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Sample records for active intrinsically unstructured

  1. Bioinformatic analysis and molecular modelling of human ameloblastin suggest a two-domain intrinsically unstructured calcium-binding protein

    Czech Academy of Sciences Publication Activity Database

    Vymětal, Jiří; Slabý, I.; Spahr, A.; Vondrášek, Jiří; Lyngstadaas, S. P.

    2008-01-01

    Roč. 116, č. 2 (2008), s. 124-134 ISSN 0909-8836 R&D Projects: GA ČR GA203/05/0009; GA ČR GA203/06/1727; GA MŠk LC512 Grant - others:EU(XE) QLK3-CT-2001-00090 Institutional research plan: CEZ:AV0Z40550506 Keywords : ameloblastin * bioinformatic modelling * calcium * intrinsically unstructured protein Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.957, year: 2008

  2. Organized and Unstructured Activity Participation among Adolescents Involved with Child Protective Services in the United States

    Science.gov (United States)

    Kwak, Yoonyoung; Lu, Ting; Christ, Sharon L.

    2017-01-01

    Background: Many adolescents are referred to Child Protective Services for possible maltreatment every year, but not much is known about their organized and unstructured activity participation. Objective: The purposes of this study are to provide a description of organized and unstructured activity participation for adolescents who were possible…

  3. Organized Sports and Unstructured Active Play as Physical Activity Sources in Children From Low-Income, Chicago Households.

    Science.gov (United States)

    Appelhans, Bradley M; Li, Hong

    2016-08-01

    This study tested associations of organized sports participation and unstructured active play with overall moderate and vigorous physical activity (MVPA) in low-income children and examined factors associated with participation frequency. Research staff visited 88 low-income Chicago households with children ages 6-13 years. MVPA was assessed through 7-day accelerometry. Researchers documented the home availability of physical activity equipment. Caregivers reported on child participation in organized sports and unstructured active play, family support for physical activity, perceived neighborhood safety, and access to neighborhood physical activity venues. Despite similar participation in organized sports and unstructured active play, boys accumulated more MVPA than girls. MVPA was predicted by an interaction between gender and unstructured active play. Boys accumulated 23-45 additional minutes of weekday MVPA and 53-62 additional minutes of weekend MVPA through unstructured active play, with no such associations in girls. Higher reported neighborhood safety and family support for physical activity were associated with engagement in unstructured active play for both genders, and with participation in organized sports for girls. Physical activity interventions for low-income, urban children should emphasize unstructured active play, particularly in boys. Fostering family support for physical activity and safe play environments may be critical intervention components.

  4. Does Aerobic Exercise Influence Intrinsic Brain Activity?

    DEFF Research Database (Denmark)

    Flodin, Pär; Jonasson, Lars S; Riklund, Katrin

    2017-01-01

    Previous studies have indicated that aerobic exercise could reduce age related decline in cognition and brain functioning. Here we investigated the effects of aerobic exercise on intrinsic brain activity. Sixty sedentary healthy males and females (64-78 years) were randomized into either an aerobic...... exercise group or an active control group. Both groups recieved supervised training, 3 days a week for 6 months. Multimodal brain imaging data was acquired before and after the intervention, including 10 min of resting state brain functional magnetic resonance imaging (rs-fMRI) and arterial spin labeling...... group improved more. Contrary to our hypothesis, we did not observe any significant group by time interactions with regard to any measure of intrinsic activity. To further probe putative relationships between fitness and brain activity, we performed post hoc analyses disregarding group belongings...

  5. The Development of Intrinsic Motivation for Physical Activity

    Science.gov (United States)

    2005-07-01

    The Development of Intrinsic Motivation for Physical Activity by James Dunigan Beaty Bachelor of Science Central Washington...2. REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE The Development of Intrinsic Motivation for Physical Activity 5a. CONTRACT...Government." 3 ABSTRACT The Development of Intrinsic Motivation for Physical Activity by James Dunigan Beaty Cynthia Carruthers, Ph.D

  6. The Development of Intrinsic Motivation for Physical Activity

    National Research Council Canada - National Science Library

    Beaty, James D

    2005-01-01

    .... Having found this to be so, it is worthy of researchers' efforts to determine the constructs that will move individuals to become more intrinsically motivated to engage in regular exercise and/or physical activity...

  7. Social influence and adolescent health-related physical activity in structured and unstructured settings: role of channel and type.

    Science.gov (United States)

    Spink, Kevin S; Wilson, Kathleen S; Ulvick, Jocelyn

    2012-08-01

    Social influence channels (e.g., parents) and types (e.g., compliance) have each been related to physical activity independently, but little is known about how these two categories of influence may operate in combination. This study examined the relationships between various combinations of social influence and physical activity among youth across structured and unstructured settings. Adolescents (N=304), classified as high or low active, reported the social influence combinations they received for being active. Participants identified three channels and three types of influence associated with being active. For structured activity, compliance with peers and significant others predicted membership in the high active group (values of psocial influence, when examining health-related physical activity.

  8. The Calponin Regulatory Region Is Intrinsically Unstructured: Novel Insight into Actin-Calponin and Calmodulin-Calponin Interfaces Using NMR Spectroscopy

    Science.gov (United States)

    Pfuhl, Mark; Al-Sarayreh, Sameeh; El-Mezgueldi, Mohammed

    2011-01-01

    Calponin is an actin- and calmodulin-binding protein believed to regulate the function of actin. Low-resolution studies based on proteolysis established that the recombinant calponin fragment 131–228 contained actin and calmodulin recognition sites but failed to precisely identify the actin-binding determinants. In this study, we used NMR spectroscopy to investigate the structure of this functionally important region of calponin and map its interaction with actin and calmodulin at amino-acid resolution. Our data indicates that the free calponin peptide is largely unstructured in solution, although four short amino-acid stretches corresponding to residues 140–146, 159–165, 189–195, and 199–205 display the propensity to form α-helices. The presence of four sequential transient helices probably provides the conformational malleability needed for the promiscuous nature of this region of calponin. We identified all amino acids involved in actin binding and demonstrated for the first time, to our knowledge, that the N-terminal flanking region of Lys137-Tyr144 is an integral part of the actin-binding site. We have also delineated the second actin-binding site to amino acids Thr180-Asp190. Ca2+-calmodulin binding extends beyond the previously identified minimal sequence of 153–163 and includes most amino acids within the stretch 143–165. In addition, we found that calmodulin induces chemical shift perturbations of amino acids 188–190 demonstrating for the first time, to our knowledge, an effect of Ca2+-calmodulin on this region. The spatial relationship of the actin and calmodulin contacts as well as the transient α-helical structures within the regulatory region of calponin provides a structural framework for understanding the Ca2+-dependent regulation of the actin-calponin interaction by calmodulin. PMID:21463585

  9. The restless brain: how intrinsic activity organizes brain function.

    Science.gov (United States)

    Raichle, Marcus E

    2015-05-19

    Traditionally studies of brain function have focused on task-evoked responses. By their very nature such experiments tacitly encourage a reflexive view of brain function. While such an approach has been remarkably productive at all levels of neuroscience, it ignores the alternative possibility that brain functions are mainly intrinsic and ongoing, involving information processing for interpreting, responding to and predicting environmental demands. I suggest that the latter view best captures the essence of brain function, a position that accords well with the allocation of the brain's energy resources, its limited access to sensory information and a dynamic, intrinsic functional organization. The nature of this intrinsic activity, which exhibits a surprising level of organization with dimensions of both space and time, is revealed in the ongoing activity of the brain and its metabolism. As we look to the future, understanding the nature of this intrinsic activity will require integrating knowledge from cognitive and systems neuroscience with cellular and molecular neuroscience where ion channels, receptors, components of signal transduction and metabolic pathways are all in a constant state of flux. The reward for doing so will be a much better understanding of human behaviour in health and disease.

  10. Older adults' intrinsic and extrinsic motivation toward physical activity.

    Science.gov (United States)

    Dacey, Marie; Baltzell, Amy; Zaichkowsky, Len

    2008-01-01

    To examine how motives discriminate 3 physical activity levels of inactive, active, and sustained maintainers. Six hundred forty-five adults (M age = 63.8) completed stage-of-change and Exercise Motivations Inventory (EMI-2) scales. Exploratory factor analysis established psychometric properties of the EMI-2 suitable for older adults. Six factors emerged in the EMI-2: health and fitness, social/emotional benefits, weight management, stress management, enjoyment, and appearance. Enjoyment contributed most to differentiating activity levels. Moderators of age and gender were delineated. Intrinsic motivation and self-determined extrinsic motivation distinguish older adults' activity levels.

  11. BQP35 is a novel member of the intrinsically unstructured protein (IUP) family which is a potential antigen for the sero-diagnosis of Babesia sp. BQ1 (Lintan) infection.

    Science.gov (United States)

    Guan, Guiquan; Moreau, Emmanuelle; Liu, Junlong; Ma, Miling; Rogniaux, Hélène; Liu, Aihong; Niu, Qingli; Li, Youquan; Ren, Qiaoyun; Luo, Jianxun; Chauvin, Alain; Yin, Hong

    2012-07-06

    A new gene of Babesia sp. BQ1 (Lintan) (BQP35) was cloned by screening a merozoite cDNA expression library with infected sheep serum and using rapid amplification of cDNA ends (RACE). The nucleotide sequence of the cDNA was 1140bp with an open reading frame (ORF) of 936bp encoding a 35-kDa predicted polypeptide with 311 amino acid residues. Comparison of BQP35 cDNA and genomic DNA sequences showed that BQP35 does not possess an intron. Recombinant BQP35 (rBQP35), expressed in a prokaryotic expression system, showed abnormally slow migration on SDS-PAGE. Gel shifting, amino acid sequence and in silico disorder region prediction indicated that BQP35 protein has characteristics of intrinsically unstructured proteins (IUPs). This is the first description of such proteins in the Babesia genus. BQP35 induced antibodies production as early as one week after Babesia sp. BQ1 (Lintan) infection in sheep. No cross-reaction was observed with sera from sheep infected with other ovine piroplasms dominant in China, except with Babesia sp. Tianzhu. The interest of BQP35 as a diagnostic antigen is discussed. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Pilgrimage: Intrinsic Motivation and Active Behavior in the Eldery

    Directory of Open Access Journals (Sweden)

    Eichberg Henning

    2017-10-01

    Full Text Available Can intrinsic religious motivation have relevant effects on the motor activity of older people? How are processions and pilgrimages related to the dominant imagination of old age as a period of fatigue and gray hair, suffering and loneliness, retirement and rest – and of waiting: waiting for a call from a loved one, waiting for the visit of a good companion, or, finally, expecting the end of life?

  13. Pilgrimage: Intrinsic Motivation and Active Behavior in the Eldery

    OpenAIRE

    Eichberg Henning; Kosiewicz Jerzy; Contiero Danilo

    2017-01-01

    Can intrinsic religious motivation have relevant effects on the motor activity of older people? How are processions and pilgrimages related to the dominant imagination of old age as a period of fatigue and gray hair, suffering and loneliness, retirement and rest – and of waiting: waiting for a call from a loved one, waiting for the visit of a good companion, or, finally, expecting the end of life?

  14. Pilgrimage:Intrinsic Motivation and Active Behavior in the Eldery

    OpenAIRE

    Eichberg, Henning; Kosiewicz, Jerzy; Contiero, Danilo

    2017-01-01

    Can intrinsic religious motivation have relevant effects on the motor activity of older people? How are processions and pilgrimages related to the dominant imagination of old age as a period of fatigue and gray hair, suffering and loneliness, retirement and rest - and of waiting: waiting for a call from a loved one, waiting for the visit of a good companion, or, finally, expecting the end of life? This study is based on interviews with people from different countries, cultures, and religions....

  15. Intrinsic-mediated caspase activation is essential for cardiomyocyte hypertrophy

    Science.gov (United States)

    Putinski, Charis; Abdul-Ghani, Mohammad; Stiles, Rebecca; Brunette, Steve; Dick, Sarah A.; Fernando, Pasan; Megeney, Lynn A.

    2013-01-01

    Cardiomyocyte hypertrophy is the cellular response that mediates pathologic enlargement of the heart. This maladaptation is also characterized by cell behaviors that are typically associated with apoptosis, including cytoskeletal reorganization and disassembly, altered nuclear morphology, and enhanced protein synthesis/translation. Here, we investigated the requirement of apoptotic caspase pathways in mediating cardiomyocyte hypertrophy. Cardiomyocytes treated with hypertrophy agonists displayed rapid and transient activation of the intrinsic-mediated cell death pathway, characterized by elevated levels of caspase 9, followed by caspase 3 protease activity. Disruption of the intrinsic cell death pathway at multiple junctures led to a significant inhibition of cardiomyocyte hypertrophy during agonist stimulation, with a corresponding reduction in the expression of known hypertrophic markers (atrial natriuretic peptide) and transcription factor activity [myocyte enhancer factor-2, nuclear factor kappa B (NF-κB)]. Similarly, in vivo attenuation of caspase activity via adenoviral expression of the biologic effector caspase inhibitor p35 blunted cardiomyocyte hypertrophy in response to agonist stimulation. Treatment of cardiomyocytes with procaspase 3 activating compound 1, a small-molecule activator of caspase 3, resulted in a robust induction of the hypertrophy response in the absence of any agonist stimulation. These results suggest that caspase-dependent signaling is necessary and sufficient to promote cardiomyocyte hypertrophy. These results also confirm that cell death signal pathways behave as active remodeling agents in cardiomyocytes, independent of inducing an apoptosis response. PMID:24101493

  16. Uncovering intrinsic modular organization of spontaneous brain activity in humans.

    Directory of Open Access Journals (Sweden)

    Yong He

    Full Text Available The characterization of topological architecture of complex brain networks is one of the most challenging issues in neuroscience. Slow (<0.1 Hz, spontaneous fluctuations of the blood oxygen level dependent (BOLD signal in functional magnetic resonance imaging are thought to be potentially important for the reflection of spontaneous neuronal activity. Many studies have shown that these fluctuations are highly coherent within anatomically or functionally linked areas of the brain. However, the underlying topological mechanisms responsible for these coherent intrinsic or spontaneous fluctuations are still poorly understood. Here, we apply modern network analysis techniques to investigate how spontaneous neuronal activities in the human brain derived from the resting-state BOLD signals are topologically organized at both the temporal and spatial scales. We first show that the spontaneous brain functional networks have an intrinsically cohesive modular structure in which the connections between regions are much denser within modules than between them. These identified modules are found to be closely associated with several well known functionally interconnected subsystems such as the somatosensory/motor, auditory, attention, visual, subcortical, and the "default" system. Specifically, we demonstrate that the module-specific topological features can not be captured by means of computing the corresponding global network parameters, suggesting a unique organization within each module. Finally, we identify several pivotal network connectors and paths (predominantly associated with the association and limbic/paralimbic cortex regions that are vital for the global coordination of information flow over the whole network, and we find that their lesions (deletions critically affect the stability and robustness of the brain functional system. Together, our results demonstrate the highly organized modular architecture and associated topological properties in

  17. Measure of synchrony in the activity of intrinsic cardiac neurons

    International Nuclear Information System (INIS)

    Longpré, Jean-Philippe; Salavatian, Siamak; Jacquemet, Vincent; Beaumont, Eric; Armour, J Andrew; Ardell, Jeffrey L

    2014-01-01

    Recent multielectrode array recordings in ganglionated plexi of canine atria have opened the way to the study of population dynamics of intrinsic cardiac neurons. These data provide critical insights into the role of local processing that these ganglia play in the regulation of cardiac function. Low firing rates, marked non-stationarity, interplay with the cardiovascular and pulmonary systems and artifacts generated by myocardial activity create new constraints not present in brain recordings for which almost all neuronal analysis techniques have been developed. We adapted and extended the jitter-based synchrony index (SI) to (1) provide a robust and computationally efficient tool for assessing the level and statistical significance of SI between cardiac neurons, (2) estimate the bias on SI resulting from neuronal activity possibly hidden in myocardial artifacts, (3) quantify the synchrony or anti-synchrony between neuronal activity and the phase in the cardiac and respiratory cycles. The method was validated on firing time series from a total of 98 individual neurons identified in 8 dog experiments. SI ranged from −0.14 to 0.66, with 23 pairs of neurons with SI > 0.1. The estimated bias due to artifacts was typically <1%. Strongly cardiovascular- and pulmonary-related neurons (SI > 0.5) were found. Results support the use of jitter-based SI in the context of intrinsic cardiac neurons. (paper)

  18. Enzyme activation through the utilization of intrinsic dianion binding energy.

    Science.gov (United States)

    Amyes, T L; Malabanan, M M; Zhai, X; Reyes, A C; Richard, J P

    2017-03-01

    We consider 'the proposition that the intrinsic binding energy that results from the noncovalent interaction of a specific substrate with the active site of the enzyme is considerably larger than is generally believed. An important part of this binding energy may be utilized to provide the driving force for catalysis, so that the observed binding energy represents only what is left over after this utilization' [Jencks,W.P. (1975) Adv. Enzymol. Relat. Areas. Mol. Biol. , , 219-410]. The large ~12 kcal/mol intrinsic substrate phosphodianion binding energy for reactions catalyzed by triosephosphate isomerase (TIM), orotidine 5'-monophosphate decarboxylase and glycerol-3-phosphate dehydrogenase is divided into 4-6 kcal/mol binding energy that is expressed on the formation of the Michaelis complex in anchoring substrates to the respective enzyme, and 6-8 kcal/mol binding energy that is specifically expressed at the transition state in activating the respective enzymes for catalysis. A structure-based mechanism is described where the dianion binding energy drives a conformational change that activates these enzymes for catalysis. Phosphite dianion plays the active role of holding TIM in a high-energy closed active form, but acts as passive spectator in showing no effect on transition-state structure. The result of studies on mutant enzymes is presented, which support the proposal that the dianion-driven enzyme conformational change plays a role in enhancing the basicity of side chain of E167, the catalytic base, by clamping the base between a pair of hydrophobic side chains. The insight these results provide into the architecture of enzyme active sites and the development of strategies for the de novo design of protein catalysts is discussed.

  19. Biocompatibility selenium nanoparticles with an intrinsic oxidase-like activity

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Leilei; Huang, Kaixun; Liu, Hongmei, E-mail: hmliu2004@126.com [Huazhong University of Science and Technology, School of Chemistry and Chemical Engineering (China)

    2016-03-15

    Selenium nanoparticles (SeNPs) are considered to be the new selenium supplement forms with high biological activity and low toxicity; however, the molecular mechanism by which SeNPs exert the biological function is unclear. Here, we reported that biocompatibility SeNPs possessed intrinsic oxidase-like activity. Using Na{sub 2}SeO{sub 3} as a precursor and glutathione as a reductant, biocompatibility SeNPs were synthesized by the wet chemical reduction method in the presence of bovine serum albumin (BSA). The results of structure characterization revealed that synthesized SeNPs were amorphous red elementary selenium with spherical morphology, and ranged in size from 25 to 70 nm size with a narrow distribution (41.4 ± 6.7 nm). The oxidase-like activity of the as-synthesized SeNPs was tested with 3,3′,5,5′-tetramethylbenzidine (TMB) as a substrate. The results indicated that SeNPs could catalyze the oxidization of TMB by dissolved oxygen. These SeNPs showed an optimum catalytic activity at pH 4 and 30 °C, and the oxidase-like activity was higher as the concentration of SeNPs increased and the size of SeNPs decreased. The Michaelis constant (K{sub m}) values and maximal reaction velocity (V{sub max}) of the SeNPs for TMB oxidation were 0.0083 mol/L and 3.042 μmol/L min, respectively.

  20. HIRENASD medium unstructured

    Data.gov (United States)

    National Aeronautics and Space Administration — Unstructured HIRENASD mesh: - medium size (16 million nodes, 39 million elements) - for node centered solvers - 31.05.2011 - caution: dimensions in mm

  1. HIRENASD coarse unstructured

    Data.gov (United States)

    National Aeronautics and Space Administration — Unstructured HIRENASD mesh: - coarse size (5.7 million nodes, 14.4 million elements) - for node centered solvers - 01.06.2011 - caution: dimensions in mm

  2. The effect of an unstructured, moderate to vigorous, before-school physical activity program in elementary school children on academics, behavior, and health.

    Science.gov (United States)

    Tompkins, Connie L; Hopkins, Jacob; Goddard, Lauren; Brock, David W

    2012-07-05

    Physical inactivity has been deemed a significant, contributing factor to childhood overweight and obesity. In recent years, many school systems removed recess and/or physical education from their curriculum due to growing pressure to increase academic scores. With the vast majority of children's time spent in school, alternative strategies to re-introduce physical activity back into schools are necessary. A creative yet underutilized solution to engage children in physical activity may be in before-school programs. The objective of the proposed study is to examine the effect of an unstructured, moderate to vigorous, before-school physical activity program on academic performance, classroom behavior, emotions, and other health related measures. Children in 3rd-5th grade will participate in a before-school (7:30-8:15 a.m.), physical activity program for 12 weeks, 3 days a week. Children will be able to choose their preferred activity and asked to sustain physical activity of moderate to vigorous intensity with individual heart rate monitored during each session. The proposed study explores an innovative method of engaging and increasing physical activity in children. The results of this study will provide evidence to support the feasibility of an unstructured, moderate to vigorous, before-school physical activity program in children and provide insight regarding the ideal physical activity intensity and duration necessary to achieve a positive increase in academic performance. ClinicalTrials.gov Identifier: NCT01505244.

  3. The effect of an unstructured, moderate to vigorous, before-school physical activity program in elementary school children on academics, behavior, and health

    Directory of Open Access Journals (Sweden)

    Tompkins Connie L

    2012-07-01

    Full Text Available Abstract Background Physical inactivity has been deemed a significant, contributing factor to childhood overweight and obesity. In recent years, many school systems removed recess and/or physical education from their curriculum due to growing pressure to increase academic scores. With the vast majority of children’s time spent in school, alternative strategies to re-introduce physical activity back into schools are necessary. A creative yet underutilized solution to engage children in physical activity may be in before-school programs. The objective of the proposed study is to examine the effect of an unstructured, moderate to vigorous, before-school physical activity program on academic performance, classroom behavior, emotions, and other health related measures. Methods/Design Children in 3rd–5th grade will participate in a before-school (7:30–8:15 a.m., physical activity program for 12 weeks, 3 days a week. Children will be able to choose their preferred activity and asked to sustain physical activity of moderate to vigorous intensity with individual heart rate monitored during each session. Discussion The proposed study explores an innovative method of engaging and increasing physical activity in children. The results of this study will provide evidence to support the feasibility of an unstructured, moderate to vigorous, before-school physical activity program in children and provide insight regarding the ideal physical activity intensity and duration necessary to achieve a positive increase in academic performance. Trial registration ClinicalTrials.gov Identifier: NCT01505244

  4. The Unstructured Clinical Interview

    Science.gov (United States)

    Jones, Karyn Dayle

    2010-01-01

    In mental health, family, and community counseling settings, master's-level counselors engage in unstructured clinical interviewing to develop diagnoses based on the "Diagnostic and Statistical Manual of Mental Disorders" (4th ed., text rev.; "DSM-IV-TR"; American Psychiatric Association, 2000). Although counselors receive education about…

  5. Do people differentiate between intrinsic and extrinsic goals for physical activity?

    Science.gov (United States)

    McLachlan, Sarah; Hagger, Martin S

    2011-04-01

    The distinction between intrinsic and extrinsic goals, and between goal pursuit for intrinsically and extrinsically motivated reasons, is a central premise of self-determination theory. Proponents of the theory have proposed that the pursuit of intrinsic goals and intrinsically motivated goal striving each predict adaptive psychological and behavioral outcomes relative to the pursuit of extrinsic goals and extrinsically motivated goal striving. Despite evidence to support these predictions, research has not explored whether individuals naturally differentiate between intrinsic and extrinsic goals. Two studies tested whether people make this differentiation when recalling goals for leisure-time physical activity. Using memory-recall methods, participants in Study 1 were asked to freely generate physical activity goals. A subsample (N = 43) was asked to code their freely generated goals as intrinsic or extrinsic. In Study 2, participants were asked to recall intrinsic and extrinsic goals after making a decision regarding their future physical activity. Results of these studies revealed that individuals' goal generation and recall exhibited significant clustering by goal type. Participants encountered some difficulties when explicitly coding goals. Findings support self-determination theory and indicate that individuals discriminate between intrinsic and extrinsic goals.

  6. Size matters to function: Brain volume correlates with intrinsic brain activity across healthy individuals.

    Science.gov (United States)

    Qing, Zhao; Gong, Gaolang

    2016-10-01

    A fundamental issue in neuroscience is to understand the structural substrates of neural activities. Intrinsic brain activity has been increasingly recognized as an important functional activity mode and is tightly linked with various cognitive functions. Structurally, cognitive functions have also shown a relation with brain volume/size. Therefore, an association between intrinsic brain activities and brain volume/size can be hypothesized, and brain volume/size may impact intrinsic brain activity in human brains. The present study aimed to explicitly investigate this brain structure-function relationship using two large independent cohorts of 176 and 236 young adults. Structural-MRI was performed to estimate the brain volume, and resting-state functional-MRI was applied to extract the amplitude of low-frequency fluctuations (ALFF), an imaging measure of intrinsic brain activity. Intriguingly, our results revealed a robust linear correlation between whole-brain size and ALFF. Moreover, specific brain lobes/regions, including the frontal lobe, the left middle frontal gyrus, anterior cingulate gyrus, Rolandic operculum, and insula, also showed a reliable, positive volume-ALFF correlation in the two cohorts. These findings offer direct, empirical evidence of a strong association between brain size/volume and intrinsic brain activity, as well as provide novel insight into the structural substrates of the intrinsic brain activity of the human brain. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Comparison of structured and unstructured physical activity training on predicted VO2max and heart rate variability in adolescents - a randomized control trial.

    Science.gov (United States)

    Sharma, Vivek Kumar; Subramanian, Senthil Kumar; Radhakrishnan, Krishnakumar; Rajendran, Rajathi; Ravindran, Balasubramanian Sulur; Arunachalam, Vinayathan

    2017-05-01

    Physical inactivity contributes to many health issues. The WHO-recommended physical activity for adolescents encompasses aerobic, resistance, and bone strengthening exercises aimed at achieving health-related physical fitness. Heart rate variability (HRV) and maximal aerobic capacity (VO2max) are considered as noninvasive measures of cardiovascular health. The objective of this study is to compare the effect of structured and unstructured physical training on maximal aerobic capacity and HRV among adolescents. We designed a single blinded, parallel, randomized active-controlled trial (Registration No. CTRI/2013/08/003897) to compare the physiological effects of 6 months of globally recommended structured physical activity (SPA), with that of unstructured physical activity (USPA) in healthy school-going adolescents. We recruited 439 healthy student volunteers (boys: 250, girls: 189) in the age group of 12-17 years. Randomization across the groups was done using age and gender stratified randomization method, and the participants were divided into two groups: SPA (n=219, boys: 117, girls: 102) and USPA (n=220, boys: 119, girls: 101). Depending on their training status and gender the participants in both SPA and USPA groups were further subdivided into the following four sub-groups: SPA athlete boys (n=22) and girls (n=17), SPA nonathlete boys (n=95) and girls (n=85), USPA athlete boys (n=23) and girls (n=17), and USPA nonathlete boys (n=96) and girls (n=84). We recorded HRV, body fat%, and VO2 max using Rockport Walk Fitness test before and after the intervention. Maximum aerobic capacity and heart rate variability increased significantly while heart rate, systolic blood pressure, diastolic blood pressure, and body fat percentage decreased significantly after both SPA and USPA intervention. However, the improvement was more in SPA as compared to USPA. SPA is more beneficial for improving cardiorespiratory fitness, HRV, and reducing body fat percentage in terms of

  8. The Development of Intrinsic Motivation for Physical Activity

    National Research Council Canada - National Science Library

    Beaty, James D

    2005-01-01

    Being physically active can improve a person's health and mental well being. A physically active society could reduce the nation's cost of caring for the preventable diseases associated with the sedentary lifestyle...

  9. Impaired prefrontal activity to regulate the intrinsic motivation-action link in schizophrenia.

    Science.gov (United States)

    Takeda, Kazuyoshi; Matsumoto, Madoka; Ogata, Yousuke; Maida, Keiko; Murakami, Hiroki; Murayama, Kou; Shimoji, Keigo; Hanakawa, Takashi; Matsumoto, Kenji; Nakagome, Kazuyuki

    2017-01-01

    A core feature of schizophrenia (SCZ) is impairment in intrinsic motivation. Although intrinsic motivation plays an important role in enhancing improvement of the social functioning, its neural mechanisms of impairment have yet to be clarified. We hypothesized that abnormal function of the frontostriatal loop consisting of the striatum and lateral prefrontal cortex (LPFC) may be related to impaired intrinsic motivation in SCZ. We tested this by comparing the brain activity measured by functional magnetic resonance imaging and behavioral parameters associated with movement, motivation, and cognitive control between 18 stable SCZ patients and 17 healthy control (HC) participants during a task that elicits intrinsic motivation. We also compared the functional connectivity during resting-state and the fractional anisotropy using diffusion tensor imaging analysis between the two groups. We adopted an enjoyable timing task to stop a stopwatch at an exact time, which in our previous study has demonstrated to elicit intrinsic motivation. Although the performance level in general was not different between groups, the SCZ group performed worse than the HC group in trials following "overshoot" errors (i.e., the response was too late). SCZ participants showed lower intrinsic motivation to the task than the HC group in an inventory report. The striatal activity during the prediction at the task cue period was consistently lower in SCZ participants than in HC. The LPFC activity at the task cue period positively correlated with intrinsic motivation and also with the rate of success following overshoot errors in the HC group, but not in the SCZ group. The LPFC activity at the task cue period was also positively correlated with the striatal activity in both groups. The striatal activity during the feedback period was not significantly different between groups. These results suggest that, unlike HC, the neural activity in the LPFC fails to mediate between prediction of hedonic

  10. Impaired prefrontal activity to regulate the intrinsic motivation-action link in schizophrenia

    Directory of Open Access Journals (Sweden)

    Kazuyoshi Takeda

    2017-01-01

    Full Text Available A core feature of schizophrenia (SCZ is impairment in intrinsic motivation. Although intrinsic motivation plays an important role in enhancing improvement of the social functioning, its neural mechanisms of impairment have yet to be clarified. We hypothesized that abnormal function of the frontostriatal loop consisting of the striatum and lateral prefrontal cortex (LPFC may be related to impaired intrinsic motivation in SCZ. We tested this by comparing the brain activity measured by functional magnetic resonance imaging and behavioral parameters associated with movement, motivation, and cognitive control between 18 stable SCZ patients and 17 healthy control (HC participants during a task that elicits intrinsic motivation. We also compared the functional connectivity during resting-state and the fractional anisotropy using diffusion tensor imaging analysis between the two groups. We adopted an enjoyable timing task to stop a stopwatch at an exact time, which in our previous study has demonstrated to elicit intrinsic motivation. Although the performance level in general was not different between groups, the SCZ group performed worse than the HC group in trials following “overshoot” errors (i.e., the response was too late. SCZ participants showed lower intrinsic motivation to the task than the HC group in an inventory report. The striatal activity during the prediction at the task cue period was consistently lower in SCZ participants than in HC. The LPFC activity at the task cue period positively correlated with intrinsic motivation and also with the rate of success following overshoot errors in the HC group, but not in the SCZ group. The LPFC activity at the task cue period was also positively correlated with the striatal activity in both groups. The striatal activity during the feedback period was not significantly different between groups. These results suggest that, unlike HC, the neural activity in the LPFC fails to mediate between

  11. Intrinsic Motivation.

    Science.gov (United States)

    the activity. There has been very little research and theorizing which considers the topic of intrinsic motivation , yet there is a substantial amount...reported within the framework of intrinsic motivation , yet the paper reinterprets the work within that framework. It considers several approaches of

  12. Intrinsically active nanobody-modified polymeric micelles for tumor-targeted combination therapy

    NARCIS (Netherlands)

    Talelli, M.; Oliveira, S.; Rijcken, C.J.; Pieters, E.H.; Etrych, T.; Ulbrich, K.; van Nostrum, C.F.; Storm, Gerrit; Hennink, W.E.; Lammers, Twan Gerardus Gertudis Maria

    2013-01-01

    Various different passively and actively targeted nanomedicines have been designed and evaluated over the years, in particular for the treatment of cancer. Reasoning that the potential of ligand-modified nanomedicines can be substantially improved if intrinsically active targeting moieties are used,

  13. Relations of perception of responsibility to intrinsic motivation and physical activity among Korean middle school students.

    Science.gov (United States)

    Lee, Okseon; Kim, Younhee; Kim, Oung Jun

    2012-12-01

    To validate the Personal and Social Responsibility Questionnaire, the relations between perceived responsibility and intrinsic motivation were examined among Korean middle school students. The relations of change in stages of physical activity and students' perceived responsibility were also examined. Participants were 357 middle school students (160 boys, 197 girls) from three schools in the Seoul metropolitan area. Exploratory factor analysis supported a three-factor structure with effort and self-direction merged into one factor and the responsibilities of respect and caring for others constituted separate factors. Pearson correlations among factors showed perceptions of personal responsibility were associated with more intrinsic motivation toward physical education and a higher stage of physical activity. A moderate or low association between perceived social responsibility and intrinsic motivation implied a need to develop strategies for Korean students to use social responsibility for promoting physical activity.

  14. Task-free presurgical mapping using functional magnetic resonance imaging intrinsic activity.

    Science.gov (United States)

    Liu, Hesheng; Buckner, Randy L; Talukdar, Tanveer; Tanaka, Naoaki; Madsen, Joseph R; Stufflebeam, Steven M

    2009-10-01

    Low-frequency components of the spontaneous functional MR imaging signal provide information about the intrinsic functional and anatomical organization of the brain. The ability to use such methods in individual patients may provide a powerful tool for presurgical planning. The authors explore the feasibility of presurgical motor function mapping in which a task-free paradigm is used. Six surgical candidates with tumors or epileptic foci near the motor cortex participated in this study. The investigators directly compared task-elicited activation of the motor system to activation obtained from intrinsic activity correlations. The motor network within the unhealthy hemisphere was identified based on intrinsic activity correlations, allowing distortions of functional anatomy caused by the tumor and epilepsy to be directly visualized. The precision of the motor function mapping was further explored in 1 participant by using direct cortical stimulation. The motor regions localized based on the spontaneous activity correlations were quite similar to the regions defined by actual movement tasks and cortical stimulation. Using intrinsic activity correlations, it was possible to map the motor cortex in presurgical patients. This task-free paradigm may provide a powerful approach to map functional anatomy in patients without task compliance and allow multiple brain systems to be determined in a single scanning session.

  15. Opposing Effects of Intrinsic Conductance and Correlated Synaptic Input on V-Fluctuations during Network Activity

    DEFF Research Database (Denmark)

    Kolind, Jens; Hounsgaard, Jørn Dybkjær; Berg, Rune W

    2012-01-01

    Neurons often receive massive concurrent bombardment of synaptic inhibition and excitation during functional network activity. This increases membrane conductance and causes fluctuations in membrane potential (V(m)) and spike timing. The conductance increase is commonly attributed to synaptic...... conductance, but also includes the intrinsic conductances recruited during network activity. These two sources of conductance have contrasting dynamic properties at sub-threshold membrane potentials. Synaptic transmitter gated conductance changes abruptly and briefly with each presynaptic action potential...... input we find that the magnitude of the membrane fluctuations uniquely determines the relative contribution of synaptic and intrinsic conductance. We also quantify how V(m)-fluctuations vary with synaptic correlations for fixed ratios of synaptic and intrinsic conductance. Interestingly, the levels of V...

  16. Activity-dependent changes in intrinsic excitability of human spinal motoneurones produced by natural activity.

    Science.gov (United States)

    Rossi, Alessandro; Rossi, Simone; Ginanneschi, Federica

    2012-11-01

    The current study was designed to evaluate activity-dependent changes intrinsic to the spinal motoneurones (MNs) associated with sustained contractions. The excitability of spinal MNs (reflected by the antidromically evoked F-wave) innervating the abductor digiti minimi muscle (ADM) was measured in 12 healthy subjects following maximum voluntary contractions (MVCs) of ADM lasting 5 s, 15 s, 30 s, and 60 s. Upon cessation of the contractions, F-waves showed a depression, which increased in depth and duration with increasing duration of contraction. Following a 5-s contraction, there was a 20% decrease, which waned in 2 min, whereas a 60-s contraction produced a 40% decrease and waned in over 15 min. The changes in excitability of peripheral motor axons produced by the MVCs were measured by recording an ADM compound muscle action potential (CMAP) of ~50% of maximum to a constant ulnar nerve electrical stimulation. On cessation of the contractions, there was a prominent decrease in size of the CMAP: following a 5-s MVC, it produced a 10% decrease in the size of the test CMAP, which recovered in 2 min, whereas following a 60-s MVC, it produced a 30% decrease, which recovered in over 15 min. Statistical analysis (correntropy) showed a high-order mutual dependence between F-wave and CMAP, and both were significantly dependent on MVC duration. Because of the parallel excitability changes in peripheral axons and spinal MNs, our interpretation is that intrinsic excitability of the axon initial segment (i.e., where the action potential is generated) and peripheral axon segments changed in a similar, activity-dependent manner.

  17. Intrinsically active and pacemaker neurons in pluripotent stem cell-derived neuronal populations.

    Science.gov (United States)

    Illes, Sebastian; Jakab, Martin; Beyer, Felix; Gelfert, Renate; Couillard-Despres, Sébastien; Schnitzler, Alfons; Ritter, Markus; Aigner, Ludwig

    2014-03-11

    Neurons generated from pluripotent stem cells (PSCs) self-organize into functional neuronal assemblies in vitro, generating synchronous network activities. Intriguingly, PSC-derived neuronal assemblies develop spontaneous activities that are independent of external stimulation, suggesting the presence of thus far undetected intrinsically active neurons (IANs). Here, by using mouse embryonic stem cells, we provide evidence for the existence of IANs in PSC-neuronal networks based on extracellular multielectrode array and intracellular patch-clamp recordings. IANs remain active after pharmacological inhibition of fast synaptic communication and possess intrinsic mechanisms required for autonomous neuronal activity. PSC-derived IANs are functionally integrated in PSC-neuronal populations, contribute to synchronous network bursting, and exhibit pacemaker properties. The intrinsic activity and pacemaker properties of the neuronal subpopulation identified herein may be particularly relevant for interventions involving transplantation of neural tissues. IANs may be a key element in the regulation of the functional activity of grafted as well as preexisting host neuronal networks.

  18. Chromospheric Mass Motions and Intrinsic Sunspot Rotations for NOAA Active Regions 10484, 10486, and 10488 Using ISOON Data (Postprint)

    Science.gov (United States)

    2013-08-10

    AFRL-RV-PS- AFRL-RV-PS- TP-2013-0009 TP-2013-0009 CHROMOSPHERIC MASS MOTIONS AND INTRINSIC SUNSPOT ROTATIONS FOR NOAA ACTIVE REGIONS...SUBTITLE Chromospheric Mass Motions and Intrinsic Sunspot Rotations for NOAA Active Regions 10484, 10486, and 10488 Using ISOON Data (Postprint...Improved Solar Observing Optical Network continuum (630.2 nm) and Hα (656.2 nm) data to: (1) detect and measure intrinsic sunspot rotations occurring in

  19. Photochemical Proteolysis of an Unstructured Linker of the GABAAR Extracellular Domain Prevents GABA but Not Pentobarbital Activation

    Science.gov (United States)

    Hanek, Ariele P.; Lester, Henry A.

    2010-01-01

    The GABA type A receptor (GABAAR) is the major inhibitory receptor in the mammalian central nervous system and the target of numerous pharmaceuticals. The α-subunit of these pentameric Cys-loop neurotransmitter-gated ion channels contributes to the binding of both GABA and allosteric modulators such as the benzodiazepines, suggesting a role for this subunit in the conformational changes associated with activation of the receptor. Herein we use the nonsense suppression methodology to incorporate a photoactivatable unnatural amino acid and photochemically cleave the backbone of the α subunit of the α1β2 GABAAR in a linker region that is believed to span the subunit. Proteolytic cleavage impairs GABA but not pentobarbital activation, strongly suggesting that conformational changes involving this linker region are critical to the GABA activation pathway. PMID:20363860

  20. Physical Effort, Energy Expenditure, and Motivation in Structured and Unstructured Active Video Games: A Randomized Controlled Trial

    Directory of Open Access Journals (Sweden)

    de Brito-Gomes Jorge Luiz

    2016-09-01

    Full Text Available Purpose. The goals of the study were: a to compare the way that two types of active video games (AVG influenced physical effort and motivation in young adults; b to compare direct and indirect instruments and use an indirect instrument (heart rate analysis as a practical tool to verify physical effort in AVGs.

  1. Proinflammatory cytokines activate the intrinsic apoptotic pathway in beta-cells

    DEFF Research Database (Denmark)

    Grunnet, Lars G; Aikin, Reid; Tonnesen, Morten F

    2009-01-01

    OBJECTIVE: Proinflammatory cytokines are cytotoxic to beta-cells and have been implicated in the pathogenesis of type 1 diabetes and islet graft failure. The importance of the intrinsic mitochondrial apoptotic pathway in cytokine-induced beta-cell death is unclear. Here, cytokine activation...... of the intrinsic apoptotic pathway and the role of the two proapoptotic Bcl-2 proteins, Bad and Bax, were examined in beta-cells. RESEARCH DESIGN AND METHODS: Human and rat islets and INS-1 cells were exposed to a combination of proinflammatory cytokines (interleukin-1beta, interferon-gamma, and/or tumor necrosis...... to investigate the role of Bad and Bax activation, respectively. RESULTS: We found that proinflammatory cytokines induced calcineurin-dependent dephosphorylation of Bad Ser136, mitochondrial stress, cytochrome c release, activation of caspase-9 and -3, and DNA fragmentation. Inhibition of Bad Ser136...

  2. Evidence from intrinsic activity that asymmetry of the human brain is controlled by multiple factors.

    Science.gov (United States)

    Liu, Hesheng; Stufflebeam, Steven M; Sepulcre, Jorge; Hedden, Trey; Buckner, Randy L

    2009-12-01

    Cerebral lateralization is a fundamental property of the human brain and a marker of successful development. Here we provide evidence that multiple mechanisms control asymmetry for distinct brain systems. Using intrinsic activity to measure asymmetry in 300 adults, we mapped the most strongly lateralized brain regions. Both men and women showed strong asymmetries with a significant, but small, group difference. Factor analysis on the asymmetric regions revealed 4 separate factors that each accounted for significant variation across subjects. The factors were associated with brain systems involved in vision, internal thought (the default network), attention, and language. An independent sample of right- and left-handed individuals showed that hand dominance affects brain asymmetry but differentially across the 4 factors supporting their independence. These findings show the feasibility of measuring brain asymmetry using intrinsic activity fluctuations and suggest that multiple genetic or environmental mechanisms control cerebral lateralization.

  3. Identification of intrinsic catalytic activity for electrochemical reduction of water molecules to generate hydrogen

    KAUST Repository

    Shinagawa, Tatsuya

    2015-01-01

    Insufficient hydronium ion activities at near-neutral pH and under unbuffered conditions induce diffusion-limited currents for hydrogen evolution, followed by a reaction with water molecules to generate hydrogen at elevated potentials. The observed constant current behaviors at near neutral pH reflect the intrinsic electrocatalytic reactivity of the metal electrodes for water reduction. This journal is © the Owner Societies.

  4. Evidence from intrinsic activity that asymmetry of the human brain is controlled by multiple factors

    OpenAIRE

    Liu, Hesheng; Stufflebeam, Steven M.; Sepulcre, Jorge; Hedden, Trey; Buckner, Randy L.

    2009-01-01

    Cerebral lateralization is a fundamental property of the human brain and a marker of successful development. Here we provide evidence that multiple mechanisms control asymmetry for distinct brain systems. Using intrinsic activity to measure asymmetry in 300 adults, we mapped the most strongly lateralized brain regions. Both men and women showed strong asymmetries with a significant, but small, group difference. Factor analysis on the asymmetric regions revealed 4 separate factors that each ac...

