and often closed-source; any instrumentation for screen capture can rely neither on access to structured output nor access to software internals. In this paper, we present a tool to help solve this problem: a system that combines keyboard video mouse (KVM) capture with automatic text redaction (and interactively selectable unredaction) to produce precise technical content that can enrich stakeholder communications and improve end-user influence on system evolution. KVM-based capture makes our system both application-independent and OS-independent because it eliminates software-interface dependencies on capture targets. Using a corpus of EMR screenshots, we present empirical measurements of redaction effectiveness and processing latency to demonstrate system performances. We discuss how these techniques can translate into instrumentation systems that improve real-world health IT deployments. Copyright © 2013 Elsevier Inc. All rights reserved.

Phenex: ontological annotation of phenotypic diversity.

Directory of Open Access Journals (Sweden)

James P Balhoff

2010-05-01

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

Phenex: ontological annotation of phenotypic diversity.

Science.gov (United States)

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

2010-05-05

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

Risk reductions for cardiovascular disease with pravastatin treatment by dyslipidemia phenotype: a post hoc analysis of the MEGA Study.

Science.gov (United States)

Nishiwaki, Masato; Ikewaki, Katsunori; Ayaori, Makoto; Mizuno, Kyoichi; Ohashi, Yasuo; Ohsuzu, Fumitaka; Ishikawa, Toshitsugu; Nakamura, Haruo

2013-03-01

The beneficial effect of statins for cardiovascular disease (CVD) prevention has been well established. However, the effectiveness among different phenotypes of dyslipidemia has not been confirmed. We evaluated the effect of pravastatin on the incidence of CVD in relation to the phenotype of dyslipidemia. The MEGA Study evaluated the effect of low-dose pravastatin on primary prevention of CVD in 7832 Japanese patients, who were randomized to diet alone or diet plus pravastatin and followed for more than 5 years. These patients were classified into phenotype IIa (n=5589) and IIb (n=2041) based on the electrophoretic pattern for this post hoc analysis. In the diet group there was no significant difference in the incidence of coronary heart disease (CHD), stroke, CVD, and total mortality between the two phenotypes. Phenotype IIb patients, compared to phenotype IIa, had lower levels of high-density lipoprotein cholesterol (HDL-C) and a significantly higher incidence of CVD in relation to a low HDL-C level (dyslipidemia. Significant risk reductions were observed for CHD by 38% (p=0.04) and CVD by 31% (p=0.02) in type IIa dyslipidemia but not in phenotype IIb. Pravastatin therapy provided significant risk reductions for CHD and CVD in patients with phenotype IIa dyslipidemia, but not in those with phenotype IIb dyslipidemia. Copyright © 2012 Japanese College of Cardiology. Published by Elsevier Ltd. All rights reserved.

Capturing characteristics of beryllium-7 in selected tree species

International Nuclear Information System (INIS)

Narazaki, Yukinori; Karube, Yoshiharu.

1997-01-01

With regard to 7 Be, a natural radioactive nuclide, the botanical capturing characteristics were compared between eight species of those trees which grow in a local district. The mechanism of such botanical capture by their leaves was discussed. The amounts of captured 7 Be were different by tree species. Higher radioactivities were found in the coniferous trees than in the broadleaf trees. The seasonal change of 7 Be radioactivity in leaves was significantly higher in winter and spring and lower in summer. Since airborne or fallout 7 Be particles stay on the upper face of leaves, the deposited amount depended on the surface area per weight of leaves particularly for evergreen trees. Because the 7 Be amount in leaves depended on the fallout capturing ability of leafs superficial skin as well as the cleaning effect of rain and the like, the radioactivity on the surface can change depending on the surface condition of leaves even in the case the levels of 7 Be fallout stayed the same. (author)

Correlated double electron capture in slow, highly charged ion-atom collisions

International Nuclear Information System (INIS)

Stolterfoht, N.; Havener, C.C.; Phaneuf, R.A.; Swenson, J.K.; Shafroth, S.M.; Meyer, F.W.

1986-01-01

Recent measurements of autoionization electrons produced in slow, highly charged ion-atom collisions are reviewed. Mechanisms for double electron capture into equivalent and nonequivalent configurations are analyzed by comparing the probabilities for the creation of L 1 L 23 X Coster Kronig electrons and L-Auger electrons. It is shown that the production of the Coster-Kronig electrons is due to electron correlation effects whose analysis leads beyond the independent-particle model. The importance of correlation effects on different capture mechanisms is discussed. 28 refs., 6 figs

Nuclear muon capture

CERN Document Server

Mukhopadhyay, N C

1977-01-01

Our present knowledge of the nuclear muon capture reactions is surveyed. Starting from the formation of the muonic atom, various phenomena, having a bearing on the nuclear capture, are reviewed. The nuclear reactions are then studied from two angles-to learn about the basic muon+nucleon weak interaction process, and to obtain new insights on the nuclear dynamics. Future experimental prospects with the newer generation muon 'factories' are critically examined. Possible modification of the muon+nucleon weak interaction in complex nuclei remains the most important open problem in this field. (380 refs).