  5. Effects of scanner acoustic noise on intrinsic brain activity during auditory stimulation.

    Science.gov (United States)

    Yakunina, Natalia; Kang, Eun Kyoung; Kim, Tae Su; Min, Ji-Hoon; Kim, Sam Soo; Nam, Eui-Cheol

    2015-10-01

    Although the effects of scanner background noise (SBN) during functional magnetic resonance imaging (fMRI) have been extensively investigated for the brain regions involved in auditory processing, its impact on other types of intrinsic brain activity has largely been neglected. The present study evaluated the influence of SBN on a number of intrinsic connectivity networks (ICNs) during auditory stimulation by comparing the results obtained using sparse temporal acquisition (STA) with those using continuous acquisition (CA). Fourteen healthy subjects were presented with classical music pieces in a block paradigm during two sessions of STA and CA. A volume-matched CA dataset (CAm) was generated by subsampling the CA dataset to temporally match it with the STA data. Independent component analysis was performed on the concatenated STA-CAm datasets, and voxel data, time courses, power spectra, and functional connectivity were compared. The ICA revealed 19 ICNs; the auditory, default mode, salience, and frontoparietal networks showed greater activity in the STA. The spectral peaks in 17 networks corresponded to the stimulation cycles in the STA, while only five networks displayed this correspondence in the CA. The dorsal default mode and salience networks exhibited stronger correlations with the stimulus waveform in the STA. SBN appeared to influence not only the areas of auditory response but also the majority of other ICNs, including attention and sensory networks. Therefore, SBN should be regarded as a serious nuisance factor during fMRI studies investigating intrinsic brain activity under external stimulation or task loads.

  6. Effects of scanner acoustic noise on intrinsic brain activity during auditory stimulation

    Energy Technology Data Exchange (ETDEWEB)

    Yakunina, Natalia [Kangwon National University, Institute of Medical Science, School of Medicine, Chuncheon (Korea, Republic of); Kangwon National University Hospital, Neuroscience Research Institute, Chuncheon (Korea, Republic of); Kang, Eun Kyoung [Kangwon National University Hospital, Department of Rehabilitation Medicine, Chuncheon (Korea, Republic of); Kim, Tae Su [Kangwon National University Hospital, Department of Otolaryngology, Chuncheon (Korea, Republic of); Kangwon National University, School of Medicine, Department of Otolaryngology, Chuncheon (Korea, Republic of); Min, Ji-Hoon [University of Michigan, Department of Biopsychology, Cognition, and Neuroscience, Ann Arbor, MI (United States); Kim, Sam Soo [Kangwon National University Hospital, Neuroscience Research Institute, Chuncheon (Korea, Republic of); Kangwon National University, School of Medicine, Department of Radiology, Chuncheon (Korea, Republic of); Nam, Eui-Cheol [Kangwon National University Hospital, Neuroscience Research Institute, Chuncheon (Korea, Republic of); Kangwon National University, School of Medicine, Department of Otolaryngology, Chuncheon (Korea, Republic of)

    2015-10-15

    Although the effects of scanner background noise (SBN) during functional magnetic resonance imaging (fMRI) have been extensively investigated for the brain regions involved in auditory processing, its impact on other types of intrinsic brain activity has largely been neglected. The present study evaluated the influence of SBN on a number of intrinsic connectivity networks (ICNs) during auditory stimulation by comparing the results obtained using sparse temporal acquisition (STA) with those using continuous acquisition (CA). Fourteen healthy subjects were presented with classical music pieces in a block paradigm during two sessions of STA and CA. A volume-matched CA dataset (CAm) was generated by subsampling the CA dataset to temporally match it with the STA data. Independent component analysis was performed on the concatenated STA-CAm datasets, and voxel data, time courses, power spectra, and functional connectivity were compared. The ICA revealed 19 ICNs; the auditory, default mode, salience, and frontoparietal networks showed greater activity in the STA. The spectral peaks in 17 networks corresponded to the stimulation cycles in the STA, while only five networks displayed this correspondence in the CA. The dorsal default mode and salience networks exhibited stronger correlations with the stimulus waveform in the STA. SBN appeared to influence not only the areas of auditory response but also the majority of other ICNs, including attention and sensory networks. Therefore, SBN should be regarded as a serious nuisance factor during fMRI studies investigating intrinsic brain activity under external stimulation or task loads. (orig.)

  7. Effects of scanner acoustic noise on intrinsic brain activity during auditory stimulation

    International Nuclear Information System (INIS)

    Yakunina, Natalia; Kang, Eun Kyoung; Kim, Tae Su; Min, Ji-Hoon; Kim, Sam Soo; Nam, Eui-Cheol

    2015-01-01

    Although the effects of scanner background noise (SBN) during functional magnetic resonance imaging (fMRI) have been extensively investigated for the brain regions involved in auditory processing, its impact on other types of intrinsic brain activity has largely been neglected. The present study evaluated the influence of SBN on a number of intrinsic connectivity networks (ICNs) during auditory stimulation by comparing the results obtained using sparse temporal acquisition (STA) with those using continuous acquisition (CA). Fourteen healthy subjects were presented with classical music pieces in a block paradigm during two sessions of STA and CA. A volume-matched CA dataset (CAm) was generated by subsampling the CA dataset to temporally match it with the STA data. Independent component analysis was performed on the concatenated STA-CAm datasets, and voxel data, time courses, power spectra, and functional connectivity were compared. The ICA revealed 19 ICNs; the auditory, default mode, salience, and frontoparietal networks showed greater activity in the STA. The spectral peaks in 17 networks corresponded to the stimulation cycles in the STA, while only five networks displayed this correspondence in the CA. The dorsal default mode and salience networks exhibited stronger correlations with the stimulus waveform in the STA. SBN appeared to influence not only the areas of auditory response but also the majority of other ICNs, including attention and sensory networks. Therefore, SBN should be regarded as a serious nuisance factor during fMRI studies investigating intrinsic brain activity under external stimulation or task loads. (orig.)

  8. Intrinsic and induced isoproturon catabolic activity in dissimilar soils and soils under dissimilar land use

    International Nuclear Information System (INIS)

    Reid, Brian J.; Papanikolaou, Niki D.; Wilcox, Ronah K.

    2005-01-01

    The catabolic activity with respect to the systemic herbicide isoproturon was determined in soil samples by 14 C-radiorespirometry. The first experiment assessed levels of intrinsic catabolic activity in soil samples that represented three dissimilar soil series under arable cultivation. Results showed average extents of isoproturon mineralisation (after 240 h assay time) in the three soil series to be low. A second experiment assessed the impact of addition of isoproturon (0.05 μg kg -1 ) into these soils on the levels of catabolic activity following 28 days of incubation. Increased catabolic activity was observed in all three soils. A third experiment assessed levels of intrinsic catabolic activity in soil samples representing a single soil series managed under either conventional agricultural practice (including the use of isoproturon) or organic farming practice (with no use of isoproturon). Results showed higher (and more consistent) levels of isoproturon mineralisation in the soil samples collected from conventional land use. The final experiment assessed the impact of isoproturon addition on the levels of inducible catabolic activity in these soils. The results showed no significant difference in the case of the conventional farm soil samples while the induction of catabolic activity in the organic farm soil samples was significant. - Dissimilar levels of isoproturon catabolic activity in dissimilar soils and soils under dissimilar land use influence inferred risk

  9. Intrinsic survival advantage of social insect queens depends on reproductive activation.

    Science.gov (United States)

    Rueppell, O; Königseder, F; Heinze, J; Schrempf, A

    2015-12-01

    The central trade-off between reproduction and longevity dominates most species' life history. However, no mortality cost of reproduction is apparent in eusocial species, particularly social insects in the order Hymenoptera: one or a few individuals (typically referred to as queens) in a group specialize on reproduction and are generally longer lived than all other group members (typically referred to as workers), despite having the same genome. However, it is unclear whether this survival advantage is due to social facilitation by the group or an intrinsic, individual property. Furthermore, it is unknown whether the correlation between reproduction and longevity is due to a direct mechanistic link or an indirect consequence of the social role of the reproductives. To begin addressing these questions, we performed a comparison of queen and worker longevity in the ant Cardiocondyla obscurior under social isolation conditions. Survival of single queens and workers was compared under laboratory conditions, monitoring and controlling for brood production. Our results indicate that there is no intrinsic survival advantage of queens relative to workers unless individuals are becoming reproductively active. This interactive effect of caste and reproduction on life expectancy outside of the normal social context suggests that the positive correlation between reproduction and longevity in social insect queens is due to a direct link that can activate intrinsic survival mechanisms to ensure queen longevity. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

  10. Intrinsic Xenobiotic Metabolizing Enzyme Activities in Early Life Stages of Zebrafish (Danio rerio).

    Science.gov (United States)

    Otte, Jens C; Schultz, Bernadette; Fruth, Daniela; Fabian, Eric; van Ravenzwaay, Bennard; Hidding, Björn; Salinas, Edward R

    2017-09-01

    Early life stages of zebrafish (Danio rerio, zf) are gaining attention as an alternative invivo test system for drug discovery, early developmental toxicity screenings and chemical testing in ecotoxicological and toxicological testing strategies. Previous studies have demonstrated transcriptional evidence for xenobiotic metabolizing enzymes (XME) during early zf development. However, elaborate experiments on XME activities during development are incomplete. In this work, the intrinsic activities of representative phase I and II XME were monitored by transformation of putative zf model substrates analyzed using photometry and high pressure liquid chromatography techniques. Six different defined stages of zf development (between 2.5 h postfertilization (hpf) to 120 hpf) were investigated by preparing a subcellular fraction from whole organism homogenates. We demonstrated that zf embryos as early as 2.5 hpf possess intrinsic metabolic activities for esterase, Aldh, Gst, and Cyp1a above the methodological detection limit. The activities of the enzymes Cyp3a and Nat were measurable during later stages in development. Activities represent dynamic patterns during development. The role of XME activities revealed in this work is relevant for the assessing toxicity in this test system and therefore contributes to a valuable characterization of zf embryos as an alternative testing organism in toxicology. © The Author 2017. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  11. Predictive features of persistent activity emergence in regular spiking and intrinsic bursting model neurons.

    Directory of Open Access Journals (Sweden)

    Kyriaki Sidiropoulou

    Full Text Available Proper functioning of working memory involves the expression of stimulus-selective persistent activity in pyramidal neurons of the prefrontal cortex (PFC, which refers to neural activity that persists for seconds beyond the end of the stimulus. The mechanisms which PFC pyramidal neurons use to discriminate between preferred vs. neutral inputs at the cellular level are largely unknown. Moreover, the presence of pyramidal cell subtypes with different firing patterns, such as regular spiking and intrinsic bursting, raises the question as to what their distinct role might be in persistent firing in the PFC. Here, we use a compartmental modeling approach to search for discriminatory features in the properties of incoming stimuli to a PFC pyramidal neuron and/or its response that signal which of these stimuli will result in persistent activity emergence. Furthermore, we use our modeling approach to study cell-type specific differences in persistent activity properties, via implementing a regular spiking (RS and an intrinsic bursting (IB model neuron. We identify synaptic location within the basal dendrites as a feature of stimulus selectivity. Specifically, persistent activity-inducing stimuli consist of activated synapses that are located more distally from the soma compared to non-inducing stimuli, in both model cells. In addition, the action potential (AP latency and the first few inter-spike-intervals of the neuronal response can be used to reliably detect inducing vs. non-inducing inputs, suggesting a potential mechanism by which downstream neurons can rapidly decode the upcoming emergence of persistent activity. While the two model neurons did not differ in the coding features of persistent activity emergence, the properties of persistent activity, such as the firing pattern and the duration of temporally-restricted persistent activity were distinct. Collectively, our results pinpoint to specific features of the neuronal response to a given

  12. Glucocorticoid receptor (GR) β has intrinsic, GRα-independent transcriptional activity

    International Nuclear Information System (INIS)

    Kino, Tomoshige; Manoli, Irini; Kelkar, Sujata; Wang, Yonghong; Su, Yan A.; Chrousos, George P.

    2009-01-01

    The human glucocorticoid receptor (GR) gene produces C-terminal GRβ and GRα isoforms through alternative use of specific exons 9β and α, respectively. We explored the transcriptional activity of GRβ on endogenous genes by developing HeLa cells stably expressing EGFP-GRβ or EGFP. Microarray analyses revealed that GRβ had intrinsic gene-specific transcriptional activity, regulating mRNA expression of a large number of genes negatively or positively. Majority of GRβ-responsive genes was distinct from those modulated by GRα, while GRβ and GRα mutually modulated each other's transcriptional activity in a subpopulation of genes. We did not observe in HCT116 cells nuclear translocation of GRβ and activation of this receptor by RU 486, a synthetic steroid previously reported to bind GRβ and to induce nuclear translocation. Our results indicate that GRβ has intrinsic, GRα-independent, gene-specific transcriptional activity, in addition to its previously reported dominant negative effect on GRα-induced transactivation of GRE-driven promoters.

  13. Glucocorticoid receptor (GR) {beta} has intrinsic, GR{alpha}-independent transcriptional activity

    Energy Technology Data Exchange (ETDEWEB)

    Kino, Tomoshige, E-mail: kinot@mail.nih.gov [Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bldg. 10, CRC, Rm. 1-3140, 10 Center Drive MSC 1109, Bethesda, MD 20892-1109 (United States); Manoli, Irini [Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine (United States); First Department of Pediatrics, Athens University Medical School (United States); Kelkar, Sujata [Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bldg. 10, CRC, Rm. 1-3140, 10 Center Drive MSC 1109, Bethesda, MD 20892-1109 (United States); Wang, Yonghong [Clinical Molecular Profiling Core, Advanced Technology Center, National Cancer Institute (United States); Su, Yan A. [Department of Biochemistry and Molecular Biology, The Catherine Birch McCormick Genomics Center, George Washington University School of Medicine and Health Sciences (United States); Chrousos, George P. [First Department of Pediatrics, Athens University Medical School (United States)

    2009-04-17

    The human glucocorticoid receptor (GR) gene produces C-terminal GR{beta} and GR{alpha} isoforms through alternative use of specific exons 9{beta} and {alpha}, respectively. We explored the transcriptional activity of GR{beta} on endogenous genes by developing HeLa cells stably expressing EGFP-GR{beta} or EGFP. Microarray analyses revealed that GR{beta} had intrinsic gene-specific transcriptional activity, regulating mRNA expression of a large number of genes negatively or positively. Majority of GR{beta}-responsive genes was distinct from those modulated by GR{alpha}, while GR{beta} and GR{alpha} mutually modulated each other's transcriptional activity in a subpopulation of genes. We did not observe in HCT116 cells nuclear translocation of GR{beta} and activation of this receptor by RU 486, a synthetic steroid previously reported to bind GR{beta} and to induce nuclear translocation. Our results indicate that GR{beta} has intrinsic, GR{alpha}-independent, gene-specific transcriptional activity, in addition to its previously reported dominant negative effect on GR{alpha}-induced transactivation of GRE-driven promoters.

  14. Does Aerobic Exercise Influence Intrinsic Brain Activity? An Aerobic Exercise Intervention among Healthy Old Adults

    Directory of Open Access Journals (Sweden)

    Pär Flodin

    2017-08-01

    Full Text Available Previous studies have indicated that aerobic exercise could reduce age related decline in cognition and brain functioning. Here we investigated the effects of aerobic exercise on intrinsic brain activity. Sixty sedentary healthy males and females (64–78 years were randomized into either an aerobic exercise group or an active control group. Both groups recieved supervised training, 3 days a week for 6 months. Multimodal brain imaging data was acquired before and after the intervention, including 10 min of resting state brain functional magnetic resonance imaging (rs-fMRI and arterial spin labeling (ASL. Additionally, a comprehensive battery of cognitive tasks assessing, e.g., executive function and episodic memory was administered. Both the aerobic and the control group improved in aerobic capacity (VO2-peak over 6 months, but a significant group by time interaction confirmed that the aerobic group improved more. Contrary to our hypothesis, we did not observe any significant group by time interactions with regard to any measure of intrinsic activity. To further probe putative relationships between fitness and brain activity, we performed post hoc analyses disregarding group belongings. At baseline, VO2-peak was negativly related to BOLD-signal fluctuations (BOLDSTD in mid temporal areas. Over 6 months, improvements in aerobic capacity were associated with decreased connectivity between left hippocampus and contralateral precentral gyrus, and positively to connectivity between right mid-temporal areas and frontal and parietal regions. Independent component analysis identified a VO2-related increase in coupling between the default mode network and left orbitofrontal cortex, as well as a decreased connectivity between the sensorimotor network and thalamus. Extensive exploratory data analyses of global efficiency, connectome wide multivariate pattern analysis (connectome-MVPA, as well as ASL, did not reveal any relationships between aerobic fitness

  15. Aberrant Intrinsic Activity and Connectivity in Cognitively Normal Parkinson’s Disease

    Directory of Open Access Journals (Sweden)

    Deborah L. Harrington

    2017-06-01

    Full Text Available Disturbances in intrinsic activity during resting-state functional MRI (rsfMRI are common in Parkinson’s disease (PD, but have largely been studied in a priori defined subnetworks. The cognitive significance of abnormal intrinsic activity is also poorly understood, as are abnormalities that precede the onset of mild cognitive impairment. To address these limitations, we leveraged three different analytic approaches to identify disturbances in rsfMRI metrics in 31 cognitively normal PD patients (PD-CN and 30 healthy adults. Subjects were screened for mild cognitive impairment using the Movement Disorders Society Task Force Level II criteria. Whole-brain data-driven analytic approaches first analyzed the amplitude of low-frequency intrinsic fluctuations (ALFF and regional homogeneity (ReHo, a measure of local connectivity amongst functionally similar regions. We then examined if regional disturbances in these metrics altered functional connectivity with other brain regions. We also investigated if abnormal rsfMRI metrics in PD-CN were related to brain atrophy and executive, visual organization, and episodic memory functioning. The results revealed abnormally increased and decreased ALFF and ReHo in PD-CN patients within the default mode network (posterior cingulate, inferior parietal cortex, parahippocampus, entorhinal cortex, sensorimotor cortex (primary motor, pre/post-central gyrus, basal ganglia (putamen, caudate, and posterior cerebellar lobule VII, which mediates cognition. For default mode network regions, we also observed a compound profile of altered ALFF and ReHo. Most regional disturbances in ALFF and ReHo were associated with strengthened long-range interactions in PD-CN, notably with regions in different networks. Stronger long-range functional connectivity in PD-CN was also partly expanded to connections that were outside the networks of the control group. Abnormally increased activity and functional connectivity appeared to have a

  16. Perceptions of the activity, the social climate, and the self during group exercise classes regulate intrinsic satisfaction.

    Science.gov (United States)

    Maher, Jaclyn P; Gottschall, Jinger S; Conroy, David E

    2015-01-01

    Engaging in regular physical activity is a challenging task for many adults. Intrinsic satisfaction with exercise classes is thought to promote adherence to physical activity. This study examined the characteristics of exercise classes that impact within-person changes in intrinsic satisfaction over the course of an extended group exercise program. A 30-week physical activity trial was conducted with assessments at the end of each class. Community-living adults (n = 29) were instructed to complete at least six group exercise classes each week and, following each exercise class, complete a questionnaire asking about the characteristics of the class and the participant's evaluation of the class. Intrinsic satisfaction was high, on average, but varied as much within-person from class-to-class as it did between exercisers. Participants reported the greatest intrinsic satisfaction when classes placed greater emphasis on exercisers' involvement with the group task, feelings of competence, and encouragement from the instructor. For the most part, exercise classes that were more intense than usual were perceived by exercisers as less intrinsically satisfying. Some overall characteristics of the exercise classes were also associated with intrinsic satisfaction. The social and motivational characteristics of group exercise classes contribute to exercisers' intrinsic satisfaction with classes and attention to those dynamics, as well as the intensity of the exercise, may improve adherence for exercise regimens.

  17. Correlation between Traits of Emotion-Based Impulsivity and Intrinsic Default-Mode Network Activity

    Directory of Open Access Journals (Sweden)

    Jizheng Zhao

    2017-01-01

    Full Text Available Negative urgency (NU and positive urgency (PU are implicated in several high-risk behaviors, such as eating disorders, substance use disorders, and nonsuicidal self-injury behavior. The current study aimed to explore the possible link between trait of urgency and brain activity at rest. We assessed the amplitude of low-frequency fluctuations (ALFF of the resting-state functional magnetic resonance imaging (fMRI signal in 85 healthy volunteers. Trait urgency measures were related to ALFF in the lateral orbitofrontal cortex, dorsolateral prefrontal cortex, ventral and dorsal medial frontal cortex, anterior cingulate, and posterior cingulate cortex/precuneus. In addition, trait urgency measures showed significant correlations with the functional connectivity of the posterior cingulate cortex/precuneus seed with the thalamus and midbrain region. These findings suggest an association between intrinsic brain activity and impulsive behaviors in healthy humans.

  18. The Role of Intrinsic Pathway in Apoptosis Activation and Progression in Peyronie’s Disease

    Directory of Open Access Journals (Sweden)

    Carla Loreto

    2014-01-01

    Full Text Available Peyronie’s disease (PD is characterized with formation of fibrous plaques which result in penile deformity, pain, and erectile dysfunction. The aim of this study was to investigate the activation of the intrinsic apoptotic pathway in plaques from PD patients. Tunica albuginea from either PD or control patients was assessed for the expression of bax, bcl-2 and caspases 9 and 3 using immunohistochemistry and by measurement of apoptotic cells using TUNEL assay. Bax overexpression was observed in metaplastic bone tissue, in fibroblasts, and in myofibroblast of plaques from PD patients. Little or no bcl-2 immunostaining was detected in samples from either patients or controls. Caspase 3 immunostaining was very strong in fibrous tissue, in metaplasic bone osteocytes, and in primary ossification center osteoblasts. Moderate caspase 9 immunostaining was seen in fibrous cells plaques and in osteocytes and osteoblasts of primary ossification centers from PD patients. Control samples were negative for caspase 9 immunostaining. In PD patients the TUNEL immunoassay showed intense immunostaining of fibroblasts and myofibroblasts, the absence of apoptotic cells in metaplasic bone tissue and on the border between fibrous and metaplastic bone tissue. Apoptosis occurs in stabilized PD plaques and is partly induced by the intrinsic pathway.

  19. Intrinsic Characteristics of Neighboring DNA Modulate Transposable Element Activity in Drosophila melanogaster

    Science.gov (United States)

    Esnault, Caroline; Palavesam, Azhahianambi; Pilitt, Kristina; O'Brochta, David A.

    2011-01-01

    Identifying factors influencing transposable element activity is essential for understanding how these elements impact genomes and their evolution as well as for fully exploiting them as functional genomics tools and gene-therapy vectors. Using a genetics-based approach, the influence of genomic position on piggyBac mobility in Drosophila melanogaster was assessed while controlling for element structure, genetic background, and transposase concentration. The mobility of piggyBac elements varied over more than two orders of magnitude solely as a result of their locations within the genome. The influence of genomic position on element activities was independent of factors resulting in position-dependent transgene expression (“position effects”). Elements could be relocated to new genomic locations without altering their activity if ≥500 bp of genomic DNA originally flanking the element was also relocated. Local intrinsic factors within the neighboring DNA that determined the activity of piggyBac elements were portable not only within the genome but also when elements were moved to plasmids. The predicted bendability of the first 50 bp flanking the 5′ and 3′ termini of piggyBac elements could account for 60% of the variance in position-dependent activity observed among elements. These results are significant because positional influences on transposable element activities will impact patterns of accumulation of elements within genomes. Manipulating and controlling the local sequence context of piggyBac elements could be a powerful, novel way of optimizing gene vector activity. PMID:20944016

  20. Intrinsic Levanase Activity of Bacillus subtilis 168 Levansucrase (SacB.

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    Luz Méndez-Lorenzo

    Full Text Available Levansucrase catalyzes the synthesis of fructose polymers through the transfer of fructosyl units from sucrose to a growing fructan chain. Levanase activity of Bacillus subtilis levansucrase has been described since the very first publications dealing with the mechanism of levan synthesis. However, there is a lack of qualitative and quantitative evidence regarding the importance of the intrinsic levan hydrolysis of B. subtilis levansucrase and its role in the levan synthesis process. Particularly, little attention has been paid to the long-term hydrolysis products, including its participation in the final levan molecules distribution. Here, we explored the hydrolytic and transferase activity of the B. subtilis levansucrase (SacB when levans produced by the same enzyme are used as substrate. We found that levan is hydrolyzed through a first order exo-type mechanism, which is limited to a conversion extent of around 30% when all polymer molecules reach a structure no longer suitable to SacB hydrolysis. To characterize the reaction, Isothermal Titration Calorimetry (ITC was employed and the evolution of the hydrolysis products profile followed by HPLC, GPC and HPAEC-PAD. The ITC measurements revealed a second step, taking place at the end of the reaction, most probably resulting from disproportionation of accumulated fructo-oligosaccharides. As levanase, levansucrase may use levan as substrate and, through a fructosyl-enzyme complex, behave as a hydrolytic enzyme or as a transferase, as demonstrated when glucose and fructose are added as acceptors. These reactions result in a wide variety of oligosaccharides that are also suitable acceptors for fructo-oligosaccharide synthesis. Moreover, we demonstrate that SacB in the presence of levan and glucose, through blastose and sucrose synthesis, results in the same fructooligosaccharides profile as that observed in sucrose reactions. We conclude that SacB has an intrinsic levanase activity that

  1. Intrinsic Activity of Inulinase from Kluyveromyces marxianus ATCC 16045 and Carbon and Nitrogen Balances

    Directory of Open Access Journals (Sweden)

    Bernardo Onagar Yépez Silva-Santisteban

    2006-01-01

    Full Text Available Kluyveromyces marxianus ATCC 16045 was cultivated in a batch on minimal medium to overproduce inulinase. The fermented broth was purified by fast protein liquid chromatography and ultrafiltration, and a pure enzyme fraction was obtained. SDS-PAGE electrophoresis allowed calculating molecular mass of 59 kDa, while nitrogen determination by the micro-Kjeldahl method allowed evaluating intrinsic inulinase activity of 879 IU/mg. These results were then used to perform material balances of the fermentation process, which suggested that no more than 0.1 % either of carbon or nitrogen initially present in the medium were incorporated in the extracellular inulinase released under different cultivation conditions. The information obtained in this study can be used for future proposal of metabolic models describing inulinase overproduction by this yeast.

  2. A Subtype of Inhibitory Interneuron with Intrinsic Persistent Activity in Human and Monkey Neocortex

    Directory of Open Access Journals (Sweden)

    Bo Wang

    2015-03-01

    Full Text Available A critical step in understanding the neural basis of human cognitive functions is to identify neuronal types in the neocortex. In this study, we performed whole-cell recording from human cortical slices and found a distinct subpopulation of neurons with intrinsic persistent activity that could be triggered by single action potentials (APs but terminated by bursts of APs. This persistent activity was associated with a depolarizing plateau potential induced by the activation of a persistent Na+ current. Single-cell RT-PCR revealed that these neurons were inhibitory interneurons. This type of neuron was found in different cortical regions, including temporal, frontal, occipital, and parietal cortices in human and also in frontal and temporal lobes of nonhuman primate but not in rat cortical tissues, suggesting that it could be unique to primates. The characteristic persistent activity in these inhibitory interneurons may contribute to the regulation of pyramidal cell activity and participate in cortical processing.

  3. Discovery of Cryoprotective Activity in Human Genome-Derived Intrinsically Disordered Proteins

    Directory of Open Access Journals (Sweden)

    Naoki Matsuo

    2018-01-01

    Full Text Available Intrinsically disordered proteins (IDPs are an emerging phenomenon. They may have a high degree of flexibility in their polypeptide chains, which lack a stable 3D structure. Although several biological functions of IDPs have been proposed, their general function is not known. The only finding related to their function is the genetically conserved YSK2 motif present in plant dehydrins. These proteins were shown to be IDPs with the YSK2 motif serving as a core region for the dehydrins’ cryoprotective activity. Here we examined the cryoprotective activity of randomly selected IDPs toward the model enzyme lactate dehydrogenase (LDH. All five IDPs that were examined were in the range of 35–45 amino acid residues in length and were equally potent at a concentration of 50 μg/mL, whereas folded proteins, the PSD-95/Dlg/ZO-1 (PDZ domain, and lysozymes had no potency. We further examined their cryoprotective activity toward glutathione S-transferase as an example of the other enzyme, and toward enhanced green fluorescent protein as a non-enzyme protein example. We further examined the lyophilization protective activity of the peptides toward LDH, which revealed that some IDPs showed a higher activity than that of bovine serum albumin (BSA. Based on these observations, we propose that cryoprotection is a general feature of IDPs. Our findings may become a clue to various industrial applications of IDPs in the future.

  4. Higher frequency network activity flow predicts lower frequency node activity in intrinsic low-frequency BOLD fluctuations.

    Science.gov (United States)

    Bajaj, Sahil; Adhikari, Bhim Mani; Dhamala, Mukesh

    2013-01-01

    The brain remains electrically and metabolically active during resting conditions. The low-frequency oscillations (LFO) of the blood oxygen level-dependent (BOLD) signal of functional magnetic resonance imaging (fMRI) coherent across distributed brain regions are known to exhibit features of this activity. However, these intrinsic oscillations may undergo dynamic changes in time scales of seconds to minutes during resting conditions. Here, using wavelet-transform based time-frequency analysis techniques, we investigated the dynamic nature of default-mode networks from intrinsic BOLD signals recorded from participants maintaining visual fixation during resting conditions. We focused on the default-mode network consisting of the posterior cingulate cortex (PCC), the medial prefrontal cortex (mPFC), left middle temporal cortex (LMTC) and left angular gyrus (LAG). The analysis of the spectral power and causal flow patterns revealed that the intrinsic LFO undergo significant dynamic changes over time. Dividing the frequency interval 0 to 0.25 Hz of LFO into four intervals slow-5 (0.01-0.027 Hz), slow-4 (0.027-0.073 Hz), slow-3 (0.073-0.198 Hz) and slow-2 (0.198-0.25 Hz), we further observed significant positive linear relationships of slow-4 in-out flow of network activity with slow-5 node activity, and slow-3 in-out flow of network activity with slow-4 node activity. The network activity associated with respiratory related frequency (slow-2) was found to have no relationship with the node activity in any of the frequency intervals. We found that the net causal flow towards a node in slow-3 band was correlated with the number of fibers, obtained from diffusion tensor imaging (DTI) data, from the other nodes connecting to that node. These findings imply that so-called resting state is not 'entirely' at rest, the higher frequency network activity flow can predict the lower frequency node activity, and the network activity flow can reflect underlying structural

  5. Intrinsic Activity of MnOx-CeO2 Catalysts in Ethanol Oxidation

    Directory of Open Access Journals (Sweden)

    Dimitrios Delimaris

    2017-11-01

    Full Text Available MnOx-CeO2 mixed oxides are considered efficient oxidation catalysts superior to the corresponding single oxides. Although these oxides have been the subject of numerous studies, their fundamental performance indicators, such as turnover frequency (TOF or specific activity, are scarcely reported. The purpose of the present work is to investigate the effect of catalyst composition on the concentration of active sites and intrinsic activity in ethanol oxidation by the employment of temperature-programmed desorption and oxidation of isotopically-labelled ethanol, 12CH313CH2OH. The transformation pathways of preadsorbed ethanol in the absence of gaseous oxygen refer to dehydrogenation to acetaldehyde followed by its dissociation combined with oxidation by lattice oxygen. In the presence of gaseous oxygen, lattice oxygen is rapidly restored and the main products are acetaldehyde, CO2, and water. CO2 forms less easily on mixed oxides than on pure MnOx. The TOF of ethanol oxidation has been calculated assuming that the amount of adsorbed ethanol and CO2 produced during temperature-programmed oxidation (TPO is a reliable indicator of the concentration of the active sites.

  6. Surface electromyography can quantify temporal and spatial patterns of activation of intrinsic human foot muscles.

    Science.gov (United States)

    Ferrari, E; Cooper, G; Reeves, N D; Hodson-Tole, E F

    2018-04-01

    Intrinsic foot muscles (IFM) are a crucial component within the human foot. Investigating their functioning can help understand healthy and pathological behaviour of foot and ankle, fundamental for everyday activities. Recording muscle activation from IFM has been attempted with invasive techniques, mainly investigating single muscles. Here we present a novel methodology, to investigate the feasibility of recording physiological surface EMG (sEMG) non-invasively and quantify patterns of activation across the whole plantar region of the foot. sEMG were recorded with a 13 × 5 array from the sole of the foot (n = 25) during two-foot stance, two-foot tiptoe and anterior/posterior sways. Physiological features of sEMG were analysed. During anterior/posterior epochs within the sway task, sEMG patterns were analysed in terms of signal amplitude (intensity) and structure (Sample Entropy) distribution, by evaluating the centre of gravity (CoG) of each topographical map. Results suggest signals are physiological and not affected by loading. Both amplitude and sample entropy CoG coordinates were grouped in one region and overlapped, suggesting that the region with highest amplitude corresponds with the most predictable signal. Therefore, both spatial and temporal features of IFM activation may be recorded non-invasively, providing opportunity for more detailed investigation of IFM function in healthy and patient populations. Copyright © 2018. Published by Elsevier Ltd.

  7. Thermodynamic activity-based intrinsic enzyme kinetic sheds light on enzyme-solvent interactions.

    Science.gov (United States)

    Grosch, Jan-Hendrik; Wagner, David; Nistelkas, Vasilios; Spieß, Antje C

    2017-01-01

    The reaction medium has major impact on biocatalytic reaction systems and on their economic significance. To allow for tailored medium engineering, thermodynamic phenomena, intrinsic enzyme kinetics, and enzyme-solvent interactions have to be discriminated. To this end, enzyme reaction kinetic modeling was coupled with thermodynamic calculations based on investigations of the alcohol dehydrogenase from Lactobacillus brevis (LbADH) in monophasic water/methyl tert-butyl ether (MTBE) mixtures as a model solvent. Substrate concentrations and substrate thermodynamic activities were varied separately to identify the individual thermodynamic and kinetic effects on the enzyme activity. Microkinetic parameters based on concentration and thermodynamic activity were derived to successfully identify a positive effect of MTBE on the availability of the substrate to the enzyme, but a negative effect on the enzyme performance. In conclusion, thermodynamic activity-based kinetic modeling might be a suitable tool to initially curtail the type of enzyme-solvent interactions and thus, a powerful first step to potentially understand the phenomena that occur in nonconventional media in more detail. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:96-103, 2017. © 2016 American Institute of Chemical Engineers.

  8. Intrinsic muscle strength and voluntary activation of both lower limbs and functional performance after stroke.

    Science.gov (United States)

    Horstman, Astrid M; Beltman, Marijke J; Gerrits, Karin H; Koppe, Peter; Janssen, Thomas W; Elich, Peter; de Haan, Arnold

    2008-07-01

    The objective of this study was to assess the nature of muscle weakness in both legs after stroke compared with able-bodied control individuals and to examine whether there is a relationship between the degree of muscle weakness and coactivation of knee extensors and flexors as well as voluntary activation capacity of knee extensors of both paretic and non-paretic legs and indices of functional performance. Maximal voluntary isometric torques of knee extensors (MVCe) and flexors (MVCf) were determined in 14 patients (bilaterally) and 12 able-bodied controls. Simultaneous measurements were made of torque and surface EMG from agonist and antagonist muscles. Coactivation was calculated. Supramaximal triplets were evoked with electrical stimulation to estimate maximal torque capacity and degree of voluntary activation of knee extensors. MVCs, activation and coactivation parameters were correlated to scores of seven functional performance tests. MVCe, MVCf and voluntary activation were lower in paretic lower limb (PL) compared with both non-paretic lower limb (NL) and control. Besides, all these parameters of NL were also lower than control. Electrically evoked torque capacity of knee extensors of PL was about 60% of both NL and control, which were not significantly different from each other. Strong significant correlations between strength, as well as voluntary activation, and functional performance were found. Coactivation did not correlate well with functional performance. Thus, whereas for NL activation failure can explain weakness, for PL both activation failure and reduced intrinsic torque capacity are responsible for the severe weakness. Activation capacity and muscle strength correlated strongly to functional performance, while coactivation did not.

  9. Being Eager to Prove Oneself: U-Shaped Relationship between Competence Frustration and Intrinsic Motivation in Another Activity.

    Science.gov (United States)

    Fang, Hui; He, Bin; Fu, Huijian; Meng, Liang

    2017-01-01

    Competence frustration has been consistently found to undermine one's intrinsic motivation in the same activity. However, the relationship between competence frustration in a preceding activity and one's intrinsic motivation in a subsequent one remains unclear. In order to explore this relationship, self-reported data were collected from 617 undergraduate students of a large comprehensive university in southern China, who took varied courses immediately before taking a less-demanding one. Results suggested a U-shaped relationship between students' competence frustration in a preceding course and intrinsic motivation in a subsequent one. To be specific, for students whose competence frustration reached the inflection point, a restoration process would be activated if the current course would help restore their competence. Importantly, these students' competence frustration in a preceding course was found to positively predict their intrinsic motivation level in a subsequent course. As far as we are concerned, this is the first study to reveal a potential positive effect of need frustration outside of its primary thwarting context, which complements and extends existing literatures on the dynamics between need frustration and intrinsic motivation.

  10. Being Eager to Prove Oneself: U-Shaped Relationship between Competence Frustration and Intrinsic Motivation in Another Activity

    Science.gov (United States)

    Fang, Hui; He, Bin; Fu, Huijian; Meng, Liang

    2017-01-01

    Competence frustration has been consistently found to undermine one’s intrinsic motivation in the same activity. However, the relationship between competence frustration in a preceding activity and one’s intrinsic motivation in a subsequent one remains unclear. In order to explore this relationship, self-reported data were collected from 617 undergraduate students of a large comprehensive university in southern China, who took varied courses immediately before taking a less-demanding one. Results suggested a U-shaped relationship between students’ competence frustration in a preceding course and intrinsic motivation in a subsequent one. To be specific, for students whose competence frustration reached the inflection point, a restoration process would be activated if the current course would help restore their competence. Importantly, these students’ competence frustration in a preceding course was found to positively predict their intrinsic motivation level in a subsequent course. As far as we are concerned, this is the first study to reveal a potential positive effect of need frustration outside of its primary thwarting context, which complements and extends existing literatures on the dynamics between need frustration and intrinsic motivation. PMID:29312025

  11. Crystal structures of an intrinsically active cholera toxin mutant yield insight into the toxin activation mechanism.

    Science.gov (United States)

    O'Neal, Claire J; Amaya, Edward I; Jobling, Michael G; Holmes, Randall K; Hol, Wim G J

    2004-04-06

    Cholera toxin (CT) is a heterohexameric bacterial protein toxin belonging to a larger family of A/B ADP-ribosylating toxins. Each of these toxins undergoes limited proteolysis and/or disulfide bond reduction to form the enzymatically active toxic fragment. Nicking and reduction render both CT and the closely related heat-labile enterotoxin from Escherichia coli (LT) unstable in solution, thus far preventing a full structural understanding of the conformational changes resulting from toxin activation. We present the first structural glimpse of an active CT in structures from three crystal forms of a single-site A-subunit CT variant, Y30S, which requires no activational modifications for full activity. We also redetermined the structure of the wild-type, proenzyme CT from two crystal forms, both of which exhibit (i) better geometry and (ii) a different A2 "tail" conformation than the previously determined structure [Zhang et al. (1995) J. Mol. Biol. 251, 563-573]. Differences between wild-type CT and active CTY30S are observed in A-subunit loop regions that had been previously implicated in activation by analysis of the structure of an LT A-subunit R7K variant [van den Akker et al. (1995) Biochemistry 34, 10996-11004]. The 25-36 activation loop is disordered in CTY30S, while the 47-56 active site loop displays varying degrees of order in the three CTY30S structures, suggesting that disorder in the activation loop predisposes the active site loop to a greater degree of flexibility than that found in unactivated wild-type CT. On the basis of these six new views of the CT holotoxin, we propose a model for how the activational modifications experienced by wild-type CT are communicated to the active site.

  12. Toward An Unstructured Mesh Database

    Science.gov (United States)

    Rezaei Mahdiraji, Alireza; Baumann, Peter Peter

    2014-05-01

    Unstructured meshes are used in several application domains such as earth sciences (e.g., seismology), medicine, oceanography, cli- mate modeling, GIS as approximate representations of physical objects. Meshes subdivide a domain into smaller geometric elements (called cells) which are glued together by incidence relationships. The subdivision of a domain allows computational manipulation of complicated physical structures. For instance, seismologists model earthquakes using elastic wave propagation solvers on hexahedral meshes. The hexahedral con- tains several hundred millions of grid points and millions of hexahedral cells. Each vertex node in the hexahedrals stores a multitude of data fields. To run simulation on such meshes, one needs to iterate over all the cells, iterate over incident cells to a given cell, retrieve coordinates of cells, assign data values to cells, etc. Although meshes are used in many application domains, to the best of our knowledge there is no database vendor that support unstructured mesh features. Currently, the main tool for querying and manipulating unstructured meshes are mesh libraries, e.g., CGAL and GRAL. Mesh li- braries are dedicated libraries which includes mesh algorithms and can be run on mesh representations. The libraries do not scale with dataset size, do not have declarative query language, and need deep C++ knowledge for query implementations. Furthermore, due to high coupling between the implementations and input file structure, the implementations are less reusable and costly to maintain. A dedicated mesh database offers the following advantages: 1) declarative querying, 2) ease of maintenance, 3) hiding mesh storage structure from applications, and 4) transparent query optimization. To design a mesh database, the first challenge is to define a suitable generic data model for unstructured meshes. We proposed ImG-Complexes data model as a generic topological mesh data model which extends incidence graph model to multi

  13. The effect of additional activation of the plantar intrinsic foot muscles on foot dynamics during gait.

    Science.gov (United States)

    Okamura, Kazunori; Kanai, Shusaku; Hasegawa, Masaki; Otsuka, Akira; Oki, Sadaaki

    2017-08-18

    The plantar intrinsic foot muscles (PIFMs) contribute to support the medial longitudinal arch. But the functional role of the PIFMs during dynamic activities is not clear. The purpose of this study was to examine the change in the foot dynamics during gait accompanied with the change in the PIFMs activity to determine the functional role of the PIFMs during gait. Twenty healthy male subjects were randomly assigned to the electrical stimulation group (ESG) or control group (CG). In the ESG, the electrical stimulation to the PIFMs was provided from mid-stance to pre-swing using surface electrodes to simulate reinforcement of the PIFMs. The foot dynamics during the stance phase of gait was measured using a 3D motion analysis, and the amount of change from baseline (electrical stimulation was not provided) was compared between groups using an independent sample t-test. In the ESG, the timing for the navicular height to reach the minimum value was significantly later, and the vertical ground reaction force (2nd peak) significantly decreased more. There were no group differences in the amount of change from baseline on gait velocity, stance phase duration, minimum navicular height and ground reaction force in other directions. Results from this study showed that the functions of the PIFMs most likely include shock absorption and facilitation of efficient foot ground force transmission during the stance phase of gait. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Altered intrinsic brain activity after chemotherapy in patients with gastric cancer: A preliminary study

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyun Gi [Ajou University Medical Center, Department of Radiology, Ajou University School of Medicine, Suwon (Korea, Republic of); Shin, Na-Young [Ewha Womans University School of Medicine, Department of Radiology, Seoul (Korea, Republic of); Yonsei University College of Medicine, Department of Radiology, Research Institute of Radiological Science, Seoul (Korea, Republic of); Bak, Yunjin; Lim, Soo Mee [Ewha Womans University School of Medicine, Department of Radiology, Seoul (Korea, Republic of); Kim, Kyung Ran; Jung, Young-Chul [Yonsei University College of Medicine, Department of Psychiatry, Seoul (Korea, Republic of); Han, Kyunghwa; Lee, Seung-Koo [Yonsei University College of Medicine, Department of Radiology, Research Institute of Radiological Science, Seoul (Korea, Republic of)

    2017-07-15

    To characterize the pattern of altered intrinsic brain activity in gastric cancer patients after chemotherapy (CTx). Patients before and after CTx (n = 14) and control subjects (n = 11) underwent resting-state functional MRI (rsfMRI) at baseline and 3 months after CTx. Regional homogeneity (ReHo), amplitude of low-frequency fluctuation (ALFF), and fractional ALFF (fALFF) were calculated and compared between the groups using the two-sample t test. Correlation analysis was also performed between rsfMRI values (i.e., ReHo, ALFF, and fALFF) and neuropsychological test results. Patients showed poor performance in verbal memory and executive function and decreased rsfMRI values in the frontal areas even before CTx and showed decreased attention/working memory and executive function after CTx compared to the control subjects. In direct comparison of values before and after CTx, there were no significant differences in neuropsychological test scores, but decreased rsfMRI values were observed at the frontal lobes and right cerebellar region. Among rsfMRI values, lower ALFF in the left inferior frontal gyrus was significantly associated with poor performance of the executive function test. We observed decreased attention/working memory and executive function that corresponded to the decline of frontal region activation in gastric cancer patients who underwent CTx. (orig.)