Machine learning and computer vision approaches for phenotypic profiling.

Science.gov (United States)

Grys, Ben T; Lo, Dara S; Sahin, Nil; Kraus, Oren Z; Morris, Quaid; Boone, Charles; Andrews, Brenda J

2017-01-02

With recent advances in high-throughput, automated microscopy, there has been an increased demand for effective computational strategies to analyze large-scale, image-based data. To this end, computer vision approaches have been applied to cell segmentation and feature extraction, whereas machine-learning approaches have been developed to aid in phenotypic classification and clustering of data acquired from biological images. Here, we provide an overview of the commonly used computer vision and machine-learning methods for generating and categorizing phenotypic profiles, highlighting the general biological utility of each approach. © 2017 Grys et al.

The effect of modeled recharge distribution on simulated groundwater availability and capture.

Science.gov (United States)

Tillman, F D; Pool, D R; Leake, S A

2015-01-01

Simulating groundwater flow in basin-fill aquifers of the semiarid southwestern United States commonly requires decisions about how to distribute aquifer recharge. Precipitation can recharge basin-fill aquifers by direct infiltration and transport through faults and fractures in the high-elevation areas, by flowing overland through high-elevation areas to infiltrate at basin-fill margins along mountain fronts, by flowing overland to infiltrate along ephemeral channels that often traverse basins in the area, or by some combination of these processes. The importance of accurately simulating recharge distributions is a current topic of discussion among hydrologists and water managers in the region, but no comparative study has been performed to analyze the effects of different recharge distributions on groundwater simulations. This study investigates the importance of the distribution of aquifer recharge in simulating regional groundwater flow in basin-fill aquifers by calibrating a groundwater-flow model to four different recharge distributions, all with the same total amount of recharge. Similarities are seen in results from steady-state models for optimized hydraulic conductivity values, fit of simulated to observed hydraulic heads, and composite scaled sensitivities of conductivity parameter zones. Transient simulations with hypothetical storage properties and pumping rates produce similar capture rates and storage change results, but differences are noted in the rate of drawdown at some well locations owing to the differences in optimized hydraulic conductivity. Depending on whether the purpose of the groundwater model is to simulate changes in groundwater levels or changes in storage and capture, the distribution of aquifer recharge may or may not be of primary importance. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Debunching and Capture in the LEB for the SSC

Energy Technology Data Exchange (ETDEWEB)

Mahale, N.; Furman, M.

1991-05-01

The authors present the details of the capture process in the Low Energy Booster (LEB) for the SSC. They consider only the longitudinal dynamics. Space charge forces are computed quasistatically. The beam pipe is considered to be perfectly conducting. With respect to maximizing the capture efficiency and minimizing the space charge tune spread, initial few milliseconds are very important. They present only the first few milliseconds of the cycle, during which space charge effects are significant. For the numerical simulation they use the code ESME.

Effects of moonlight on the capturability of frugivorous phyllostomid bats (Chiroptera: Phyllostomidae at different time scales

Directory of Open Access Journals (Sweden)

Marco A. R. Mello

2013-08-01

Full Text Available Some bat species seem to be lunar phobic, i.e., they avoid flying in bright areas or during bright periods of the night; however, the evidence is still controversial. We think that part of this controversy comes from pooling data on bat captures and moonlight intensity according to broad categories, such as moon phases, which conceal the high variability among nights. Therefore, we used detailed, long-term field data on three phyllostomid bat species, in order to test the hypothesis of lunar phobia at two different time scales: 1 among nights, by pooling data of different nights according to moon phases and testing for differences in the distribution of captures; and 2 within a night, by analyzing the relationship between capturability and moonlight intensity (measured as illuminance in one-hour intervals for 29 individual nights. Although most captures of the studied bat species occurred in the first half of the night, their activity pattern varied largely among nights, and was not always unimodal as commonly assumed. At the larger time scale, all studied bat species showed evidence of lunar phobia, as they were more frequently captured on dark moon phases. Nevertheless, at the smaller time scale, only Carollia perspicillata (Linnaeus, 1758 was less frequently captured on brighter periods of the night. We propose that the unimodal activity pattern assumed for frugivorous phyllostomid bats may be an artifact of data organization, and that activity and lunar phobia are much more variable than previously assumed.

Dynamics and control of robot for capturing objects in space

Science.gov (United States)

Huang, Panfeng

Space robots are expected to perform intricate tasks in future space services, such as satellite maintenance, refueling, and replacing the orbital replacement unit (ORU). To realize these missions, the capturing operation may not be avoided. Such operations will encounter some challenges because space robots have some unique characteristics unfound on ground-based robots, such as, dynamic singularities, dynamic coupling between manipulator and space base, limited energy supply and working without a fixed base, and so on. In addition, since contacts and impacts may not be avoided during capturing operation. Therefore, dynamics and control problems of space robot for capturing objects are significant research topics if the robots are to be deployed for the space services. A typical servicing operation mainly includes three phases: capturing the object, berthing and docking the object, then repairing the target. Therefore, this thesis will focus on resolving some challenging problems during capturing the object, berthing and docking, and so on. In this thesis, I study and analyze the dynamics and control problems of space robot for capturing objects. This work has potential impact in space robotic applications. I first study the contact and impact dynamics of space robot and objects. I specifically focus on analyzing the impact dynamics and mapping the relationship of influence and speed. Then, I develop the fundamental theory for planning the minimum-collision based trajectory of space robot and designing the configuration of space robot at the moment of capture. To compensate for the attitude of the space base during the capturing approach operation, a new balance control concept which can effectively balance the attitude of the space base using the dynamic couplings is developed. The developed balance control concept helps to understand of the nature of space dynamic coupling, and can be readily applied to compensate or minimize the disturbance to the space base

Cattle phenotypes can disguise their maternal ancestry.

Science.gov (United States)

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

2017-06-26

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

Recombination methods for boron neutron capture therapy dosimetry

International Nuclear Information System (INIS)

Golnik, N.; Tulik, P.; Zielczynski, M.

2003-01-01

The radiation effects of boron neutron capture therapy (BNCT) are associated with four-dose-compartment radiation field - boron dose (from 10 B(n,α) 7 Li) reaction), proton dose from 14 N(n,p) 14 C reaction, neutron dose (mainly fast and epithermal neutrons) and gamma-ray dose (external and from capture reaction 1 H(n,γ) 2 D). Because of this the relation between the absorbed dose and the biological effects is very complex and all the above mentioned absorbed dose components should be determined. From this point of view, the recombination chambers can be very useful instruments for characterization of the BNCT beams. They can be used for determination of gamma and high-LET dose components for the characterization of radiation quality of mixed radiation fields by recombination microdosimetric method (RMM). In present work, a graphite high-pressure recombination chamber filled with nitrogen, 10 BF 3 and tissue equivalent gas was used for studies on application of RMM for BNCT dosimetry. The use of these gases or their mixtures opens a possibility to design a recombination chamber for determination of the dose fractions due to gamma radiation, fast neutrons, neutron capture on nitrogen and high LET particles from (n, 10 B) reaction in simulated tissue with different content of 10 B. (author)

The effects of perceived phenotypic racial stereotypicality and social identity threat on racial minorities' attitudes about police.

Science.gov (United States)

Kahn, Kimberly Barsamian; Lee, J Katherine; Renauer, Brian; Henning, Kris R; Stewart, Greg

2017-01-01

This study examines the role of perceived phenotypic racial stereotypicality and race-based social identity threat on racial minorities' trust and cooperation with police. We hypothesize that in police interactions, racial minorities' phenotypic racial stereotypicality may increase race-based social identity threat, which will lead to distrust and decreased participation with police. Racial minorities (Blacks, Latinos, Native Americans, and multi-racials) and Whites from a representative random sample of city residents were surveyed about policing attitudes. A serial multiple mediation model confirmed that racial minorities' self-rated phenotypic racial stereotypicality indirectly affected future cooperation through social identity threat and trust. Due to the lack of negative group stereotypes in policing, the model did not hold for Whites. This study provides evidence that phenotypic stereotypicality influences racial minorities' psychological experiences interacting with police.

Subtask 2.18 - Advancing CO₂ Capture Technology: Partnership for CO₂ Capture (PCO₂C) Phase III

Energy Technology Data Exchange (ETDEWEB)

Kay, John; Azenkeng, Alexander; Fiala, Nathan; Jensen, Melanie; Laumb, Jason; Leroux, Kerryanne; McCollor, Donald; Stanislowski, Joshua; Tolbert, Scott; Curran, Tyler