  15. Activation of intrinsic apoptotic signaling pathway in cancer cells by Cymbopogon citratus polysaccharide fractions.

    Science.gov (United States)

    Thangam, Ramar; Sathuvan, Malairaj; Poongodi, Arasu; Suresh, Veeraperumal; Pazhanichamy, Kalailingam; Sivasubramanian, Srinivasan; Kanipandian, Nagarajan; Ganesan, Nalini; Rengasamy, Ramasamy; Thirumurugan, Ramasamy; Kannan, Soundarapandian

    2014-07-17

    Essential oils of Cymbopogon citratus were already reported to have wide ranging medical and industrial applications. However, information on polysaccharides from the plant and their anticancer activities are limited. In the present study, polysaccharides from C. citratus were extracted and fractionated by anion exchange and gel filtration chromatography. Two different polysaccharide fractions such as F1 and F2 were obtained, and these fractions were found to have distinct acidic polysaccharides as characterized by their molecular weight and sugar content. NMR spectral analysis revealed the presence of (1→4) linked b-d-Xylofuranose moiety in these polysaccharides. Using these polysaccharide fractions F1 and F2, anti-inflammatory and anticancer activities were evaluated against cancer cells in vitro and the mechanism of action of the polysaccharides in inducing apoptosis in cancer cells via intrinsic pathway was also proposed. Two different reproductive cancer cells such as Siha and LNCap were employed for in vitro studies on cytotoxicity, induction of apoptosis and apoptotic DNA fragmentation, changes in mitochondrial membrane potential, and profiles of gene and protein expression in response to treatment of cells by the polysaccharide fractions. These polysaccharide fractions exhibited potential cytotoxic and apoptotic effects on carcinoma cells, and they induced apoptosis in these cells through the events of up-regulation of caspase 3, down-regulation of bcl-2 family genes followed by cytochrome c release. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Altered intrinsic brain activity after chemotherapy in patients with gastric cancer: A preliminary study

    International Nuclear Information System (INIS)

    Kim, Hyun Gi; Shin, Na-Young; Bak, Yunjin; Lim, Soo Mee; Kim, Kyung Ran; Jung, Young-Chul; Han, Kyunghwa; Lee, Seung-Koo

    2017-01-01

    To characterize the pattern of altered intrinsic brain activity in gastric cancer patients after chemotherapy (CTx). Patients before and after CTx (n = 14) and control subjects (n = 11) underwent resting-state functional MRI (rsfMRI) at baseline and 3 months after CTx. Regional homogeneity (ReHo), amplitude of low-frequency fluctuation (ALFF), and fractional ALFF (fALFF) were calculated and compared between the groups using the two-sample t test. Correlation analysis was also performed between rsfMRI values (i.e., ReHo, ALFF, and fALFF) and neuropsychological test results. Patients showed poor performance in verbal memory and executive function and decreased rsfMRI values in the frontal areas even before CTx and showed decreased attention/working memory and executive function after CTx compared to the control subjects. In direct comparison of values before and after CTx, there were no significant differences in neuropsychological test scores, but decreased rsfMRI values were observed at the frontal lobes and right cerebellar region. Among rsfMRI values, lower ALFF in the left inferior frontal gyrus was significantly associated with poor performance of the executive function test. We observed decreased attention/working memory and executive function that corresponded to the decline of frontal region activation in gastric cancer patients who underwent CTx. (orig.)

  17. Alloying Au surface with Pd reduces the intrinsic activity in catalyzing CO oxidation

    KAUST Repository

    Qian, Kun

    2016-03-30

    © 2016. Various Au-Pd/SiO2 catalysts with a fixed Au loading but different Au:Pd molar ratios were prepared via deposition-precipitation method followed by H2 reduction. The structures were characterized and the catalytic activities in CO oxidation were evaluated. The formation of Au-Pd alloy particles was identified. The Au-Pd alloy particles exhibit enhanced dispersions on SiO2 than Au particles. Charge transfer from Pd to Au within Au-Pd alloy particles. Isolated Pd atoms dominate the surface of Au-Pd alloy particles with large Au:Pd molar ratios while contiguous Pd atoms dominate the surface of Au-Pd alloy particles with small Au:Pd molar ratios. Few synergetic effect of Au-Pd alloy occurs on catalyzing CO oxidation under employed reaction conditions. Alloying Au with Pd reduces the intrinsic activity in catalyzing CO oxidation, and contiguous Pd atoms on the Au-Pd alloy particles are capable of catalyzing CO oxidation while isolated Pd atoms are not. These results advance the fundamental understandings of Au-Pd alloy surfaces in catalyzing CO oxidation.

  18. Biventricular pacing with ventricular fusion by intrinsic activation in cardiac resynchronization therapy.

    Science.gov (United States)

    Guo, Tao; Li, Ruijie; Zhang, Limei; Luo, Zhiling; Zhao, Ling; Yang, Jun; Pu, Lijin; Hua, Baotong

    2015-05-13

    We sought to evaluate the impact of biventricular (BiV) pacing with ventricular fusion by intrinsic atrioventricular nodal (AVN) conduction (BiV + intrinsic pacing) on clinical outcomes in patients with chronic heart failure (CHF) receiving cardiac resynchronization therapy (CRT).A total of 44 patients were randomized to receive either BiV or BiV + intrinsic pacing for one month. Echocardiographic optimization was performed for the BiV pacing mode, while the BiV + intrinsic pacing mode was achieved by titrating AV delay under electrocardiography (ECG) monitoring. Symptoms, quality of life, ECG, echocardiography, and cardiovascular events were recorded at baseline and the end of the follow-up for each pacing mode.Patients undergoing BiV + intrinsic pacing mode had shorter QRS duration compared to those with conventional BiV pacing (118.4 ± 21.6 ms versus 146.4 ± 5.3 ms, P Heart Failure Questionnaire (MLHFQ) scores (12.5 ± 6.6 versus 18.2 ± 12.3, P = 0.0001).Treating CHF patients with BiV+intrinsic pacing resulted in improved cardiac function and quality of life. BiV + intrinsic pacing can be used in CHF patients with sinus rhythm and normal AV nodal conduction to improve CRT efficacy.

  19. Ocean modeling on unstructured meshes

    Science.gov (United States)

    Danilov, S.

    2013-09-01

    Unstructured meshes are common in coastal modeling, but still rarely used for modeling the large-scale ocean circulation. Existing and new projects aim at changing this situation by proposing models enabling a regional focus (multiresolution) in global setups, without nesting and open boundaries. Among them, finite-volume models using the C-grid discretization on Voronoi-centroidal meshes or cell-vertex quasi-B-grid discretization on triangular meshes work well and offer the multiresolution functionality at a price of being 2 to 4 times slower per degree of freedom than structured-mesh models. This is already sufficient for many practical tasks and will be further improved as the number of vertical layers is increased. Approaches based on the finite-element method, both used or proposed, are as a rule slower at present. Most of staggered discretizations on triangular or Voronoi meshes allow spurious modes which are difficult to filter on unstructured meshes. The ongoing research seeks how to handle them and explores new approaches where such modes are absent. Issues of numerical efficiency and accurate transport schemes are still important, and the question on parameterizations for multiresolution meshes is hardly explored at all. The review summarizes recent developments the main practical result of which is the emergence of multiresolution models for simulating large-scale ocean circulation.

  20. Intrinsic predictive factors for ankle sprain in active university students: a prospective study.

    Science.gov (United States)

    de Noronha, M; França, L C; Haupenthal, A; Nunes, G S

    2013-10-01

    The ankle is the joint most affected among the sports-related injuries. The current study investigated whether certain intrinsic factors could predict ankle sprains in active students. The 125 participants were submitted to a baseline assessment in a single session were then followed-up for 52 weeks regarding the occurrence of sprain. The baseline assessment were performed in both ankles and included the questionnaire Cumberland ankle instability tool - Portuguese, the foot lift test, dorsiflexion range of motion, Star Excursion Balance Test (SEBT), the side recognition task, body mass index, and history of previous sprain. Two groups were used for analysis: one with those who suffered an ankle sprain and the other with those who did not suffer an ankle sprain. After Cox regression analysis, participants with history of previous sprain were twice as likely to suffer subsequent sprains [hazard ratio (HR) 2.21 and 95% confidence interval (CI) 1.07-4.57] and people with better performance on the SEBT in the postero-lateral (PL) direction were less likely to suffer a sprain (HR 0.96 and 95% CI 0.92-0.99). History of previous sprain was the strongest predictive factor and a weak performance on SEBT PL was also considered a predictive factor for ankle sprains. © 2012 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  1. Effect of vanadate on glucose transporter (GLUT4) intrinsic activity in skeletal muscle plasma membrane giant vesicles

    DEFF Research Database (Denmark)

    Kristiansen, S; Youn, J; Richter, Erik

    1996-01-01

    Maximally effective concentrations of vanadate (a phosphotyrosine phosphatase inhibitor) increase glucose transport in muscle less than maximal insulin stimulation. This might be due to vanadate-induced decreased intrinsic activity of GLUT4 accompanying GLUT4 translocation. Thus, the effect of va...

  2. Intrinsic Brain Activity Responsible for Sex Differences in Shyness and Social Anxiety.

    Science.gov (United States)

    Yang, Xun; Zhou, Ming; Lama, Sunima; Chen, Lizhou; Hu, Xinyu; Wang, Song; Chen, Taolin; Shi, Yan; Huang, Xiaoqi; Gong, Qiyong

    2017-01-01

    Male and female show significant differences in important behavioral features such as shyness, yet the neural substrates of these differences remain poorly understood. Previous neuroimaging studies have demonstrated that both shyness and social anxiety in healthy subjects are associated with increased activation in the fronto-limbic and cognitive control areas. However, it remains unknown whether these brain abnormalities would be shared by different genders. Therefore, in the current study, we used resting-state fMRI (r-fMRI) to investigate sex differences in intrinsic cerebral activity that may contribute to shyness and social anxiety. Sixty subjects (28 males, 32 females) participated in r-fMRI scans, and the amplitude of low-frequency fluctuations (ALFF) and fractional ALFF (fALFF) were used to measure the spontaneous regional cerebral activity in all subjects. We first compared the differences between male and female both in the ALFF and fALFF and then we also examined the whole brain correlation between the ALFF/fALFF and the severity of shyness as well as social anxiety by genders. Referring to shyness measure, we found a significant positive correlation between shyness scores (CBSS) and ALFF/fALFF value in the frontoparietal control network and a negative correlation in the cingulo-insular network in female; while in male, there is no such correlation. For the social anxiety level, we found positive correlations between Leibowitz Social Anxiety Scale (LSAS) scores and spontaneous activity in the frontal-limbic network in male and negative correlation between the frontal-parietal network; however, such correlation was not prominent in female. This pattern suggests that shy female individuals engaged a proactive control process, driven by a positive association with activity in frontoparietal network and negative association in cingulo-insular network, whereas social anxiety males relied more on a reactive control process, driven by a positive correlation of

  3. Modulation of intrinsic brain activity by electroconvulsive therapy in major depression

    Science.gov (United States)

    Leaver, Amber M.; Espinoza, Randall; Pirnia, Tara; Joshi, Shantanu H.; Woods, Roger P.; Narr, Katherine L.

    2015-01-01

    Introduction One of the most effective interventions for intractable major depressive episodes is electroconvulsive therapy (ECT). Because ECT is also relatively fast-acting, longitudinal study of its neurobiological effects offers critical insight into the mechanisms underlying depression and antidepressant response. Here we assessed modulation of intrinsic brain activity in corticolimbic networks associated with ECT and clinical response. Methods We measured resting-state functional connectivity (RSFC) in patients with treatment-resistant depression (n=30), using functional magnetic resonance imaging (fMRI) acquired before and after completing a treatment series with right-unilateral ECT. Using independent component analysis, we assessed changes in RSFC with 1) symptom improvement and 2) ECT regardless of treatment outcome in patients, with reference to healthy controls (n=33, also scanned twice). Results After ECT, consistent changes in RSFC within targeted depression-relevant functional networks were observed in the dorsal anterior cingulate (ACC), mediodorsal thalamus (mdTh), hippocampus, and right anterior temporal, medial parietal, and posterior cingulate cortex in all patients. In a separate analysis, changes in depressive symptoms were associated with RSFC changes in the dorsal ACC, mdTh, putamen, medial prefrontal, and lateral parietal cortex. RSFC of these regions did not change in healthy controls. Conclusions Neuroplasticity underlying clinical change was in part separable from changes associated with the effects of ECT observed in all patients. However, both ECT and clinical change were associated with RSFC modulation in dorsal ACC, mdTh and hippocampus, which may indicate that these regions underlie the mechanisms of clinical outcome in ECT and may be effective targets for future neurostimulation therapies. PMID:26878070

  4. Data on the effect of conductive hearing loss on auditory and visual cortex activity revealed by intrinsic signal imaging.

    Science.gov (United States)

    Teichert, Manuel; Bolz, Jürgen

    2017-10-01

    This data article provides additional data related to the research article entitled "Simultaneous intrinsic signal imaging of auditory and visual cortex reveals profound effects of acute hearing loss on visual processing" (Teichert and Bolz, 2017) [1]. The primary auditory and visual cortex (A1 and V1) of adult male C57BL/6J mice (P120-P240) were mapped simultaneously using intrinsic signal imaging (Kalatsky and Stryker, 2003) [2]. A1 and V1 activity evoked by combined auditory and visual stimulation were measured before and after conductive hearing loss (CHL) induced by bilateral malleus removal. We provide data showing that A1 responsiveness evoked by sounds of different sound pressure levels (SPL) decreased after CHL whereas visually evoked V1 activity increased after this intervention. In addition, we also provide imaging data on percentage of V1 activity increases after CHL compared to pre-CHL.

  5. Parallel adaptive simulations on unstructured meshes

    International Nuclear Information System (INIS)

    Shephard, M S; Jansen, K E; Sahni, O; Diachin, L A

    2007-01-01

    This paper discusses methods being developed by the ITAPS center to support the execution of parallel adaptive simulations on unstructured meshes. The paper first outlines the ITAPS approach to the development of interoperable mesh, geometry and field services to support the needs of SciDAC application in these areas. The paper then demonstrates the ability of unstructured adaptive meshing methods built on such interoperable services to effectively solve important physics problems. Attention is then focused on ITAPs' developing ability to solve adaptive unstructured mesh problems on massively parallel computers

  6. Best Practices for Unstructured Grid Shock Fitting

    Science.gov (United States)

    McCloud, Peter L.

    2017-01-01

    Unstructured grid solvers have well-known issues predicting surface heat fluxes when strong shocks are present. Various efforts have been made to address the underlying numerical issues that cause the erroneous predictions. The present work addresses some of the shortcomings of unstructured grid solvers, not by addressing the numerics, but by applying structured grid best practices to unstructured grids. A methodology for robust shock detection and shock fitting is outlined and applied to production relevant cases. Results achieved by using the Loci-CHEM Computational Fluid Dynamics solver are provided.

  7. Machine Learning Classification of Cirrhotic Patients with and without Minimal Hepatic Encephalopathy Based on Regional Homogeneity of Intrinsic Brain Activity.

    Science.gov (United States)

    Chen, Qiu-Feng; Chen, Hua-Jun; Liu, Jun; Sun, Tao; Shen, Qun-Tai

    2016-01-01

    Machine learning-based approaches play an important role in examining functional magnetic resonance imaging (fMRI) data in a multivariate manner and extracting features predictive of group membership. This study was performed to assess the potential for measuring brain intrinsic activity to identify minimal hepatic encephalopathy (MHE) in cirrhotic patients, using the support vector machine (SVM) method. Resting-state fMRI data were acquired in 16 cirrhotic patients with MHE and 19 cirrhotic patients without MHE. The regional homogeneity (ReHo) method was used to investigate the local synchrony of intrinsic brain activity. Psychometric Hepatic Encephalopathy Score (PHES) was used to define MHE condition. SVM-classifier was then applied using leave-one-out cross-validation, to determine the discriminative ReHo-map for MHE. The discrimination map highlights a set of regions, including the prefrontal cortex, anterior cingulate cortex, anterior insular cortex, inferior parietal lobule, precentral and postcentral gyri, superior and medial temporal cortices, and middle and inferior occipital gyri. The optimized discriminative model showed total accuracy of 82.9% and sensitivity of 81.3%. Our results suggested that a combination of the SVM approach and brain intrinsic activity measurement could be helpful for detection of MHE in cirrhotic patients.

  8. Machine Learning Classification of Cirrhotic Patients with and without Minimal Hepatic Encephalopathy Based on Regional Homogeneity of Intrinsic Brain Activity.

    Directory of Open Access Journals (Sweden)

    Qiu-Feng Chen

    Full Text Available Machine learning-based approaches play an important role in examining functional magnetic resonance imaging (fMRI data in a multivariate manner and extracting features predictive of group membership. This study was performed to assess the potential for measuring brain intrinsic activity to identify minimal hepatic encephalopathy (MHE in cirrhotic patients, using the support vector machine (SVM method. Resting-state fMRI data were acquired in 16 cirrhotic patients with MHE and 19 cirrhotic patients without MHE. The regional homogeneity (ReHo method was used to investigate the local synchrony of intrinsic brain activity. Psychometric Hepatic Encephalopathy Score (PHES was used to define MHE condition. SVM-classifier was then applied using leave-one-out cross-validation, to determine the discriminative ReHo-map for MHE. The discrimination map highlights a set of regions, including the prefrontal cortex, anterior cingulate cortex, anterior insular cortex, inferior parietal lobule, precentral and postcentral gyri, superior and medial temporal cortices, and middle and inferior occipital gyri. The optimized discriminative model showed total accuracy of 82.9% and sensitivity of 81.3%. Our results suggested that a combination of the SVM approach and brain intrinsic activity measurement could be helpful for detection of MHE in cirrhotic patients.

  9. Histidine-rich glycoprotein binds DNA and RNA and attenuates their capacity to activate the intrinsic coagulation pathway.

    Science.gov (United States)

    Vu, Trang T; Leslie, Beverly A; Stafford, Alan R; Zhou, Ji; Fredenburgh, James C; Weitz, Jeffrey I

    2016-01-01

    When triggered by factor (F) XII and nucleic acids, we showed that thrombosis in HRG-deficient mice is accelerated compared with that in wild-type mice. In this study, we set out to identify the mechanisms by which nucleic acids promote contact activation, and to determine whether HRG attenuates their effects. DNA or RNA addition to human plasma enhances thrombin generation via the intrinsic pathway and shortens the clotting time. Their effect on the clotting time is seven- to 14-fold greater in HRG-deficient plasma than in control plasma. Investigations into the mechanisms of activation reveal that nucleic acids a) promote FXII activation in the presence of prekallikrein- and high molecular weight kininogen (HK), and b) enhance thrombin-mediated FXI activation by 10- to 12-fold. Surface plasmon resonance studies show that DNA and RNA bind FXII, FXIIa, HK, FXI, FXIa and thrombin with high affinity. HRG attenuates DNA- and RNA-mediated FXII activation, and FXI activation by FXIIa or by thrombin, suggesting that HRG down regulates the capacity of DNA and RNA to activate the intrinsic pathway. Therefore, HRG attenuates the procoagulant activity of nucleic acids at multiple levels.

  10. Effects of Extrinsic and Intrinsic Proton Activity on The Mechanism of Oxygen Reduction in Ionic Liquids

    Science.gov (United States)

    Zeller, Robert August

    Mechanisms for oxygen reduction are proposed for three distinct cases covering two ionic liquids of fundamentally different archetypes and almost thirty orders of magnitude of proton activity. Proton activity is treated both extrinsically by varying the concentration and intrinsically by selecting proton donors with a wide range of aqueous pKa values. The mechanism of oxygen reduction in ionic liquids is introduced by way of the protic ionic liquid (pIL) triethylammonium triflate (TEATf) which shares some similarities with aqueous acid solutions. Oxygen reduction in TEATf begins as the one electron rate limited step to form superoxide, O2 *-, which is then rapidly protonated by the pIL cation forming the perhydroxyl radical, HO2*. The perhydroxyl radical is further reduced to peroxidate (HO2-) and hydrogen peroxide in proportions in accordance with their pKa. The reaction does not proceed beyond this point due to the adsorption of the conjugate base triethylammine interfering with the disproportionation of hydrogen peroxide. This work demonstrates that this mechanism is consistent across Pt, Au, Pd, and Ag electrodes. Two related sets of experiments were performed in the inherently aprotic ionic liquid 1-butyl-2,3-dimethylimidazolium triflate (C4dMImTf). The first involved the titration of acidic species of varying aqueous pKa into the IL while monitoring the extent of oxygen reduction as a function of pKa and potential on Pt and glassy carbon (GC) electrodes. These experiments confirmed the greater propensity of Pt to reduce oxygen by its immediate and abrupt transition from one electron reduction to four electron reduction, while oxygen reduction on GC gradually approaches four electron reduction as the potentials were driven more cathodic. The potential at which oxygen reduction initiates shows general agreement with the Nernst equation and the acid's tabulated aqueous pKa value, however at the extremely acidic end, a small deviation is observed. The second set

  11. Pharmacological targeting of HSP90 with 17-AAG induces apoptosis of myogenic cells through activation of the intrinsic pathway.

    Science.gov (United States)

    Wagatsuma, Akira; Takayama, Yuzo; Hoshino, Takayuki; Shiozuka, Masataka; Yamada, Shigeru; Matsuda, Ryoichi; Mabuchi, Kunihiko

    2017-12-16

    We have shown that pharmacological inhibition of HSP90 ATPase activity induces apoptosis of myoblasts during their differentiation. However, the signaling pathways remain not fully characterized. We report that pharmacological targeting of HSP90 with 17-AAG activates the intrinsic pathway including caspase-dependent and caspase-independent pathways. 17-AAG induces the typical apoptotic phenotypes including PARP cleavage, chromatin condensation, and nuclear fragmentation with mitochondrial release of cytochrome c, Smac/DIABLO, procaspase-9 processing, and caspase-3 activation. AIF and EndoG redistribute from the mitochondria into the cytosol and are partially translocated to the nucleus in 17-AAG-treated cells. These results suggest that caspase-dependent and caspase-independent pathways should be considered in apoptosis of myogenic cells induced by inhibition of HSP90 ATPase activity.

  12. Enhancement of intrinsic antitumor activity in spore-endotoxin mixtures of Bacillus thuringiensis by exposure to ultraviolet radiation

    International Nuclear Information System (INIS)

    Zamola, B.; Karminski-Zamola, G.; Fuks, Z.; Kubovic, M.; Wrishcer, M.

    1985-01-01

    Irradiation of spore-endotoxin mixtures from Bacillus thuringiensis cultures at 254 nm (60 μW cm -2 ) enhances their intrinsic antitumor potency as well as that of either component. The extent of enhancement depends on the length of exposure (optimum: 35 min) and may thus be due to photochemical changes of the endotoxin protein or/and to photoproduction of additional compounds with antitumor activity. Antitumor effects, expressed as survival rates of C57BL/6 mice inoculated with Lewis' mouse lung carcinoma and subjected to treatments 24 h later, depended on the number of doses of preparations administered (mixture, separated components). (author)

  13. Intrinsic and chemo-sensitizing activity of SMAC-mimetics on high-risk childhood acute lymphoblastic leukemia.

    Science.gov (United States)

    Schirmer, M; Trentin, L; Queudeville, M; Seyfried, F; Demir, S; Tausch, E; Stilgenbauer, S; Eckhoff, S M; Meyer, L H; Debatin, K-M

    2016-01-14

    SMAC-mimetics represent a targeted therapy approach to overcome apoptosis resistance in many tumors. Here, we investigated the efficacy of the SMAC-mimetic BV6 in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). In ALL cell lines, intrinsic apoptosis sensitivity was associated with rapid cIAP degradation, NF-κB activation, TNF-α secretion and induction of an autocrine TNF-α-dependent cell death loop. This pattern of responsiveness was also observed upon ex vivo analysis of 40 primograft BCP-ALL samples. Treatment with BV6 induced cell death in the majority of ALL primografts including leukemias with high-risk and poor-prognosis features. Inhibition of cell death by the TNF receptor fusion protein etanercept demonstrated that BV6 activity is dependent on TNF-α. In a preclinical NOD/SCID/huALL model of high-risk ALL, marked anti-leukemia effectivity and significantly prolonged survival were observed upon BV6 treatment. Interestingly, also in vivo, intrinsic SMAC-mimetic activity was mediated by TNF-α. Importantly, BV6 increased the effectivity of conventional induction therapy including vincristine, dexamethasone and asparaginase leading to prolonged remission induction. These data suggest SMAC-mimetics as an important addendum to efficient therapy of pediatric BCP-ALL.

  14. Regorafenib induces extrinsic and intrinsic apoptosis through inhibition of ERK/NF-κB activation in hepatocellular carcinoma cells.

    Science.gov (United States)

    Tsai, Jai-Jen; Pan, Po-Jung; Hsu, Fei-Ting

    2017-02-01

    The aim of the present study was to investigate the role of NF-κB inactivation in regorafenib-induced apoptosis in human hepatocellular carcinoma SK-HEP-1 cells. SK-HEP-1 cells were treated with different concentrations of the NF-κB inhibitor 4-N-[2-(4-phenoxyphenyl)ethyl]quinazoline-4,6-diamine (QNZ) or regorafenib for different periods. The effects of QNZ and regorafenib on cell viability, expression of NF-κB-modulated anti-apoptotic proteins and apoptotic pathways were analyzed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, western blotting, DNA gel electrophoresis, flow cytometry and NF-κB reporter gene assay. Inhibitors of various kinases including AKT, c-Jun N-terminal kinase (JNK), P38 and extracellular signal-regulated kinase (ERK) were used to evaluate the mechanism of regorafenib-induced NF-κB inactivation. The results demonstrated that both QNZ and regorafenib significantly inhibited the expression of anti-apoptotic proteins and triggered extrinsic and intrinsic apoptosis. We also demonstrated that regorafenib inhibited NF-κB activation through ERK dephosphorylation. Taken all together, our findings indicate that regorafenib triggers extrinsic and intrinsic apoptosis through suppression of ERK/NF-κB activation in SK-HEP-1 cells.

  15. Constitutively active signaling by the G protein βγ-subunit mediates intrinsically increased phosphodiesterase-4 activity in human asthmatic airway smooth muscle cells.

    Directory of Open Access Journals (Sweden)

    Aihua Hu

    Full Text Available Signaling by the Gβγ subunit of Gi protein, leading to downstream c-Src-induced activation of the Ras/c-Raf1/MEK-ERK1/2 signaling pathway and its upregulation of phosphodiesterase-4 (PDE4 activity, was recently shown to mediate the heightened contractility in proasthmatic sensitized isolated airway smooth muscle (ASM, as well as allergen-induced airway hyperresponsiveness and inflammation in an in vivo animal model of allergic asthma. This study investigated whether cultured human ASM (HASM cells derived from asthmatic donor lungs exhibit constitutively increased PDE activity that is attributed to intrinsically upregulated Gβγ signaling coupled to c-Src activation of the Ras/MEK/ERK1/2 cascade. We show that, relative to normal cells, asthmatic HASM cells constitutively exhibit markedly increased intrinsic PDE4 activity coupled to heightened Gβγ-regulated phosphorylation of c-Src and ERK1/2, and direct co-localization of the latter with the PDE4D isoform. These signaling events and their induction of heightened PDE activity are acutely suppressed by treating asthmatic HASM cells with a Gβγ inhibitor. Importantly, along with increased Gβγ activation, asthmatic HASM cells also exhibit constitutively increased direct binding of the small Rap1 GTPase-activating protein, Rap1GAP, to the α-subunit of Gi protein, which serves to cooperatively facilitate Ras activation and, thereby, enable enhanced Gβγ-regulated ERK1/2-stimulated PDE activity. Collectively, these data are the first to identify that intrinsically increased signaling via the Gβγ subunit, facilitated by Rap1GAP recruitment to the α-subunit, mediates the constitutively increased PDE4 activity detected in asthmatic HASM cells. These new findings support the notion that interventions targeted at suppressing Gβγ signaling may lead to novel approaches to treat asthma.

  16. Unstructured mesh adaptivity for urban flooding modelling

    Science.gov (United States)

    Hu, R.; Fang, F.; Salinas, P.; Pain, C. C.

    2018-05-01

    Over the past few decades, urban floods have been gaining more attention due to their increase in frequency. To provide reliable flooding predictions in urban areas, various numerical models have been developed to perform high-resolution flood simulations. However, the use of high-resolution meshes across the whole computational domain causes a high computational burden. In this paper, a 2D control-volume and finite-element flood model using adaptive unstructured mesh technology has been developed. This adaptive unstructured mesh technique enables meshes to be adapted optimally in time and space in response to the evolving flow features, thus providing sufficient mesh resolution where and when it is required. It has the advantage of capturing the details of local flows and wetting and drying front while reducing the computational cost. Complex topographic features are represented accurately during the flooding process. For example, the high-resolution meshes around the buildings and steep regions are placed when the flooding water reaches these regions. In this work a flooding event that happened in 2002 in Glasgow, Scotland, United Kingdom has been simulated to demonstrate the capability of the adaptive unstructured mesh flooding model. The simulations have been performed using both fixed and adaptive unstructured meshes, and then results have been compared with those published 2D and 3D results. The presented method shows that the 2D adaptive mesh model provides accurate results while having a low computational cost.

  17. The activity of myrosinase from broccoli (Brassica oleracea L. cv. Italica): influence of intrinsic and extrinsic factors.

    Science.gov (United States)

    Ludikhuyze, L; Rodrigo, L; Hendrickx, M

    2000-03-01

    The potential of some intrinsic (MgCl2, ascorbic acid, pH) and extrinsic (temperature, pressure) factors for controlling/altering activity of myrosinase from broccoli was investigated in this paper. A combination of MgCl2 and ascorbic acid was found to enhance enzyme activity. Concentrations resulting in optimal activity were determined as 0.1 g/liter and 2 g/liter, respectively. Both in the absence and presence of this enzyme activator, the optimal pH was situated between 6.5 and 7, corresponding to the natural pH of fresh broccoli juice. At atmospheric pressure, the enzyme was optimally active at a temperature about 30 degrees C. Application of low pressure (50 to 100 MPa) slightly enhanced the activity while at higher pressure (300 MPa), the activity was largely reduced. Future work should focus on the extension of this work to real food products in order to take cellular disruption into account. In intact vegetable tissues, the enzyme myrosinase is present in compartments separated from its substrate, the glucosinolates. Hence, enzymatic hydrolysis can merely occur after cellular disruption. In this respect, processes such as cutting, cooking, freezing, or pressurizing of the vegetables will have a large effect on the glucosinolate hydrolysis by myrosinase. This work could then be the basis for controlling glucosinolate hydrolysis in food preparation and processing.

  18. The intrinsically disordered tails of PTEN and PTEN-L have distinct roles in regulating substrate specificity and membrane activity

    Science.gov (United States)

    Masson, Glenn R.; Perisic, Olga; Burke, John E.; Williams, Roger L.

    2015-01-01

    Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is a lipid and protein phosphatase, and both activities are necessary for its role as a tumour suppressor. PTEN activity is controlled by phosphorylation of its intrinsically disordered C-terminal tail. A recently discovered variant of PTEN, PTEN-long (PTEN-L), has a 173-residue N-terminal extension that causes PTEN-L to exhibit unique behaviour, such as movement from one cell to another. Using hydrogen/deuterium exchange mass spectrometry (HDX–MS) and biophysical assays, we show that both the N-terminal extension of PTEN-L and C-terminal tail of PTEN affect the phosphatase activity using unique mechanisms. Phosphorylation of six residues in the C-terminal tail of PTEN results in auto-inhibitory interactions with the phosphatase and C2 domains, effectively blocking both the active site and the membrane-binding interface of PTEN. Partially dephosphorylating PTEN on pThr366/pSer370 results in sufficient exposure of the active site to allow a selective activation for soluble substrates. Using HDX–MS, we identified a membrane-binding element in the N-terminal extension of PTEN-L, termed the membrane-binding helix (MBH). The MBH radically alters the membrane binding mechanism of PTEN-L compared with PTEN, switching PTEN-L to a ‘scooting’ mode of catalysis from the ‘hopping’ mode that is characteristic of PTEN. PMID:26527737

  19. Functional Trade-Offs in Promiscuous Enzymes Cannot Be Explained by Intrinsic Mutational Robustness of the Native Activity.

    Directory of Open Access Journals (Sweden)

    Miriam Kaltenbach

    2016-10-01

    Full Text Available The extent to which an emerging new function trades off with the original function is a key characteristic of the dynamics of enzyme evolution. Various cases of laboratory evolution have unveiled a characteristic trend; a large increase in a new, promiscuous activity is often accompanied by only a mild reduction of the native, original activity. A model that associates weak trade-offs with "evolvability" was put forward, which proposed that enzymes possess mutational robustness in the native activity and plasticity in promiscuous activities. This would enable the acquisition of a new function without compromising the original one, reducing the benefit of early gene duplication and therefore the selection pressure thereon. Yet, to date, no experimental study has examined this hypothesis directly. Here, we investigate the causes of weak trade-offs by systematically characterizing adaptive mutations that occurred in two cases of evolutionary transitions in enzyme function: (1 from phosphotriesterase to arylesterase, and (2 from atrazine chlorohydrolase to melamine deaminase. Mutational analyses in various genetic backgrounds revealed that, in contrast to the prevailing model, the native activity is less robust to mutations than the promiscuous activity. For example, in phosphotriesterase, the deleterious effect of individual mutations on the native phosphotriesterase activity is much larger than their positive effect on the promiscuous arylesterase activity. Our observations suggest a revision of the established model: weak trade-offs are not caused by an intrinsic robustness of the native activity and plasticity of the promiscuous activity. We propose that upon strong adaptive pressure for the new activity without selection against the original one, selected mutations will lead to the largest possible increases in the new function, but whether and to what extent they decrease the old function is irrelevant, creating a bias towards initially weak

  20. Redox enzyme-mimicking activities of CeO2nanostructures: Intrinsic influence of exposed facets.

    Science.gov (United States)

    Yang, Yushi; Mao, Zhou; Huang, Wenjie; Liu, Lihua; Li, Junli; Li, Jialiang; Wu, Qingzhi

    2016-10-17

    CeO 2 nanoparticles (NPs) have been well demonstrated as an antioxidant in protecting against oxidative stress-induced cellular damages and a potential therapeutic agent for various diseases thanks to their redox enzyme-mimicking activities. The Ce 3+ /Ce 4+ ratio and oxygen vacancies on the surface have been considered as the major originations responsible for the redox enzyme-mimicking activities of CeO 2 NPs. Herein, CeO 2 nanostructures (nanocubes and nanorods) exposed different facets were synthesized via a facile hydrothermal method. The characterizations by X-ray photoelectron spectroscopy, Raman spectroscopy, and UV-Vis spectroscopy show that the Ce 3+ /Ce 4+ ratio and oxygen vacancy content on the surfaces of as-synthesized CeO 2 nanostructures are nearly at the same levels. Meanwhile, the enzymatic activity measurements indicate that the redox enzyme-mimicking activities of as-synthesized CeO 2 nanostructures are greatly dependent on their exposed facets. CeO 2 nanocubes with exposed {100} facets exhibit a higher peroxidase but lower superoxide dismutase activity than those of the CeO 2 nanorods with exposed {110} facets. Our results provide new insights into the redox enzyme-mimicking activities of CeO 2 nanostructures, as well as the design and synthesis of inorganic nanomaterials-based artificial enzymes.

  1. Study on the relationships between intrinsic functional connectivity of the default mode network and transient epileptic activity

    Directory of Open Access Journals (Sweden)

    Renaud eLopes

    2014-10-01

    Full Text Available Rationale. Simultaneous recording of electroencephalogram and functional MRI (EEG-fMRI is a powerful tool for localizing epileptic networks via the detection of hemodynamic changes correlated with interictal epileptic discharges (IEDs. FMRI can be used to study the long-lasting effect of epileptic activity by assessing stationary functional connectivity during the resting-state period (especially the connectivity of the default mode network (DMN. Temporal lobe epilepsy (TLE and idiopathic generalized epilepsy (IGE are associated with low responsiveness and disruption of DMN activity. A dynamic functional connectivity approach might enable us to determine the effect of IEDs on DMN connectivity and to better understand the correlation between DMN connectivity changes and altered consciousness. Method. We studied dynamic changes in DMN intrinsic connectivity and their relation to IEDs. Six IGE patients (with generalized spike and slow waves and 6 TLE patients (with unilateral left temporal spikes were included. Functional connectivity before, during and after IEDs was estimated using a sliding window approach and compared with the baseline period.Results. No dependence on window size was observed. The baseline DMN connectivity was decreased in the left hemisphere (ipsilateral to the epileptic focus in TLEs and was less strong but remained bilateral in IGEs. We observed an overall increase in DMN intrinsic connectivity prior to the onset of IEDs in both IGEs and TLEs. After IEDs in TLEs, we found that DMN connectivity increased before it returned to baseline values. Most of the DMN regions with increased connectivity before and after IEDs were lateralized to the left hemisphere in TLE (i.e., ipsilateral to the epileptic focus.Conclusion. Results suggest that DMN connectivity may facilitate IED generation and may be affected at the time of the IED. However, these results need to be confirmed in a larger independent cohort.

  2. Mechanism of the Ca2+-induced enhancement of the intrinsic factor VIIa activity

    DEFF Research Database (Denmark)

    Bjelke, Jais R; Olsen, Ole H; Fodje, Michel

    2008-01-01

    between the loop and Lys(161) in the N-terminal tail. In support of the first mechanism, the mutations E296V and D212N resulted in similar, about 2-fold, enhancements of the amidolytic activity. Moreover, mutation of the Lys(161)-interactive residue Asp(217) or Asp(219) to Ala reduced the amidolytic...... activity by 40-50%, whereas the K161A mutation resulted in 80% reduction. Hence one of these Asp residues in the Ca(2+)-binding loop appears to suffice for some residual interaction with Lys(161), whereas the more severe effect upon replacement of Lys(161) is due to abrogation of the interaction with the N......-terminal tail. However, Ca(2+) attenuation of the repulsion between Asp(212) and Glu(296) keeps the activity above that of apoFVIIa. Altogether, our data suggest that repulsion involving Asp(212) in the Ca(2+)-binding loop suppresses FVIIa activity and that optimal activity requires a favorable interaction...

  3. Molecular-level insights into intrinsic peroxidase-like activity of nanocarbon oxides.

    Science.gov (United States)

    Zhao, Ruisheng; Zhao, Xiang; Gao, Xingfa

    2015-01-12

    Nanocarbon oxides have been proved to possess great peroxidase-like activity, catalyzing the oxidation of many peroxidase substrates, such as 3,3',5,5'-tetramethylbenzidine (TMB) and o-phenylenediamine dihydrochloride (OPD), accompanied by a significant color change. This chromogenic reaction is widely used to detect glucose and occult blood. The chromogenic reaction was intensively investigated with density functional theory and molecular-level insights into the nature of peroxidase-like activity were gained. A radical mechanism was unraveled and the carboxyl groups of nanocarbon oxides were identified as the reactive sites. Aromatic domains connected with the carboxyl groups were critical to the peroxidase-like activity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Albinism-causing mutations in recombinant human tyrosinase alter intrinsic enzymatic activity.

    Directory of Open Access Journals (Sweden)

    Monika B Dolinska

    Full Text Available Tyrosinase (TYR catalyzes the rate-limiting, first step in melanin production and its gene (TYR is mutated in many cases of oculocutaneous albinism (OCA1, an autosomal recessive cause of childhood blindness. Patients with reduced TYR activity are classified as OCA1B; some OCA1B mutations are temperature-sensitive. Therapeutic research for OCA1 has been hampered, in part, by the absence of purified, active, recombinant wild-type and mutant human enzymes.The intra-melanosomal domain of human tyrosinase (residues 19-469 and two OCA1B related temperature-sensitive mutants, R422Q and R422W were expressed in insect cells and produced in T. ni larvae. The short trans-membrane fragment was deleted to avoid potential protein insolubility, while preserving all other functional features of the enzymes. Purified tyrosinase was obtained with a yield of >1 mg per 10 g of larval biomass. The protein was a monomeric glycoenzyme with maximum enzyme activity at 37°C and neutral pH. The two purified mutants when compared to the wild-type protein were less active and temperature sensitive. These differences are associated with conformational perturbations in secondary structure.The intramelanosomal domains of recombinant wild-type and mutant human tyrosinases are soluble monomeric glycoproteins with activities which mirror their in vivo function. This advance allows for the structure - function analyses of different mutant TYR proteins and correlation with their corresponding human phenotypes; it also provides an important tool to discover drugs that may improve tyrosinase activity and treat OCA1.

  5. Albinism-Causing Mutations in Recombinant Human Tyrosinase Alter Intrinsic Enzymatic Activity

    Science.gov (United States)

    Dolinska, Monika B.; Kovaleva, Elena; Backlund, Peter; Wingfield, Paul T.; Brooks, Brian P.; Sergeev, Yuri V.

    2014-01-01

    Background Tyrosinase (TYR) catalyzes the rate-limiting, first step in melanin production and its gene (TYR) is mutated in many cases of oculocutaneous albinism (OCA1), an autosomal recessive cause of childhood blindness. Patients with reduced TYR activity are classified as OCA1B; some OCA1B mutations are temperature-sensitive. Therapeutic research for OCA1 has been hampered, in part, by the absence of purified, active, recombinant wild-type and mutant human enzymes. Methodology/Principal Findings The intra-melanosomal domain of human tyrosinase (residues 19–469) and two OCA1B related temperature-sensitive mutants, R422Q and R422W were expressed in insect cells and produced in T. ni larvae. The short trans-membrane fragment was deleted to avoid potential protein insolubility, while preserving all other functional features of the enzymes. Purified tyrosinase was obtained with a yield of >1 mg per 10 g of larval biomass. The protein was a monomeric glycoenzyme with maximum enzyme activity at 37°C and neutral pH. The two purified mutants when compared to the wild-type protein were less active and temperature sensitive. These differences are associated with conformational perturbations in secondary structure. Conclusions/Significance The intramelanosomal domains of recombinant wild-type and mutant human tyrosinases are soluble monomeric glycoproteins with activities which mirror their in vivo function. This advance allows for the structure – function analyses of different mutant TYR proteins and correlation with their corresponding human phenotypes; it also provides an important tool to discover drugs that may improve tyrosinase activity and treat OCA1. PMID:24392141

  6. Albinism-causing mutations in recombinant human tyrosinase alter intrinsic enzymatic activity.

    Science.gov (United States)

    Dolinska, Monika B; Kovaleva, Elena; Backlund, Peter; Wingfield, Paul T; Brooks, Brian P; Sergeev, Yuri V

    2014-01-01

    Tyrosinase (TYR) catalyzes the rate-limiting, first step in melanin production and its gene (TYR) is mutated in many cases of oculocutaneous albinism (OCA1), an autosomal recessive cause of childhood blindness. Patients with reduced TYR activity are classified as OCA1B; some OCA1B mutations are temperature-sensitive. Therapeutic research for OCA1 has been hampered, in part, by the absence of purified, active, recombinant wild-type and mutant human enzymes. The intra-melanosomal domain of human tyrosinase (residues 19-469) and two OCA1B related temperature-sensitive mutants, R422Q and R422W were expressed in insect cells and produced in T. ni larvae. The short trans-membrane fragment was deleted to avoid potential protein insolubility, while preserving all other functional features of the enzymes. Purified tyrosinase was obtained with a yield of >1 mg per 10 g of larval biomass. The protein was a monomeric glycoenzyme with maximum enzyme activity at 37°C and neutral pH. The two purified mutants when compared to the wild-type protein were less active and temperature sensitive. These differences are associated with conformational perturbations in secondary structure. The intramelanosomal domains of recombinant wild-type and mutant human tyrosinases are soluble monomeric glycoproteins with activities which mirror their in vivo function. This advance allows for the structure - function analyses of different mutant TYR proteins and correlation with their corresponding human phenotypes; it also provides an important tool to discover drugs that may improve tyrosinase activity and treat OCA1.