2016-03-31

Industries and utilities continue to investigate ways to decrease their carbon footprint. Carbon capture and storage (CCS) can enable existing power generation facilities to meet the current national CO₂ reduction goals. The Partnership for CO2 Capture Phase III focused on several important research areas in an effort to find ways to decrease the cost of capture across both precombustion and postcombustion platforms. Two flue gas pretreatment technologies for postcombustion capture, an SO₂ reduction scrubbing technology from Cansolv Technologies Inc. and the Tri-Mer filtration technology that combines particulate, NOx, and SO₂ control, were evaluated on the Energy & Environmental Research Center’s (EERC’s) pilot-scale test system. Pretreating the flue gas should enable more efficient, and therefore less expensive, CO₂ capture. Both technologies were found to be effective in pretreating flue gas prior to CO₂ capture. Two new postcombustion capture solvents were tested, one from the Korea Carbon Capture and Sequestration R&D Center (KCRC) and one from CO₂ Solutions Incorporated. Both of these solvents showed the ability to capture CO₂ while requiring less regeneration energy, which would reduce the cost of capture. Hydrogen separation membranes from Commonwealth Scientific and Industrial Research Organisation were evaluated through precombustion testing. They are composed of vanadium alloy, which is less expensive than the palladium alloys that are typically used. Their performance was comparable to that of other membranes that have been tested at the EERC. Aspen Plus® software was used to model the KCRC and CO₂ Solutions solvents and found that they would result in significantly improved overall plant performance. The modeling effort also showed that the parasitic steam load at partial capture of 45% is less than half that of 90% overall capture, indicating savings that

MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

Science.gov (United States)

Blank, Carrine E; Cui, Hong; Moore, Lisa R; Walls, Ramona L

2016-01-01

MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. MicrO currently has ~14550 classes (~2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by ~24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we

Nucleic acid hybridization assays employing dA-tailed capture probes. II. Advanced multiple capture methods

International Nuclear Information System (INIS)

Hunsaker, W.R.; Badri, H.; Lombardo, M.; Collins, M.L.

1989-01-01

A fourth capture is added to the reversible target capture procedure. This results in an improved radioisotopic detection limit of 7.3 x 10(-21) mol of target. In addition, the standard triple capture method is converted into a nonradioactive format with a detection limit of under 1 amol of target. The principal advantage of nonradioactive detection is that the entire assay can be performed in about 1 h. Nucleic acids are released from cells in the presence of the (capture probe) which contains a 3'-poly(dA) sequence and the (labeled probe) which contains a detectable nonradioactive moiety such as biotin. After a brief hybridization in solution, the target is captured on oligo(dT) magnetic particles. The target is further purified from sample impurities and excess labeled probe by recapture either once or twice more on fresh magnetic particles. The highly purified target is then concentrated to 200 nl by recapture onto a poly(dT) nitrocellulose filter and rapidly detected with streptavidin-alkaline phosphatase using bromochloroindolyl phosphate and nitroblue tetrazolium. Using this procedure, as little as 0.25 amol of a target plasmid has been detected nonradioactively in crude samples in just 1 h without prior purification of the DNA and RNA. Finally, a new procedure called background capture is introduced to complement the background-reducing power of RTC

Looking beyond the exome: a phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases

Science.gov (United States)

Pena, Loren DM; Jiang, Yong-Hui; Schoch, Kelly; Spillmann, Rebecca C.; Walley, Nicole; Stong, Nicholas; Horn, Sarah Rapisardo; Sullivan, Jennifer A.; McConkie-Rosell, Allyn; Kansagra, Sujay; Smith, Edward C.; El-Dairi, Mays; Bellet, Jane; Ann Keels, Martha; Jasien, Joan; Kranz, Peter G.; Noel, Richard; Nagaraj, Shashi K.; Lark, Robert K.; Wechsler, Daniel SG; del Gaudio, Daniela; Leung, Marco L.; Hendon, Laura G.; Parker, Collette C.; Jones, Kelly L.; Goldstein, David B.; Shashi, Vandana

2017-01-01

Purpose To describe examples of missed pathogenic variants on whole exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing. Methods Guided by phenotypic information, three children with negative WES underwent targeted single gene testing. Results Individual 1 had a clinical diagnosis consistent with infantile systemic hyalinosis, although WES and an NGS-based ANTXR2 test were negative. Sanger sequencing of ANTXR2 revealed a homozygous single base pair insertion, previously missed by the WES variant caller software. Individual 2 had neurodevelopmental regression and cerebellar atrophy, with no diagnosis on WES. New clinical findings prompted Sanger sequencing and copy number testing of PLA2G6. A novel homozygous deletion of the non-coding exon 1 (not included in the WES capture kit) was detected, with extension into the promoter, confirming the clinical suspicion of infantile neuroaxonal dystrophy. Individual 3 had progressive ataxia, spasticity and MRI changes of vanishing white matter leukoencephalopathy. An NGS leukodystrophy gene panel and WES showed a heterozygous pathogenic variant in EIF2B5; no deletions/duplications were detected. Sanger sequencing of EIF2B5 showed a frameshift indel, likely missed due to failure of alignment. Conclusions These cases illustrate potential pitfalls of WES/NGS testing, and the importance of phenotype-guided molecular testing in yielding diagnoses. PMID:28914269

Capture cross sections on unstable nuclei

Science.gov (United States)

Tonchev, A. P.; Escher, J. E.; Scielzo, N.; Bedrossian, P.; Ilieva, R. S.; Humby, P.; Cooper, N.; Goddard, P. M.; Werner, V.; Tornow, W.; Rusev, G.; Kelley, J. H.; Pietralla, N.; Scheck, M.; Savran, D.; Löher, B.; Yates, S. W.; Crider, B. P.; Peters, E. E.; Tsoneva, N.; Goriely, S.

2017-09-01

Accurate neutron-capture cross sections on unstable nuclei near the line of beta stability are crucial for understanding the s-process nucleosynthesis. However, neutron-capture cross sections for short-lived radionuclides are difficult to measure due to the fact that the measurements require both highly radioactive samples and intense neutron sources. Essential ingredients for describing the γ decays following neutron capture are the γ-ray strength function and level densities. We will compare different indirect approaches for obtaining the most relevant observables that can constrain Hauser-Feshbach statistical-model calculations of capture cross sections. Specifically, we will consider photon scattering using monoenergetic and 100% linearly polarized photon beams. Challenges that exist on the path to obtaining neutron-capture cross sections for reactions on isotopes near and far from stability will be discussed.

Capture cross sections on unstable nuclei

Directory of Open Access Journals (Sweden)

Tonchev A.P.

2017-01-01

Full Text Available Accurate neutron-capture cross sections on unstable nuclei near the line of beta stability are crucial for understanding the s-process nucleosynthesis. However, neutron-capture cross sections for short-lived radionuclides are difficult to measure due to the fact that the measurements require both highly radioactive samples and intense neutron sources. Essential ingredients for describing the γ decays following neutron capture are the γ-ray strength function and level densities. We will compare different indirect approaches for obtaining the most relevant observables that can constrain Hauser-Feshbach statistical-model calculations of capture cross sections. Specifically, we will consider photon scattering using monoenergetic and 100% linearly polarized photon beams. Challenges that exist on the path to obtaining neutron-capture cross sections for reactions on isotopes near and far from stability will be discussed.

Correlated double electron capture in slow, highly charged ion-atom collisions

Energy Technology Data Exchange (ETDEWEB)

Stolterfoht, N.; Havener, C.C.; Phaneuf, R.A.; Swenson, J.K.; Shafroth, S.M.; Meyer, F.W.

1986-01-01

Recent measurements of autoionization electrons produced in slow, highly charged ion-atom collisions are reviewed. Mechanisms for double electron capture into equivalent and nonequivalent configurations are analyzed by comparing the probabilities for the creation of L/sub 1/L/sub 23/X Coster Kronig electrons and L-Auger electrons. It is shown that the production of the Coster-Kronig electrons is due to electron correlation effects whose analysis leads beyond the independent-particle model. The importance of correlation effects on different capture mechanisms is discussed. 28 refs., 6 figs.

Plant phenomics and the need for physiological phenotyping across scales to narrow the genotype-to-phenotype knowledge gap

Czech Academy of Sciences Publication Activity Database

Grosskinsky, D. K.; Svensgaard, J.; Christensen, S.; Roitsch, Thomas

2015-01-01

Roč. 66, č. 18 (2015), s. 5429-5440 ISSN 0022-0957 Institutional support: RVO:67179843 Keywords : External phenotype * genome–environment–management interaction * genome–phenome map * internal phenotype * phenomics * physiological traits * physiology * plant phenotyping * predictors Subject RIV: EH - Ecology, Behaviour Impact factor: 5.677, year: 2015

Phenotypic variation in nurse traits and community feedbacks define an alpine community.

Science.gov (United States)

Michalet, Richard; Xiao, Sa; Touzard, Blaise; Smith, David S; Cavieres, Lohengrin A; Callaway, Ragan M; Whitham, Thomas G

2011-05-01

Much is known about facilitation, but virtually nothing about the underlying genetic and evolutionary consequences of this important interaction. We assessed the potential of phenotypic differences in facilitative effects of a foundation species to determine the composition of an Alpine community in Arizona. Two phenotypes of Geum rossii occur along a gradient of disturbance, with 'tight' competitive cushions in stable conditions and 'loose' facilitative cushions in disturbed conditions. A common-garden study suggested that field-based traits may have a genetic basis. Field experiments showed that the reproductive fitness of G. rossii cushions decreased with increasing facilitation. Finally, using a dual-lattice model we showed that including the cost and benefit of facilitation may contribute to the co-occurrence of genotypes with contrasting facilitative effects. Our results indicate that changes in community composition due to phenotypic differences in facilitative effects of a foundation species may in turn affect selective pressures on the foundation species. © 2011 Blackwell Publishing Ltd/CNRS.

Nordic research infrastructures for plant phenotyping

Directory of Open Access Journals (Sweden)

Kristiina Himanen

2018-03-01

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

Knowledge-based analysis of phenotypes

KAUST Repository

Hoendorf, Robert

2016-01-01

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

Evolution of the androgen-induced male phenotype.