  7. The construction of hierarchical structure on Ti substrate with superior osteogenic activity and intrinsic antibacterial capability

    Science.gov (United States)

    Huang, Ying; Zha, Guangyu; Luo, Qiaojie; Zhang, Jianxiang; Zhang, Feng; Li, Xiaohui; Zhao, Shifang; Zhu, Weipu; Li, Xiaodong

    2014-01-01

    The deficient osseointegration and implant-associated infections are pivotal issues for the long-term clinical success of endosteal Ti implants, while development of functional surfaces that can simultaneously overcome these problems remains highly challenging. This study aimed to fabricate sophisticated Ti implant surface with both osteogenic inducing activity and inherent antibacterial ability simply via tailoring surface topographical features. Micro/submciro/nano-scale structure was constructed on Ti by three cumulative subtractive methods, including sequentially conducted sandblasting as well as primary and secondary acid etching treatment. Topographical features of this hierarchical structure can be well tuned by the time of the secondary acid treatment. Ti substrate with mere micro/submicro-scale structure (MS0-Ti) served as a control to examine the influence of hierarchical structures on surface properties and biological activities. Surface analysis indicated that all hierarchically structured surfaces possessed exactly the same surface chemistry as that of MS0-Ti, and all of them showed super-amphiphilicity, high surface free energy, and high protein adsorption capability. Biological evaluations revealed surprisingly antibacterial ability and excellent osteogenic activity for samples with optimized hierarchical structure (MS30-Ti) when compared with MS0-Ti. Consequently, for the first time, a hierarchically structured Ti surface with topography-induced inherent antibacterial capability and excellent osteogenic activity was constructed. PMID:25146099

  8. Intrinsically active nanobody-modified polymeric micelles for tumor-targeted combination therapy

    Czech Academy of Sciences Publication Activity Database

    Talelli, M.; Oliveira, S.; Rijcken, C. J. F.; Pieters, E. H. E.; Etrych, Tomáš; Ulbrich, Karel; van Nostrum, R. C. F.; Storm, G.; Hennink, W. E.; Lammers, T.

    2013-01-01

    Roč. 34, č. 4 (2013), s. 1255-1260 ISSN 0142-9612 R&D Projects: GA AV ČR IAA400500806; GA ČR GAP301/11/0325 Institutional research plan: CEZ:AV0Z40500505 Keywords : polymeric micelle * doxorubicin * active targeting Subject RIV: CD - Macromolecular Chemistry Impact factor: 8.312, year: 2013

  9. Keeping women active: an examination of the impacts of self-efficacy, intrinsic motivation, and leadership on women's persistence in physical activity.

    Science.gov (United States)

    Lloyd, Kathleen M; Little, Donna E

    2010-10-01

    Physical inactivity in women is a worldwide problem that has not only been well-documented but has provoked much government concern and policy activity. However, an even more important issue is encouraging women's persistence in physical activity. The purpose of this study was to examine the links between women's experiences of participation in a government-funded physical activity festival, their intentions to continue participation, and their participation behavior six months after the festival. Results from semi-structured, in-depth interviews with 20 women revealed that enhanced self-efficacy, intrinsic motivation, and supportive leadership had motivated the women's future intentions to participate. Follow-up surveys showed their levels of interest and participation in physical activity had been maintained. These results enhance our understanding of the relationship between key outcomes of women's physical activity participation and their persistence in physical activity.

  10. ABIN1 Determines Severity of Glomerulonephritis via Activation of Intrinsic Glomerular Inflammation.

    Science.gov (United States)

    Korte, Erik A; Caster, Dawn J; Barati, Michelle T; Tan, Min; Zheng, Shirong; Berthier, Celine C; Brosius, Frank C; Vieyra, Mark B; Sheehan, Ryan M; Kosiewicz, Michele; Wysoczynski, Marcin; Gaffney, Patrick M; Salant, David J; McLeish, Kenneth R; Powell, David W

    2017-12-01

    Transcription factor NF-κB regulates expression of numerous genes that control inflammation and is activated in glomerular cells in glomerulonephritis (GN). We previously identified genetic variants for a NF-κB regulatory, ubiquitin-binding protein ABIN1 as risk factors for GN in systemic autoimmunity. The goal was to define glomerular inflammatory events controlled by ABIN1 function in GN. Nephrotoxic serum nephritis was induced in wild-type (WT) and ubiquitin-binding deficient ABIN1[D485N] mice, and renal pathophysiology and glomerular inflammatory phenotypes were assessed. Proteinuria was also measured in ABIN1[D485N] mice transplanted with WT mouse bone marrow. Inflammatory activation of ABIN1[D472N] (D485N homolog) cultured human-derived podocytes, and interaction with primary human neutrophils were also assessed. Disruption of ABIN1 function exacerbated proteinuria, podocyte injury, glomerular NF-κB activity, glomerular expression of inflammatory mediators, and glomerular recruitment and retention of neutrophils in antibody-mediated nephritis. Transplantation of WT bone marrow did not prevent the increased proteinuria in ABIN1[D845N] mice. Tumor necrosis factor-stimulated enhanced expression and secretion of NF-κB-targeted proinflammatory mediators in ABIN1[D472N] cultured podocytes compared with WT cells. Supernatants from ABIN1[D472N] podocytes accelerated chemotaxis of human neutrophils, and ABIN1[D472N] podocytes displayed a greater susceptibility to injurious morphologic findings induced by neutrophil granule contents. These studies define a novel role for ABIN1 dysfunction and NF-κB in mediating GN through proinflammatory activation of podocytes. Copyright © 2017 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  11. Inhibition of the intrinsic factor X activating complex by protein S: evidence for a specific binding of protein S to factor VIII

    NARCIS (Netherlands)

    Koppelman, S.J.

    1995-01-01

    Protein S is a vitamin K-dependent nonenzymatic anticoagulant protein that acts as a cofactor to activated protein C. Recently it was shown that protein S inhibits the prothrombinase reaction independent of activated protein C. In this study, we show that protein S can also inhibit the intrinsic

  12. Energy transfer in structured and unstructured environments

    DEFF Research Database (Denmark)

    Iles-Smith, Jake; Dijkstra, Arend G.; Lambert, Neill

    2016-01-01

    We explore excitonic energy transfer dynamics in a molecular dimer system coupled to both structured and unstructured oscillator environments. By extending the reaction coordinate master equation technique developed by Iles-Smith et al. [Phys. Rev. A 90, 032114 (2014)], we go beyond the commonly...... used Born-Markov approximations to incorporate system-environment correlations and the resultant non-Markovian dynamical effects. We obtain energy transfer dynamics for both underdamped and overdamped oscillator environments that are in perfect agreement with the numerical hierarchical equations....... We find that though an enhancement of the dimer energy transfer rate can be obtained when compared to an unstructured environment, its magnitude is rather sensitive to both the dimer-peak resonance conditions and the relative strengths of the underdamped and overdamped contributions. (C) 2016 AIP...

  13. A Denotational Semantics for Communicating Unstructured Code

    Directory of Open Access Journals (Sweden)

    Nils Jähnig

    2015-03-01

    Full Text Available An important property of programming language semantics is that they should be compositional. However, unstructured low-level code contains goto-like commands making it hard to define a semantics that is compositional. In this paper, we follow the ideas of Saabas and Uustalu to structure low-level code. This gives us the possibility to define a compositional denotational semantics based on least fixed points to allow for the use of inductive verification methods. We capture the semantics of communication using finite traces similar to the denotations of CSP. In addition, we examine properties of this semantics and give an example that demonstrates reasoning about communication and jumps. With this semantics, we lay the foundations for a proof calculus that captures both, the semantics of unstructured low-level code and communication.

  14. Seeing diabetes: visual detection of glucose based on the intrinsic peroxidase-like activity of MoS2 nanosheets

    Science.gov (United States)

    Lin, Tianran; Zhong, Liangshuang; Guo, Liangqia; Fu, Fengfu; Chen, Guonan

    2014-09-01

    Molybdenum disulfide (MoS2) has attracted increasing research interest recently due to its unique physical, optical and electrical properties, correlated with its 2D ultrathin atomic-layered structure. Until now, however, great efforts have focused on its applications such as lithium ion batteries, transistors, and hydrogen evolution reactions. Herein, for the first time, MoS2 nanosheets are discovered to possess an intrinsic peroxidase-like activity and can catalytically oxidize 3,3',5,5'-tetramethylbenzidine (TMB) by H2O2 to produce a color reaction. The catalytic activity follows the typical Michaelis-Menten kinetics and is dependent on temperature, pH, H2O2 concentration, and reaction time. Based on this finding, a highly sensitive and selective colorimetric method for H2O2 and glucose detection is developed and applied to detect glucose in serum samples. Moreover, a simple, inexpensive, instrument-free and portable test kit for the visual detection of glucose in normal and diabetic serum samples is constructed by utilizing agarose hydrogel as a visual detection platform.Molybdenum disulfide (MoS2) has attracted increasing research interest recently due to its unique physical, optical and electrical properties, correlated with its 2D ultrathin atomic-layered structure. Until now, however, great efforts have focused on its applications such as lithium ion batteries, transistors, and hydrogen evolution reactions. Herein, for the first time, MoS2 nanosheets are discovered to possess an intrinsic peroxidase-like activity and can catalytically oxidize 3,3',5,5'-tetramethylbenzidine (TMB) by H2O2 to produce a color reaction. The catalytic activity follows the typical Michaelis-Menten kinetics and is dependent on temperature, pH, H2O2 concentration, and reaction time. Based on this finding, a highly sensitive and selective colorimetric method for H2O2 and glucose detection is developed and applied to detect glucose in serum samples. Moreover, a simple, inexpensive

  15. Longitudinal intrinsic brain activity changes in cirrhotic patients before and one month after liver transplantation

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Yue; Huang, Li Xiang; Xie, Shuang [Dept. of Radiology, Tianjin First Central Hospital, Tianjin (China); and others

    2017-04-15

    To evaluate the spontaneous brain activity alterations in liver transplantation (LT) recipients using resting-state functional MRI. Twenty cirrhotic patients as transplant candidates and 25 healthy controls (HCs) were included in this study. All patients repeated the MRI study one month after LT. Amplitude of low-frequency fluctuation (ALFF) values were compared between cirrhotic patients (both pre- and post-LT) and HCs as well as between the pre- and post-LT groups. The relationship between ALFF changes and venous blood ammonia levels and neuropsychological tests were investigated using Pearson's correlation analysis. In the cirrhotic patients, decreased ALFF in the vision-related regions (left lingual gyrus and calcarine), sensorimotor-related regions (left postcentral gyrus and middle cingulate cortex), and the default-mode network (bilateral precuneus and left inferior parietal lobule) were restored, and the increased ALFF in the temporal and frontal lobe improved in the early period after LT. The ALFF decreases persisted in the right supplementary motor area, inferior parietal lobule, and calcarine. The ALFF changes in the right precuneus were negatively correlated with changes in number connection test-A scores (r = 0.507, p < 0.05). LT improved spontaneous brain activity and the results for associated cognition tests. However, decreased ALFF in some areas persisted, and new-onset abnormal ALFF were possible, indicating that complete cognitive function recovery may need more time.

  16. LOLA Object Manipulation in an Unstructured Environment

    OpenAIRE

    LeGrand, Richard; Luo, Ren C.

    1996-01-01

    LOLA won the Office Cleanup event at the 1995 Robot Competition and Exhibition, held as part of the Fourteenth International Conference on Artificial Intelligence. The event called for a robot to pick up trash in an unstructured environment and sort it such that the recyclable trash winded up in the recycle bin and the regular trash in the trash bin. The only allowable information lola was given beforehand were model-based descriptions of the trash and recyclables, which it located using colo...

  17. Domain decomposition multigrid for unstructured grids

    Energy Technology Data Exchange (ETDEWEB)

    Shapira, Yair

    1997-01-01

    A two-level preconditioning method for the solution of elliptic boundary value problems using finite element schemes on possibly unstructured meshes is introduced. It is based on a domain decomposition and a Galerkin scheme for the coarse level vertex unknowns. For both the implementation and the analysis, it is not required that the curves of discontinuity in the coefficients of the PDE match the interfaces between subdomains. Generalizations to nonmatching or overlapping grids are made.

  18. Unstructured Polyhedral Mesh Thermal Radiation Diffusion

    International Nuclear Information System (INIS)

    Palmer, T.S.; Zika, M.R.; Madsen, N.K.

    2000-01-01

    Unstructured mesh particle transport and diffusion methods are gaining wider acceptance as mesh generation, scientific visualization and linear solvers improve. This paper describes an algorithm that is currently being used in the KULL code at Lawrence Livermore National Laboratory to solve the radiative transfer equations. The algorithm employs a point-centered diffusion discretization on arbitrary polyhedral meshes in 3D. We present the results of a few test problems to illustrate the capabilities of the radiation diffusion module

  19. The Tera Multithreaded Architecture and Unstructured Meshes

    Science.gov (United States)

    Bokhari, Shahid H.; Mavriplis, Dimitri J.

    1998-01-01

    The Tera Multithreaded Architecture (MTA) is a new parallel supercomputer currently being installed at San Diego Supercomputing Center (SDSC). This machine has an architecture quite different from contemporary parallel machines. The computational processor is a custom design and the machine uses hardware to support very fine grained multithreading. The main memory is shared, hardware randomized and flat. These features make the machine highly suited to the execution of unstructured mesh problems, which are difficult to parallelize on other architectures. We report the results of a study carried out during July-August 1998 to evaluate the execution of EUL3D, a code that solves the Euler equations on an unstructured mesh, on the 2 processor Tera MTA at SDSC. Our investigation shows that parallelization of an unstructured code is extremely easy on the Tera. We were able to get an existing parallel code (designed for a shared memory machine), running on the Tera by changing only the compiler directives. Furthermore, a serial version of this code was compiled to run in parallel on the Tera by judicious use of directives to invoke the "full/empty" tag bits of the machine to obtain synchronization. This version achieves 212 and 406 Mflop/s on one and two processors respectively, and requires no attention to partitioning or placement of data issues that would be of paramount importance in other parallel architectures.

  20. Computing Flows Using Chimera and Unstructured Grids

    Science.gov (United States)

    Liou, Meng-Sing; Zheng, Yao

    2006-01-01

    DRAGONFLOW is a computer program that solves the Navier-Stokes equations of flows in complexly shaped three-dimensional regions discretized by use of a direct replacement of arbitrary grid overlapping by nonstructured (DRAGON) grid. A DRAGON grid (see figure) is a combination of a chimera grid (a composite of structured subgrids) and a collection of unstructured subgrids. DRAGONFLOW incorporates modified versions of two prior Navier-Stokes-equation-solving programs: OVERFLOW, which is designed to solve on chimera grids; and USM3D, which is used to solve on unstructured grids. A master module controls the invocation of individual modules in the libraries. At each time step of a simulated flow, DRAGONFLOW is invoked on the chimera portion of the DRAGON grid in alternation with USM3D, which is invoked on the unstructured subgrids of the DRAGON grid. The USM3D and OVERFLOW modules then immediately exchange their solutions and other data. As a result, USM3D and OVERFLOW are coupled seamlessly.

  1. SP-R210 (Myo18A Isoforms as Intrinsic Modulators of Macrophage Priming and Activation.

    Directory of Open Access Journals (Sweden)

    Linlin Yang

    Full Text Available The surfactant protein (SP-A receptor SP-R210 has been shown to increase phagocytosis of SP-A-bound pathogens and to modulate cytokine secretion by immune cells. SP-A plays an important role in pulmonary immunity by enhancing opsonization and clearance of pathogens and by modulating macrophage inflammatory responses. Alternative splicing of the Myo18A gene results in two isoforms: SP-R210S and SP-R210L, with the latter predominantly expressed in alveolar macrophages. In this study we show that SP-A is required for optimal expression of SP-R210L on alveolar macrophages. Interestingly, pre-treatment with SP-A prepared by different methods either enhances or suppresses responsiveness to LPS, possibly due to differential co-isolation of SP-B or other proteins. We also report that dominant negative disruption of SP-R210L augments expression of receptors including SR-A, CD14, and CD36, and enhances macrophages' inflammatory response to TLR stimulation. Finally, because SP-A is known to modulate CD14, we used a variety of techniques to investigate how SP-R210 mediates the effect of SP-A on CD14. These studies revealed a novel physical association between SP-R210S, CD14, and SR-A leading to an enhanced response to LPS, and found that SP-R210L and SP-R210S regulate internalization of CD14 via distinct macropinocytosis-like mechanisms. Together, our findings support a model in which SP-R210 isoforms differentially regulate trafficking, expression, and activation of innate immune receptors on macrophages.

  2. Molecular aspects of core-shell intrinsic defect induced enhanced antibacterial activity of ZnO nanocrystals.

    Science.gov (United States)

    Verma, Suresh K; Jha, Ealisha; Panda, Pritam Kumar; Das, Jugal K; Thirumurugan, Arun; Suar, Mrutyunjay; Parashar, Sks

    2018-01-01

    To investigate molecular aspects of the antibacterial effect of size-dependent core-shell intrinsic defects of nanocrystalline ZnO synthesized through high energy ball milling technique. Mechanically synthesized and characterized 7, 10 and 15 h milled ZnO nanoparticles were evaluated for antibacterial activity with molecular investigation by computational molecular docking. Synthesized ZnO nanoparticles displayed shrinkage of core and increase of shell with reduction in size of bulk ZnO particles from 250 to 80, 40 and 20 nm and increase in zeta potential up to -19 mV in 7, 10 and 15 h nano ZnO. Antibacterial activity was found increased with decrease in size due to increased reactive oxygen species and membrane damage in bacteria. Synthesized nano ZnO exhibit size-dependent antibacterial action as consequences of interactions with cell membrane proteins via hydrogen bond interaction with amino acid residues followed by internalization, membrane depolarization and induction of reactive oxygen species generation.

  3. Peptide affinity analysis of proteins that bind to an unstructured NH2-terminal region of the osmoprotective transcription factor NFAT5

    Science.gov (United States)

    DuMond, Jenna F.; Ramkissoon, Kevin; Zhang, Xue; Izumi, Yuichiro; Wang, Xujing; Eguchi, Koji; Gao, Shouguo; Mukoyama, Masashi; Ferraris, Joan D.

    2016-01-01

    NFAT5 is an osmoregulated transcription factor that particularly increases expression of genes involved in protection against hypertonicity. Transcription factors often contain unstructured regions that bind co-regulatory proteins that are crucial for their function. The NH2-terminal region of NFAT5 contains regions predicted to be intrinsically disordered. We used peptide aptamer-based affinity chromatography coupled with mass spectrometry to identify protein preys pulled down by one or more overlapping 20 amino acid peptide baits within a predicted NH2-terminal unstructured region of NFAT5. We identify a total of 467 unique protein preys that associate with at least one NH2-terminal peptide bait from NFAT5 in either cytoplasmic or nuclear extracts from HEK293 cells treated with elevated, normal, or reduced NaCl concentrations. Different sets of proteins are pulled down from nuclear vs. cytoplasmic extracts. We used GeneCards to ascertain known functions of the protein preys. The protein preys include many that were previously known, but also many novel ones. Consideration of the novel ones suggests many aspects of NFAT5 regulation, interaction and function that were not previously appreciated, for example, hypertonicity inhibits NFAT5 by sumoylating it and the NFAT5 protein preys include components of the CHTOP complex that desumoylate proteins, an action that should contribute to activation of NFAT5. PMID:26757802

  4. Two Isoforms of Yersinia pestis Plasminogen Activator Pla: Intraspecies Distribution, Intrinsic Disorder Propensity, and Contribution to Virulence.

    Science.gov (United States)

    Dentovskaya, Svetlana V; Platonov, Mikhail E; Svetoch, Tat'yana E; Kopylov, Pavel Kh; Kombarova, Tat'yana I; Ivanov, Sergey A; Shaikhutdinova, Rima Z; Kolombet, Lyubov' V; Chauhan, Sadhana; Ablamunits, Vitaly G; Motin, Vladimir L; Uversky, Vladimir N; Anisimov, Andrey P

    2016-01-01

    It has been shown previously that several endemic Y. pestis isolates with limited virulence contained the I259 isoform of the outer membrane protease Pla, while the epidemic highly virulent strains possessed only the T259 Pla isoform. Our sequence analysis of the pla gene from 118 Y. pestis subsp. microtus strains revealed that the I259 isoform was present exclusively in the endemic strains providing a convictive evidence of more ancestral origin of this isoform. Analysis of the effects of the I259T polymorphism on the intrinsic disorder propensity of Pla revealed that the I259T mutation slightly increases the intrinsic disorder propensity of the C-terminal tail of Pla and makes this protein slightly more prone for disorder-based protein-protein interactions, suggesting that the T259 Pla could be functionally more active than the I259 Pla. This assumption was proven experimentally by assessing the coagulase and fibrinolytic activities of the two Pla isoforms in human plasma, as well as in a direct fluorometric assay with the Pla peptide substrate. The virulence testing of Pla-negative or expressing the I259 and T259 Pla isoforms Y. pestis subsp. microtus and subsp. pestis strains did not reveal any significant difference in LD50 values and dose-dependent survival assays between them by using a subcutaneous route of challenge of mice and guinea pigs or intradermal challenge of mice. However, a significant decrease in time-to-death was observed in animals infected with the epidemic T259 Pla-producing strains as compared to the parent Pla-negative variants. Survival curves of the endemic I259 Pla+ strains fit between them, but significant difference in mean time to death post infection between the Pla-strains and their I259 Pla+ variants could be seen only in the isogenic set of subsp. pestis strains. These findings suggest an essential role for the outer membrane protease Pla evolution in Y. pestis bubonic infection exacerbation that is necessary for intensification

  5. Novel Role for Protein Inhibitor of Activated STAT 4 (PIAS4) in the Restriction of Herpes Simplex Virus 1 by the Cellular Intrinsic Antiviral Immune Response.

    Science.gov (United States)

    Conn, Kristen L; Wasson, Peter; McFarlane, Steven; Tong, Lily; Brown, James R; Grant, Kyle G; Domingues, Patricia; Boutell, Chris

    2016-05-01

    Small ubiquitin-like modifier (SUMO) is used by the intrinsic antiviral immune response to restrict viral pathogens, such as herpes simplex virus 1 (HSV-1). Despite characterization of the host factors that rely on SUMOylation to exert their antiviral effects, the enzymes that mediate these SUMOylation events remain to be defined. We show that unconjugated SUMO levels are largely maintained throughout infection regardless of the presence of ICP0, the HSV-1 SUMO-targeted ubiquitin ligase. Moreover, in the absence of ICP0, high-molecular-weight SUMO-conjugated proteins do not accumulate if HSV-1 DNA does not replicate. These data highlight the continued importance for SUMO signaling throughout infection. We show that the SUMO ligase protein inhibitor of activated STAT 4 (PIAS4) is upregulated during HSV-1 infection and localizes to nuclear domains that contain viral DNA. PIAS4 is recruited to sites associated with HSV-1 genome entry through SUMO interaction motif (SIM)-dependent mechanisms that are destabilized by ICP0. In contrast, PIAS4 accumulates in replication compartments through SIM-independent mechanisms irrespective of ICP0 expression. Depletion of PIAS4 enhances the replication of ICP0-null mutant HSV-1, which is susceptible to restriction by the intrinsic antiviral immune response. The mechanisms of PIAS4-mediated restriction are synergistic with the restriction mechanisms of a characterized intrinsic antiviral factor, promyelocytic leukemia protein, and are antagonized by ICP0. We provide the first evidence that PIAS4 is an intrinsic antiviral factor. This novel role for PIAS4 in intrinsic antiviral immunity contrasts with the known roles of PIAS proteins as suppressors of innate immunity. Posttranslational modifications with small ubiquitin-like modifier (SUMO) proteins regulate multiple aspects of host immunity and viral replication. The protein inhibitor of activated STAT (PIAS) family of SUMO ligases is predominantly associated with the suppression of

  6. About some new possibilities of increasing the intrinsic output power of the photon beam: for definite laser active media

    Science.gov (United States)

    Isarie, Claudiu; Voineag, Anca; Isarie, Ilie; Oprean, Constantin; Nastase, Dan

    2006-02-01

    Producers and users of laser beam equipment have some wishes as: to have economic machines, the machines must be as small and light as possible, the power supply must be also very light and small. All mentioned desires - and other related with them - may be accomplished by an adequate efficiency of laser beam process. As we know, the first laser began with 2% efficiency. In the process of time, the efficiency increased progressive, and in this way was possible after the year 2000 to have laser weapons mounted on jet planes, including the power supply. In a laser system, there are many points where photons are lost. To reduce this losses, we must treat with the utmost care all points of the "chain" where photons could be lost. We mention: the resonance cavity - inside -, the exit from the resonance cavity, the mirrors and lenses and also other related factors. Each improvement in one of the mentioned points could contribute to the general raising of the laser machine efficiency. Authors were concerned first with some possibilities of increasing the intrinsic output of the photon beam, for definite laser active media, by applying some fields inside the resonance cavity. Such fields, characterized by nature, energy, frequency and other parameters could influence positive the efficiency of the photon beam emission.

  7. Natural Optical Activity of Chiral Epoxides: the Influence of Structure and Environment on the Intrinsic Chiroptical Response

    Science.gov (United States)

    Lemler, Paul M.; Craft, Clayton L.; Vaccaro, Patrick

    2017-06-01

    Chiral epoxides built upon nominally rigid frameworks that incorporate aryl substituents have been shown to provide versatile backbones for asymmetric syntheses designed to generate novel pharmaceutical and catalytic agents. The ubiquity of these species has motivated the present studies of their intrinsic (solvent-free) circular birefringence (CB), the measurement of which serves as a benchmark for quantum-chemical predictions of non-resonant chiroptical behavior and as a beachhead for understanding the often-pronounced mediation of such properties by environmental perturbations (e.g., solvation). The optical rotatory dispersion (or wavelength-resolved CB) of (R)-styrene oxide (R-SO) and (S,S)-phenylpropylene oxide (S-PPO) have been interrogated under ambient solvated and isolated conditions, where the latter efforts exploited the ultrasensitive techniques of cavity ring-down polarimetry. Both of the targeted systems display marked solvation effects as evinced by changes the magnitude and (in the case of R-SO) the sign of the extracted specific optical rotation, with the anomalously large response evoked from S-PPO distinguishing it from other members of the epoxide family. Linear-response calculations of dispersive optical activity have been performed at both density-functional and coupled-cluster levels of theory to unravel the structural and electronic origins of experimental findings, thereby suggesting the possible involvement of hindered torsional motion along dihedral coordinates adjoining phenyl and epoxide moieties.

  8. The glucagon-like peptide 1 receptor agonist enhances intrinsic peroxisome proliferator-activated receptor γ activity in endothelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Onuma, Hirohisa; Inukai, Kouichi, E-mail: kinukai@ks.kyorin-u.ac.jp; Kitahara, Atsuko; Moriya, Rie; Nishida, Susumu; Tanaka, Toshiaki; Katsuta, Hidenori; Takahashi, Kazuto; Sumitani, Yoshikazu; Hosaka, Toshio; Ishida, Hitoshi

    2014-08-22

    Highlights: • PPARγ activation was involved in the GLP-1-mediated anti-inflammatory action. • Exendin-4 enhanced endogenous PPARγ transcriptional activity in HUVECs. • H89, a PKA inhibitor, abolished GLP-1-induced PPARγ enhancement. • The anti-inflammatory effects of GLP-1 may be explained by PPARγ activation. - Abstract: Recent studies have suggested glucagon-like peptide-1 (GLP-1) signaling to exert anti-inflammatory effects on endothelial cells, although the precise underlying mechanism remains to be elucidated. In the present study, we investigated whether PPARγ activation is involved in the GLP-1-mediated anti-inflammatory action on endothelial cells. When we treated HUVEC cells with 0.2 ng/ml exendin-4, a GLP-1 receptor agonist, endogenous PPARγ transcriptional activity was significantly elevated, by approximately 20%, as compared with control cells. The maximum PPARγ activity enhancing effect of exendin-4 was observed 12 h after the initiation of incubation with exendin-4. As H89, a PKA inhibitor, abolished GLP-1-induced PPARγ enhancement, the signaling downstream from GLP-1 cross-talk must have been involved in PPARγ activation. In conclusion, our results suggest that GLP-1 has the potential to induce PPARγ activity, partially explaining the anti-inflammatory effects of GLP-1 on endothelial cells. Cross-talk between GLP-1 signaling and PPARγ activation would have major impacts on treatments for patients at high risk for cardiovascular disease.

  9. 3D Feature Extraction for Unstructured Grids

    Science.gov (United States)

    Silver, Deborah

    1996-01-01

    Visualization techniques provide tools that help scientists identify observed phenomena in scientific simulation. To be useful, these tools must allow the user to extract regions, classify and visualize them, abstract them for simplified representations, and track their evolution. Object Segmentation provides a technique to extract and quantify regions of interest within these massive datasets. This article explores basic algorithms to extract coherent amorphous regions from two-dimensional and three-dimensional scalar unstructured grids. The techniques are applied to datasets from Computational Fluid Dynamics and those from Finite Element Analysis.

  10. Best Practices for Unstructured Grid Shock-Fitting

    Science.gov (United States)

    McCoud, Peter L.

    2017-01-01

    Unstructured grid solvers have well-known issues predicting surface heat fluxes when strong shocks are present. Various efforts have been made to address the underlying numerical issues that cause the erroneous predictions. The present work addresses some of the shortcomings of unstructured grid solvers, not by addressing the numerics, but by applying structured grid best practices to unstructured grids. A methodology for robust shock detection and shock-fitting is outlined and applied to production-relevant cases. Results

  11. Unstructured Navier-Stokes Analysis of Full TCA Configuration

    Science.gov (United States)

    Frink, Neal T.; Pirzadeh, Shahyar Z.

    1999-01-01

    This paper presents an Unstructured Navier-Stokes Analysis of Full TCA (Technology Concept Airplane) Configuration. The topics include: 1) Motivation; 2) Milestone and approach; 3) Overview of the unstructured-grid system; 4) Results on full TCA W/B/N/D/E configuration; 5) Concluding remarks; and 6) Future directions.

  12. Multiphase Flow of Immiscible Fluids on Unstructured Moving Meshes

    DEFF Research Database (Denmark)

    Misztal, Marek Krzysztof; Erleben, Kenny; Bargteil, Adam

    2013-01-01

    In this paper, we present a method for animating multiphase flow of immiscible fluids using unstructured moving meshes. Our underlying discretization is an unstructured tetrahedral mesh, the deformable simplicial complex (DSC), that moves with the flow in a Lagrangian manner. Mesh optimization op...

  13. Extraction of information from unstructured text

    Energy Technology Data Exchange (ETDEWEB)

    Irwin, N.H.; DeLand, S.M.; Crowder, S.V.

    1995-11-01

    Extracting information from unstructured text has become an emphasis in recent years due to the large amount of text now electronically available. This status report describes the findings and work done by the end of the first year of a two-year LDRD. Requirements of the approach included that it model the information in a domain independent way. This means that it would differ from current systems by not relying on previously built domain knowledge and that it would do more than keyword identification. Three areas that are discussed and expected to contribute to a solution include (1) identifying key entities through document level profiling and preprocessing, (2) identifying relationships between entities through sentence level syntax, and (3) combining the first two with semantic knowledge about the terms.

  14. Partitioning of unstructured meshes for load balancing

    International Nuclear Information System (INIS)

    Martin, O.C.; Otto, S.W.

    1994-01-01

    Many large-scale engineering and scientific calculations involve repeated updating of variables on an unstructured mesh. To do these types of computations on distributed memory parallel computers, it is necessary to partition the mesh among the processors so that the load balance is maximized and inter-processor communication time is minimized. This can be approximated by the problem, of partitioning a graph so as to obtain a minimum cut, a well-studied combinatorial optimization problem. Graph partitioning algorithms are discussed that give good but not necessarily optimum solutions. These algorithms include local search methods recursive spectral bisection, and more general purpose methods such as simulated annealing. It is shown that a general procedure enables to combine simulated annealing with Kernighan-Lin. The resulting algorithm is both very fast and extremely effective. (authors) 23 refs., 3 figs., 1 tab

  15. Recognition and characterization of unstructured environmental sounds

    Science.gov (United States)

    Chu, Selina

    2011-12-01

    Environmental sounds are what we hear everyday, or more generally sounds that surround us ambient or background audio. Humans utilize both vision and hearing to respond to their surroundings, a capability still quite limited in machine processing. The first step toward achieving multimodal input applications is the ability to process unstructured audio and recognize audio scenes (or environments). Such ability would have applications in content analysis and mining of multimedia data or improving robustness in context aware applications through multi-modality, such as in assistive robotics, surveillances, or mobile device-based services. The goal of this thesis is on the characterization of unstructured environmental sounds for understanding and predicting the context surrounding of an agent or device. Most research on audio recognition has focused primarily on speech and music. Less attention has been paid to the challenges and opportunities for using audio to characterize unstructured audio. My research focuses on investigating challenging issues in characterizing unstructured environmental audio and to develop novel algorithms for modeling the variations of the environment. The first step in building a recognition system for unstructured auditory environment was to investigate on techniques and audio features for working with such audio data. We begin by performing a study that explore suitable features and the feasibility of designing an automatic environment recognition system using audio information. In my initial investigation to explore the feasibility of designing an automatic environment recognition system using audio information, I have found that traditional recognition and feature extraction for audio were not suitable for environmental sound, as they lack any type of structures, unlike those of speech and music which contain formantic and harmonic structures, thus dispelling the notion that traditional speech and music recognition techniques can simply

  16. Protein intrinsic disorder in plants.

    Science.gov (United States)

    Pazos, Florencio; Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto

    2013-09-12

    To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously) with different partners. Similarly, they also serve as signal integrators in signaling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms cannot escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.

  17. Protein intrinsic disorder in plants

    Directory of Open Access Journals (Sweden)

    Florencio ePazos

    2013-09-01

    Full Text Available To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously with different partners. Similarly, they also serve as signal integrators in signalling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms can not escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.

  18. Fresh tar (from biomass gasification) destruction with downstream catalysts: comparison of their intrinsic activity with a realistic kinetic model

    Energy Technology Data Exchange (ETDEWEB)

    Corella, J.; Narvaez, I.; Orio, A. [Complutense Univ. of Madrid (Spain). Dept. of Chemical Engineering

    1996-12-31

    A model for fresh tar destruction over catalysts placed downstream a biomass gasifier is presented. It includes the stoichio-metry and the calculation of the kinetic constants for the tar destruction. Catalysts studied include commercial Ni steam reforming catalysts and calcinated dolomites. Kinetic constants for tar destruction are calculated for several particle sizes, times- on-stream and temperatures of the catalyst and equivalence ratios in the gasifier. Such intrinsic kinetic constants allow a rigorous or scientific comparison of solids and conditions to be used in an advanced gasification process. (orig.) 4 refs.

  19. Mesh Adaptation and Shape Optimization on Unstructured Meshes, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — In this SBIR CRM proposes to implement the entropy adjoint method for solution adaptive mesh refinement into the Loci/CHEM unstructured flow solver. The scheme will...

  20. High Performance Parallel Multigrid Algorithms for Unstructured Grids

    Science.gov (United States)

    Frederickson, Paul O.

    1996-01-01

    We describe a high performance parallel multigrid algorithm for a rather general class of unstructured grid problems in two and three dimensions. The algorithm PUMG, for parallel unstructured multigrid, is related in structure to the parallel multigrid algorithm PSMG introduced by McBryan and Frederickson, for they both obtain a higher convergence rate through the use of multiple coarse grids. Another reason for the high convergence rate of PUMG is its smoother, an approximate inverse developed by Baumgardner and Frederickson.

  1. Diagnostic tools for 3D unstructured oceanographic data

    Science.gov (United States)

    Cotter, C. J.; Gorman, G. J.

    2008-01-01

    Most ocean models in current use are built upon structured meshes. It follows that most existing tools for extracting diagnostic quantities (volume and surface integrals, for example) from ocean model output are constructed using techniques and software tools which assume structured meshes. The greater complexity inherent in unstructured meshes (especially fully unstructured grids which are unstructured in the vertical as well as the horizontal direction) has left some oceanographers, accustomed to traditional methods, unclear on how to calculate diagnostics on these meshes. In this paper we show that tools for extracting diagnostic data from the new generation of unstructured ocean models can be constructed with relative ease using open source software. Higher level languages such as Python, in conjunction with packages such as NumPy, SciPy, VTK and MayaVi, provide many of the high-level primitives needed to perform 3D visualisation and evaluate diagnostic quantities, e.g. density fluxes. We demonstrate this in the particular case of calculating flux of vector fields through isosurfaces, using flow data obtained from the unstructured mesh finite element ocean code ICOM, however this tool can be applied to model output from any unstructured grid ocean code.

  2. Distinctive activation patterns under intrinsically versus extrinsically driven cognitive loads in prefrontal cortex: a near-infrared spectroscopy study using a driving video game.

    Science.gov (United States)

    Liu, Tao; Saito, Hirofumi; Oi, Misato

    2012-01-11

    To investigate the neural bases of intrinsically and extrinsically driven cognitive loads in daily life, we measured repetitively prefrontal activation in three (one control and two experimental) groups during a driving video game using near-infrared spectroscopy. The control group drove to goal four times with distinct route-maps illustrating default turning points. In contrast, the memory group drove the memorized default route without a route-map, and the emergency group drove with a route-map, but was instructed to change the default route by an extrinsically given verbal command (turn left or right) as an envisioned emergency. The predictability of a turning point in the route in each group was relatively different: due to extrinsic dictate of others in the emergency group, intrinsic memory in the memory group, and route-map aid in the control group. We analyzed concentration changes of oxygenated hemoglobin (CoxyHb) in the three critical periods (pre-turning, actual-turning, and post-turning). The emergency group showed a significantly increasing pattern of CoxyHb throughout the three periods, and a significant reduction in CoxyHb throughout the repetitive trials, but the memory group did not, even though both experimental groups showed higher activation than the control group in the pre-turning period. These results suggest that the prefrontal cortex differentiates the intrinsically (memory) and the extrinsically (dictate of others) driven cognitive loads according to the predictability of turning behavior, although the two types of cognitive loads commonly show increasing activation in the pre-turning period as the preparation effect. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  3. Arsenite induces apoptosis in human mesenchymal stem cells by altering Bcl-2 family proteins and by activating intrinsic pathway

    International Nuclear Information System (INIS)

    Yadav, Santosh; Shi Yongli; Wang Feng; Wang He

    2010-01-01

    Purpose: Environmental exposure to arsenic is an important public health issue. The effects of arsenic on different tissues and organs have been intensively studied. However, the effects of arsenic on bone marrow mesenchymal stem cells (MSCs) have not been reported. This study is designed to investigate the cell death process caused by arsenite and its related underlying mechanisms on MSCs. The rationale is that absorbed arsenic in the blood circulation can reach to the bone marrow and may affect the cell survival of MSCs. Methods: MSCs of passage 1 were purchased from Tulane University, grown till 70% confluency level and plated according to the experimental requirements followed by treatment with arsenite at various concentrations and time points. Arsenite (iAs III ) induced cytotoxic effects were confirmed by cell viability and cell cycle analysis. For the presence of canonic apoptosis markers; DNA damage, exposure of intramembrane phosphotidylserine, protein and m-RNA expression levels were analyzed. Results: iAs III induced growth inhibition, G2-M arrest and apoptotic cell death in MSCs, the apoptosis induced by iAs III in the cultured MSCs was, via altering Bcl-2 family proteins and by involving intrinsic pathway. Conclusion: iAs III can induce apoptosis in bone marrow-derived MSCs via Bcl-2 family proteins, regulating intrinsic apoptotic pathway. Due to the multipotency of MSC, acting as progenitor cells for a variety of connective tissues including bone, adipose, cartilage and muscle, these effects of arsenic may be important in assessing the health risk of the arsenic compounds and understanding the mechanisms of arsenic-induced harmful effects.

  4. Roles of visual experience and intrinsic mechanism in the activity-dependent self-organization of orientation maps: theory and experiment.

    Science.gov (United States)

    Tanaka, Shigeru; Miyashita, Masanobu; Ribot, Jérôme

    2004-01-01

    It is widely accepted that functional maps in the mammalian visual cortex such as ocular dominance columns and orientation columns are formed depending on neural activity. There is still, however, controversy on how much visual experience contributes to the map formation during development. In the present study, we address this issue from mathematical modeling and experimental investigation. Using a model of activity-dependent self-organization of geniculo-cortical afferent inputs, we showed that spontaneous activity in the LGN can produce orientation maps, while the exposure to drifting gratings results in sharply segregated orientation maps as observed in cat visual cortex. The restricted exposure to a single orientation of the grating led to the over-representation of the exposed orientation, which was moderated by the contribution of learning based on the spontaneous activity. These theoretical results were confirmed by intrinsic optical recordings from area 18 of kittens reared under various visual conditions.

  5. Carbon monoxide and cyanide as intrinsic ligands to iron in the active site of [NiFe]-hydrogenases. NiFe(CN)2CO, biology's way to activate H2

    NARCIS (Netherlands)

    Pierik, A.J.; Roseboom, W.; Happe, R.P.; Bagley, K.A.; Albracht, S.P.J.

    1999-01-01

    Infrared-spectroscopic studies on the [NiFe]-hydrogenase of Chromatium vinosum-enriched in 15N or 13C, as well as chemical analyses, show that this enzyme contains three non-exchangeable, intrinsic, diatomic molecules as ligands to the active site, one carbon monoxide molecule and two cyanide

  6. Numerical treatment of wave breaking on unstructured finite volume approximations for extended Boussinesq-type equations

    Science.gov (United States)

    Kazolea, M.; Delis, A. I.; Synolakis, C. E.

    2014-08-01

    A new methodology is presented to handle wave breaking over complex bathymetries in extended two-dimensional Boussinesq-type (BT) models which are solved by an unstructured well-balanced finite volume (FV) scheme. The numerical model solves the 2D extended BT equations proposed by Nwogu (1993), recast in conservation law form with a hyperbolic flux identical to that of the Non-linear Shallow Water (NSW) equations. Certain criteria, along with their proper implementation, are established to characterize breaking waves. Once breaking waves are recognized, we switch locally in the computational domain from the BT to NSW equations by suppressing the dispersive terms in the vicinity of the wave fronts. Thus, the shock-capturing features of the FV scheme enable an intrinsic representation of the breaking waves, which are handled as shocks by the NSW equations. An additional methodology is presented on how to perform a stable switching between the BT and NSW equations within the unstructured FV framework. Extensive validations are presented, demonstrating the performance of the proposed wave breaking treatment, along with some comparisons with other well-established wave breaking mechanisms that have been proposed for BT models.

  7. Nonlinear Projective-Iteration Methods for Solving Transport Problems on Regular and Unstructured Grids

    International Nuclear Information System (INIS)

    Dmitriy Y. Anistratov; Adrian Constantinescu; Loren Roberts; William Wieselquist

    2007-01-01

    This is a project in the field of fundamental research on numerical methods for solving the particle transport equation. Numerous practical problems require to use unstructured meshes, for example, detailed nuclear reactor assembly-level calculations, large-scale reactor core calculations, radiative hydrodynamics problems, where the mesh is determined by hydrodynamic processes, and well-logging problems in which the media structure has very complicated geometry. Currently this is an area of very active research in numerical transport theory. main issues in developing numerical methods for solving the transport equation are the accuracy of the numerical solution and effectiveness of iteration procedure. The problem in case of unstructured grids is that it is very difficult to derive an iteration algorithm that will be unconditionally stable

  8. Delayed intrinsic activation of an NMDA-independent CaM-kinase II in a critical time window is necessary for late consolidation of an associative memory.

    Science.gov (United States)

    Wan, Huimin; Mackay, Beth; Iqbal, Hassan; Naskar, Souvik; Kemenes, György

    2010-01-06

    Calcium/calmodulin-dependent kinases (CaM-kinases) are central to various forms of long-term memory (LTM) in a number of evolutionarily diverse organisms. However, it is still largely unknown what contributions specific CaM-kinases make to different phases of the same specific type of memory, such as acquisition, or early, intermediate, and late consolidation of associative LTM after classical conditioning. Here, we investigated the involvement of CaM-kinase II (CaMKII) in different phases of associative LTM induced by single-trial reward classical conditioning in Lymnaea, a well established invertebrate experimental system for studying molecular mechanisms of learning and memory. First, by using a general CaM-kinase inhibitor, KN-62, we found that CaM-kinase activation was necessary for acquisition and late consolidation, but not early or intermediate consolidation or retrieval of LTM. Then, we used Western blot-based phosphorylation assays and treatment with CaMKIINtide to identify CaMKII as the main CaM-kinase, the intrinsic activation of which, in a critical time window ( approximately 24 h after learning), is central to late consolidation of LTM. Additionally, using MK-801 and CaMKIINtide we found that acquisition was dependent on both NMDA receptor and CaMKII activation. However, unlike acquisition, CaMKII-dependent late memory consolidation does not require the activation of NMDA receptors. Our new findings support the notion that even apparently stable memory traces may undergo further molecular changes and identify NMDA-independent intrinsic activation of CaMKII as a mechanism underlying this "lingering consolidation." This process may facilitate the preservation of LTM in the face of protein turnover or active molecular processes that underlie forgetting.

  9. Identifying the neural substrates of intrinsic motivation during task performance.

    Science.gov (United States)

    Lee, Woogul; Reeve, Johnmarshall

    2017-10-01

    Intrinsic motivation is the inherent tendency to seek out novelty and challenge, to explore and investigate, and to stretch and extend one's capacities. When people imagine performing intrinsically motivating tasks, they show heightened anterior insular cortex (AIC) activity. To fully explain the neural system of intrinsic motivation, however, requires assessing neural activity while people actually perform intrinsically motivating tasks (i.e., while answering curiosity-inducing questions or solving competence-enabling anagrams). Using event-related functional magnetic resonance imaging, we found that the neural system of intrinsic motivation involves not only AIC activity, but also striatum activity and, further, AIC-striatum functional interactions. These findings suggest that subjective feelings of intrinsic satisfaction (associated with AIC activations), reward processing (associated with striatum activations), and their interactions underlie the actual experience of intrinsic motivation. These neural findings are consistent with the conceptualization of intrinsic motivation as the pursuit and satisfaction of subjective feelings (interest and enjoyment) as intrinsic rewards.

  10. Reduced Hyperpolarization-Activated Current Contributes to Enhanced Intrinsic Excitability in Cultured Neonatal Hippocampal Neurons from PrP−/− Mice

    Directory of Open Access Journals (Sweden)

    Jing eFan

    2016-03-01

    Full Text Available Genetic ablation of cellular prion protein (PrPC has been linked to increased neuronal excitability and synaptic activity in the hippocampus. We have previously shown that synaptic activity in hippocampi of PrP-null mice is increased due to enhanced N-methyl-D-aspartate receptor (NMDAR function. Here, we focused on the effect of PRNP gene knock-out (KO on intrinsic neuronal excitability, and in particular, the underlying ionic mechanism in hippocampal neurons cultured from P0 mouse pups. We found that the absence of PrPC profoundly affected the firing properties of cultured hippocampal neurons in the presence of synaptic blockers. The membrane impedance was greater in PrP-null neurons, and this difference was abolished by the hyperpolarization-activated cyclic nucleotide-gated (HCN channel blocker ZD7288 (100 µM. HCN channel activity appeared to be functionally regulated by PrPC. The amplitude of voltage sag, a characteristic of activating HCN channel current (Ih, was decreased in null mice. Moreover, Ih peak current was reduced, along with a hyperpolarizing shift in activation gating and slower kinetics. However, neither HCN1 nor HCN2 formed a biochemical complex with PrPC. These results suggest that the absence of PrP downregulates the activity of HCN channels through activation of a cell signaling pathway rather than through direct interactions. This in turn contributes to an increase in membrane impedance to potentiate neuronal excitability.

  11. Older but still fluent? Insights from the intrinsically active baseline configuration of the aging brain using a data driven graph-theoretical approach.

    Science.gov (United States)

    Muller, Angela M; Mérillat, Susan; Jäncke, Lutz

    2016-02-15

    A major part of our knowledge about the functioning of the aging brain comes from task-induced activation paradigms. However, the aging brain's intrinsic functional organization may be already a limiting factor for the outcome of an actual behavior. In order to get a better understanding of how this functional baseline configuration of the aging brain may affect cognitive performance, we analyzed task-free fMRI data of older 186 participants (mean age=70.4, 97 female) and their performance data in verbal fluency: First, we conducted an intrinsic connectivity contrast analysis (ICC) for the purpose of evaluating the brain regions whose degree of connectedness was significantly correlated with fluency performance. Secondly, using connectivity analyses we investigated how the clusters from the ICC functionally related to the other major resting-state networks. Apart from the importance of intact fronto-parietal long-range connections, the preserved capacity of the DMN for a finely attuned interaction with the executive-control network and the language network seems to be crucial for successful verbal fluency performance in older people. We provide further evidence that the right frontal regions might be more prominently affected by age-related decline. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Semantic Annotation of Unstructured Documents Using Concepts Similarity

    Directory of Open Access Journals (Sweden)

    Fernando Pech

    2017-01-01

    Full Text Available There is a large amount of information in the form of unstructured documents which pose challenges in the information storage, search, and retrieval. This situation has given rise to several information search approaches. Some proposals take into account the contextual meaning of the terms specified in the query. Semantic annotation technique can help to retrieve and extract information in unstructured documents. We propose a semantic annotation strategy for unstructured documents as part of a semantic search engine. In this proposal, ontologies are used to determine the context of the entities specified in the query. Our strategy for extracting the context is focused on concepts similarity. Each relevant term of the document is associated with an instance in the ontology. The similarity between each of the explicit relationships is measured through the combination of two types of associations: the association between each pair of concepts and the calculation of the weight of the relationships.

  13. An efficient massively parallel Euler solver for unstructured grids

    International Nuclear Information System (INIS)

    Hammond, S.W.; Barth, T.J.

    1991-01-01

    A data parallel mesh-vertex upwind finite-volume scheme for solving the Euler equations on triangular unstructured meshes is described. A novel vertex-based partitioning of the problem is introduced which minimizes the computation and communication costs associated with distributing the computation to the processors of a massively parallel computer. Finally, the performance of this unstructured computation on 8K processors of the Connection Machine CM-2 is compared with one processor of a Cray-YMP. The experiments show that 8K processors of the CM-2 achieve approximately 70 percent of the performance of one processor of the Cray-YMP on the unstructured mesh computations described here. 8 refs

  14. Synergistic inhibition of the intrinsic factor X activation by protein S and C4b-binding protein

    NARCIS (Netherlands)

    Koppelman, S. J.; van't Veer, C.; Sixma, J. J.; Bouma, B. N.

    1995-01-01

    The complement protein C4b-binding protein plays an important role in the regulation of the protein C anticoagulant pathway. C4b-binding protein can bind to protein S, thereby inhibiting the cofactor activity of protein S for activated protein C. In this report, we describe a new role for

  15. Implementation of LDG method for 3D unstructured meshes

    Directory of Open Access Journals (Sweden)

    Filander A. Sequeira Chavarría

    2012-07-01

    Full Text Available This paper describes an implementation of the Local Discontinuous Galerkin method (LDG applied to elliptic problems in 3D. The implementation of the major operators is discussed. In particular the use of higher-order approximations and unstructured meshes. Efficient data structures that allow fast assembly of the linear system in the mixed formulation are described in detail. Keywords: Discontinuous finite element methods, high-order approximations, unstructured meshes, object-oriented programming. Mathematics Subject Classification: 65K05, 65N30, 65N55.

  16. Role of ongoing, intrinsic activity of neuronal populations for quantitative neuroimaging of functional magnetic resonance imaging-based networks.

    Science.gov (United States)

    Hyder, Fahmeed; Herman, Peter; Sanganahalli, Basavaraju G; Coman, Daniel; Blumenfeld, Hal; Rothman, Douglas L

    2011-01-01

    A primary objective in neuroscience is to determine how neuronal populations process information within networks. In humans and animal models, functional magnetic resonance imaging (fMRI) is gaining increasing popularity for network mapping. Although neuroimaging with fMRI-conducted with or without tasks-is actively discovering new brain networks, current fMRI data analysis schemes disregard the importance of the total neuronal activity in a region. In task fMRI experiments, the baseline is differenced away to disclose areas of small evoked changes in the blood oxygenation level-dependent (BOLD) signal. In resting-state fMRI experiments, the spotlight is on regions revealed by correlations of tiny fluctuations in the baseline (or spontaneous) BOLD signal. Interpretation of fMRI-based networks is obscured further, because the BOLD signal indirectly reflects neuronal activity, and difference/correlation maps are thresholded. Since the small changes of BOLD signal typically observed in cognitive fMRI experiments represent a minimal fraction of the total energy/activity in a given area, the relevance of fMRI-based networks is uncertain, because the majority of neuronal energy/activity is ignored. Thus, another alternative for quantitative neuroimaging of fMRI-based networks is a perspective in which the activity of a neuronal population is accounted for by the demanded oxidative energy (CMR(O2)). In this article, we argue that network mapping can be improved by including neuronal energy/activity of both the information about baseline and small differences/fluctuations of BOLD signal. Thus, total energy/activity information can be obtained through use of calibrated fMRI to quantify differences of ΔCMR(O2) and through resting-state positron emission tomography/magnetic resonance spectroscopy measurements for average CMR(O2).

  17. Role of Ongoing, Intrinsic Activity of Neuronal Populations for Quantitative Neuroimaging of Functional Magnetic Resonance Imaging–Based Networks

    Science.gov (United States)

    Herman, Peter; Sanganahalli, Basavaraju G.; Coman, Daniel; Blumenfeld, Hal; Rothman, Douglas L.

    2011-01-01

    Abstract A primary objective in neuroscience is to determine how neuronal populations process information within networks. In humans and animal models, functional magnetic resonance imaging (fMRI) is gaining increasing popularity for network mapping. Although neuroimaging with fMRI—conducted with or without tasks—is actively discovering new brain networks, current fMRI data analysis schemes disregard the importance of the total neuronal activity in a region. In task fMRI experiments, the baseline is differenced away to disclose areas of small evoked changes in the blood oxygenation level-dependent (BOLD) signal. In resting-state fMRI experiments, the spotlight is on regions revealed by correlations of tiny fluctuations in the baseline (or spontaneous) BOLD signal. Interpretation of fMRI-based networks is obscured further, because the BOLD signal indirectly reflects neuronal activity, and difference/correlation maps are thresholded. Since the small changes of BOLD signal typically observed in cognitive fMRI experiments represent a minimal fraction of the total energy/activity in a given area, the relevance of fMRI-based networks is uncertain, because the majority of neuronal energy/activity is ignored. Thus, another alternative for quantitative neuroimaging of fMRI-based networks is a perspective in which the activity of a neuronal population is accounted for by the demanded oxidative energy (CMRO2). In this article, we argue that network mapping can be improved by including neuronal energy/activity of both the information about baseline and small differences/fluctuations of BOLD signal. Thus, total energy/activity information can be obtained through use of calibrated fMRI to quantify differences of ΔCMRO2 and through resting-state positron emission tomography/magnetic resonance spectroscopy measurements for average CMRO2. PMID:22433047

  18. The influence of thermal activation and the intrinsic temperature dependence of the spin torque effect in current-induced domain wall motion

    International Nuclear Information System (INIS)

    Dagras, P; Klaeui, M; Laufenberg, M; Bedau, D; Vila, L; Faini, G; Vaz, C A F; Bland, J A C; Ruediger, U

    2007-01-01

    An experimental study of domain wall motion in Ni 80 Fe 20 ring structures induced by current pulses as well as conventional magnetic fields is presented. Using constrictions we demonstrate that current-induced domain wall motion can be used to displace walls into parts of the structure where no pulsed currents are flowing. Measurements at variable temperatures between 2 and 300 K show that the fields necessary for wall motion decrease with increasing temperature, which can be explained by thermal activation. For the current-induced case we find, depending on the geometry and temperature range, that the current densities necessary for displacement can increase or decrease with rising temperature. This indicates that, in addition to thermal excitations, an intrinsic temperature dependence of the efficiency of the spin torque effect is present and leads to an increase in the critical current density with increasing temperature

  19. Repetition priming of motor activity mediated by a central pattern generator: the importance of extrinsic vs. intrinsic program initiators

    Science.gov (United States)

    Siniscalchi, Michael J.; Jing, Jian; Weiss, Klaudiusz R.

    2016-01-01

    Repetition priming is characterized by increased performance as a behavior is repeated. Although this phenomenon is ubiquitous, mediating mechanisms are poorly understood. We address this issue in a model system, the feeding network of Aplysia. This network generates both ingestive and egestive motor programs. Previous data suggest a chemical coding model: ingestive and egestive inputs to the feeding central pattern generator (CPG) release different modulators, which act via different second messengers to prime motor activity in different ways. The ingestive input to the CPG (neuron CBI-2) releases the peptides feeding circuit activating peptide and cerebral peptide 2, which produce an ingestive pattern of activity. The egestive input to the CPG (the esophageal nerve) releases the peptide small cardioactive peptide. This model is based on research that focused on a single aspect of motor control (radula opening). Here we ask whether repetition priming is observed if activity is triggered with a neuron within the core CPG itself and demonstrate that it is not. Moreover, previous studies demonstrated that effects of modulatory neurotransmitters that induce repetition priming persist. This suggests that it should be possible to “prime” motor programs triggered from within the CPG by first stimulating extrinsic modulatory inputs. We demonstrate that programs triggered after ingestive input activation are ingestive and programs triggered after egestive input activation are egestive. We ask where this priming occurs and demonstrate modifications within the CPG itself. This arrangement is likely to have important consequences for “task” switching, i.e., the cessation of one type of motor activity and the initiation of another. PMID:27466134

  20. Editing of misaligned 3'-termini by an intrinsic 3'-5' exonuclease activity residing in the PHP domain of a family X DNA polymerase.

    Science.gov (United States)

    Baños, Benito; Lázaro, José M; Villar, Laurentino; Salas, Margarita; de Vega, Miguel

    2008-10-01

    Bacillus subtilis gene yshC encodes a family X DNA polymerase (PolX(Bs)), whose biochemical features suggest that it plays a role during DNA repair processes. Here, we show that, in addition to the polymerization activity, PolX(Bs) possesses an intrinsic 3'-5' exonuclease activity specialized in resecting unannealed 3'-termini in a gapped DNA substrate. Biochemical analysis of a PolX(Bs) deletion mutant lacking the C-terminal polymerase histidinol phosphatase (PHP) domain, present in most of the bacterial/archaeal PolXs, as well as of this separately expressed protein region, allow us to state that the 3'-5' exonuclease activity of PolX(Bs) resides in its PHP domain. Furthermore, site-directed mutagenesis of PolX(Bs) His339 and His341 residues, evolutionary conserved in the PHP superfamily members, demonstrated that the predicted metal binding site is directly involved in catalysis of the exonucleolytic reaction. The implications of the unannealed 3'-termini resection by the 3'-5' exonuclease activity of PolX(Bs) in the DNA repair context are discussed.

  1. Relationship of shoulder activity and skin intrinsic fluorescence with low level shoulder pain and disability in people with type 2 diabetes.

    Science.gov (United States)

    Sorensen, Christopher J; Hastings, Mary K; Lang, Catherine E; McGill, Janet B; Clark, B Ruth; Bohnert, Kathryn L; Mueller, Michael J

    2017-06-01

    People with type 2 diabetes (T2DM) have a high incidence of musculoskeletal disorders thought to be influenced by high non-enzymatic advanced glycated end-products (AGEs). The goals of this study were to determine differences in shoulder activity level and AGEs in people with T2DM compared to matched controls, and to determine factors associated with shoulder pain and disability. Eighty-one participants, T2DM (n=52) and controls (n=29), were examined for magnitude and duration of shoulder activity (measured using accelerometers), skin intrinsic florescence (SIF) as a surrogate measure of AGE level, and the Shoulder Pain and Disability Index (SPADI) as a self-report of shoulder pain and disability. Compared with controls, T2DM participants had 23% less shoulder activity (p=0.01), greater SIF level (3.6±1.7 vs 2.7±0.6AU, p=0.01), less shoulder strength (pshoulder activity was moderately associated (r=0.40; pshoulder pain and disability. Shoulder pain and disability were not related to SIF level. Persons with T2DM have higher SIF levels and shoulder symptoms and disability indices than controls. Research is needed to determine if a shoulder mobility intervention to increase strength and mobility can help decrease shoulder pain and disability. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Unsupervised Ontology Generation from Unstructured Text. CRESST Report 827

    Science.gov (United States)

    Mousavi, Hamid; Kerr, Deirdre; Iseli, Markus R.

    2013-01-01

    Ontologies are a vital component of most knowledge acquisition systems, and recently there has been a huge demand for generating ontologies automatically since manual or supervised techniques are not scalable. In this paper, we introduce "OntoMiner", a rule-based, iterative method to extract and populate ontologies from unstructured or…

  3. Improving the efficiency of aerodynamic shape optimization on unstructured meshes

    NARCIS (Netherlands)

    G. Carpentieri; M.J.L. van Tooren; B. Koren (Barry)

    2006-01-01

    textabstractIn this paper the exact discrete adjoint of a finite volume formulation on unstructured meshes for the Euler equations in two dimensions is derived and implemented to support aerodynamic shape optimization. The accuracy of the discrete exact adjoint is demonstrated and compared with that

  4. Unstructured Orthogonal Meshes for Modeling Coastal and Ocean Flows

    NARCIS (Netherlands)

    Kleptsova, O.

    2013-01-01

    In this thesis a z?layer unstructured C-grid finite volume hydrostatic model is presented. An efficient and highly scalable implicit technique for the solution of the free surface equation is combined with an Eulerian approach for the advection of momentum. A consistent velocity reconstruc- tion

  5. GRIZ: Visualization of finite element analysis results on unstructured grids

    International Nuclear Information System (INIS)

    Dovey, D.; Loomis, M.D.

    1994-01-01

    GRIZ is a general-purpose post-processing application that supports interactive visualization of finite element analysis results on three-dimensional unstructured grids. GRIZ includes direct-to-videodisc animation capabilities and is being used as a production tool for creating engineering animations

  6. Unstructured Spectral Element Model for Dispersive and Nonlinear Wave Propagation

    DEFF Research Database (Denmark)

    Engsig-Karup, Allan Peter; Eskilsson, Claes; Bigoni, Daniele

    2016-01-01

    We introduce a new stabilized high-order and unstructured numerical model for modeling fully nonlinear and dispersive water waves. The model is based on a nodal spectral element method of arbitrary order in space and a -transformed formulation due to Cai, Langtangen, Nielsen and Tveito (1998). In...

  7. Neural mechanism of activity spread in the cat motor cortex and its relation to the intrinsic connectivity

    DEFF Research Database (Denmark)

    Capaday, Charles; van Vreeswijk, Carl; Ethier, Christian

    2011-01-01

    by the anatomical connections, indicating the existence of mechanisms that limit the spread of activity. Nonetheless, such an area contains the representations of a variety of muscles spanning several joints, from digits to shoulder. These results support the hypothesis that the MCx controls the forelimb...... (BIC) was inserted in the hole and driven to a depth of 1200–1400 {#956}m from the cortical surface. BIC was ejected for ∼2 min from the tip of the micropipette with positive direct current ranging between 20 and 40 nA in different experiments. This produced spontaneous nearly periodic bursts (0...

  8. Intrinsic monitoring of learning success facilitates memory encoding via the activation of the SN/VTA-Hippocampal loop

    Science.gov (United States)

    Ripollés, Pablo; Marco-Pallarés, Josep; Alicart, Helena; Tempelmann, Claus; Rodríguez-Fornells, Antoni; Noesselt, Toemme

    2016-01-01

    Humans constantly learn in the absence of explicit rewards. However, the neurobiological mechanisms supporting this type of internally-guided learning (without explicit feedback) are still unclear. Here, participants who completed a task in which no external reward/feedback was provided, exhibited enhanced fMRI-signals within the dopaminergic midbrain, hippocampus, and ventral striatum (the SN/VTA-Hippocampal loop) when successfully grasping the meaning of new-words. Importantly, new-words that were better remembered showed increased activation and enhanced functional connectivity between the midbrain, hippocampus, and ventral striatum. Moreover, enhanced emotion-related physiological measures and subjective pleasantness ratings during encoding were associated with remembered new-words after 24 hr. Furthermore, increased subjective pleasantness ratings were also related to new-words remembered after seven days. These results suggest that intrinsic—potentially reward-related—signals, triggered by self-monitoring of correct performance, can promote the storage of new information into long-term memory through the activation of the SN/VTA-Hippocampal loop, possibly via dopaminergic modulation of the midbrain. DOI: http://dx.doi.org/10.7554/eLife.17441.001 PMID:27644419

  9. Anti-tumour activity of a novel coumarin-chalcone hybrid is mediated through intrinsic apoptotic pathway by inducing PUMA and altering Bax/Bcl-2 ratio.

    Science.gov (United States)

    Singh, Neetu; Sarkar, Jayanta; Sashidhara, Koneni V; Ali, Shakir; Sinha, Sudhir

    2014-06-01

    Coumarins and chalcones are secondary plant metabolites which have shown an array of pharmacological properties including anti-tumour activity. We have previously reported on the synthesis and anti-proliferative activity of a series of novel coumarin-chalcone hybrids. Now we report on the in vivo efficacy as well as mechanism of action of the most potent molecule of the series, S009-131. Oral administration of this molecule resulted in regression of tumours induced by HeLa cell xenografts in nod SCID mice. The molecule inhibited proliferation of cervical cancer cells (HeLa and C33A) by inducing apoptosis and arresting cell cycle at G2/M phase. Apoptosis was induced through induction of caspase-dependent intrinsic pathway and alterations in the cellular levels of Bcl-2 family proteins. The mitochondrial transmembrane potential got highly depleted in S009-131 treated cells due to an increase in Bax/Bcl-2 ratio and intracellular ROS. The molecule induced release of cytochrome c into the cytosol and activation of initiator caspase-9 and executioner caspases-3/7. Tumour suppressor protein p53 and its transcriptional target PUMA were up regulated, suggesting their role in mediating the cell death. These results suggest that S009-131 is a potent candidate for the chemotherapy of cervical carcinoma.

  10. 'Unstructured Data' Practices in Polar Institutions and Networks: a Case Study with the Arctic Options Project

    Directory of Open Access Journals (Sweden)

    Paul Arthur Berkman

    2014-10-01

    Full Text Available Arctic Options: Holistic Integration for Arctic Coastal-Marine Sustainability is a new three-year research project to assess future infrastructure associated with the Arctic Ocean regarding: (1 natural and living environment; (2 built environment; (3 natural resource development; and (4 governance. For the assessments, Arctic Options will generate objective relational schema from numeric data as well as textual data. This paper will focus on the ‘long tail of smaller, heterogeneous, and often unstructured datasets’ that ‘usually receive minimal data management consideration’,as observed in the 2013 Communiqué from the International Forum on Polar Data Activities in Global Data Systems.

  11. Revelation of the Excellent Intrinsic Activity of MoS2|NiS|MoO3 Nanowires for Hydrogen Evolution Reaction in Alkaline Medium.

    Science.gov (United States)

    Wang, Chuanqin; Tian, Bin; Wu, Mei; Wang, Jiahai

    2017-03-01

    Loading an electrocatalyst on poorly conducting substrate can easily lead to undervaluation of its intrinsic property. In this study, the excellent activity of MoS 2 |NiS|MoO 3 nanowires for hydrogen evolution is revealed. The precursor NiMoO 4 synthesized on chemically polished Ti foil can be successfully converted to MoS 2 |NiS|MoO 3 catalyst via gas-phase sulfurization. Without deep polish in sulfuric acid for 2 h, the as-synthesized materials do not show competitive results. After sulfurization, the surface morphology of the precursor is transformed into rough features, and the peripheries of these electrocatalysts are coated by multilayered and misaligned MoS 2 with a high density of active sites and conductive component NiS. Further analysis shows that defect MoO 3 is embedded inside each nanowire, which may facilitate fast electron transfer. Such nanostructured architecture shows promising results for hydrogen evolution reaction in alkaline medium with only 91 mV overpotential for the current density of 10 mA cm -2 and robust long-term stability during more than 20 h of tests.

  12. Multiphase flow of immiscible fluids on unstructured moving meshes

    DEFF Research Database (Denmark)

    Misztal, Marek Krzysztof; Erleben, Kenny; Bargteil, Adam

    2012-01-01

    In this paper, we present a method for animating multiphase flow of immiscible fluids using unstructured moving meshes. Our underlying discretization is an unstructured tetrahedral mesh, the deformable simplicial complex (DSC), that moves with the flow in a Lagrangian manner. Mesh optimization...... operations improve element quality and avoid element inversion. In the context of multiphase flow, we guarantee that every element is occupied by a single fluid and, consequently, the interface between fluids is represented by a set of faces in the simplicial complex. This approach ensures...... that the underlying discretization matches the physics and avoids the additional book-keeping required in grid-based methods where multiple fluids may occupy the same cell. Our Lagrangian approach naturally leads us to adopt a finite element approach to simulation, in contrast to the finite volume approaches adopted...

  13. Jali - Unstructured Mesh Infrastructure for Multi-Physics Applications

    Energy Technology Data Exchange (ETDEWEB)

    2017-04-13

    Jali is a parallel unstructured mesh infrastructure library designed for use by multi-physics simulations. It supports 2D and 3D arbitrary polyhedral meshes distributed over hundreds to thousands of nodes. Jali can read write Exodus II meshes along with fields and sets on the mesh and support for other formats is partially implemented or is (https://github.com/MeshToolkit/MSTK), an open source general purpose unstructured mesh infrastructure library from Los Alamos National Laboratory. While it has been made to work with other mesh frameworks such as MOAB and STKmesh in the past, support for maintaining the interface to these frameworks has been suspended for now. Jali supports distributed as well as on-node parallelism. Support of on-node parallelism is through direct use of the the mesh in multi-threaded constructs or through the use of "tiles" which are submeshes or sub-partitions of a partition destined for a compute node.

  14. Microbial activity and biomass of peats in relation to the intrinsic organic matter composition, pH, moisture, and C and N inputs

    Energy Technology Data Exchange (ETDEWEB)

    Amha Amde, Yosef

    2011-03-25

    Excessive decomposition of organic matter (OM) from the potting media (e.g. peat) is known to influence plant growth by decreasing the total porosity, altering the chemical properties (pH, electrical conductivity), and releasing organic compounds that might have phytotoxic or stimulating effects. When peats are used as constitutes of the potting media, they should, therefore, maintain stability during plant production. In this study, twenty peat samples from Estonia, Finland, Germany, Ireland, Latvia, Lithuania and Sweden were evaluated for their microbial activity (measured as CO{sub 2} and N{sub 2}O emissions) and biomass with a special emphasis to the intrinsic organic matter composition, pH, moisture, and C and N inputs as such information on a wide range of peat samples is largely missing from published literature. Overall, the whole peat samples were broadly classified into three distinct groups using the hierarchical cluster analysis: the Irish and two of German peats produced the lowest CO{sub 2} while most peats from Finland produced the highest CO{sub 2}. With few exceptions, peats from the Baltic States occupied the middle ranges. Excessive decomposition of organic matter in the Finish peats might have unintended consequences if these peats are used for long-term pot plant production. With regard to botanical composition, peats containing Sphagnum imbricatum produced the lowest CO{sub 2} and S. angustifolium dominated peats mostly produced the highest CO{sub 2}. (orig.)

  15. Wave Resource Characterization Using an Unstructured Grid Modeling Approach

    Directory of Open Access Journals (Sweden)

    Wei-Cheng Wu

    2018-03-01

    Full Text Available This paper presents a modeling study conducted on the central Oregon coast for wave resource characterization, using the unstructured grid Simulating WAve Nearshore (SWAN model coupled with a nested grid WAVEWATCH III® (WWIII model. The flexibility of models with various spatial resolutions and the effects of open boundary conditions simulated by a nested grid WWIII model with different physics packages were evaluated. The model results demonstrate the advantage of the unstructured grid-modeling approach for flexible model resolution and good model skills in simulating the six wave resource parameters recommended by the International Electrotechnical Commission in comparison to the observed data in Year 2009 at National Data Buoy Center Buoy 46050. Notably, spectral analysis indicates that the ST4 physics package improves upon the ST2 physics package’s ability to predict wave power density for large waves, which is important for wave resource assessment, load calculation of devices, and risk management. In addition, bivariate distributions show that the simulated sea state of maximum occurrence with the ST4 physics package matched the observed data better than with the ST2 physics package. This study demonstrated that the unstructured grid wave modeling approach, driven by regional nested grid WWIII outputs along with the ST4 physics package, can efficiently provide accurate wave hindcasts to support wave resource characterization. Our study also suggests that wind effects need to be considered if the dimension of the model domain is greater than approximately 100 km, or O (102 km.

  16. Unstructured Models for Lactic Acid Fermentation – A Review

    Directory of Open Access Journals (Sweden)

    Abdallah Bouguettoucha

    2011-01-01

    Full Text Available To describe a microbial process, two kinds of models can be developed, structured and unstructured models. Contrary to structured models, which take into account some basic aspects of cell structure, their function and composition, no physiological characterization of cells is considered in unstructured models, which only consider total cellular concentration. However, in spite of their simplicity, unstructured models have proven to accurately describe lactic acid fermentation in a wide range of experimental conditions and media. A partial link between cell growth and production, namely the Luedeking and Piret model, is mostly considered by the authors. Culture pH is the main parameter to be considered for model development. Acidic pH leads to inhibitory concentrations of undissociated lactic acid, the main inhibitory component, which causes cessation of growth and then production. On the other hand, pH control at optimal value for LAB growth allows to overcome product inhibition (by the total lactic acid produced or its undissociated part; hence nutritional limitations have to be considered for model development. Nitrogen is mainly involved in cessation of growth, owing to the fastidious nutritional requirements of LAB, while lactic acid production ceased when carbon was exhausted from the medium. The lack of substrate inhibition when usual concentrations of carbon substrate are used should be noted.

  17. Finding geospatial pattern of unstructured data by clustering routes

    Science.gov (United States)

    Boustani, M.; Mattmann, C. A.; Ramirez, P.; Burke, W.

    2016-12-01

    Today the majority of data generated has a geospatial context to it. Either in attribute form as a latitude or longitude, or name of location or cross referenceable using other means such as an external gazetteer or location service. Our research is interested in exploiting geospatial location and context in unstructured data such as that found on the web in HTML pages, images, videos, documents, and other areas, and in structured information repositories found on intranets, in scientific environments, and otherwise. We are working together on the DARPA MEMEX project to exploit open source software tools such as the Lucene Geo Gazetteer, Apache Tika, Apache Lucene, and Apache OpenNLP, to automatically extract, and make meaning out of geospatial information. In particular, we are interested in unstructured descriptors e.g., a phone number, or a named entity, and the ability to automatically learn geospatial paths related to these descriptors. For example, a particular phone number may represent an entity that travels on a monthly basis, according to easily identifiable and somes more difficult to track patterns. We will present a set of automatic techniques to extract descriptors, and then to geospatially infer their paths across unstructured data.

  18. Unstructured Grids and the Multigroup Neutron Diffusion Equation

    Directory of Open Access Journals (Sweden)

    German Theler

    2013-01-01

    Full Text Available The neutron diffusion equation is often used to perform core-level neutronic calculations. It consists of a set of second-order partial differential equations over the spatial coordinates that are, both in the academia and in the industry, usually solved by discretizing the neutron leakage term using a structured grid. This work introduces the alternatives that unstructured grids can provide to aid the engineers to solve the neutron diffusion problem and gives a brief overview of the variety of possibilities they offer. It is by understanding the basic mathematics that lie beneath the equations that model real physical systems; better technical decisions can be made. It is in this spirit that this paper is written, giving a first introduction to the basic concepts which can be incorporated into core-level neutron flux computations. A simple two-dimensional homogeneous circular reactor is solved using a coarse unstructured grid in order to illustrate some basic differences between the finite volumes and the finite elements method. Also, the classic 2D IAEA PWR benchmark problem is solved for eighty combinations of symmetries, meshing algorithms, basic geometric entities, discretization schemes, and characteristic grid lengths, giving even more insight into the peculiarities that arise when solving the neutron diffusion equation using unstructured grids.

  19. Parallel Performance Optimizations on Unstructured Mesh-based Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Sarje, Abhinav; Song, Sukhyun; Jacobsen, Douglas; Huck, Kevin; Hollingsworth, Jeffrey; Malony, Allen; Williams, Samuel; Oliker, Leonid

    2015-01-01

    © The Authors. Published by Elsevier B.V. This paper addresses two key parallelization challenges the unstructured mesh-based ocean modeling code, MPAS-Ocean, which uses a mesh based on Voronoi tessellations: (1) load imbalance across processes, and (2) unstructured data access patterns, that inhibit intra- and inter-node performance. Our work analyzes the load imbalance due to naive partitioning of the mesh, and develops methods to generate mesh partitioning with better load balance and reduced communication. Furthermore, we present methods that minimize both inter- and intranode data movement and maximize data reuse. Our techniques include predictive ordering of data elements for higher cache efficiency, as well as communication reduction approaches. We present detailed performance data when running on thousands of cores using the Cray XC30 supercomputer and show that our optimization strategies can exceed the original performance by over 2×. Additionally, many of these solutions can be broadly applied to a wide variety of unstructured grid-based computations.

  20. Intrinsic contractures of the hand.

    Science.gov (United States)

    Paksima, Nader; Besh, Basil R

    2012-02-01

    Contractures of the intrinsic muscles of the fingers disrupt the delicate and complex balance of intrinsic and extrinsic muscles, which allows the hand to be so versatile and functional. The loss of muscle function primarily affects the interphalangeal joints but also may affect etacarpophalangeal joints. The resulting clinical picture is often termed, intrinsic contracture or intrinsic-plus hand. Disruption of the balance between intrinsic and extrinsic muscles has many causes and may be secondary to changes within the intrinsic musculature or the tendon unit. This article reviews diagnosis, etiology, and treatment algorithms in the management of intrinsic contractures of the fingers. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Predicting Intrinsic Motivation

    Science.gov (United States)

    Martens, Rob; Kirschner, Paul A.

    2004-01-01

    Intrinsic motivation can be predicted from participants' perceptions of the social environment and the task environment (Ryan & Deci, 2000)in terms of control, relatedness and competence. To determine the degree of independence of these factors 251 students in higher vocational education (physiotherapy and hotel management) indicated the…

  2. The α-Helical Structure of Prodomains Promotes Translocation of Intrinsically Disordered Neuropeptide Hormones into the Endoplasmic Reticulum*

    Science.gov (United States)

    Dirndorfer, Daniela; Seidel, Ralf P.; Nimrod, Guy; Miesbauer, Margit; Ben-Tal, Nir; Engelhard, Martin; Zimmermann, Richard; Winklhofer, Konstanze F.; Tatzelt, Jörg

    2013-01-01

    Different neuropeptide hormones, which are either too small to adopt a stable conformation or are predicted to be intrinsically disordered, are synthesized as larger precursors containing a prodomain in addition to an N-terminal signal peptide. We analyzed the biogenesis of three unstructured neuropeptide hormones and observed that translocation of these precursors into the lumen of the endoplasmic reticulum (ER) is critically dependent on the presence of the prodomain. The hormone domains could be deleted from the precursors without interfering with ER import and secretion, whereas constructs lacking the prodomain remained in the cytosol. Domain-swapping experiments revealed that the activity of the prodomains to promote productive ER import resides in their ability to adopt an α-helical structure. Removal of the prodomain from the precursor did not interfere with co-translational targeting of the nascent chain to the Sec61 translocon but with its subsequent productive translocation into the ER lumen. Our study reveals a novel function of prodomains to enable import of small or intrinsically disordered secretory proteins into the ER based on their ability to adopt an α-helical conformation. PMID:23532840

  3. The organization of intrinsic brain activity differs between genders: a resting-state fMRI study in a large cohort of young healthy subjects.

    Science.gov (United States)

    Filippi, Massimo; Valsasina, Paola; Misci, Paolo; Falini, Andrea; Comi, Giancarlo; Rocca, Maria A

    2013-06-01

    To investigate, using resting state (RS) functional MRI (fMRI), gender-related differences of functional connectivity (FC) and functional network connectivity (FNC) of the human brain. One-hundred and four young healthy subjects (48/56 men/women), aged between 20 and 29 years, underwent a 10-min RS fMRI acquisition. Independent component analysis (ICA) and statistical parametric mapping were used to assess gender-related differences in RSNs, with and without correction for regional gray matter (GM) volume. The relationships among all RSNs was also assessed using a FNC method. For all networks, significant between-group differences of RS activity were found. Between-group comparisons of RSNs changed when adjusting for GM volume, as follows: (1) there was only marginal effect on the analysis of sensory (i.e., sensorimotor, visual, and auditory) networks; and (2) there was a significantly increased difference when cognitive networks (apart from one related to attention) were considered. Compared with women, men experienced increased FC in parietal and occipital regions in most RSNs, whereas women experienced a higher RS FC in frontal and temporal regions, and in the cerebellum. When compared to women, increased FNC was found in men between several cognitive and sensory networks, whereas women showed an increased FNC only between attention and right working-memory networks. The organization of intrinsic FC and FNC differ between genders. The detected differences could contribute to the understanding of the known between-gender variation in task-related recruitments, and the patterns of abnormalities detected in neurologic and psychiatric diseases with a gender prevalence. Copyright © 2012 Wiley Periodicals, Inc.

  4. The intrinsic resistome of bacterial pathogens

    Directory of Open Access Journals (Sweden)

    Jorge Andrés Olivares Pacheco

    2013-04-01

    Full Text Available Intrinsically resistant bacteria have emerged as a relevant health problem in the last years. Those bacterial species, several of them with an environmental origin, present naturally a low-level susceptibility to several drugs. It has been proposed that intrinsic resistance is mainly the consequence of the impermeability of cellular envelopes, the activity of multidrug efflux pumps or the lack of appropriate targets for a given family of drugs. However, recently published articles indicate that the characteristic phenotype of susceptibility to antibiotics of a given bacterial species depends on the concerted activity of several elements, what has been named as intrinsic resistome. These determinants comprise not just classical resistance genes. Other elements, several of them involved in basic bacterial metabolic processes, are of relevance for the intrinsic resistance of bacterial pathogens. In the present review we analyse recent publications on the intrinsic resistomes of Escherichia coli and Pseudomonas aeruginosa. We present as well information on the role that global regulators of bacterial metabolism, as Crc from P. aeruginosa, may have on modulating bacterial susceptibility to antibiotics. Finally, we discuss the possibility of searching inhibitors of the intrinsic resistome in the aim of improving the activity of drugs currently in use for clinical practice.

  5. Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA.

    Science.gov (United States)

    Mateos-Gil, Pablo; Tsortos, Achilleas; Vélez, Marisela; Gizeli, Electra

    2016-05-05

    The sensitivity of QCM-D to molecular hydrodynamic properties is applied in this work to study conformational changes of the intrinsically disordered protein ZipA. Acoustic measurements can clearly follow ZipA's unstructured domain expansion and contraction with salt content and be correlated with changes in the hydrodynamic radius of 1.8 nm or less.

  6. Parallel performance of a preconditioned CG solver for unstructured finite element applications

    Energy Technology Data Exchange (ETDEWEB)

    Shadid, J.N.; Hutchinson, S.A.; Moffat, H.K. [Sandia National Labs., Albuquerque, NM (United States)

    1994-12-31

    A parallel unstructured finite element (FE) implementation designed for message passing MIMD machines is described. This implementation employs automated problem partitioning algorithms for load balancing unstructured grids, a distributed sparse matrix representation of the global finite element equations and a parallel conjugate gradient (CG) solver. In this paper a number of issues related to the efficient implementation of parallel unstructured mesh applications are presented. These include the differences between structured and unstructured mesh parallel applications, major communication kernels for unstructured CG solvers, automatic mesh partitioning algorithms, and the influence of mesh partitioning metrics on parallel performance. Initial results are presented for example finite element (FE) heat transfer analysis applications on a 1024 processor nCUBE 2 hypercube. Results indicate over 95% scaled efficiencies are obtained for some large problems despite the required unstructured data communication.

  7. Discontinuous Spectral Difference Method for Conservation Laws on Unstructured Grids

    Science.gov (United States)

    Liu, Yen; Vinokur, Marcel; Wang, Z. J.

    2004-01-01

    A new, high-order, conservative, and efficient method for conservation laws on unstructured grids is developed. The concept of discontinuous and high-order local representations to achieve conservation and high accuracy is utilized in a manner similar to the Discontinuous Galerkin (DG) and the Spectral Volume (SV) methods, but while these methods are based on the integrated forms of the equations, the new method is based on the differential form to attain a simpler formulation and higher efficiency. A discussion on the Discontinuous Spectral Difference (SD) Method, locations of the unknowns and flux points and numerical results are also presented.

  8. Reactor physics verification of the MCNP6 unstructured mesh capability

    International Nuclear Information System (INIS)

    Burke, T. P.; Kiedrowski, B. C.; Martz, R. L.; Martin, W. R.

    2013-01-01

    The Monte Carlo software package MCNP6 has the ability to transport particles on unstructured meshes generated from the Computed-Aided Engineering software Abaqus. Verification is performed using benchmarks with features relevant to reactor physics - Big Ten and the C5G7 computational benchmark. Various meshing strategies are tested and results are compared to reference solutions. Computational performance results are also given. The conclusions show MCNP6 is capable of producing accurate calculations for reactor physics geometries and the computational requirements for small lattice benchmarks are reasonable on modern computing platforms. (authors)

  9. An Algorithm for Parallel Sn Sweeps on Unstructured Meshes

    International Nuclear Information System (INIS)

    Pautz, Shawn D.

    2002-01-01

    A new algorithm for performing parallel S n sweeps on unstructured meshes is developed. The algorithm uses a low-complexity list ordering heuristic to determine a sweep ordering on any partitioned mesh. For typical problems and with 'normal' mesh partitionings, nearly linear speedups on up to 126 processors are observed. This is an important and desirable result, since although analyses of structured meshes indicate that parallel sweeps will not scale with normal partitioning approaches, no severe asymptotic degradation in the parallel efficiency is observed with modest (≤100) levels of parallelism. This result is a fundamental step in the development of efficient parallel S n methods

  10. Aerodynamic analysis of complex configurations using unstructured grids

    Science.gov (United States)

    Frink, Neal T.; Parikh, Paresh; Pirzadeh, Shahyar

    1991-01-01

    The purpose of this paper is to assess the accuracy and utility of a new unstructured, inviscid, upwind flow solver for the aerodynamic analysis of two aircraft configurations. The two configurations consist of a low-wing transport with nacelle/pylon on and off, and a generic high-speed civil transport. Computations are made at subsonic and transonic Mach numbers for the low-wing transport and at transonic and low-supersonic speeds for the high-speed civil transport. The results include an assessment of grid sensitivity and provide comparisons with experimental data.