Science.gov (United States)

Fuxjager, Matthew J; Miles, Meredith C; Schlinger, Barney A

2018-01-01

The masculine reproductive phenotype varies significantly across vertebrates. As a result, biologists have long recognized that many of the mechanisms that support these phenotypes-particularly the androgenic system-is evolutionarily labile, and thus susceptible to the effects of selection for different traits. However, exactly how androgenic signaling systems vary in a way which results in dramatically different functional outputs, remain largely unclear. We explore this topic here by outlining four key-but non-mutually exclusive-hypotheses that propose how the mechanisms of androgenic signaling might change over time to potentiate the emergence of phenotypical variation in masculine behavior and physiology. We anchor this framework in a review of our own studies of a tropical bird called the golden-collared manakin (Manacus vitellinus), which has evolved an exaggerated acrobatic courtship display that is heavily androgen-dependent. The result is an example of how the cellular basis of androgenic action can be modified to support a unique reproductive repertoire. We end this review by highlighting a broad pathway forward to further pursue the intricate ways by which the mechanisms of hormone action evolve to support processes of adaptation and animal design.

Gas permeation process for post combustion CO2 capture

International Nuclear Information System (INIS)

Pfister, Marc

2017-01-01

CO 2 Capture and Storage (CCS) is a promising solution to separate CO 2 from flue gas, to reduce the CO 2 emissions in the atmosphere, and hence to reduce global warming. In CCS, one important constraint is the high additional energy requirement of the different capture processes. That statement is partly explained by the low CO 2 fraction in the inlet flue gas and the high output targets in terms of CO 2 capture and purity (≥90%). Gas permeation across dense membrane can be used in post combustion CO 2 capture. Gas permeation in a dense membrane is ruled by a mass transfer mechanism and separation performance in a dense membrane are characterized by component's effective permeability and selectivity. One of the newest and encouraging type of membrane in terms of separation performance is the facilitated transport membrane. Each particular type of membrane is defined by a specific mass transfer law. The most important difference to the mass transfer behavior in a dense membrane is related to the facilitated transport mechanism and the solution diffusion mechanism and its restrictions and limitations. Permeation flux modelling across a dense membrane is required to perform a post combustion CO 2 capture process simulation. A CO 2 gas permeation separation process is composed of a two-steps membrane process, one drying step and a compression unit. Simulation on the energy requirement and surface area of the different membrane modules in the global system are useful to determine the benefits of using dense membranes in a post combustion CO 2 capture technology. (author)

Effect of sequential heat and cold shocks on nuclear phenotypes of the blood-sucking insect, Panstrongylus megistus (Burmeister (Hemiptera, Reduviidae

Directory of Open Access Journals (Sweden)

Garcia Simone L

2002-01-01

Full Text Available Thermal shocks induce changes in the nuclear phenotypes that correspond to survival (heterochromatin decondensation, nuclear fusion or death (apoptosis, necrosis responses in the Malpighian tubules of Panstrongylus megistus. Since thermal tolerance increased survival and molting rate in this species following sequential shocks, we investigated whether changes in nuclear phenotypes accompanied the insect survival response to sequential thermal shocks. Fifth instar nymphs were subjected to a single heat (35 or 40°C, 1 h or cold (5 or 0°C, 1 h shock and then subjected to a second shock for 12 h at 40 or 0°C, respectively, after 8, 18, 24 and 72 h at 28°C (control temperature. As with specimen survival, sequential heat and cold shocks induced changes in frequency of the mentioned nuclear phenotypes although their patterns differed. The heat shock tolerance involved decrease in apoptosis simultaneous to increase in cell survival responses. Sequential cold shocks did not involve cell/nuclear fusion and even elicited increase in necrosis with advancing time after shocks. The temperatures of 40 and 0ºC were more effective than the temperatures of 35 and 5ºC in eliciting the heat and cold shock tolerances, respectively, as shown by cytological analysis of the nuclear phenotypes. It is concluded that different sequential thermal shocks can trigger different mechanisms of cellular protection against stress in P. megistus, favoring the insect to adapt to various ecotopes.

Effect of water on the physical properties and carbon dioxide capture capacities of liquid-like Nanoparticle Organic Hybrid Materials and their corresponding polymers