  11. Atomic-Scale Determination of Active Facets on the MoVTeNb Oxide M1 Phase and Their Intrinsic Catalytic Activity for Ethane Oxidative Dehydrogenation.

    Science.gov (United States)

    Melzer, Daniel; Xu, Pinghong; Hartmann, Daniela; Zhu, Yuanyuan; Browning, Nigel D; Sanchez-Sanchez, Maricruz; Lercher, Johannes A

    2016-07-25

    Aberration-corrected high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) has been used to image the basal {001} plane of the catalytically relevant M1 phase in MoVTeNb complex oxides. Facets {010}, {120}, and {210} are identified as the most frequent lateral termination planes of the crystals. Combination of STEM with He ion microscopy (HIM) images, Rietveld analysis, and kinetic tests reveals that the activation of ethane is correlated to the availability of facets {001}, {120}, and {210} at the surface of M1 crystals. The lateral facets {120} and {210} expose crystalline positions related to the typical active centers described for propane oxidation. Conversely, the low activity of the facet {010} is attributed to its configuration, consisting of only stable M6 O21 units connected by a single octahedron. Thus, we quantitatively demonstrated that differences in catalytic activity among M1 samples of equal chemical composition depend primarily on the morphology of the particles, which determines the predominant terminating facets. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Unstructured Mesh Movement and Viscous Mesh Generation for CFD-Based Design Optimization Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The innovations proposed are twofold: 1) a robust unstructured mesh movement method able to handle isotropic (Euler), anisotropic (viscous), mixed element (hybrid)...

  13. Unstructured Mesh Movement and Viscous Mesh Generation for CFD-Based Design Optimization, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — The innovations proposed are twofold: 1) a robust unstructured mesh movement method able to handle isotropic (Euler), anisotropic (viscous), mixed element (hybrid)...

  14. Intrinsic and Extrinsic Motivation

    OpenAIRE

    Roland Bénabou; Jean Tirole

    2003-01-01

    A central tenet of economics is that individuals respond to incentives. For psychologists and sociologists, in contrast, rewards and punishments are often counterproductive, because they undermine "intrinsic motivation". We reconcile these two views, showing how performance incentives offered by an informed principal (manager, teacher, parent) can adversely impact an agent's (worker, child) perception of the task, or of his own abilities. Incentives are then only weak reinforcers in the short...

  15. Importance and challenges of measuring intrinsic foot muscle strength

    Science.gov (United States)

    2012-01-01

    Background Intrinsic foot muscle weakness has been implicated in a range of foot deformities and disorders. However, to establish a relationship between intrinsic muscle weakness and foot pathology, an objective measure of intrinsic muscle strength is needed. The aim of this review was to provide an overview of the anatomy and role of intrinsic foot muscles, implications of intrinsic weakness and evaluate the different methods used to measure intrinsic foot muscle strength. Method Literature was sourced from database searches of MEDLINE, PubMed, SCOPUS, Cochrane Library, PEDro and CINAHL up to June 2012. Results There is no widely accepted method of measuring intrinsic foot muscle strength. Methods to estimate toe flexor muscle strength include the paper grip test, plantar pressure, toe dynamometry, and the intrinsic positive test. Hand-held dynamometry has excellent interrater and intrarater reliability and limits toe curling, which is an action hypothesised to activate extrinsic toe flexor muscles. However, it is unclear whether any method can actually isolate intrinsic muscle strength. Also most methods measure only toe flexor strength and other actions such as toe extension and abduction have not been adequately assessed. Indirect methods to investigate intrinsic muscle structure and performance include CT, ultrasonography, MRI, EMG, and muscle biopsy. Indirect methods often discriminate between intrinsic and extrinsic muscles, but lack the ability to measure muscle force. Conclusions There are many challenges to accurately measure intrinsic muscle strength in isolation. Most studies have measured toe flexor strength as a surrogate measure of intrinsic muscle strength. Hand-held dynamometry appears to be a promising method of estimating intrinsic muscle strength. However, the contribution of extrinsic muscles cannot be excluded from toe flexor strength measurement. Future research should clarify the relative contribution of intrinsic and extrinsic muscles

  16. Unstructured Grids for Sonic Boom Analysis and Design

    Science.gov (United States)

    Campbell, Richard L.; Nayani, Sudheer N.

    2015-01-01

    An evaluation of two methods for improving the process for generating unstructured CFD grids for sonic boom analysis and design has been conducted. The process involves two steps: the generation of an inner core grid using a conventional unstructured grid generator such as VGRID, followed by the extrusion of a sheared and stretched collar grid through the outer boundary of the core grid. The first method evaluated, known as COB, automatically creates a cylindrical outer boundary definition for use in VGRID that makes the extrusion process more robust. The second method, BG, generates the collar grid by extrusion in a very efficient manner. Parametric studies have been carried out and new options evaluated for each of these codes with the goal of establishing guidelines for best practices for maintaining boom signature accuracy with as small a grid as possible. In addition, a preliminary investigation examining the use of the CDISC design method for reducing sonic boom utilizing these grids was conducted, with initial results confirming the feasibility of a new remote design approach.

  17. First benchmark of the Unstructured Grid Adaptation Working Group

    Science.gov (United States)

    Ibanez, Daniel; Barral, Nicolas; Krakos, Joshua; Loseille, Adrien; Michal, Todd; Park, Mike

    2017-01-01

    Unstructured grid adaptation is a technology that holds the potential to improve the automation and accuracy of computational fluid dynamics and other computational disciplines. Difficulty producing the highly anisotropic elements necessary for simulation on complex curved geometries that satisfies a resolution request has limited this technology's widespread adoption. The Unstructured Grid Adaptation Working Group is an open gathering of researchers working on adapting simplicial meshes to conform to a metric field. Current members span a wide range of institutions including academia, industry, and national laboratories. The purpose of this group is to create a common basis for understanding and improving mesh adaptation. We present our first major contribution: a common set of benchmark cases, including input meshes and analytic metric specifications, that are publicly available to be used for evaluating any mesh adaptation code. We also present the results of several existing codes on these benchmark cases, to illustrate their utility in identifying key challenges common to all codes and important differences between available codes. Future directions are defined to expand this benchmark to mature the technology necessary to impact practical simulation workflows.

  18. Multiphase flow of immiscible fluids on unstructured moving meshes.

    Science.gov (United States)

    Misztal, Marek Krzysztof; Erleben, Kenny; Bargteil, Adam; Fursund, Jens; Christensen, Brian Bunch; Bærentzen, Jakob Andreas; Bridson, Robert

    2014-01-01

    In this paper, we present a method for animating multiphase flow of immiscible fluids using unstructured moving meshes. Our underlying discretization is an unstructured tetrahedral mesh, the deformable simplicial complex (DSC), that moves with the flow in a Lagrangian manner. Mesh optimization operations improve element quality and avoid element inversion. In the context of multiphase flow, we guarantee that every element is occupied by a single fluid and, consequently, the interface between fluids is represented by a set of faces in the simplicial complex. This approach ensures that the underlying discretization matches the physics and avoids the additional book-keeping required in grid-based methods where multiple fluids may occupy the same cell. Our Lagrangian approach naturally leads us to adopt a finite element approach to simulation, in contrast to the finite volume approaches adopted by a majority of fluid simulation techniques that use tetrahedral meshes. We characterize fluid simulation as an optimization problem allowing for full coupling of the pressure and velocity fields and the incorporation of a second-order surface energy. We introduce a preconditioner based on the diagonal Schur complement and solve our optimization on the GPU. We provide the results of parameter studies as well as a performance analysis of our method, together with suggestions for performance optimization.

  19. 3D COMPOSITIONAL RESERVOIR SIMULATION IN CONJUNCTION WITH UNSTRUCTURED GRIDS

    Directory of Open Access Journals (Sweden)

    A. L. S. Araújo

    Full Text Available Abstract In the last decade, unstructured grids have been a very important step in the development of petroleum reservoir simulators. In fact, the so-called third generation simulators are based on Perpendicular Bisection (PEBI unstructured grids. Nevertheless, the use of PEBI grids is not very general when full anisotropic reservoirs are modeled. Another possibility is the use of the Element based Finite Volume Method (EbFVM. This approach has been tested for several reservoir types and in principle has no limitation in application. In this paper, we implement this approach in an in-house simulator called UTCOMP using four element types: hexahedron, tetrahedron, prism, and pyramid. UTCOMP is a compositional, multiphase/multi-component simulator based on an Implicit Pressure Explicit Composition (IMPEC approach designed to handle several hydrocarbon recovery processes. All properties, except permeability and porosity, are evaluated in each grid vertex. In this work, four case studies were selected to evaluate the implementation, two of them involving irregular geometries. Results are shown in terms of oil and gas rates and saturated gas field.

  20. Smooth Bézier surfaces over unstructured quadrilateral meshes

    CERN Document Server

    Bercovier, Michel

    2017-01-01

    Using an elegant mixture of geometry, graph theory and linear analysis, this monograph completely solves a problem lying at the interface of Isogeometric Analysis (IgA) and Finite Element Methods (FEM). The recent explosion of IgA, strongly tying Computer Aided Geometry Design to Analysis, does not easily apply to the rich variety of complex shapes that engineers have to design and analyse. Therefore new developments have studied the extension of IgA to unstructured unions of meshes, similar to those one can find in FEM. The following problem arises: given an unstructured planar quadrilateral mesh, construct a C1-surface, by piecewise Bézier or B-Spline patches defined over this mesh. This problem is solved for C1-surfaces defined over plane bilinear Bézier patches, the corresponding results for B-Splines then being simple consequences. The method can be extended to higher-order quadrilaterals and even to three dimensions, and the most recent developments in this direction are also mentioned here.

  1. Optimizations of Unstructured Aerodynamics Computations for Many-core Architectures

    KAUST Repository

    Al Farhan, Mohammed Ahmed

    2018-04-13

    We investigate several state-of-the-practice shared-memory optimization techniques applied to key routines of an unstructured computational aerodynamics application with irregular memory accesses. We illustrate for the Intel KNL processor, as a representative of the processors in contemporary leading supercomputers, identifying and addressing performance challenges without compromising the floating point numerics of the original code. We employ low and high-level architecture-specific code optimizations involving thread and data-level parallelism. Our approach is based upon a multi-level hierarchical distribution of work and data across both the threads and the SIMD units within every hardware core. On a 64-core KNL chip, we achieve nearly 2.9x speedup of the dominant routines relative to the baseline. These exhibit almost linear strong scalability up to 64 threads, and thereafter some improvement with hyperthreading. At substantially fewer Watts, we achieve up to 1.7x speedup relative to the performance of 72 threads of a 36-core Haswell CPU and roughly equivalent performance to 112 threads of a 56-core Skylake scalable processor. These optimizations are expected to be of value for many other unstructured mesh PDE-based scientific applications as multi and many-core architecture evolves.

  2. Reaction rates for reaction-diffusion kinetics on unstructured meshes.

    Science.gov (United States)

    Hellander, Stefan; Petzold, Linda

    2017-02-14

    The reaction-diffusion master equation is a stochastic model often utilized in the study of biochemical reaction networks in living cells. It is applied when the spatial distribution of molecules is important to the dynamics of the system. A viable approach to resolve the complex geometry of cells accurately is to discretize space with an unstructured mesh. Diffusion is modeled as discrete jumps between nodes on the mesh, and the diffusion jump rates can be obtained through a discretization of the diffusion equation on the mesh. Reactions can occur when molecules occupy the same voxel. In this paper, we develop a method for computing accurate reaction rates between molecules occupying the same voxel in an unstructured mesh. For large voxels, these rates are known to be well approximated by the reaction rates derived by Collins and Kimball, but as the mesh is refined, no analytical expression for the rates exists. We reduce the problem of computing accurate reaction rates to a pure preprocessing step, depending only on the mesh and not on the model parameters, and we devise an efficient numerical scheme to estimate them to high accuracy. We show in several numerical examples that as we refine the mesh, the results obtained with the reaction-diffusion master equation approach those of a more fine-grained Smoluchowski particle-tracking model.

  3. Extrinsic Rewards and Intrinsic Motivation in Children. Final Report.

    Science.gov (United States)

    Lepper, Mark R.

    Three experiments were conducted to examine the effects of providing extrinsic rewards for engaging in an activity on children's subsequent intrinsic interest in that activity. In each study, preschool children were asked to engage in an activity of initial intrinsic interest in individual experimental sessions. The children agreed to engage in…

  4. Intrinsic and extrinsic mortality reunited

    DEFF Research Database (Denmark)

    Koopman, Jacob J E; Wensink, Maarten J; Rozing, Maarten P

    2015-01-01

    Intrinsic and extrinsic mortality are often separated in order to understand and measure aging. Intrinsic mortality is assumed to be a result of aging and to increase over age, whereas extrinsic mortality is assumed to be a result of environmental hazards and be constant over age. However......, allegedly intrinsic and extrinsic mortality have an exponentially increasing age pattern in common. Theories of aging assert that a combination of intrinsic and extrinsic stressors underlies the increasing risk of death. Epidemiological and biological data support that the control of intrinsic as well...... as extrinsic stressors can alleviate the aging process. We argue that aging and death can be better explained by the interaction of intrinsic and extrinsic stressors than by classifying mortality itself as being either intrinsic or extrinsic. Recognition of the tight interaction between intrinsic and extrinsic...

  5. The effects of extrinsic rewards on children's intrinsic motivation

    OpenAIRE

    大槻, 千秋

    1981-01-01

    An experiment was conducted with preschool children to test whether a person's intrinsic motivation in an activity may be decreased by extrinsic salient rewards in Japan like in America. Children solved some jigsaw puzzles and received assorted candies, then they were observed how long they did other jigsaw puzzles. The results showed that the effects of extrinsic rewards on intrinsic motivation in an activity varied with the subject's social background. In uptown children's intrinsic motivat...

  6. Intrinsic bevacizumab resistance is associated with prolonged activation of autocrine VEGF signaling and hypoxia tolerance in colorectal cancer cells and can be overcome by nintedanib, a small molecule angiokinase inhibitor

    Science.gov (United States)

    Mésange, Paul; Poindessous, Virginie; Sabbah, Michèle; Escargueil, Alexandre E.; de Gramont, Aimery; Larsen, Annette K.

    2014-01-01

    Colorectal cancer (CRC) is a common tumor type with a high mortality rate, in part due to intrinsic drug resistance. Although bevacizumab, a VEGF-directed neutralizing antibody, is particularly active in this pathology, some patients never respond for reasons not well understood. We here wish to clarify the role of autocrine VEGF signaling in the response of CRC cells to angiogenesis inhibition. Our results show that CRC cells with intrinsic bevacizumab-resistance displayed pronounced upregulation of autocrine HIF-VEGF-VEGFR signaling in response to prolonged bevacizumab exposure whereas the same signaling pathway was downregulated in bevacizumab-sensitive xenografts. Importantly, both bevacizumab-sensitive and -resistant CRC xenografts were sensitive to nintedanib, a small molecule angiokinase inhibitor, which was associated with inhibition of mTORC1. In vitro studies revealed that bevacizumab-resistant cells displayed intrinsically higher HIF-VEGF signaling intensity and hypoxia tolerance compared to their bevacizumab-sensitive counterparts. Interestingly, although nintedanib showed comparable activity toward bevacizumab-sensitive cells under normoxia and hypoxia, the drug was three-fold more toxic to the resistant cells under hypoxia, suggesting that nintedanib attenuated the survival signaling that usually protects these cells from hypoxia-mediated cell death. In conclusion, our findings support a role for autocrine VEGF signaling in the survival of CRC cells to hypoxia and thus to angiogenesis inhibition. We further show that nintedanib, a small molecule angiokinase inhibitor, is active toward CRC models with intrinsic bevacizumab resistance supporting clinical trials of nintedanib in patients that do not respond to bevacizumab, alone or in combination with bevacizumab to increase angiogenesis inhibition. PMID:25015210

  7. Hanging Out with Which Friends? Friendship-Level Predictors of Unstructured and Unsupervised Socializing in Adolescence

    Science.gov (United States)

    Siennick, Sonja E.; Osgood, D. Wayne

    2012-01-01

    Companions are central to explanations of the risky nature of unstructured and unsupervised socializing, yet we know little about whom adolescents are with when hanging out. We examine predictors of how often friendship dyads hang out via multilevel analyses of longitudinal friendship-level data on over 5,000 middle schoolers. Adolescents hang out most with their most available friends and their most generally similar friends, not with their most at-risk or similarly at-risk friends. These findings vary little by gender and wave. Together, the findings suggest that the risks of hanging out stem from the nature of hanging out as an activity, not the nature of adolescents’ companions, and that hanging out is a context for friends’ mutual reinforcement of pre-existing characteristics. PMID:23204811

  8. Inhibition of Intrinsic Thrombin Generation

    Directory of Open Access Journals (Sweden)

    Thomas W. Stief MD

    2006-01-01

    Full Text Available Background The contact phase of coagulation is of physiologic/pathophysiologic importance, whenever unphysiologic polynegative substances such as cell fragments (microparticles get in contact with blood. There are several clinically used inhibitors of intrinsic thrombin generation. Here the inhibitory concentrations 50% (IC50 of these anticoagulants are measured by the highly specific thrombin generation assay INCA. Methods Unfrozen pooled normal citrated plasma in polystyrole tubes was supplemented at 23°C in duplicate with 0–2 IU/ml low molecular weight heparin (dalteparin, 0–2 IU/ml unfractionated heparin, 0–500 KIU/ml aprotinin, or 0–40 mM arginine. 50 μl plasma or 1 IU/ml thrombin standard were pipetted into a polystyrole microtiter plate with flat bottom. 5 μl SiO 2 /CaCl 2 - reagent (INCA activator were added and after 0–30 min incubation at 37°C 100 μl 2.5 M arginine, pH 8.6, were added; arginine inhibits hemostasis activation and depolymerizes generated fibrin within 20 min at 23°C. The in the physiologic 37°C incubation phase generated thrombin was then chromogenically detected. The intra-assay CV values were < 5%. Results and Discussion The approximate IC50 were 0.01 IU/ml dalteparin, 0.02 IU/ml heparin, 25 KIU/ml aprotinin, and 12 mM arginine. The efficiency of any anticoagulant on intrinsic thrombin generation should be measured for each individual patient. Abbreviations IIa, thrombin; δA, increase in absorbance; APTT, activated partial thromboplastin time; CRT, coagulation reaction time (at 37°C in water-bath; F-wells, polystyrole microtiter plates with flat bottom; IC50, inhibitory concentration 50%; INCA, intrinsic coagulation activity assay; IU, international units; KIU, kallikrein inhibiting unis; LMWH, low molecular weight heparin; mA, milli-absorbance units; PSL, pathromtin SL®; RT, room temperature (23°C; U-wells, polystyrole microtiter plates with round bottom.

  9. The impact of the unstructured contacts component in influenza pandemic modeling.

    Directory of Open Access Journals (Sweden)

    Marco Ajelli

    Full Text Available Individual based models have become a valuable tool for modeling the spatiotemporal dynamics of epidemics, e.g. influenza pandemic, and for evaluating the effectiveness of intervention strategies. While specific contacts among individuals into diverse environments (family, school/workplace can be modeled in a standard way by employing available socio-demographic data, all the other (unstructured contacts can be dealt with by adopting very different approaches. This can be achieved for instance by employing distance-based models or by choosing unstructured contacts in the local communities or by employing commuting data.Here we show how diverse choices can lead to different model outputs and thus to a different evaluation of the effectiveness of the containment/mitigation strategies. Sensitivity analysis has been conducted for different values of the first generation index G(0, which is the average number of secondary infections generated by the first infectious individual in a completely susceptible population and by varying the seeding municipality. Among the different considered models, attack rate ranges from 19.1% to 25.7% for G(0 = 1.1, from 47.8% to 50.7% for G(0 = 1.4 and from 62.4% to 67.8% for G(0 = 1.7. Differences of about 15 to 20 days in the peak day have been observed. As regards spatial diffusion, a difference of about 100 days to cover 200 km for different values of G(0 has been observed.To reduce uncertainty in the models it is thus important to employ data, which start being available, on contacts on neglected but important activities (leisure time, sport mall, restaurants, etc. and time-use data for improving the characterization of the unstructured contacts. Moreover, all the possible effects of different assumptions should be considered for taking public health decisions: not only sensitivity analysis to various model parameters should be performed, but intervention options should be based on the analysis and

  10. Euler Flow Computations on Non-Matching Unstructured Meshes

    Science.gov (United States)

    Gumaste, Udayan

    1999-01-01

    Advanced fluid solvers to predict aerodynamic performance-coupled treatment of multiple fields are described. The interaction between the fluid and structural components in the bladed regions of the engine is investigated with respect to known blade failures caused by either flutter or forced vibrations. Methods are developed to describe aeroelastic phenomena for internal flows in turbomachinery by accounting for the increased geometric complexity, mutual interaction between adjacent structural components and presence of thermal and geometric loading. The computer code developed solves the full three dimensional aeroelastic problem of-stage. The results obtained show that flow computations can be performed on non-matching finite-volume unstructured meshes with second order spatial accuracy.

  11. Domain-independent information extraction in unstructured text

    Energy Technology Data Exchange (ETDEWEB)

    Irwin, N.H. [Sandia National Labs., Albuquerque, NM (United States). Software Surety Dept.

    1996-09-01

    Extracting information from unstructured text has become an important research area in recent years due to the large amount of text now electronically available. This status report describes the findings and work done during the second year of a two-year Laboratory Directed Research and Development Project. Building on the first-year`s work of identifying important entities, this report details techniques used to group words into semantic categories and to output templates containing selective document content. Using word profiles and category clustering derived during a training run, the time-consuming knowledge-building task can be avoided. Though the output still lacks in completeness when compared to systems with domain-specific knowledge bases, the results do look promising. The two approaches are compatible and could complement each other within the same system. Domain-independent approaches retain appeal as a system that adapts and learns will soon outpace a system with any amount of a priori knowledge.

  12. Development of unstructured mesh generator on parallel computers

    International Nuclear Information System (INIS)

    Muramatsu, Kazuhiro; Shimada, Akio; Murakami, Hiroyuki; Higashida, Akihiro; Wakatsuki, Shigeto

    2000-01-01

    A general-purpose unstructured mesh generator, 'GRID3D/UNST', has been developed on parallel computers. High-speed operations and large-scale memory capacity of parallel computers enable the system to generate a large-scale mesh at high speed. As a matter of fact, the system generates large-scale mesh composed of 2,400,000 nodes and 14,000,000 elements about 1.5 hours on HITACHI SR2201, 64 PEs (Processing Elements) through 2.5 hours pre-process on SUN. Also the system is built on standard FORTRAN, C and Motif, and therefore has high portability. The system enables us to solve a large-scale problem that has been impossible to be solved, and to break new ground in the field of science and engineering. (author)

  13. Multigrid and multilevel domain decomposition for unstructured grids

    Energy Technology Data Exchange (ETDEWEB)

    Chan, T.; Smith, B.

    1994-12-31

    Multigrid has proven itself to be a very versatile method for the iterative solution of linear and nonlinear systems of equations arising from the discretization of PDES. In some applications, however, no natural multilevel structure of grids is available, and these must be generated as part of the solution procedure. In this presentation the authors will consider the problem of generating a multigrid algorithm when only a fine, unstructured grid is given. Their techniques generate a sequence of coarser grids by first forming an approximate maximal independent set of the vertices and then applying a Cavendish type algorithm to form the coarser triangulation. Numerical tests indicate that convergence using this approach can be as fast as standard multigrid on a structured mesh, at least in two dimensions.

  14. Implicit Unstructured Computational Aerodynamics on Many-Integrated Core Architecture

    KAUST Repository

    Al Farhan, Mohammed A.

    2014-05-04

    This research aims to understand the performance of PETSc-FUN3D, a fully nonlinear implicit unstructured grid incompressible or compressible Euler code with origins at NASA and the U.S. DOE, on many-integrated core architecture and how a hybridprogramming paradigm (MPI+OpenMP) can exploit Intel Xeon Phi hardware with upwards of 60 cores per node and 4 threads per core. For the current contribution, we focus on strong scaling with many-integrated core hardware. In most implicit PDE-based codes, while the linear algebraic kernel is limited by the bottleneck of memory bandwidth, the flux kernel arising in control volume discretization of the conservation law residuals and the preconditioner for the Jacobian exploits the Phi hardware well.

  15. PDF modeling of turbulent flows on unstructured grids

    Science.gov (United States)

    Bakosi, J.

    2010-06-01

    In probability density function (PDF) methods of turbulent flows, the joint PDF of several flow variables is computed by numerically integrating a system of stochastic differential equations for Lagrangian particles. A mathematically exact treatment of advection, viscous effects and arbitrarily complex chemical reactions is possible; these processes are treated without closure assumptions. A set of algorithms is proposed to provide an efficient solution of the PDF transport equation modeling the joint PDF of turbulent velocity, frequency and concentration of a passive scalar in geometrically complex configurations. An unstructured Eulerian grid is employed to extract Eulerian statistics, to solve for quantities represented at fixed locations of the domain and to track particles. All three aspects regarding the grid make use of the finite element method. Compared to hybrid methods, the current methodology is stand-alone, therefore it is consistent both numerically and at the level of turbulence closure without the use of consistency conditions. Several newly developed algorithms are described that facilitate the numerical solution in complex flow geometries, including a stabilized mean-pressure projection scheme, the estimation of conditional and unconditional Eulerian statistics and their derivatives from stochastic particle fields, particle tracking through unstructured grids, an efficient particle redistribution procedure and techniques related to efficient random number generation. The solver has been parallelized and optimized for shared memory and multi-core architectures using the OpenMP standard. Relevant aspects of performance and parallelism on cache-based shared memory machines are discussed and presented in detail. The methodology shows great promise in the simulation of high-Reynolds-number incompressible inert or reactive turbulent flows in realistic configurations.

  16. PLUM: Parallel Load Balancing for Unstructured Adaptive Meshes

    Science.gov (United States)

    Oliker, Leonid

    1998-01-01

    Dynamic mesh adaption on unstructured grids is a powerful tool for computing large-scale problems that require grid modifications to efficiently resolve solution features. Unfortunately, an efficient parallel implementation is difficult to achieve, primarily due to the load imbalance created by the dynamically-changing nonuniform grid. To address this problem, we have developed PLUM, an automatic portable framework for performing adaptive large-scale numerical computations in a message-passing environment. First, we present an efficient parallel implementation of a tetrahedral mesh adaption scheme. Extremely promising parallel performance is achieved for various refinement and coarsening strategies on a realistic-sized domain. Next we describe PLUM, a novel method for dynamically balancing the processor workloads in adaptive grid computations. This research includes interfacing the parallel mesh adaption procedure based on actual flow solutions to a data remapping module, and incorporating an efficient parallel mesh repartitioner. A significant runtime improvement is achieved by observing that data movement for a refinement step should be performed after the edge-marking phase but before the actual subdivision. We also present optimal and heuristic remapping cost metrics that can accurately predict the total overhead for data redistribution. Several experiments are performed to verify the effectiveness of PLUM on sequences of dynamically adapted unstructured grids. Portability is demonstrated by presenting results on the two vastly different architectures of the SP2 and the Origin2OOO. Additionally, we evaluate the performance of five state-of-the-art partitioning algorithms that can be used within PLUM. It is shown that for certain classes of unsteady adaption, globally repartitioning the computational mesh produces higher quality results than diffusive repartitioning schemes. We also demonstrate that a coarse starting mesh produces high quality load balancing, at

  17. 3D unstructured-mesh radiation transport codes

    International Nuclear Information System (INIS)

    Morel, J.

    1997-01-01

    Three unstructured-mesh radiation transport codes are currently being developed at Los Alamos National Laboratory. The first code is ATTILA, which uses an unstructured tetrahedral mesh in conjunction with standard Sn (discrete-ordinates) angular discretization, standard multigroup energy discretization, and linear-discontinuous spatial differencing. ATTILA solves the standard first-order form of the transport equation using source iteration in conjunction with diffusion-synthetic acceleration of the within-group source iterations. DANTE is designed to run primarily on workstations. The second code is DANTE, which uses a hybrid finite-element mesh consisting of arbitrary combinations of hexahedra, wedges, pyramids, and tetrahedra. DANTE solves several second-order self-adjoint forms of the transport equation including the even-parity equation, the odd-parity equation, and a new equation called the self-adjoint angular flux equation. DANTE also offers three angular discretization options: $S n$ (discrete-ordinates), $P n$ (spherical harmonics), and $SP n$ (simplified spherical harmonics). DANTE is designed to run primarily on massively parallel message-passing machines, such as the ASCI-Blue machines at LANL and LLNL. The third code is PERICLES, which uses the same hybrid finite-element mesh as DANTE, but solves the standard first-order form of the transport equation rather than a second-order self-adjoint form. DANTE uses a standard $S n$ discretization in angle in conjunction with trilinear-discontinuous spatial differencing, and diffusion-synthetic acceleration of the within-group source iterations. PERICLES was initially designed to run on workstations, but a version for massively parallel message-passing machines will be built. The three codes will be described in detail and computational results will be presented

  18. Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides

    International Nuclear Information System (INIS)

    Oh, Kwang-Im; Jung, Young-Sang; Hwang, Geum-Sook; Cho, Minhaeng

    2012-01-01

    Understanding intrinsic conformational preferences of amino-acids in unfolded proteins is important for elucidating the underlying principles of their stability and re-folding on biological timescales. Here, to investigate the neighbor interaction effects on the conformational propensities of amino-acids, we carried out 1 H NMR experiments for a comprehensive set of blocked dipeptides and measured the scalar coupling constants between alpha protons and amide protons as well as their chemical shifts. Detailed inspection of these NMR properties shows that, irrespective of amino-acid side-chain properties, the distributions of the measured coupling constants and chemical shifts of the dipeptides are comparatively narrow, indicating small variances of their conformation distributions. They are further compared with those of blocked amino-acids (Ac–X–NHMe), oligopeptides (Ac–GGXGG–NH 2 ), and native (lysozyme), denatured (lysozyme and outer membrane protein X from Escherichia coli), unstructured (Domain 2 of the protein 5A of Hepatitis C virus), and intrinsically disordered (hNlg3cyt: intracellular domain of human NL3) proteins. These comparative investigations suggest that the conformational preferences and local solvation environments of the blocked dipeptides are quite similar to not only those of other short oligopeptides but also those of denatured and natively unfolded proteins.

  19. Cell intrinsic control of axon regeneration

    Science.gov (United States)

    Mar, Fernando M; Bonni, Azad; Sousa, Mónica M

    2014-01-01

    Although neurons execute a cell intrinsic program of axonal growth during development, following the establishment of connections, the developmental growth capacity declines. Besides environmental challenges, this switch largely accounts for the failure of adult central nervous system (CNS) axons to regenerate. Here, we discuss the cell intrinsic control of axon regeneration, including not only the regulation of transcriptional and epigenetic mechanisms, but also the modulation of local protein translation, retrograde and anterograde axonal transport, and microtubule dynamics. We further explore the causes underlying the failure of CNS neurons to mount a vigorous regenerative response, and the paradigms demonstrating the activation of cell intrinsic axon growth programs. Finally, we present potential mechanisms to support axon regeneration, as these may represent future therapeutic approaches to promote recovery following CNS injury and disease. PMID:24531721

  20. Intrinsic Chevrolets at the SSC

    International Nuclear Information System (INIS)

    Brodsky, S.J.; Collins, J.C.; Ellis, S.D.; Gunion, J.F.; Mueller, A.H.

    1984-01-01

    The possibility of the production at high energy of heavy quarks, supersymmetric particles and other large mass colored systems via the intrinsic twist-six components in the proton wave function is discussed. While the existing data do not rule out the possible relevance of intrinsic charm production at present energies, the extrapolation of such intrinsic contributions to very high masses and energies suggests that they will not play an important role at the SSC

  1. Intrinsically dynamic population models

    Directory of Open Access Journals (Sweden)

    Robert Schoen

    2005-03-01

    Full Text Available Intrinsically dynamic models (IDMs depict populations whose cumulative growth rate over a number of intervals equals the product of the long term growth rates (that is the dominant roots or dominant eigenvalues associated with each of those intervals. Here the focus is on the birth trajectory produced by a sequence of population projection (Leslie matrices. The elements of a Leslie matrix are represented as straightforward functions of the roots of the matrix, and new relationships are presented linking the roots of a matrix to its Net Reproduction Rate and stable mean age of childbearing. Incorporating mortality changes in the rates of reproduction yields an IDM when the subordinate roots are held constant over time. In IDMs, the birth trajectory generated by any specified sequence of Leslie matrices can be found analytically. In the Leslie model with 15 year age groups, the constant subordinate root assumption leads to reasonable changes in the age pattern of fertility, and equations (27 and (30 provide the population size and structure that result from changing levels of net reproduction. IDMs generalize the fixed rate stable population model. They can characterize any observed population, and can provide new insights into dynamic demographic behavior, including the momentum associated with gradual or irregular paths to zero growth.

  2. Finite volume methods for the incompressible Navier-Stokes equations on unstructured grids

    Energy Technology Data Exchange (ETDEWEB)

    Meese, Ernst Arne

    1998-07-01

    Most solution methods of computational fluid dynamics (CFD) use structured grids based on curvilinear coordinates for compliance with complex geometries. In a typical industry application, about 80% of the time used to produce the results is spent constructing computational grids. Recently the use of unstructured grids has been strongly advocated. For unstructured grids there are methods for generating them automatically on quite complex domains. This thesis focuses on the design of Navier-Stokes solvers that can cope with unstructured grids and ''low quality grids'', thus reducing the need for human intervention in the grid generation.

  3. Incompressible Navier-Stokes inverse design method based on adaptive unstructured meshes

    International Nuclear Information System (INIS)

    Rahmati, M.T.; Charlesworth, D.; Zangeneh, M.

    2005-01-01

    An inverse method for blade design based on Navier-Stokes equations on adaptive unstructured meshes has been developed. In the method, unlike the method based on inviscid equations, the effect of viscosity is directly taken into account. In the method, the pressure (or pressure loading) is prescribed. The design method then computes the blade shape that would accomplish the target prescribed pressure distribution. The method is implemented using a cell-centered finite volume method, which solves the incompressible Navier-Stokes equations on unstructured meshes. An adaptive unstructured mesh method based on grid subdivision and local adaptive mesh method is utilized for increasing the accuracy. (author)

  4. Unstructured Computational Aerodynamics on Many Integrated Core Architecture

    KAUST Repository

    Al Farhan, Mohammed A.

    2016-06-08

    Shared memory parallelization of the flux kernel of PETSc-FUN3D, an unstructured tetrahedral mesh Euler flow code previously studied for distributed memory and multi-core shared memory, is evaluated on up to 61 cores per node and up to 4 threads per core. We explore several thread-level optimizations to improve flux kernel performance on the state-of-the-art many integrated core (MIC) Intel processor Xeon Phi “Knights Corner,” with a focus on strong thread scaling. While the linear algebraic kernel is bottlenecked by memory bandwidth for even modest numbers of cores sharing a common memory, the flux kernel, which arises in the control volume discretization of the conservation law residuals and in the formation of the preconditioner for the Jacobian by finite-differencing the conservation law residuals, is compute-intensive and is known to exploit effectively contemporary multi-core hardware. We extend study of the performance of the flux kernel to the Xeon Phi in three thread affinity modes, namely scatter, compact, and balanced, in both offload and native mode, with and without various code optimizations to improve alignment and reduce cache coherency penalties. Relative to baseline “out-of-the-box” optimized compilation, code restructuring optimizations provide about 3.8x speedup using the offload mode and about 5x speedup using the native mode. Even with these gains for the flux kernel, with respect to execution time the MIC simply achieves par with optimized compilation on a contemporary multi-core Intel CPU, the 16-core Sandy Bridge E5 2670. Nevertheless, the optimizations employed to reduce the data motion and cache coherency protocol penalties of the MIC are expected to be of value for CFD and many other unstructured applications as many-core architecture evolves. We explore large-scale distributed-shared memory performance on the Cray XC40 supercomputer, to demonstrate that optimizations employed on Phi hybridize to this context, where each of

  5. Intrinsic Motivation and Flow Condition on the Music Teacher's Performance

    Science.gov (United States)

    Torres Delgado, Gabriela

    2017-01-01

    The aim of these research is to identify if music teachers and teachers from other areas are intrinsically or extrinsically motivated, to identify the dimensions of the flow state, and to identify if there is a relationship between intrinsic motivation and flow state in these teachers. The sample was made up of 738 active teachers. The presence of…

  6. Unstructured CFD Aerodynamic Analysis of a Generic UCAV Configuration

    Science.gov (United States)

    Frink, Neal T.; Tormalm, Magnus; Schmidt, Stefan

    2011-01-01

    Three independent studies from the United States (NASA), Sweden (FOI), and Australia (DSTO) are analyzed to assess the state of current unstructured-grid computational fluid dynamic tools and practices for predicting the complex static and dynamic aerodynamic and stability characteristics of a generic 53-degree swept, round-leading-edge uninhabited combat air vehicle configuration, called SACCON. NASA exercised the USM3D tetrahedral cell-centered flow solver, while FOI and DSTO applied the FOI/EDGE general-cell vertex-based solver. The authors primarily employ the Reynolds Averaged Navier-Stokes (RANS) assumption, with a limited assessment of the EDGE Detached Eddy Simulation (DES) extension, to explore sensitivities to grids and turbulence models. Correlations with experimental data are provided for force and moments, surface pressure, and off-body flow measurements. The vortical flow field over SACCON proved extremely difficult to model adequately. As a general rule, the prospect of obtaining reasonable correlations of SACCON pitching moment characteristics with the RANS formulation is not promising, even for static cases. Yet, dynamic pitch oscillation results seem to produce a promising characterization of shapes for the lift and pitching moment hysteresis curves. Future studies of this configuration should include more investigation with higher-fidelity turbulence models, such as DES.

  7. Adaptive unstructured meshes for finite element ocean modelling

    Science.gov (United States)

    Power, P. W.; Pain, C. C.; Piggott, M. D.; Marshall, D. P.; Fang, F.; Umpleby, A. P.; de Oliveira, C. R. E.; Goddard, A. J. H.

    2003-04-01

    Flow in the world's oceans occurs at a wide range of spatial scales, from micro-metres to mega-metres. In particular, regions of intense flow are often highly localised, for example Western Boundary Currents. Conventional numerical ocean models generally use static meshes. The Imperial College Ocean Model (ICOM) uses advanced finite element methods to evolve the mesh to follow regions of intense flow, where high resolution may be required. Coarser resolution can be used in other areas of the flow domain. Evolution of the unstructured mesh is achieved by the use of a variety of error norms which control a self-adaptive anisotrophic meshing algorithm. The objective of this work is a reduction in computational cost, ensuring areas of fine resolution are used only where and when they are required. In this work we present some examples of an error measure being used to obtain high-quality solutions to a set of benchmark problems, for example flow over a seamount and a wind driven gyre, while using a minimal number of elements. The long term objective of this work is to define a rigorous self-adaptive technique for use in an Oceanographic context, and we present plans for the implimentation of a sensitivity based error measure.

  8. Mathematical modeling of polymer flooding using the unstructured Voronoi grid

    Science.gov (United States)

    Kireev, T. F.; Bulgakova, G. T.; Khatmullin, I. F.

    2017-12-01

    Effective recovery of unconventional oil reserves necessitates development of enhanced oil recovery techniques such as polymer flooding. The study investigated the model of polymer flooding with effects of adsorption and water salinity. The model takes into account six components that include elements of the classic black oil model. These components are polymer, salt, water, dead oil, dry gas and dissolved gas. Solution of the problem is obtained by finite volume method on unstructured Voronoi grid using fully implicit scheme and the Newton’s method. To compare several different grid configurations numerical simulation of polymer flooding is performed. The oil rates obtained by a hexagonal locally refined Voronoi grid are shown to be more accurate than the oil rates obtained by a rectangular grid with the same number of cells. The latter effect is caused by high solution accuracy near the wells due to the local grid refinement. Minimization of the grid orientation effect caused by the hexagonal pattern is also demonstrated. However, in the inter-well regions with large Voronoi cells flood front tends to flatten and the water breakthrough moment is smoothed.

  9. Development and acceleration of unstructured mesh-based cfd solver

    Science.gov (United States)

    Emelyanov, V.; Karpenko, A.; Volkov, K.

    2017-06-01

    The study was undertaken as part of a larger effort to establish a common computational fluid dynamics (CFD) code for simulation of internal and external flows and involves some basic validation studies. The governing equations are solved with ¦nite volume code on unstructured meshes. The computational procedure involves reconstruction of the solution in each control volume and extrapolation of the unknowns to find the flow variables on the faces of control volume, solution of Riemann problem for each face of the control volume, and evolution of the time step. The nonlinear CFD solver works in an explicit time-marching fashion, based on a three-step Runge-Kutta stepping procedure. Convergence to a steady state is accelerated by the use of geometric technique and by the application of Jacobi preconditioning for high-speed flows, with a separate low Mach number preconditioning method for use with low-speed flows. The CFD code is implemented on graphics processing units (GPUs). Speedup of solution on GPUs with respect to solution on central processing units (CPU) is compared with the use of different meshes and different methods of distribution of input data into blocks. The results obtained provide promising perspective for designing a GPU-based software framework for applications in CFD.

  10. Constructing Social Networks from Unstructured Group Dialog in Virtual Worlds

    Science.gov (United States)

    Shah, Fahad; Sukthankar, Gita

    Virtual worlds and massively multi-player online games are rich sources of information about large-scale teams and groups, offering the tantalizing possibility of harvesting data about group formation, social networks, and network evolution. However these environments lack many of the cues that facilitate natural language processing in other conversational settings and different types of social media. Public chat data often features players who speak simultaneously, use jargon and emoticons, and only erratically adhere to conversational norms. In this paper, we present techniques for inferring the existence of social links from unstructured conversational data collected from groups of participants in the Second Life virtual world. We present an algorithm for addressing this problem, Shallow Semantic Temporal Overlap (SSTO), that combines temporal and language information to create directional links between participants, and a second approach that relies on temporal overlap alone to create undirected links between participants. Relying on temporal overlap is noisy, resulting in a low precision and networks with many extraneous links. In this paper, we demonstrate that we can ameliorate this problem by using network modularity optimization to perform community detection in the noisy networks and severing cross-community links. Although using the content of the communications still results in the best performance, community detection is effective as a noise reduction technique for eliminating the extra links created by temporal overlap alone.

  11. The quasidiffusion method for transport problems on unstructured meshes

    Science.gov (United States)

    Wieselquist, William A.

    2009-06-01

    In this work, we develop a quasidiffusion (QD) method for solving radiation transport problems on unstructured quadrilateral meshes in 2D Cartesian geometry, for example hanging-node meshes from adaptive mesh refinement (AMR) applications or skewed quadrilateral meshes from radiation hydrodynamics with Lagrangian meshing. The main result of the work is a new low-order quasidiffusion (LOQD) discretization on arbitrary quadrilaterals and a strategy for the efficient iterative solution which uses Krylov methods and incomplete LU factorization (ILU) preconditioning. The LOQD equations are a non-symmetric set of first-order PDEs that in second-order form resembles convection- diffusion with a diffusion tensor, with the difference that the LOQD equations contain extra cross-derivative terms. Our finite volume (FV) discretization of the LOQD equations is compared with three LOQD discretizations from literature. We then present a conservative, short characteristics discretization based on subcell balances (SCSB) that uses polynomial exponential moments to achieve robust behavior in various limits (e.g. small cells and voids) and is second- order accurate in space. A linear representation of the isotropic component of the scattering source based on face-average and cell-average scalar fluxes is also proposed and shown to be effective in some problems. In numerical tests, our QD method with linear scattering source representation shows some advantages compared to other transport methods. We conclude with avenues for future research and note that this QD method may easily be extended to arbitrary meshes in 3D Cartesian geometry.