KAUST Repository

Petit, Camille; Bhatnagar, Sonali; Park, Ah-Hyung Alissa

2013-01-01

Binary systems composed of liquid-like Nanoparticle Organic Hybrid Materials (NOHMs) and the secondary fluid (i.e., water) were prepared, and their thermal stabilities, densities, viscosities, and CO2 absorption capacities were investigated. Recent work has suggested NOHMs as an alternative CO2 capture media with interesting chemical and physical tunability. Anhydrous CO2 capture solvents often degrade when they are exposed to water, while flue gas generally contains about 8-16% water. Thus, this study was conducted to investigate the effect of water on the NOHMs' properties relevant to CO2 capture as well as the chemical and thermal stabilities of H2O-loaded NOHMs. It was found that water acted as an antisolvent of NOHMs, and therefore, caused a decreased CO2 capture capacity. On the other hand, the results indicated that while water did not affect the NOHMs' thermal stability, it significantly helped lowering their density and viscosity. In order to investigate the effect of intermolecular interactions among two fluids on the density and viscosity, the excess volumes and viscosity deviations were calculated and correlated with Redlich-Kister equations. The trends revealed the existence of strong intermolecular interactions between water molecules and the poly(ethlyne glycol) component of NOHMs, which may have caused the drastic decrease in the NOHMs' viscosity with the addition of water. © 2013 Elsevier Inc.

Effect of water on the physical properties and carbon dioxide capture capacities of liquid-like Nanoparticle Organic Hybrid Materials and their corresponding polymers

KAUST Repository

Petit, Camille

2013-10-01

Binary systems composed of liquid-like Nanoparticle Organic Hybrid Materials (NOHMs) and the secondary fluid (i.e., water) were prepared, and their thermal stabilities, densities, viscosities, and CO2 absorption capacities were investigated. Recent work has suggested NOHMs as an alternative CO2 capture media with interesting chemical and physical tunability. Anhydrous CO2 capture solvents often degrade when they are exposed to water, while flue gas generally contains about 8-16% water. Thus, this study was conducted to investigate the effect of water on the NOHMs\\' properties relevant to CO2 capture as well as the chemical and thermal stabilities of H2O-loaded NOHMs. It was found that water acted as an antisolvent of NOHMs, and therefore, caused a decreased CO2 capture capacity. On the other hand, the results indicated that while water did not affect the NOHMs\\' thermal stability, it significantly helped lowering their density and viscosity. In order to investigate the effect of intermolecular interactions among two fluids on the density and viscosity, the excess volumes and viscosity deviations were calculated and correlated with Redlich-Kister equations. The trends revealed the existence of strong intermolecular interactions between water molecules and the poly(ethlyne glycol) component of NOHMs, which may have caused the drastic decrease in the NOHMs\\' viscosity with the addition of water. © 2013 Elsevier Inc.

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

DEFF Research Database (Denmark)

Riis, Tenna; Lambertini, Carla; Olesen, Birgit

2010-01-01

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

Sublethal effects of catch-and-release fishing: measuring capture stress, fish impairment, and predation risk using a condition index

Science.gov (United States)

Campbell, Matthew D.; Patino, Reynaldo; Tolan, J.M.; Strauss, R.E.; Diamond, S.

2009-01-01

The sublethal effects of simulated capture of red snapper (Lutjanus campechanus) were analysed using physiological responses, condition indexing, and performance variables. Simulated catch-and-release fishing included combinations of depth of capture and thermocline exposure reflective of environmental conditions experienced in the Gulf of Mexico. Frequency of occurrence of barotrauma and lack of reflex response exhibited considerable individual variation. When combined into a single condition or impairment index, individual variation was reduced, and impairment showed significant increases as depth increased and with the addition of thermocline exposure. Performance variables, such as burst swimming speed (BSS) and simulated predator approach distance (AD), were also significantly different by depth. BSSs and predator ADs decreased with increasing depth, were lowest immediately after release, and were affected for up to 15 min, with longer recovery times required as depth increased. The impairment score developed was positively correlated with cortisol concentration and negatively correlated with both BSS and simulated predator AD. The impairment index proved to be an efficient method to estimate the overall impairment of red snapper in the laboratory simulations of capture and shows promise for use in field conditions, to estimate release mortality and vulnerability to predation.

Theory of inelastic multiphonon scattering and carrier capture by defects in semiconductors: Application to capture cross sections

Science.gov (United States)

Barmparis, Georgios D.; Puzyrev, Yevgeniy S.; Zhang, X.-G.; Pantelides, Sokrates T.

2015-12-01

Inelastic scattering and carrier capture by defects in semiconductors are the primary causes of hot-electron-mediated degradation of power devices, which holds up their commercial development. At the same time, carrier capture is a major issue in the performance of solar cells and light-emitting diodes. A theory of nonradiative (multiphonon) inelastic scattering by defects, however, is nonexistent, while the theory for carrier capture by defects has had a long and arduous history. Here we report the construction of a comprehensive theory of inelastic scattering by defects, with carrier capture being a special case. We distinguish between capture under thermal equilibrium conditions and capture under nonequilibrium conditions, e.g., in the presence of an electrical current or hot carriers where carriers undergo scattering by defects and are described by a mean free path. In the thermal-equilibrium case, capture is mediated by a nonadiabatic perturbation Hamiltonian, originally identified by Huang and Rhys and by Kubo, which is equal to linear electron-phonon coupling to first order. In the nonequilibrium case, we demonstrate that the primary capture mechanism is within the Born-Oppenheimer approximation (adiabatic transitions), with coupling to the defect potential inducing Franck-Condon electronic transitions, followed by multiphonon dissipation of the transition energy, while the nonadiabatic terms are of secondary importance (they scale with the inverse of the mass of typical atoms in the defect complex). We report first-principles density-functional-theory calculations of the capture cross section for a prototype defect using the projector-augmented wave, which allows us to employ all-electron wave functions. We adopt a Monte Carlo scheme to sample multiphonon configurations and obtain converged results. The theory and the results represent a foundation upon which to build engineering-level models for hot-electron degradation of power devices and the performance

Ontology-based validation and identification of regulatory phenotypes

KAUST Repository

Kulmanov, Maxat

2018-01-31

Motivation: Function annotations of gene products, and phenotype annotations of genotypes, provide valuable information about molecular mechanisms that can be utilized by computational methods to identify functional and phenotypic relatedness, improve our understanding of disease and pathobiology, and lead to discovery of drug targets. Identifying functions and phenotypes commonly requires experiments which are time-consuming and expensive to carry out; creating the annotations additionally requires a curator to make an assertion based on reported evidence. Support to validate the mutual consistency of functional and phenotype annotations as well as a computational method to predict phenotypes from function annotations, would greatly improve the utility of function annotations Results: We developed a novel ontology-based method to validate the mutual consistency of function and phenotype annotations. We apply our method to mouse and human annotations, and identify several inconsistencies that can be resolved to improve overall annotation quality. Our method can also be applied to the rule-based prediction of phenotypes from functions. We show that the predicted phenotypes can be utilized for identification of protein-protein interactions and gene-disease associations. Based on experimental functional annotations, we predict phenotypes for 1,986 genes in mouse and 7,301 genes in human for which no experimental phenotypes have yet been determined.

Ontology-based validation and identification of regulatory phenotypes

KAUST Repository

Kulmanov, Maxat; Schofield, Paul N; Gkoutos, Georgios V; Hoehndorf, Robert

2018-01-01

Motivation: Function annotations of gene products, and phenotype annotations of genotypes, provide valuable information about molecular mechanisms that can be utilized by computational methods to identify functional and phenotypic relatedness, improve our understanding of disease and pathobiology, and lead to discovery of drug targets. Identifying functions and phenotypes commonly requires experiments which are time-consuming and expensive to carry out; creating the annotations additionally requires a curator to make an assertion based on reported evidence. Support to validate the mutual consistency of functional and phenotype annotations as well as a computational method to predict phenotypes from function annotations, would greatly improve the utility of function annotations Results: We developed a novel ontology-based method to validate the mutual consistency of function and phenotype annotations. We apply our method to mouse and human annotations, and identify several inconsistencies that can be resolved to improve overall annotation quality. Our method can also be applied to the rule-based prediction of phenotypes from functions. We show that the predicted phenotypes can be utilized for identification of protein-protein interactions and gene-disease associations. Based on experimental functional annotations, we predict phenotypes for 1,986 genes in mouse and 7,301 genes in human for which no experimental phenotypes have yet been determined.

Phenotypic Profiling of Antibiotic Response Signatures in Escherichia coli Using Raman Spectroscopy

Science.gov (United States)

Athamneh, A. I. M.; Alajlouni, R. A.; Wallace, R. S.; Seleem, M. N.

2014-01-01

Identifying the mechanism of action of new potential antibiotics is a necessary but time-consuming and costly process. Phenotypic profiling has been utilized effectively to facilitate the discovery of the mechanism of action and molecular targets of uncharacterized drugs. In this research, Raman spectroscopy was used to profile the phenotypic response of Escherichia coli to applied antibiotics. The use of Raman spectroscopy is advantageous because it is noninvasive, label free, and prone to automation, and its results can be obtained in real time. In this research, E. coli cultures were subjected to three times the MICs of 15 different antibiotics (representing five functional antibiotic classes) with known mechanisms of action for 30 min before being analyzed by Raman spectroscopy (using a 532-nm excitation wavelength). The resulting Raman spectra contained sufficient biochemical information to distinguish between profiles induced by individual antibiotics belonging to the same class. The collected spectral data were used to build a discriminant analysis model that identified the effects of unknown antibiotic compounds on the phenotype of E. coli cultures. Chemometric analysis showed the ability of Raman spectroscopy to predict the functional class of an unknown antibiotic and to identify individual antibiotics that elicit similar phenotypic responses. Results of this research demonstrate the power of Raman spectroscopy as a cellular phenotypic profiling methodology and its potential impact on antibiotic drug development research. PMID:24295982

Effects of blood transportation on human peripheral mononuclear cell yield, phenotype and function: implications for immune cell biobanking.