  12. Improved Degree Search Algorithms in Unstructured P2P Networks

    Directory of Open Access Journals (Sweden)

    Guole Liu

    2012-01-01

    Full Text Available Searching and retrieving the demanded correct information is one important problem in networks; especially, designing an efficient search algorithm is a key challenge in unstructured peer-to-peer (P2P networks. Breadth-first search (BFS and depth-first search (DFS are the current two typical search methods. BFS-based algorithms show the perfect performance in the aspect of search success rate of network resources, while bringing the huge search messages. On the contrary, DFS-based algorithms reduce the search message quantity and also cause the dropping of search success ratio. To address the problem that only one of performances is excellent, we propose two memory function degree search algorithms: memory function maximum degree algorithm (MD and memory function preference degree algorithm (PD. We study their performance including the search success rate and the search message quantity in different networks, which are scale-free networks, random graph networks, and small-world networks. Simulations show that the two performances are both excellent at the same time, and the performances are improved at least 10 times.

  13. Numerical study of Taylor bubbles with adaptive unstructured meshes

    Science.gov (United States)

    Xie, Zhihua; Pavlidis, Dimitrios; Percival, James; Pain, Chris; Matar, Omar; Hasan, Abbas; Azzopardi, Barry

    2014-11-01

    The Taylor bubble is a single long bubble which nearly fills the entire cross section of a liquid-filled circular tube. This type of bubble flow regime often occurs in gas-liquid slug flows in many industrial applications, including oil-and-gas production, chemical and nuclear reactors, and heat exchangers. The objective of this study is to investigate the fluid dynamics of Taylor bubbles rising in a vertical pipe filled with oils of extremely high viscosity (mimicking the ``heavy oils'' found in the oil-and-gas industry). A modelling and simulation framework is presented here which can modify and adapt anisotropic unstructured meshes to better represent the underlying physics of bubble rise and reduce the computational effort without sacrificing accuracy. The numerical framework consists of a mixed control-volume and finite-element formulation, a ``volume of fluid''-type method for the interface capturing based on a compressive control volume advection method, and a force-balanced algorithm for the surface tension implementation. Numerical examples of some benchmark tests and the dynamics of Taylor bubbles are presented to show the capability of this method. EPSRC Programme Grant, MEMPHIS, EP/K0039761/1.

  14. Parallel unstructured AMR and gigabit networking for Beowulf-class clusters

    Science.gov (United States)

    Norton, C. D.; Cwik, T. A.

    2001-01-01

    The impact of gigabit networking with Myrinet 2000 hardware and MPICH-GM software on a 2-way SMP Beowulf-class cluster for parallel unstructured adaptive mesh refinement using the PYRAMID library is described.

  15. An efficient approach to unstructured mesh hydrodynamics on the cell broadband engine (u)

    Energy Technology Data Exchange (ETDEWEB)

    Ferenbaugh, Charles R [Los Alamos National Laboratory

    2010-12-14

    Unstructured mesh physics for the Cell Broadband Engine (CBE) has received little or no attention to date, largely because the CBE architecture poses particular challenges for unstructured mesh algorithms. SPU memory management strategies such as data preloading cannot be applied to the irregular memory storage patterns of unstructured meshes; and the SPU vector instruction set does not support the indirect addressing needed by connectivity arrays. This paper presents an approach to unstructured mesh physics that addresses these challenges, by creating a new mesh data structure and reorganizing code to give efficient CBE performance. The approach is demonstrated on the FLAG production hydrodynamics code using standard test problems, and results show an average speedup of more than 5x over the original code.

  16. An efficient approach to unstructured mesh hydrodynamics on the cell broadband engine

    Energy Technology Data Exchange (ETDEWEB)

    Ferenbaugh, Charles R [Los Alamos National Laboratory

    2010-01-01

    Unstructured mesh physics for the Cell Broadband Engine (CBE) has received little or no attention to date, largely because the CBE architecture poses particular challenges for unstructured mesh algorithms. The most common SPU memory management strategies cannot be applied to the irregular memory access patterns of unstructured meshes, and the SPU vector instruction set does not support the indirect addressing needed by connectivity arrays. This paper presents an approach to unstructured mesh physics that addresses these challenges, by creating a new mesh data structure and reorganizing code to give efficient CBE performance. The approach is demonstrated on the FLAG production hydrodynamics code using standard test problems, and results show an average speedup of more than 5x over the original code.

  17. Multigrid on unstructured grids using an auxiliary set of structured grids

    Energy Technology Data Exchange (ETDEWEB)

    Douglas, C.C.; Malhotra, S.; Schultz, M.H. [Yale Univ., New Haven, CT (United States)

    1996-12-31

    Unstructured grids do not have a convenient and natural multigrid framework for actually computing and maintaining a high floating point rate on standard computers. In fact, just the coarsening process is expensive for many applications. Since unstructured grids play a vital role in many scientific computing applications, many modifications have been proposed to solve this problem. One suggested solution is to map the original unstructured grid onto a structured grid. This can be used as a fine grid in a standard multigrid algorithm to precondition the original problem on the unstructured grid. We show that unless extreme care is taken, this mapping can lead to a system with a high condition number which eliminates the usefulness of the multigrid method. Theorems with lower and upper bounds are provided. Simple examples show that the upper bounds are sharp.

  18. Comparative reliability of structured versus unstructured interviews in the admission process of a residency program.

    Science.gov (United States)

    Blouin, Danielle; Day, Andrew G; Pavlov, Andrey

    2011-12-01

    Although never directly compared, structured interviews are reported as being more reliable than unstructured interviews. This study compared the reliability of both types of interview when applied to a common pool of applicants for positions in an emergency medicine residency program. In 2008, one structured interview was added to the two unstructured interviews traditionally used in our resident selection process. A formal job analysis using the critical incident technique guided the development of the structured interview tool. This tool consisted of 7 scenarios assessing 4 of the domains deemed essential for success as a resident in this program. The traditional interview tool assessed 5 general criteria. In addition to these criteria, the unstructured panel members were asked to rate each candidate on the same 4 essential domains rated by the structured panel members. All 3 panels interviewed all candidates. Main outcomes were the overall, interitem, and interrater reliabilities, the correlations between interview panels, and the dimensionality of each interview tool. Thirty candidates were interviewed. The overall reliability reached 0.43 for the structured interview, and 0.81 and 0.71 for the unstructured interviews. Analyses of the variance components showed a high interrater, low interitem reliability for the structured interview, and a high interrater, high interitem reliability for the unstructured interviews. The summary measures from the 2 unstructured interviews were significantly correlated, but neither was correlated with the structured interview. Only the structured interview was multidimensional. A structured interview did not yield a higher overall reliability than both unstructured interviews. The lower reliability is explained by a lower interitem reliability, which in turn is due to the multidimensionality of the interview tool. Both unstructured panels consistently rated a single dimension, even when prompted to assess the 4 specific domains

  19. Learning intrinsic excitability in medium spiny neurons.

    Science.gov (United States)

    Scheler, Gabriele

    2013-01-01

    We present an unsupervised, local activation-dependent learning rule for intrinsic plasticity (IP) which affects the composition of ion channel conductances for single neurons in a use-dependent way. We use a single-compartment conductance-based model for medium spiny striatal neurons in order to show the effects of parameterization of individual ion channels on the neuronal membrane potential-curent relationship (activation function). We show that parameter changes within the physiological ranges are sufficient to create an ensemble of neurons with significantly different activation functions. We emphasize that the effects of intrinsic neuronal modulation on spiking behavior require a distributed mode of synaptic input and can be eliminated by strongly correlated input. We show how modulation and adaptivity in ion channel conductances can be utilized to store patterns without an additional contribution by synaptic plasticity (SP). The adaptation of the spike response may result in either "positive" or "negative" pattern learning. However, read-out of stored information depends on a distributed pattern of synaptic activity to let intrinsic modulation determine spike response. We briefly discuss the implications of this conditional memory on learning and addiction.

  20. Intrinsically Passive Handling and Grasping

    NARCIS (Netherlands)

    Stramigioli, Stefano; Scherpen, Jacquelien M.A.; Khodabandehloo, Koorosh

    2000-01-01

    The paper presents a control philosophy called Intrinsically Passive Control, which has the feature to properly behave during interaction with any passive objects. The controlled robot will never become unstable due to the physical structure of the controller.

  1. Helical propensity in an intrinsically disordered protein accelerates ligand binding

    DEFF Research Database (Denmark)

    Iesmantavicius, Vytautas; Dogan, Jakob; Jemth, Per

    2014-01-01

    domain of the activator for thyroid hormone and retinoid receptors (ACTR) is intrinsically disordered and folds upon binding to the nuclear coactivator binding domain (NCBD) of the CREB binding protein. A number of mutants was designed that selectively perturbs the amount of secondary structure......Many intrinsically disordered proteins fold upon binding to other macromolecules. The secondary structure present in the well-ordered complex is often formed transiently in the unbound state. The consequence of such transient structure for the binding process is, however, not clear. The activation...... the notion of preformed secondary structure as an important determinant for molecular recognition in intrinsically disordered proteins....

  2. 3D Digitisation of Large-Scale Unstructured Great Wall Heritage Sites by a Small Unmanned Helicopter

    Directory of Open Access Journals (Sweden)

    Fucheng Deng

    2017-04-01

    Full Text Available The ancient Great Wall of China has long suffered from damage due to natural factors and human activities. A small low-cost unmanned helicopter system with a laser scanner and a digital camera is developed to efficiently visualize the status of the huge Great Wall area. The goal of the system is to achieve 3D digitisation of the large-scale Great Wall using a combination of fly-hover-scan and flying-scan modes. However, pose uncertainties of the unmanned helicopter could cause mismatching among point clouds acquired by each hovering-scan. This problem would become more severe as the target area becomes larger and more unstructured. Therefore, a hierarchical optimization framework is proposed in this paper to achieve 3D digitisation of the large-scale unstructured Great Wall with unpredictable pose uncertainties of the unmanned helicopter. In this framework, different optimization methodologies are proposed for the fly-hover-scan and flying-scan modes, respectively, because different scan modes would result in different features of point clouds. Moreover, a user-friendly interface based on WebGL has been developed for 3D model visualization and comparison. Experimental results demonstrate the feasibility of the proposed framework for 3D digitisation of the Great Wall segments.

  3. A Parallel Multiblock Structured Grid Method with Automated Interblocked Unstructured Grids for Chemically Reacting Flows

    Science.gov (United States)

    Spiegel, Seth Christian

    An automated method for using unstructured grids to patch non- C0 interfaces between structured blocks has been developed in conjunction with a finite-volume method for solving chemically reacting flows on unstructured grids. Although the standalone unstructured solver, FVFLO-NCSU, is capable of resolving flows for high-speed aeropropulsion devices with complex geometries, unstructured-mesh algorithms are inherently inefficient when compared to their structured counterparts. However, the advantages of structured algorithms in developing a flow solution in a timely manner can be negated by the amount of time required to develop a mesh for complex geometries. The global domain can be split up into numerous smaller blocks during the grid-generation process to alleviate some of the difficulties in creating these complex meshes. An even greater abatement can be found by allowing the nodes on abutting block interfaces to be nonmatching or non-C 0 continuous. One code capable of solving chemically reacting flows on these multiblock grids is VULCAN, which uses a nonconservative approach for patching non-C0 block interfaces. The developed automated unstructured-grid patching algorithm has been installed within VULCAN to provide it the capability of a fully conservative approach for patching non-C0 block interfaces. Additionally, the FVFLO-NCSU solver algorithms have been deeply intertwined with the VULCAN source code to solve chemically reacting flows on these unstructured patches. Finally, the CGNS software library was added to the VULCAN postprocessor so structured and unstructured data can be stored in a single compact file. This final upgrade to VULCAN has been successfully installed and verified using test cases with particular interest towards those involving grids with non- C0 block interfaces.

  4. Estimating abundance of mountain lions from unstructured spatial sampling

    Science.gov (United States)

    Russell, Robin E.; Royle, J. Andrew; Desimone, Richard; Schwartz, Michael K.; Edwards, Victoria L.; Pilgrim, Kristy P.; Mckelvey, Kevin S.

    2012-01-01

    distance x sex on detection probability). These numbers translate to a total estimate of 293 mountain lions (95% Cl 182–451) to 529 (95% Cl 245–870) within the Blackfoot drainage. Results from the distance model are similar to previous estimates of 3.6 mountain lions/100 km2 for the study area; however, results from all other models indicated greater numbers of mountain lions. Our results indicate that unstructured spatial sampling combined with spatial capture–recapture analysis can be an effective method for estimating large carnivore densities.

  5. Extrinsic and intrinsic determinants of nerve regeneration

    Directory of Open Access Journals (Sweden)

    Toby A. Ferguson

    2011-01-01

    Full Text Available After central nervous system (CNS injury axons fail to regenerate often leading to persistent neurologic deficit although injured peripheral nervous system (PNS axons mount a robust regenerative response that may lead to functional recovery. Some of the failures of CNS regeneration arise from the many glial-based inhibitory molecules found in the injured CNS, whereas the intrinsic regenerative potential of some CNS neurons is actively curtailed during CNS maturation and limited after injury. In this review, the molecular basis for extrinsic and intrinsic modulation of axon regeneration within the nervous system is evaluated. A more complete understanding of the factors limiting axonal regeneration will provide a rational basis, which is used to develop improved treatments for nervous system injury.

  6. Verification of Unstructured Mesh Capabilities in MCNP6 for Reactor Physics Problems

    International Nuclear Information System (INIS)

    Burke, Timothy P.; Martz, Roger L.; Kiedrowski, Brian C.; Martin, William R.

    2012-01-01

    New unstructured mesh capabilities in MCNP6 (developmental version during summer 2012) show potential for conducting multi-physics analyses by coupling MCNP to a finite element solver such as Abaqus/CAE[2]. Before these new capabilities can be utilized, the ability of MCNP to accurately estimate eigenvalues and pin powers using an unstructured mesh must first be verified. Previous work to verify the unstructured mesh capabilities in MCNP was accomplished using the Godiva sphere [1], and this work attempts to build on that. To accomplish this, a criticality benchmark and a fuel assembly benchmark were used for calculations in MCNP using both the Constructive Solid Geometry (CSG) native to MCNP and the unstructured mesh geometry generated using Abaqus/CAE. The Big Ten criticality benchmark [3] was modeled due to its geometry being similar to that of a reactor fuel pin. The C5G7 3-D Mixed Oxide (MOX) Fuel Assembly Benchmark [4] was modeled to test the unstructured mesh capabilities on a reactor-type problem.

  7. Unstructured mesh based elastic wave modelling on GPU: a double-mesh grid method

    Science.gov (United States)

    Yang, Kai; Zhang, Jianfeng; Gao, Hongwei

    2017-11-01

    We present an unstructured mesh based numerical technique for modelling elastic wave propagation in heterogeneous media with complex geometrical settings. The scheme is developed by adapting the so-called grid method with a double-mesh implementation. The double-mesh is generated by subdividing each triangular grid of the first-level mesh into a group of congruent smaller grids with equally dividing each edge of the triangle. The resulting double-mesh grid method incorporates the advantages of structured- and unstructured-mesh schemes. The irregular, unstructured first-level mesh, which is generated by centroidal Voronoi tessellation based on Delaunay triangulation with a velocity-dependent density function, can accurately describe the surface topography and interfaces, and the size of the grid cells can vary according to local velocities. Congruent smaller grids within each grid cell of the first-level mesh greatly reduce the memory requirement of geometrical coefficients compared to a whole irregular, unstructured mesh. Applying the double-mesh approach can also alleviate the discontinuity of memory accessing mainly caused by adoption of fully unstructured mesh. As a result, the GPU implementation of the proposed scheme can obtain a high speedup rate. Numerical examples demonstrate the good behaviour of the double-mesh elastic grid method.

  8. V(2)O(5) nanowires with an intrinsic iodination activity leading to the formation of self-assembled melanin-like biopolymers

    NARCIS (Netherlands)

    Natalio, F.; André, R.; Pihan, S.A.; Humanes, M.; Wever, R.; Tremel, W.

    2011-01-01

    V2O5 nanowires act as biomimetic catalysts resembling vanadium haloperoxidases (V-HPO). The nanowires display iodinating activity as confirmed by a colorimetric assay using thymol blue (TB), UV/Vis spectrophotometry and mass spectrometry (FD-MS). In the presence of dopamine these nanowires catalyze

  9. Effect of pH on the denitrifying enzyme activity in pasture soils in relation to the intrinsic differences in denitrifier communities

    Czech Academy of Sciences Publication Activity Database

    Čuhel, Jiří; Šimek, Miloslav

    2011-01-01

    Roč. 56, č. 3 (2011), s. 230-235 ISSN 0015-5632 R&D Projects: GA MŠk LC06066; GA AV ČR IAA600660605 Institutional research plan: CEZ:AV0Z60660521 Keywords : pH * denitrifying enzyme activity * pasture soils Subject RIV: EH - Ecology, Behaviour Impact factor: 0.677, year: 2011

  10. Effects of Gold Substrates on the Intrinsic and Extrinsic Activity of High-Loading Nickel-Based Oxyhydroxide Oxygen Evolution Catalysts

    DEFF Research Database (Denmark)

    Chakthranont, Pongkarn; Kibsgaard, Jakob; Gallo, Alessandro

    2017-01-01

    We systematically investigate the effects of Au substrates on the oxygen evolution activities of cathodically electrodeposited nickel oxyhydroxide (NiOOH), nickel–iron oxyhydroxide (NiFeOOH), and nickel–cerium oxyhydroxide (NiCeOOH) at varying loadings from 0 to 2000 nmol of metal/cm2. We determine...

  11. Editing of misaligned 3′-termini by an intrinsic 3′–5′ exonuclease activity residing in the PHP domain of a family X DNA polymerase

    Science.gov (United States)

    Baños, Benito; Lázaro, José M.; Villar, Laurentino; de Vega, Miguel

    2008-01-01

    Bacillus subtilis gene yshC encodes a family X DNA polymerase (PolXBs), whose biochemical features suggest that it plays a role during DNA repair processes. Here, we show that, in addition to the polymerization activity, PolXBs possesses an intrinsic 3′–5′ exonuclease activity specialized in resecting unannealed 3′-termini in a gapped DNA substrate. Biochemical analysis of a PolXBs deletion mutant lacking the C-terminal polymerase histidinol phosphatase (PHP) domain, present in most of the bacterial/archaeal PolXs, as well as of this separately expressed protein region, allow us to state that the 3′–5′ exonuclease activity of PolXBs resides in its PHP domain. Furthermore, site-directed mutagenesis of PolXBs His339 and His341 residues, evolutionary conserved in the PHP superfamily members, demonstrated that the predicted metal binding site is directly involved in catalysis of the exonucleolytic reaction. The implications of the unannealed 3′-termini resection by the 3′–5′ exonuclease activity of PolXBs in the DNA repair context are discussed. PMID:18776221

  12. The intrinsic antimicrobial activity of citric acid-coated manganese ferrite nanoparticles is enhanced after conjugation with the antifungal peptide Cm-p5

    Science.gov (United States)

    Lopez-Abarrategui, Carlos; Figueroa-Espi, Viviana; Lugo-Alvarez, Maria B; Pereira, Caroline D; Garay, Hilda; Barbosa, João ARG; Falcão, Rosana; Jiménez-Hernández, Linnavel; Estévez-Hernández, Osvaldo; Reguera, Edilso; Franco, Octavio L; Dias, Simoni C; Otero-Gonzalez, Anselmo J

    2016-01-01

    Diseases caused by bacterial and fungal pathogens are among the major health problems in the world. Newer antimicrobial therapies based on novel molecules urgently need to be developed, and this includes the antimicrobial peptides. In spite of the potential of antimicrobial peptides, very few of them were able to be successfully developed into therapeutics. The major problems they present are molecule stability, toxicity in host cells, and production costs. A novel strategy to overcome these obstacles is conjugation to nanomaterial preparations. The antimicrobial activity of different types of nanoparticles has been previously demonstrated. Specifically, magnetic nanoparticles have been widely studied in biomedicine due to their physicochemical properties. The citric acid-modified manganese ferrite nanoparticles used in this study were characterized by high-resolution transmission electron microscopy, which confirmed the formation of nanocrystals of approximately 5 nm diameter. These nanoparticles were able to inhibit Candida albicans growth in vitro. The minimal inhibitory concentration was 250 µg/mL. However, the nanoparticles were not capable of inhibiting Gram-negative bacteria (Escherichia coli) or Gram-positive bacteria (Staphylococcus aureus). Finally, an antifungal peptide (Cm-p5) from the sea animal Cenchritis muricatus (Gastropoda: Littorinidae) was conjugated to the modified manganese ferrite nanoparticles. The antifungal activity of the conjugated nanoparticles was higher than their bulk counterparts, showing a minimal inhibitory concentration of 100 µg/mL. This conjugate proved to be nontoxic to a macrophage cell line at concentrations that showed antimicrobial activity. PMID:27563243

  13. The intrinsic antimicrobial activity of citric acid-coated manganese ferrite nanoparticles is enhanced after conjugation with the antifungal peptide Cm-p5.

    Science.gov (United States)

    Lopez-Abarrategui, Carlos; Figueroa-Espi, Viviana; Lugo-Alvarez, Maria B; Pereira, Caroline D; Garay, Hilda; Barbosa, João Arg; Falcão, Rosana; Jiménez-Hernández, Linnavel; Estévez-Hernández, Osvaldo; Reguera, Edilso; Franco, Octavio L; Dias, Simoni C; Otero-Gonzalez, Anselmo J

    2016-01-01

    Diseases caused by bacterial and fungal pathogens are among the major health problems in the world. Newer antimicrobial therapies based on novel molecules urgently need to be developed, and this includes the antimicrobial peptides. In spite of the potential of antimicrobial peptides, very few of them were able to be successfully developed into therapeutics. The major problems they present are molecule stability, toxicity in host cells, and production costs. A novel strategy to overcome these obstacles is conjugation to nanomaterial preparations. The antimicrobial activity of different types of nanoparticles has been previously demonstrated. Specifically, magnetic nanoparticles have been widely studied in biomedicine due to their physicochemical properties. The citric acid-modified manganese ferrite nanoparticles used in this study were characterized by high-resolution transmission electron microscopy, which confirmed the formation of nanocrystals of approximately 5 nm diameter. These nanoparticles were able to inhibit Candida albicans growth in vitro. The minimal inhibitory concentration was 250 µg/mL. However, the nanoparticles were not capable of inhibiting Gram-negative bacteria (Escherichia coli) or Gram-positive bacteria (Staphylococcus aureus). Finally, an antifungal peptide (Cm-p5) from the sea animal Cenchritis muricatus (Gastropoda: Littorinidae) was conjugated to the modified manganese ferrite nanoparticles. The antifungal activity of the conjugated nanoparticles was higher than their bulk counterparts, showing a minimal inhibitory concentration of 100 µg/mL. This conjugate proved to be nontoxic to a macrophage cell line at concentrations that showed antimicrobial activity.

  14. Cis-trimethoxy resveratrol induces intrinsic apoptosis via prometaphase arrest and prolonged CDK1 activation pathway in human Jurkat T cells.

    Science.gov (United States)

    Kim, Chae Eun; Jun, Do Youn; Kim, Jong-Sik; Kim, Young Ho

    2018-01-12

    Cis-trimethoxy resveratrol (cis-3M-RES) induced dose-dependent cytotoxicity and apoptotic DNA fragmentation in Jurkat T cell clones (JT/Neo); however, it induced only cytostasis in BCL-2-overexpressing cells (JT/BCL-2). Treatment with 0.25 μM cis-3M-RES induced G 2 /M arrest, BAK activation, Δψm loss, caspase-9 and caspase-3 activation, and poly (ADP-ribose) polymerase (PARP) cleavage in JT/Neo cells time-dependently but did not induce these events, except G 2 /M arrest, in JT/BCL-2 cells. Moreover, cis-3M-RES induced CDK1 activation, BCL-2 phosphorylation at Ser-70, MCL-1 phosphorylation at Ser-159/Thr-163, and BIM (BIM EL and BIM L ) phosphorylation irrespective of BCL-2 overexpression. Enforced G 1 /S arrest by using a G 1 /S blocker aphidicolin completely inhibited cis-3M-RES-induced apoptotic events. Cis-3M-RES-induced phosphorylation of BCL-2 family proteins and mitochondrial apoptotic events were suppressed by a validated CDK1 inhibitor RO3306. Immunofluorescence microscopy showed that cis-3M-RES induced mitotic spindle defects and prometaphase arrest. The rate of intracellular polymeric tubulin to monomeric tubulin decreased markedly by cis-3M-RES (0.1-1.0 μM). Wild-type Jurkat clone A3, FADD-deficient Jurkat clone I2.1, and caspase-8-deficient Jurkat clone I9.2 exhibited similar susceptibilities to the cytotoxicity of cis-3M-RES, excluding contribution of the extrinsic death receptor-dependent pathway to the apoptosis. IC 50 values of cis-3M-RES against Jurkat E6.1, U937, HL-60, and HeLa cells were 0.07-0.17 μM, whereas those against unstimulated human peripheral T cells and phytohaemagglutinin A-stimulated peripheral T cells were >10.0 and 0.23 μM, respectively. These results indicate that the antitumor activity of cis-3M-RES is mediated by microtubule damage, and subsequent prometaphase arrest and prolonged CDK1 activation that cause BAK-mediated mitochondrial apoptosis, and suggest that cis-3M-RES is a promising agent to treat leukemia.

  15. An assessment of unstructured grid finite volume schemes for cold gas hypersonic flow calculations

    Directory of Open Access Journals (Sweden)

    João Luiz F. Azevedo

    2009-06-01

    Full Text Available A comparison of five different spatial discretization schemes is performed considering a typical high speed flow application. Flowfields are simulated using the 2-D Euler equations, discretized in a cell-centered finite volume procedure on unstructured triangular meshes. The algorithms studied include a central difference-type scheme, and 1st- and 2nd-order van Leer and Liou flux-vector splitting schemes. These methods are implemented in an efficient, edge-based, unstructured grid procedure which allows for adaptive mesh refinement based on flow property gradients. Details of the unstructured grid implementation of the methods are presented together with a discussion of the data structure and of the adaptive refinement strategy. The application of interest is the cold gas flow through a typical hypersonic inlet. Results for different entrance Mach numbers and mesh topologies are discussed in order to assess the comparative performance of the various spatial discretization schemes.

  16. Downregulation of PI3-K/Akt/PTEN pathway and activation of mitochondrial intrinsic apoptosis by Diclofenac and Curcumin in colon cancer.

    Science.gov (United States)

    Rana, Chandan; Piplani, Honit; Vaish, Vivek; Nehru, Bimla; Sanyal, S N

    2015-04-01

    Phosphatidylinositol 3-kinase (PI3-K)/PTEN/Akt signaling is over activated in various tumors including colon cancer. Activation of this pathway regulates multiple biological processes such as apoptosis, metabolism, cell proliferation, and cell growth that underlie the biology of a cancer cell. In the present study, the chemopreventive effects have been observed of Diclofenac, a preferential COX-2 inhibitory non-steroidal anti-inflammatory drugs, and Curcumin, a natural anti-inflammatory agent, in the early stage of colorectal carcinogenesis induced by 1,2-dimethylhydrazine dihydrochloride in rats. The tumor-promoting role of PI3-K/Akt/PTEN signal transduction pathway and its association with anti-apoptotic family of proteins are also observed. Both Diclofenac and Curcumin downregulated the PI3-K and Akt expression while promoting the apoptotic mechanism. Diclofenac and Curcumin administration significantly increased the expression of pro-apoptotic Bcl-2 family members (Bad and Bax) while decreasing the anti-apoptotic Bcl-2 protein. An up-regulation of cysteine protease family apoptosis executioner, such as caspase-3 and -9, is seen. Diclofenac and Curcumin inhibited the Bcl-2 protein by directly interacting at the active site by multiple hydrogen bonding, as also evident by negative glide score of Bcl-2. These drugs stimulated apoptosis by increasing reactive oxygen species (ROS) generation and simultaneously decreasing the mitochondrial membrane potential (ΔΨ M). Diclofenac and Curcumin showed anti-neoplastic effects by downregulating PI3-K/Akt/PTEN pathway, inducing apoptosis, increasing ROS generation, and decreasing ΔΨ M. The anti-neoplastic and apoptotic effects were found enhanced when both Diclofenac and Curcumin were administered together, rather than individually.

  17. Orexin receptor activation generates gamma band input to cholinergic and serotonergic arousal system neurons and drives an intrinsic Ca2+-dependent resonance in LDT and PPT cholinergic neurons.

    Directory of Open Access Journals (Sweden)

    Masaru eIshibashi

    2015-06-01

    Full Text Available A hallmark of the waking state is a shift in EEG power to higher frequencies with epochs of synchronized intracortical gamma activity (30-60 Hz - a process associated with high-level cognitive functions. The ascending arousal system, including cholinergic laterodorsal (LDT and pedunculopontine (PPT tegmental neurons and serotonergic dorsal raphe (DR neurons, promotes this state. Recently, this system has been proposed as a gamma wave generator, in part, because some neurons produce high-threshold, Ca2+-dependent oscillations at gamma frequencies. However, it is not known whether arousal-related inputs to these neurons generate such oscillations, or whether such oscillations are ever transmitted to neuronal targets. Since key arousal input arises from hypothalamic orexin (hypocretin neurons, we investigated whether the unusually noisy, depolarizing orexin current could provide significant gamma input to cholinergic and serotonergic neurons, and whether such input could drive Ca2+-dependent oscillations. Whole-cell recordings in brain slices were obtained from mice expressing Cre-induced fluorescence in cholinergic LDT and PPT, and serotonergic DR neurons. After first quantifying reporter expression accuracy in cholinergic and serotonergic neurons, we found that the orexin current produced significant high frequency, including gamma, input to both cholinergic and serotonergic neurons. Then, by using a dynamic clamp, we found that adding a noisy orexin conductance to cholinergic neurons induced a Ca2+-dependent resonance that peaked in the theta and alpha frequency range (4 - 14 Hz and extended up to 100 Hz. We propose that this orexin current noise and the Ca2+ dependent resonance work synergistically to boost the encoding of high-frequency synaptic inputs into action potentials and to help ensure cholinergic neurons fire during EEG activation. This activity could reinforce thalamocortical states supporting arousal, REM sleep and intracortical

  18. A Selective Assay to Detect Chitin and Biologically Active Nano-Machineries for Chitin-Biosynthesis with Their Intrinsic Chitin-Synthase Molecules

    OpenAIRE

    Herasimenka, Yury; Kotasinska, Marta; Walter, Stefan; Schrempf, Hildgund

    2010-01-01

    A new assay system for chitin has been developed. It comprises the chitin-binding protein ChbB in fusion with a His-tag as well as with a Strep-tag, the latter of which was chemically coupled to horseradish peroxidase. With the resulting complex, minimal quantities of chitin are photometrically detectable. In addition, the assay allows rapid scoring of the activity of chitin-synthases. As a result, a refined procedure for the rapid purification of yeast chitosomes (nano-machineries for chitin...

  19. Development and verification of unstructured adaptive mesh technique with edge compatibility

    International Nuclear Information System (INIS)

    Ito, Kei; Ohshima, Hiroyuki; Kunugi, Tomoaki

    2010-01-01

    In the design study of the large-sized sodium-cooled fast reactor (JSFR), one key issue is suppression of gas entrainment (GE) phenomena at a gas-liquid interface. Therefore, the authors have been developed a high-precision CFD algorithm to evaluate the GE phenomena accurately. The CFD algorithm has been developed on unstructured meshes to establish an accurate modeling of JSFR system. For two-phase interfacial flow simulations, a high-precision volume-of-fluid algorithm is employed. It was confirmed that the developed CFD algorithm could reproduce the GE phenomena in a simple GE experiment. Recently, the authors have been developed an important technique for the simulation of the GE phenomena in JSFR. That is an unstructured adaptive mesh technique which can apply fine cells dynamically to the region where the GE occurs in JSFR. In this paper, as a part of the development, a two-dimensional unstructured adaptive mesh technique is discussed. In the two-dimensional adaptive mesh technique, each cell is refined isotropically to reduce distortions of the mesh. In addition, connection cells are formed to eliminate the edge incompatibility between refined and non-refined cells. The two-dimensional unstructured adaptive mesh technique is verified by solving well-known lid-driven cavity flow problem. As a result, the two-dimensional unstructured adaptive mesh technique succeeds in providing a high-precision solution, even though poor-quality distorted initial mesh is employed. In addition, the simulation error on the two-dimensional unstructured adaptive mesh is much less than the error on the structured mesh with a larger number of cells. (author)

  20. A Selective Assay to Detect Chitin and Biologically Active Nano-Machineries for Chitin-Biosynthesis with Their Intrinsic Chitin-Synthase Molecules

    Directory of Open Access Journals (Sweden)

    Hildgund Schrempf

    2010-09-01

    Full Text Available A new assay system for chitin has been developed. It comprises the chitin-binding protein ChbB in fusion with a His-tag as well as with a Strep-tag, the latter of which was chemically coupled to horseradish peroxidase. With the resulting complex, minimal quantities of chitin are photometrically detectable. In addition, the assay allows rapid scoring of the activity of chitin-synthases. As a result, a refined procedure for the rapid purification of yeast chitosomes (nano-machineries for chitin biosynthesis has been established. Immuno-electronmicroscopical studies of purified chitosomes, gained from a yeast strain carrying a chitin-synthase gene fused to that for GFP (green-fluorescence protein, has led to the in situ localization of chitin-synthase-GFP molecules within chitosomes.

  1. Characterization of Partial Intrinsic Symmetries

    NARCIS (Netherlands)

    Shehu, Aurela; Brunton, Alan; Wuhrer, Stefanie; Wand, Michael

    2014-01-01

    We present a mathematical framework and algorithm for characterizing and extracting partial intrinsic symmetries of surfaces, which is a fundamental building block for many modern geometry processing algorithms. Our goal is to compute all “significant” symmetry information of the shape, which we

  2. Reading: Intrinsic versus Extrinsic Motivation.

    Science.gov (United States)

    Ediger, Marlow

    Much debate centers on motivating student in reading achievement. Should students feel motivated from within (intrinsic motivation), or is it better to have extrinsic motivation whereby external stimuli are used to help learners achieve optimally in reading? This paper aims to analyze the two points of view about motivating students in reading…

  3. Intrinsic volumes of symmetric cones

    OpenAIRE

    Amelunxen, Dennis; Bürgisser, Peter

    2012-01-01

    We compute the intrinsic volumes of the cone of positive semidefinite matrices over the real numbers, over the complex numbers, and over the quaternions, in terms of integrals related to Mehta's integral. Several applications for the probabilistic analysis of semidefinite programming are given.

  4. Acoustic resonance spectroscopy intrinsic seals

    International Nuclear Information System (INIS)

    Olinger, C.T.; Burr, T.; Vnuk, D.R.

    1994-01-01

    We have begun to quantify the ability of acoustic resonance spectroscopy (ARS) to detect the removal and replacement of the lid of a simulated special nuclear materials drum. Conceptually, the acoustic spectrum of a container establishcs a baseline fingerprint, which we refer to as an intrinsic seal, for the container. Simply removing and replacing the lid changes some of the resonant frequencies because it is impossible to exactly duplicate all of the stress patterns between the lid and container. Preliminary qualitative results suggested that the ARS intrinsic seal could discriminate between cases where a lid has or has not been removed. The present work is directed at quantifying the utility of the ARS intrinsic seal technique, including the technique's sensitivity to ''nuisance'' effects, such as temperature swings, movement of the container, and placement of the transducers. These early quantitative tests support the potential of the ARS intrinsic seal application, but also reveal a possible sensitivity to nuisance effects that could limit environments or conditions under which the technique is effective

  5. Intrinsic Motivation in Physical Education

    Science.gov (United States)

    Davies, Benjamin; Nambiar, Nathan; Hemphill, Caroline; Devietti, Elizabeth; Massengale, Alexandra; McCredie, Patrick

    2015-01-01

    This article describes ways in which educators can use Harter's perceived competence motivation theory, the achievement goal theory, and self-determination theory to develop students' intrinsic motivation to maintain physical fitness, as demonstrated by the Sound Body Sound Mind curriculum and proven effective by the 2013 University of…

  6. A hierarchy of intrinsic timescales across primate cortex.

    Science.gov (United States)

    Murray, John D; Bernacchia, Alberto; Freedman, David J; Romo, Ranulfo; Wallis, Jonathan D; Cai, Xinying; Padoa-Schioppa, Camillo; Pasternak, Tatiana; Seo, Hyojung; Lee, Daeyeol; Wang, Xiao-Jing

    2014-12-01

    Specialization and hierarchy are organizing principles for primate cortex, yet there is little direct evidence for how cortical areas are specialized in the temporal domain. We measured timescales of intrinsic fluctuations in spiking activity across areas and found a hierarchical ordering, with sensory and prefrontal areas exhibiting shorter and longer timescales, respectively. On the basis of our findings, we suggest that intrinsic timescales reflect areal specialization for task-relevant computations over multiple temporal ranges.

  7. Identification of intrinsically disordered regions in PTEN and delineation of its function via a network approach.

    Science.gov (United States)

    Malaney, Prerna; Uversky, Vladimir N; Davé, Vrushank

    2015-05-01

    Intrinsically disordered proteins (IDPs) are proteins that lack stable higher order structures for the entire protein molecule or a significant portion of it. The discovery of IDPs evolved as an antithesis to the conventional structure-function paradigm wherein a higher order structure dictates protein function. Over the last decade, a number of proteins with functionally relevant unstructured regions have been discovered, which includes tumor suppressor PTEN. The protein domains that lack structure provide "hot-spots" for post-translational modifications (PTMs) and protein-protein interactions (PPIs), which facilitate their regulation and participation in multiple cellular processes. Consequently, dysregulation in IDPs contribute to aberrant cellular pathophysiology. Herein, we present PTEN and its translational isoform PTEN-L as a hybrid protein possessing ordered domain and intrinsically disordered C-terminal and an N-terminal tails. We review the role of intrinsic disorder in PTEN function and propose a methodology for the use of intrinsic disorder to study PTEN-regulated higher order protein-networks by associating basic principles of network biology to functional pathway analysis at the systems level. Published by Elsevier Inc.

  8. A Four-Week Unstructured Break Improved Athletic Performance in Collegiate Rugby Players.

    Science.gov (United States)

    Jensen, C D; Gleason, D; VanNess, J M

    2018-01-24

    This study analyzed the changes in athletic performance and anthropometric characteristics in collegiate male club rugby athletes (n=14) following a four-week winter break. All measurements were collected prior to and after the break. Body composition was assessed by body mass index and hydrostatic weighing. Performance measurements were: VO2 max, vertical jump, 10-yard sprint, squat max, and bench press max. Prior to testing, each subject was acclimated to the protocols to reduce learning effects. During the four-week break, no workouts were provided for the athletes; it was unsupervised and unstructured. Participants were required to maintain and submit self-reported nutritional and activity logs during this period. After the break, the athletes demonstrated a 5.0% improvement in VO2 max (absolute increase of 2.25 ml/kg/min), 6.8% improvement in vertical jump (1.50 inches), and a 14.3% increase in squat max (38.64lb). Although increases in bodyweight (1.0%) were not significant, body fat percentage exhibited a relative increase of 19.3% (absolute change from 13.35% to 15.93%). A significant discriminate function analysis indicated statistical differences between groups based on these variables. Self-report behavior logs confirmed participation in >3 days of moderate to intense physical activity per week, but somewhat poor dietary habits. These results indicate that collegiate rugby athletes may not need prescribed exercise routines during seasonal breaks in the athletic schedule. However, it may be beneficial to provide structured nutritional advice during unsupervised periods.

  9. Innate and intrinsic antiviral immunity in skin.

    Science.gov (United States)

    Kawamura, Tatsuyoshi; Ogawa, Youichi; Aoki, Rui; Shimada, Shinji

    2014-09-01

    As the body's most exposed interface with the environment, the skin is constantly challenged by potentially pathogenic microbes, including viruses. To sense the invading viruses, various types of cells resident in the skin express many different pattern-recognition receptors (PRRs) such as C-type lectin receptors (CLRs), Toll-like receptors (TLRs), nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) and cytosolic DNA sensors, that can detect the pathogen-associated molecular patterns (PAMPs) of the viruses. The detection of viral PAMPs initiates two major innate immune signaling cascades: the first involves the activation of the downstream transcription factors, such as interferon regulatory factors (IRFs), nuclear factor kappa B (NF-κB) and activator protein 1 (AP-1), which cooperate to induce the transcription of type I interferons and pro-inflammatory cytokines. The second signaling pathway involves the caspase-1-mediated processing of IL-1β and IL-18 through the formation of an inflammasome complex. Cutaneous innate immunity including the production of the innate cytokines constitutes the first line of host defence that limits the virus dissemination from the skin, and also plays an important role in the activation of adaptive immune response, which represents the second line of defence. More recently, the third immunity "intrinsic immunity" has emerged, that provides an immediate and direct antiviral defense mediated by host intrinsic restriction factors. This review focuses on the recent advances regarding the antiviral immune systems, highlighting the innate and intrinsic immunity against the viral infections in the skin, and describes how viral components are recognized by cutaneous immune systems. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  10. Ferulago angulata activates intrinsic pathway of apoptosis in MCF-7 cells associated with G1 cell cycle arrest via involvement of p21/p27

    Directory of Open Access Journals (Sweden)

    Karimian H

    2014-09-01

    Full Text Available Hamed Karimian,1 Soheil Zorofchian Moghadamtousi,2 Mehran Fadaeinasab,3 Shahram Golbabapour,2 Mahboubeh Razavi,1 Maryam Hajrezaie,2 Aditya Arya,1 Mahmood Ameen Abdulla,4 Syam Mohan,5 Hapipah Mohd Ali,2 Mohamad Ibrahim Noordin1 1Department of Pharmacy, Faculty of Medicine, 2Institute of Biological Sciences, Faculty of Science, 3Department of Chemistry, 4Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, 5Medical Research Centre, Jazan University, Jazan, Saudi Arabia Abstract: Ferulago angulata is a medicinal plant that is traditionally known for its ­anti-inflammatory and antiulcer properties. The present study was aimed to evaluate its anticancer activity and the possible mechanism of action using MCF-7 as an in vitro model. F. angulata leaf extracts were prepared using solvents in the order of increasing polarity. As determined by MTT assay, F. angulata leaves hexane extract (FALHE revealed the strongest cytotoxicity against MCF-7 cells with the half maximal inhibitory concentration (IC50 value of 5.3±0.82 µg/mL. The acute toxicity study of FALHE provided evidence of the safety of the plant extract. Microscopic and flow cytometric analysis using annexin-V probe showed an induction of apoptosis in MCF-7 by FALHE. Treatment of MCF-7 cells with FALHE encouraged the intrinsic pathway of apoptosis, with cell death transducing signals that reduced the mitochondrial membrane potential with cytochrome c release from mitochondria to cytosol. The released cytochrome c triggered the activation of caspase-9. Meanwhile, the overexpression of caspase-8 suggested the involvement of an extrinsic pathway in the induced apoptosis at the late stage of treatment. Moreover, flow cytometric analysis showed that FALHE treatment significantly arrested MCF-7 cells in the G1 phase, which was associated with upregulation of p21 and p27 assessed by quantitative polymerase chain reaction. Immunofluorescence

  11. On the performance of a 2D unstructured computational rheology code on a GPU

    NARCIS (Netherlands)

    Pereira, S.P.; Vuik, K.; Pinho, F.T.; Nobrega, J.M.

    2013-01-01

    The present work explores the massively parallel capabilities of the most advanced architecture of graphics processing units (GPUs) code named “Fermi”, on a two-dimensional unstructured cell-centred finite volume code. We use the SIMPLE algorithm to solve the continuity and momentum equations that

  12. Efficient scheme for the shallow water equations on unstructured grids with application to the Continental Shelf

    NARCIS (Netherlands)

    Kernkamp, H.W.J.; Van Dam, A.; Stelling, G.S.; De Goede, E.D.

    2011-01-01

    In this paper, a shallow-water flow solver is presented, based on the finite-volume method on unstructured grids The method is suitable for flows that occur in rivers, channels, sewer systems (1D), shallow seas, rivers, overland flow (2D), and estuaries, lakes and shelf breaks (3D). We present an

  13. Symmetry-preserving discretization of Navier-Stokes equations on collocated unstructured grids

    NARCIS (Netherlands)

    Trias, F.X.; Lehmkuhl, O.; Oliva, A.; Pérez-Segarra, C.D.; Verstappen, R.W.C.P.

    2014-01-01

    A fully-conservative discretization is presented in this paper. The same principles followed earlier are generalized for unstructured meshes. Here, a collocated-mesh scheme is preferred over a staggered one due to its simpler form for such meshes. The basic idea behind this approach remains the

  14. Multigrid Approaches to Non-linear Diffusion Problems on Unstructured Meshes

    Science.gov (United States)

    2001-02-01

    The efficiency of three multigrid methods for solving highly non-linear diffusion problems on two-dimensional unstructured meshes is examined. The...three multigrid methods differ mainly in the manner in which the non-linearities of the governing equations are handled. These comprise a non-linear

  15. 36 CFR 1236.24 - What are the additional requirements for managing unstructured electronic records?

    Science.gov (United States)

    2010-07-01

    ... requirements for managing unstructured electronic records? 1236.24 Section 1236.24 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION RECORDS MANAGEMENT ELECTRONIC RECORDS MANAGEMENT Additional Requirements for Electronic Records § 1236.24 What are the additional requirements for managing...

  16. Parallel Sn Sweeps on Unstructured Grids: Algorithms for Prioritization, Grid Partitioning, and Cycle Detection

    International Nuclear Information System (INIS)

    Plimpton, Steven J.; Hendrickson, Bruce; Burns, Shawn P.; McLendon, William III; Rauchwerger, Lawrence

    2005-01-01

    The method of discrete ordinates is commonly used to solve the Boltzmann transport equation. The solution in each ordinate direction is most efficiently computed by sweeping the radiation flux across the computational grid. For unstructured grids this poses many challenges, particularly when implemented on distributed-memory parallel machines where the grid geometry is spread across processors. We present several algorithms relevant to this approach: (a) an asynchronous message-passing algorithm that performs sweeps simultaneously in multiple ordinate directions, (b) a simple geometric heuristic to prioritize the computational tasks that a processor works on, (c) a partitioning algorithm that creates columnar-style decompositions for unstructured grids, and (d) an algorithm for detecting and eliminating cycles that sometimes exist in unstructured grids and can prevent sweeps from successfully completing. Algorithms (a) and (d) are fully parallel; algorithms (b) and (c) can be used in conjunction with (a) to achieve higher parallel efficiencies. We describe our message-passing implementations of these algorithms within a radiation transport package. Performance and scalability results are given for unstructured grids with up to 3 million elements (500 million unknowns) running on thousands of processors of Sandia National Laboratories' Intel Tflops machine and DEC-Alpha CPlant cluster

  17. Using Text Analytics to Derive Customer Service Management Benefits from Unstructured Data

    DEFF Research Database (Denmark)

    Müller, Oliver; Junglas, Iris; Debortoli, Stefan

    2016-01-01

    Deriving value from structured data is now commonplace. The value of unstructured textual data, however, remains mostly untapped and often unrecognized. This article describes the text analytics journeys of three organizations in the customer service management area. Based on their experiences, we...

  18. Young Children's Opportunities for Unstructured Environmental Exploration of Nature: Links to Adults' Experiences in Childhood

    Science.gov (United States)

    Laird, Shelby Gull; McFarland-Piazza, Laura; Allen, Sydnye

    2014-01-01

    Outdoor environmental education and provision of unstructured exploration of nature are often forgotten aspects of the early childhood experience. The aim of this study was to understand how adults' early experiences in nature relate to their attitudes and practices in providing such experiences for young children. This study surveyed 33 parents…

  19. LanguageNet: A Novel Framework for Processing Unstructured Text Information

    DEFF Research Database (Denmark)

    Qureshi, Pir Abdul Rasool; Memon, Nasrullah; Wiil, Uffe Kock

    2011-01-01

    In this paper we present LanguageNet—a novel framework for processing unstructured text information from human generated content. The state of the art information processing frameworks have some shortcomings: modeled in generalized form, trained on fixed (limited) data sets, and leaving...

  20. A point-centered diffusion differencing for unstructured meshes in 3-D

    International Nuclear Information System (INIS)

    Palmer, T.S.

    1994-01-01

    We describe a point-centered diffusion discretization for 3-D unstructured meshes of polyhedra. The method has several attractive qualities, including second-order accuracy and preservation of linear solutions. A potential drawback to the scheme is that the diffusion matrix is asymmetric, in general. Results of numerical test problems illustrate the behavior of the scheme

  1. Heritability and temporal stability of ambulatory autonomic stress reactivity in unstructured 24-hour recordings

    NARCIS (Netherlands)

    Neijts, Melanie; van Lien, Rene; Kupper, Nina; Boomsma, Dorret; Willemsen, Gonneke; de Geus, Eco J C

    2015-01-01

    Objective: Measurements of ambulatory autonomic reactivity can help with our understanding of the long-term health consequences of exposure to psychosocial stress in real-life settings. Methods: In this study, unstructured 24-hour ambulatory recordings of cardiac parasympathetic and sympathetic

  2. Verification & Validation of High-Order Short-Characteristics-Based Deterministic Transport Methodology on Unstructured Grids

    International Nuclear Information System (INIS)

    Azmy, Yousry; Wang, Yaqi

    2013-01-01

    The research team has developed a practical, high-order, discrete-ordinates, short characteristics neutron transport code for three-dimensional configurations represented on unstructured tetrahedral grids that can be used for realistic reactor physics applications at both the assembly and core levels. This project will perform a comprehensive verification and validation of this new computational tool against both a continuous-energy Monte Carlo simulation (e.g. MCNP) and experimentally measured data, an essential prerequisite for its deployment in reactor core modeling. Verification is divided into three phases. The team will first conduct spatial mesh and expansion order refinement studies to monitor convergence of the numerical solution to reference solutions. This is quantified by convergence rates that are based on integral error norms computed from the cell-by-cell difference between the code's numerical solution and its reference counterpart. The latter is either analytic or very fine- mesh numerical solutions from independent computational tools. For the second phase, the team will create a suite of code-independent benchmark configurations to enable testing the theoretical order of accuracy of any particular discretization of the discrete ordinates approximation of the transport equation. For each tested case (i.e. mesh and spatial approximation order), researchers will execute the code and compare the resulting numerical solution to the exact solution on a per cell basis to determine the distribution of the numerical error. The final activity comprises a comparison to continuous-energy Monte Carlo solutions for zero-power critical configuration measurements at Idaho National Laboratory's Advanced Test Reactor (ATR). Results of this comparison will allow the investigators to distinguish between modeling errors and the above-listed discretization errors introduced by the deterministic method, and to separate the sources of uncertainty.

  3. Verification & Validation of High-Order Short-Characteristics-Based Deterministic Transport Methodology on Unstructured Grids

    Energy Technology Data Exchange (ETDEWEB)

    Azmy, Yousry [North Carolina State Univ., Raleigh, NC (United States); Wang, Yaqi [North Carolina State Univ., Raleigh, NC (United States)

    2013-12-20

    The research team has developed a practical, high-order, discrete-ordinates, short characteristics neutron transport code for three-dimensional configurations represented on unstructured tetrahedral grids that can be used for realistic reactor physics applications at both the assembly and core levels. This project will perform a comprehensive verification and validation of this new computational tool against both a continuous-energy Monte Carlo simulation (e.g. MCNP) and experimentally measured data, an essential prerequisite for its deployment in reactor core modeling. Verification is divided into three phases. The team will first conduct spatial mesh and expansion order refinement studies to monitor convergence of the numerical solution to reference solutions. This is quantified by convergence rates that are based on integral error norms computed from the cell-by-cell difference between the code’s numerical solution and its reference counterpart. The latter is either analytic or very fine- mesh numerical solutions from independent computational tools. For the second phase, the team will create a suite of code-independent benchmark configurations to enable testing the theoretical order of accuracy of any particular discretization of the discrete ordinates approximation of the transport equation. For each tested case (i.e. mesh and spatial approximation order), researchers will execute the code and compare the resulting numerical solution to the exact solution on a per cell basis to determine the distribution of the numerical error. The final activity comprises a comparison to continuous-energy Monte Carlo solutions for zero-power critical configuration measurements at Idaho National Laboratory’s Advanced Test Reactor (ATR). Results of this comparison will allow the investigators to distinguish between modeling errors and the above-listed discretization errors introduced by the deterministic method, and to separate the sources of uncertainty.

  4. Kelussia odoratissima Mozaff. activates intrinsic pathway of apoptosis in breast cancer cells associated with S phase cell cycle arrest via involvement of p21/p27 in vitro and in vivo

    Directory of Open Access Journals (Sweden)

    Karimian H

    2017-02-01

    Full Text Available Hamed Karimian,1 Aditya Arya,2 Mehran Fadaeinasab,3 Mahboubeh Razavi,1 Maryam Hajrezaei,4 Ataul Karim Khan,1 Hapipah Mohd Ali,3 Mahmood Ameen Abdulla,4 Mohamad Ibrahim Noordin1,5 1Department of Pharmacy, Faculty of Medicine, University of Malaya, Kuala Lumpur, 2School of Medicine, Taylor’s University, Subang Jaya, 3Centre for Natural Products Research and Drug Discovery, 4Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, 5Malaysian Institute of Pharmaceuticals and Nutraceuticals (IPharm, Pulau Pinang, Malaysia Background: The aim of this study was to evaluate the anticancer potential of Kelussia odoratissima. Several in vitro and in vivo biological assays were applied to explore the direct effect of an extract and bioactive compound of this plant against breast cancer cells and its possible mechanism of action. Materials and methods: K. odoratissima methanol extract (KME was prepared, and MTT assay was used to evaluate the cytotoxicity. To identify the cytotoxic compound, a bioassay-guided investigation was performed on methanol extract. 8-Hydroxy-ar-turmerone was isolated as a bioactive compound. In vivo study was performed in the breast cancer rat model. LA7 cell line was used to induce the breast tumor. Histopathological and expression changes of PCNA, Bcl-2, Bax, p27 and p21 and caspase-3 were examined. The induction of apoptosis was tested using Annexin V-fluorescein isothiocyanate (FITC assay. To confirm the intrinsic pathway of apoptosis, caspase-7 and caspase-9 assays were utilized. In addition, cell cycle arrest was evaluated. Results: Our results demonstrated that K. odoratissima has an obvious effect on the arrest of proliferation of cancer cells. It induced apoptosis, transduced the cell death signals, decreased the threshold of mitochondrial membrane potential (MMP, upregulated Bax and downregulated Bcl-2. Conclusion: This study demonstrated that K. odoratissima exhibits antitumor activity

  5. Detecting Nosocomial Intrinsic Infections through Relating Bacterial ...

    African Journals Online (AJOL)

    Sierra Leone Journal of Biomedical Research ... Surgical procedures often lead to both intrinsic and extrinsic infections. ... This study demonstrated surgical procedures as precursory to intrinsic infections and that bacterial pathogens found on wounds and endogenous indicators of surgery are links to intrinsic infection.

  6. Unstructured medical image query using big data - An epilepsy case study.

    Science.gov (United States)

    Istephan, Sarmad; Siadat, Mohammad-Reza

    2016-02-01

    Big data technologies are critical to the medical field which requires new frameworks to leverage them. Such frameworks would benefit medical experts to test hypotheses by querying huge volumes of unstructured medical data to provide better patient care. The objective of this work is to implement and examine the feasibility of having such a framework to provide efficient querying of unstructured data in unlimited ways. The feasibility study was conducted specifically in the epilepsy field. The proposed framework evaluates a query in two phases. In phase 1, structured data is used to filter the clinical data warehouse. In phase 2, feature extraction modules are executed on the unstructured data in a distributed manner via Hadoop to complete the query. Three modules have been created, volume comparer, surface to volume conversion and average intensity. The framework allows for user-defined modules to be imported to provide unlimited ways to process the unstructured data hence potentially extending the application of this framework beyond epilepsy field. Two types of criteria were used to validate the feasibility of the proposed framework - the ability/accuracy of fulfilling an advanced medical query and the efficiency that Hadoop provides. For the first criterion, the framework executed an advanced medical query that spanned both structured and unstructured data with accurate results. For the second criterion, different architectures were explored to evaluate the performance of various Hadoop configurations and were compared to a traditional Single Server Architecture (SSA). The surface to volume conversion module performed up to 40 times faster than the SSA (using a 20 node Hadoop cluster) and the average intensity module performed up to 85 times faster than the SSA (using a 40 node Hadoop cluster). Furthermore, the 40 node Hadoop cluster executed the average intensity module on 10,000 models in 3h which was not even practical for the SSA. The current study is

  7. INTRINSIC AND EXTRINSIC MOTIVATION - AN INVESTIGATION OF PERFORMANCE CORRELATION

    Directory of Open Access Journals (Sweden)

    Abrudan Maria-Madela

    2011-07-01

    Full Text Available A series of research untaken in the last decade have revealed some interesting aspects regarding the effects of different types of motivation on performance. Among the researchers who have shown interest in this field we can number: Richard Ryan, Edward Deci, Sam Glucksberg, Dan Ariely, Robert Eisenhower, Linda Shanock, analysts from London School of Economics, and others. Their findings suggest that extrinsic incentives may have a negative impact on overall performance, but a general agreement in this respect has not been reached. In this paper we intend to shed some light upon the relationship between intrinsic and extrinsic motivation and performance. Experts define intrinsic motivation as being the execution of a task or activity because of the inherent satisfaction arising from it rather than due to some separate outcome. In contrast with intrinsic motivation, we speak of extrinsic motivation whenever an activity is done in order to attain some separable outcome. With the purpose of contributing to the clarification of the links between concepts, we initiated and conducted an explanatory research. The research is based on the analysis of the relations between the results obtained by third year students and their predominant type of motivation. For this, we formulated and tested four work hypotheses using a combination of quantitative methods (investigation and qualitative methods (focus group. After the validation of the questionnaires, the respondents were divided into four categories: intrinsically motivated, extrinsically motivated, both intrinsically and extrinsically motivated and unmotivated. To analyze the collected data, we made use of Excel and SPSS. Some of the primary conclusions of the research are as follows: as the average increases, the percent of individuals having both extrinsic and intrinsic motivation is decreasing; the highest percentage of unmotivated students is concentrated in the highest average category; Female

  8. Intrinsic cylindrical and spherical waves

    International Nuclear Information System (INIS)

    Ludlow, I K

    2008-01-01

    Intrinsic waveforms associated with cylindrical and spherical Bessel functions are obtained by eliminating the factors responsible for the inverse radius and inverse square radius laws of wave power per unit area of wavefront. The resulting expressions are Riccati-Bessel functions for both cases and these can be written in terms of amplitude and phase functions of order v and wave variable z. When z is real, it is shown that a spatial phase angle of the intrinsic wave can be defined and this, together with its amplitude function, is systematically investigated for a range of fixed orders and varying z. The derivatives of Riccati-Bessel functions are also examined. All the component functions exhibit different behaviour in the near field depending on the order being less than, equal to or greater than 1/2. Plots of the phase angle can be used to display the locations of the zeros of the general Riccati-Bessel functions and lead to new relations concerning the ordering of the real zeros of Bessel functions and the occurrence of multiple zeros when the argument of the Bessel function is fixed

  9. The Neglected Intrinsic Resistome of Bacterial Pathogens

    Science.gov (United States)

    Fajardo, Alicia; Martínez-Martín, Nadia; Mercadillo, María; Galán, Juan C.; Ghysels, Bart; Matthijs, Sandra; Cornelis, Pierre; Wiehlmann, Lutz; Tümmler, Burkhard; Baquero, Fernando; Martínez, José L.

    2008-01-01

    Bacteria with intrinsic resistance to antibiotics are a worrisome health problem. It is widely believed that intrinsic antibiotic resistance of bacterial pathogens is mainly the consequence of cellular impermeability and activity of efflux pumps. However, the analysis of transposon-tagged Pseudomonas aeruginosa mutants presented in this article shows that this phenotype emerges from the action of numerous proteins from all functional categories. Mutations in some genes make P. aeruginosa more susceptible to antibiotics and thereby represent new targets. Mutations in other genes make P. aeruginosa more resistant and therefore define novel mechanisms for mutation-driven acquisition of antibiotic resistance, opening a new research field based in the prediction of resistance before it emerges in clinical environments. Antibiotics are not just weapons against bacterial competitors, but also natural signalling molecules. Our results demonstrate that antibiotic resistance genes are not merely protective shields and offer a more comprehensive view of the role of antibiotic resistance genes in the clinic and in nature. PMID:18286176

  10. A tonoplast intrinsic protein in Gardenia jasminoides

    Science.gov (United States)

    Gao, Lan; Li, Hao-Ming

    2017-08-01

    Physiological and molecular studies proved that plasma membrane intrinsic proteins (PIPs) and tonoplast intrinsic proteins (TIPs) subfamily of aquaporins play key functions in plant water homeostasis. Five specialized subgroups (TIP1-5) of TIPs have been found in higher plants, in which the TIP1 and TIP2 isoforms are the largest arbitrary groups. TIPs have high water-transport activity than PIPs, some TIPs can transport other small molecule such as urea, ammonia, hydrogen peroxide, and carbon dioxide. In this work, the structure of the putative tonoplast aquaporin from Gardenia jasminoides (GjTIP) was analyzed. Its transcript level has increased during fruit maturation. A phylogenetic analysis indicates that the protein belongs to TIP1 subfamily. A three-dimensional model structure of GjTIP was built based on crystal structure of an ammonia-permeable AtTIP2-1 from Arabidopsis thaliana. The model structure displayed as a homo-tetramer, each monomer has six trans-membrane and two half-membrane-spanning α helices. The data suggests that the GjTIP has tendency to be a mixed function aquaporin, might involve in water, urea and hydrogen peroxide transport, and the gating machanism founded in some AQPs involving pH and phosphorylation response have not been proved in GjTIP.

  11. The neglected intrinsic resistome of bacterial pathogens.

    Directory of Open Access Journals (Sweden)

    Alicia Fajardo

    Full Text Available Bacteria with intrinsic resistance to antibiotics are a worrisome health problem. It is widely believed that intrinsic antibiotic resistance of bacterial pathogens is mainly the consequence of cellular impermeability and activity of efflux pumps. However, the analysis of transposon-tagged Pseudomonas aeruginosa mutants presented in this article shows that this phenotype emerges from the action of numerous proteins from all functional categories. Mutations in some genes make P. aeruginosa more susceptible to antibiotics and thereby represent new targets. Mutations in other genes make P. aeruginosa more resistant and therefore define novel mechanisms for mutation-driven acquisition of antibiotic resistance, opening a new research field based in the prediction of resistance before it emerges in clinical environments. Antibiotics are not just weapons against bacterial competitors, but also natural signalling molecules. Our results demonstrate that antibiotic resistance genes are not merely protective shields and offer a more comprehensive view of the role of antibiotic resistance genes in the clinic and in nature.

  12. Intrinsic terminators in Mycoplasma hyopneumoniae transcription.

    Science.gov (United States)

    Fritsch, Tiago Ebert; Siqueira, Franciele Maboni; Schrank, Irene Silveira

    2015-04-08

    Mycoplasma hyopneumoniae, an important pathogen of swine, exhibits a low guanine and cytosine (GC) content genome. M. hyopneumoniae genome is organised in long transcriptional units and promoter sequences have been mapped upstream of all transcription units. These analysis provided insights into the gene organisation and transcription initiation at the genome scale. However, the presence of transcriptional terminator sequences in the M. hyopneumoniae genome is poorly understood. In silico analyses demonstrated the presence of putative terminators in 82% of the 33 monocistronic units (mCs) and in 74% of the 116 polycistronic units (pCs) considering different classes of terminators. The functional activity of 23 intrinsic terminators was confirmed by RT-PCR and qPCR. Analysis of all terminators found by three software algorithms, combined with experimental results, allowed us to propose a pattern of RNA hairpin formation during the termination process and to predict the location of terminators in the M. hyopneumoniae genome sequence. The stem-loop structures of intrinsic terminators of mycoplasma diverge from the pattern of terminators found in other bacteria due the low content of guanine and cytosine. In M. hyopneumoniae, transcription can end after a transcriptional unit and before its terminator sequence and can also continue past the terminator sequence with RNA polymerases gradually releasing the RNA.

  13. Implicit Unstructured Aerodynamics on Emerging Multi- and Many-Core HPC Architectures

    KAUST Repository

    Al Farhan, Mohammed A.

    2017-03-13

    Shared memory parallelization of PETSc-FUN3D, an unstructured tetrahedral mesh Euler code previously characterized for distributed memory Single Program, Multiple Data (SPMD) for thousands of nodes, is hybridized with shared memory Single Instruction, Multiple Data (SIMD) for hundreds of threads per node. We explore thread-level performance optimizations on state-of-the-art multi- and many-core Intel processors, including the second generation of Xeon Phi, Knights Landing (KNL). We study the performance on the KNL with different configurations of memory and cluster modes, with code optimizations to minimize indirect addressing and enhance the cache locality. The optimizations employed are expected to be of value other unstructured applications as many-core architecture evolves.

  14. How to Measure Quality of Service Using Unstructured Data Analysis: A General Method Design

    Directory of Open Access Journals (Sweden)

    Lucie Sperková,

    2015-10-01

    Full Text Available The aim of the paper is to design a general method usable for measuring the quality of the service from the customer’s point of view with the help of content analytics. Large amount of unstructured data is created by customers of the service. This data can provide a valuable feedback from the service usage. Customers talk among themselves about their experiences and feelings from consumption of the service. The design of the method is based on a systematic literature review in the area of the service quality and unstructured data analysis. Analytics and quality measurement models are collected and critically evaluated regarding their potential use for measuring IT service quality. The method can be used by IT service provider to measure and monitor service quality based on World-of-Mouth in order to continual service improvement.

  15. From Pore Scale to Turbulent Flow with the Unstructured Lattice Boltzmann Method

    DEFF Research Database (Denmark)

    Matin, Rastin

    region depends on the method of time integration. The formulation based on the finite element method exhibits improved stability and is therefore used for two applications. Firstly, together with a free-energy model two-phase flow is simulated at large density and kinematic viscosity contrasts including......Abstract: The lattice Boltzmann method is a class of methods in computational fluid dynamics for simulating fluid flow. Implementations on unstructured grids are particularly relevant for various engineering applications, where geometric flexibility or high resolution near a body or a wall...... is required. The main topic of this thesis is to further develop unstructured lattice Boltzmann methods for simulations of Newtonian fluid flow in three dimensions, in particular porous flow. Two methods are considered in this thesis based on the finite volume method and finite element method, respectively...

  16. A local level set method based on a finite element method for unstructured meshes

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, Long Cu; Choi, Hyoung Gwon [School of Mechanical Engineering, Seoul National University of Science and Technology, Seoul (Korea, Republic of)

    2016-12-15

    A local level set method for unstructured meshes has been implemented by using a finite element method. A least-square weighted residual method was employed for implicit discretization to solve the level set advection equation. By contrast, a direct re-initialization method, which is directly applicable to the local level set method for unstructured meshes, was adopted to re-correct the level set function to become a signed distance function after advection. The proposed algorithm was constructed such that the advection and direct reinitialization steps were conducted only for nodes inside the narrow band around the interface. Therefore, in the advection step, the Gauss–Seidel method was used to update the level set function using a node-by-node solution method. Some benchmark problems were solved by using the present local level set method. Numerical results have shown that the proposed algorithm is accurate and efficient in terms of computational time.

  17. Formation flight and collision avoidance for multiple UAVs based on modified tentacle algorithm in unstructured environments.

    Directory of Open Access Journals (Sweden)

    Minghuan Zhang

    Full Text Available This paper presents a method for formation flight and collision avoidance of multiple UAVs. Due to the shortcomings such as collision avoidance caused by UAV's high-speed and unstructured environments, this paper proposes a modified tentacle algorithm to ensure the high performance of collision avoidance. Different from the conventional tentacle algorithm which uses inverse derivation, the modified tentacle algorithm rapidly matches the radius of each tentacle and the steering command, ensuring that the data calculation problem in the conventional tentacle algorithm is solved. Meanwhile, both the speed sets and tentacles in one speed set are reduced and reconstructed so as to be applied to multiple UAVs. Instead of path iterative optimization, the paper selects the best tentacle to obtain the UAV collision avoidance path quickly. The simulation results show that the method presented in the paper effectively enhances the performance of flight formation and collision avoidance for multiple high-speed UAVs in unstructured environments.

  18. Formation flight and collision avoidance for multiple UAVs based on modified tentacle algorithm in unstructured environments.

    Science.gov (United States)

    Zhang, Minghuan

    2017-01-01

    This paper presents a method for formation flight and collision avoidance of multiple UAVs. Due to the shortcomings such as collision avoidance caused by UAV's high-speed and unstructured environments, this paper proposes a modified tentacle algorithm to ensure the high performance of collision avoidance. Different from the conventional tentacle algorithm which uses inverse derivation, the modified tentacle algorithm rapidly matches the radius of each tentacle and the steering command, ensuring that the data calculation problem in the conventional tentacle algorithm is solved. Meanwhile, both the speed sets and tentacles in one speed set are reduced and reconstructed so as to be applied to multiple UAVs. Instead of path iterative optimization, the paper selects the best tentacle to obtain the UAV collision avoidance path quickly. The simulation results show that the method presented in the paper effectively enhances the performance of flight formation and collision avoidance for multiple high-speed UAVs in unstructured environments.

  19. Computation of UH-60A Airloads Using CFD/CSD Coupling on Unstructured Meshes

    Science.gov (United States)

    Biedron, Robert T.; Lee-Rausch, Elizabeth M.

    2011-01-01

    An unsteady Reynolds-averaged Navier-Stokes solver for unstructured grids is used to compute the rotor airloads on the UH-60A helicopter at high-speed and high thrust conditions. The flow solver is coupled to a rotorcraft comprehensive code in order to account for trim and aeroelastic deflections. Simulations are performed both with and without the fuselage, and the effects of grid resolution, temporal resolution and turbulence model are examined. Computed airloads are compared to flight data.

  20. Efficient High-Order Accurate Methods using Unstructured Grids for Hydrodynamics and Acoustics

    Science.gov (United States)

    2007-08-31

    are that often-used structured mesh solution techniques, such as banded matrix approaches, line solvers, and multigrid methods , can not be used...technology [8-11] or multigrid methods [12-15] and line solution al- gorithms adapted to unstructured meshes through specialized data-structures [16...formulations and nodal multigrid methods were pursued in separate software development efforts. In the following subsections, we first describe the

  1. Emergence of Unstructured Data and Scope of Big Data in Indian Education

    OpenAIRE

    S S Kolhatkar; M Y Patil; S P Kolhatkar; M S Paranjape

    2017-01-01

    The Indian Education sector has grown exponentially in the last few decades as per various official reports[22]. Large amount of information pertaining to education sector is generated every year. This has led to the requirement for managing and analyzing the structured and unstructured information related to various stakeholders. At the same time there is a need to adapt to the dynamic global world by channelizing young talent in appropriate domains by cognizing and deriving the knowledge ab...

  2. Formation flight and collision avoidance for multiple UAVs based on modified tentacle algorithm in unstructured environments

    OpenAIRE

    Zhang, Minghuan

    2017-01-01

    This paper presents a method for formation flight and collision avoidance of multiple UAVs. Due to the shortcomings such as collision avoidance caused by UAV's high-speed and unstructured environments, this paper proposes a modified tentacle algorithm to ensure the high performance of collision avoidance. Different from the conventional tentacle algorithm which uses inverse derivation, the modified tentacle algorithm rapidly matches the radius of each tentacle and the steering command, ensuri...

  3. Beta-mangostin from Cratoxylum arborescens activates the intrinsic apoptosis pathway through reactive oxygen species with downregulation of the HSP70 gene in the HL60 cells associated with a G0/G1cell-cycle arrest.

    Science.gov (United States)

    Omer, Fatima Abdelmutaal Ahmed; Hashim, Najihah Binti Mohd; Ibrahim, Mohamed Yousif; Dehghan, Firouzeh; Yahayu, Maizatulakmal; Karimian, Hamed; Salim, Landa Zeenelabdin Ali; Mohan, Syam

    2017-11-01

    Xanthones are phytochemical compounds found in a number of fruits and vegetables. Characteristically, they are noted to be made of diverse properties based on their biological, biochemical, and pharmacological actions. Accordingly, the apoptosis mechanisms induced by beta-mangostin, a xanthone compound isolated from Cratoxylum arborescens in the human promyelocytic leukemia cell line (HL60) in vitro, were examined in this study. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay was done to estimate the cytotoxicity effect of β-mangostin on the HL60 cell line. Acridine orange/propidium iodide and Hoechst 33342 dyes and Annexin V tests were conducted to detect the apoptosis features. Caspase-3 and caspase-9 activities; reactive oxygen species; real-time polymerase chain reaction for Bcl-2, Bax, caspase-3, and caspase-9 Hsp70 genes; and western blot for p53, cytochrome c, and pro- and cleavage-caspase-3 and caspase-9 were assessed to examine the apoptosis mechanism. Cell-cycle analysis conducted revealed that β-mangostin inhibited the growth of HL60 at 58 µM in 24 h. The administration of β-mangostin with HL60 caused cell morphological changes related to apoptosis which increased the number of early and late apoptotic cells. The β-mangostin-catalyzed apoptosis action through caspase-3, caspase-7, and caspase-9 activation overproduced reactive oxygen species which downregulated the expression of antiapoptotic genes Bcl-2 and HSP70. Conversely, the expression of the apoptotic genes Bax, caspase-3, and caspase-9 were upregulated. Meanwhile, at the protein level, β-mangostin activated the formation of cleaved caspase-3 and caspase-9 and also upregulated the p53. β-mangostin arrested the cell cycle at the G 0 /G 1 phase. Overall, the results for β-mangostin showed an antiproliferative effect in HL60 via stopping the cell cycle at the G 0 /G 1 phase and prompted the intrinsic apoptosis pathway.

  4. Transcriptional profiling reveals molecular signatures associated with HIV permissiveness in Th1Th17 cells and identifies Peroxisome Proliferator-Activated Receptor Gamma as an intrinsic negative regulator of viral replication

    Science.gov (United States)

    2013-01-01

    Background We previously demonstrated that primary Th1Th17 cells are highly permissive to HIV-1, whereas Th1 cells are relatively resistant. Molecular mechanisms underlying these differences remain unknown. Results Exposure to replication competent and single-round VSV-G pseudotyped HIV strains provide evidence that superior HIV replication in Th1Th17 vs. Th1 cells was regulated by mechanisms located at entry and post-entry levels. Genome-wide transcriptional profiling identified transcripts upregulated (n = 264) and downregulated (n = 235) in Th1Th17 vs. Th1 cells (p-value Th17 (nuclear receptors, trafficking, p38/MAPK, NF-κB, p53/Ras, IL-23) vs. Th1 cells (proteasome, interferon α/β). Differentially expressed genes were classified into biological categories using Gene Ontology. Th1Th17 cells expressed typical Th17 markers (IL-17A/F, IL-22, CCL20, RORC, IL-26, IL-23R, CCR6) and transcripts functionally linked to regulating cell trafficking (CEACAM1, MCAM), activation (CD28, CD40LG, TNFSF13B, TNFSF25, PTPN13, MAP3K4, LTB, CTSH), transcription (PPARγ, RUNX1, ATF5, ARNTL), apoptosis (FASLG), and HIV infection (CXCR6, FURIN). Differential expression of CXCR6, PPARγ, ARNTL, PTPN13, MAP3K4, CTSH, SERPINB6, PTK2, and ISG20 was validated by RT-PCR, flow cytometry and/or confocal microscopy. The nuclear receptor PPARγ was preferentially expressed by Th1Th17 cells. PPARγ RNA interference significantly increased HIV replication at levels post-entry and prior HIV-DNA integration. Finally, the activation of PPARγ pathway via the agonist Rosiglitazone induced the nuclear translocation of PPARγ and a robust inhibition of viral replication. Conclusions Thus, transcriptional profiling in Th1Th17 vs. Th1 cells demonstrated that HIV permissiveness is associated with a superior state of cellular activation and limited antiviral properties and identified PPARγ as an intrinsic negative regulator of viral replication. Therefore, triggering PPARγ pathway via non

  5. Towards a supervised rescoring system for unstructured data bases used to build specialized dictionaries

    Directory of Open Access Journals (Sweden)

    Antonio Rico-Sulayes

    2014-12-01

    Full Text Available This article proposes the architecture for a system that uses previously learned weights to sort query results from unstructured data bases when building specialized dictionaries. A common resource in the construction of dictionaries, unstructured data bases have been especially useful in providing information about lexical items frequencies and examples in use. However, when building specialized dictionaries, whose selection of lexical items does not rely on frequency, the use of these data bases gets restricted to a simple provider of examples. Even in this task, the information unstructured data bases provide may not be very useful when looking for specialized uses of lexical items with various meanings and very long lists of results. In the face of this problem, long lists of hits can be rescored based on a supervised learning model that relies on previously helpful results. The allocation of a vast set of high quality training data for this rescoring system is reported here. Finally, the architecture of sucha system,an unprecedented tool in specialized lexicography, is proposed.

  6. Unsteady Non-Newtonian Solver on Unstructured Grid for the Simulation of Blood Flow

    Directory of Open Access Journals (Sweden)

    Guojie Li

    2013-01-01

    Full Text Available Blood is in fact a suspension of different cells with yield stress, shear thinning, and viscoelastic properties, which can be represented by different non-Newtonian models. Taking Casson fluid as an example, an unsteady solver on unstructured grid for non-Newtonian fluid is developed to simulate transient blood flow in complex flow region. In this paper, a steady solver for Newtonian fluid is firstly developed with the discretization of convective flux, diffusion flux, and source term on unstructured grid. For the non-Newtonian characteristics of blood, the Casson fluid is approximated by the Papanastasiou's model and treated as Newtonian fluid with variable viscosity. Then considering the transient property of blood flow, an unsteady non-Newtonian solver based on unstructured grid is developed by introducing the temporal term by first-order upwind difference scheme. Using the proposed solver, the blood flows in carotid bifurcation of hypertensive patients and healthy people are simulated. The result shows that the possibility of the genesis and development of atherosclerosis is increased, because of the increase in incoming flow shock and backflow areas of the hypertensive patients, whose WSS was 20~87.1% lower in outer vascular wall near the bifurcation than that of the normal persons and 3.7~5.5% lower in inner vascular wall downstream the bifurcation.

  7. Development of 3-D Flow Analysis Code for Fuel Assembly using Unstructured Grid System

    International Nuclear Information System (INIS)

    Myong, Hyon Kook; Kim, Jong Eun; Ahn, Jong Ki; Yang, Seung Yong

    2007-03-01

    The flow through a nuclear rod bundle with mixing vanes are very complex and required a suitable turbulence model to be predicted accurately. Final objective of this study is to develop a CFD code for fluid flow and heat transfer analysis in a nuclear fuel assembly using unstructured grid system. In order to develop a CFD code for fluid flow and heat transfer analysis in a nuclear fuel assembly using unstructured grid system, the following researches are made: - Development of numerical algorithm for CFD code's solver - Grid and geometric connectivity data - Development of software(PowerCFD code) for fluid flow and heat transfer analysis in a nuclear fuel assembly using unstructured grid system - Modulation of software(PowerCFD code) - Development of turbulence model - Development of analysis module of RANS/LES hybrid models - Analysis of turbulent flow and heat transfer - Basic study on LES analysis - Development of main frame on pre/post processors based on GUI - Algorithm for fully-developed flow

  8. Collaborative human-machine analysis to disambiguate entities in unstructured text and structured datasets

    Science.gov (United States)

    Davenport, Jack H.

    2016-05-01

    Intelligence analysts demand rapid information fusion capabilities to develop and maintain accurate situational awareness and understanding of dynamic enemy threats in asymmetric military operations. The ability to extract relationships between people, groups, and locations from a variety of text datasets is critical to proactive decision making. The derived network of entities must be automatically created and presented to analysts to assist in decision making. DECISIVE ANALYTICS Corporation (DAC) provides capabilities to automatically extract entities, relationships between entities, semantic concepts about entities, and network models of entities from text and multi-source datasets. DAC's Natural Language Processing (NLP) Entity Analytics model entities as complex systems of attributes and interrelationships which are extracted from unstructured text via NLP algorithms. The extracted entities are automatically disambiguated via machine learning algorithms, and resolution recommendations are presented to the analyst for validation; the analyst's expertise is leveraged in this hybrid human/computer collaborative model. Military capability is enhanced by these NLP Entity Analytics because analysts can now create/update an entity profile with intelligence automatically extracted from unstructured text, thereby fusing entity knowledge from structured and unstructured data sources. Operational and sustainment costs are reduced since analysts do not have to manually tag and resolve entities.

  9. Modelling and robust control of an unmanned coaxial rotor helicopter with unstructured uncertainties

    Directory of Open Access Journals (Sweden)

    Zhi-Yan Dong

    2017-01-01

    Full Text Available A complete methodology for an unmanned coaxial rotor helicopter with unstructured uncertainties was proposed to achieve high-accuracy tracking performance from modelling to robust control. An integrative approach was introduced to systematically construct a whole dynamic model. The key parameters were selected carefully after iteratively being checked by empirical coefficients to decrease the budget and risk of programme. Moreover, a new control scheme is proposed to simultaneously incorporate six inputs to control six states based on the investment of singularity value responses and the general rule of relative gain array. Coprime factor uncertainty model is considered to represent a class of unstructured uncertainties, such as unmolded actuator dynamics and unpredicted interferences between two rotors. Furthermore, the H ∞ loop-shaping control was proposed to apply the control design of the coaxial rotor helicopter to manage complicated uncertainties and multivariable coupling. Finally, simulation results show the effectiveness of the proposed controller design in the step response of the closed loop. The stable closed-loop plant is achieved and the tolerant size of unstructured uncertainty is up to 36.09%. Good step responses and satisfied decoupling were also investigated in detail.

  10. Development of 3-D Flow Analysis Code for Fuel Assembly using Unstructured Grid System

    Energy Technology Data Exchange (ETDEWEB)

    Myong, Hyon Kook; Kim, Jong Eun; Ahn, Jong Ki; Yang, Seung Yong [Kookmin Univ., Seoul (Korea, Republic of)

    2007-03-15

    The flow through a nuclear rod bundle with mixing vanes are very complex and required a suitable turbulence model to be predicted accurately. Final objective of this study is to develop a CFD code for fluid flow and heat transfer analysis in a nuclear fuel assembly using unstructured grid system. In order to develop a CFD code for fluid flow and heat transfer analysis in a nuclear fuel assembly using unstructured grid system, the following researches are made: - Development of numerical algorithm for CFD code's solver - Grid and geometric connectivity data - Development of software(PowerCFD code) for fluid flow and heat transfer analysis in a nuclear fuel assembly using unstructured grid system - Modulation of software(PowerCFD code) - Development of turbulence model - Development of analysis module of RANS/LES hybrid models - Analysis of turbulent flow and heat transfer - Basic study on LES analysis - Development of main frame on pre/post processors based on GUI - Algorithm for fully-developed flow.

  11. Coronary artery disease risk assessment from unstructured electronic health records using text mining.

    Science.gov (United States)

    Jonnagaddala, Jitendra; Liaw, Siaw-Teng; Ray, Pradeep; Kumar, Manish; Chang, Nai-Wen; Dai, Hong-Jie

    2015-12-01

    Coronary artery disease (CAD) often leads to myocardial infarction, which may be fatal. Risk factors can be used to predict CAD, which may subsequently lead to prevention or early intervention. Patient data such as co-morbidities, medication history, social history and family history are required to determine the risk factors for a disease. However, risk factor data are usually embedded in unstructured clinical narratives if the data is not collected specifically for risk assessment purposes. Clinical text mining can be used to extract data related to risk factors from unstructured clinical notes. This study presents methods to extract Framingham risk factors from unstructured electronic health records using clinical text mining and to calculate 10-year coronary artery disease risk scores in a cohort of diabetic patients. We developed a rule-based system to extract risk factors: age, gender, total cholesterol, HDL-C, blood pressure, diabetes history and smoking history. The results showed that the output from the text mining system was reliable, but there was a significant amount of missing data to calculate the Framingham risk score. A systematic approach for understanding missing data was followed by implementation of imputation strategies. An analysis of the 10-year Framingham risk scores for coronary artery disease in this cohort has shown that the majority of the diabetic patients are at moderate risk of CAD. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Exploring Shared-Memory Optimizations for an Unstructured Mesh CFD Application on Modern Parallel Systems

    KAUST Repository

    Mudigere, Dheevatsa

    2015-05-01

    In this work, we revisit the 1999 Gordon Bell Prize winning PETSc-FUN3D aerodynamics code, extending it with highly-tuned shared-memory parallelization and detailed performance analysis on modern highly parallel architectures. An unstructured-grid implicit flow solver, which forms the backbone of computational aerodynamics, poses particular challenges due to its large irregular working sets, unstructured memory accesses, and variable/limited amount of parallelism. This code, based on a domain decomposition approach, exposes tradeoffs between the number of threads assigned to each MPI-rank sub domain, and the total number of domains. By applying several algorithm- and architecture-aware optimization techniques for unstructured grids, we show a 6.9X speed-up in performance on a single-node Intel® XeonTM1 E5 2690 v2 processor relative to the out-of-the-box compilation. Our scaling studies on TACC Stampede supercomputer show that our optimizations continue to provide performance benefits over baseline implementation as we scale up to 256 nodes.

  13. Intrinsic rotation with gyrokinetic models

    International Nuclear Information System (INIS)

    Parra, Felix I.; Barnes, Michael; Catto, Peter J.; Calvo, Iván

    2012-01-01

    The generation of intrinsic rotation by turbulence and neoclassical effects in tokamaks is considered. To obtain the complex dependences observed in experiments, it is necessary to have a model of the radial flux of momentum that redistributes the momentum within the tokamak in the absence of a preexisting velocity. When the lowest order gyrokinetic formulation is used, a symmetry of the model precludes this possibility, making small effects in the gyroradius over scale length expansion necessary. These effects that are usually small become important for momentum transport because the symmetry of the lowest order gyrokinetic formulation leads to the cancellation of the lowest order momentum flux. The accuracy to which the gyrokinetic equation needs to be obtained to retain all the physically relevant effects is discussed.

  14. Computer Simulations of Intrinsically Disordered Proteins

    Science.gov (United States)

    Chong, Song-Ho; Chatterjee, Prathit; Ham, Sihyun

    2017-05-01

    The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields. Thus, achieving an accurate structural characterization of IDPs via simulations is a challenge. It is also daunting to perform a configuration-space integration over heterogeneous structural ensembles sampled by IDPs to extract, in particular, protein configurational entropy. In this review, we summarize recent efforts devoted to the development of force fields and the critical evaluations of their performance when applied to IDPs. We also survey recent advances in computational methods for protein configurational entropy that aim to provide a thermodynamic link between structural disorder and protein activity.

  15. IMPACT OF BARYONIC PHYSICS ON INTRINSIC ALIGNMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Tenneti, Ananth; Gnedin, Nickolay Y. [Particle Astrophysics Center, Fermi National Accelerator Laboratory, Batavia, IL 60510 (United States); Feng, Yu, E-mail: vat@andrew.cmu.edu [Berkeley Center for Cosmological Physics, Department of Physics, University of California Berkeley, Berkeley, CA 94720 (United States)

    2017-01-10

    We explore the effects of specific assumptions in the subgrid models of star formation and stellar and active galactic nucleus feedback on intrinsic alignments of galaxies in cosmological simulations of the “MassiveBlack-II” family. Using smaller-volume simulations, we explore the parameter space of the subgrid star formation and feedback model and find remarkable robustness of the observable statistical measures to the details of subgrid physics. The one observational probe most sensitive to modeling details is the distribution of misalignment angles. We hypothesize that the amount of angular momentum carried away by the galactic wind is the primary physical quantity that controls the orientation of the stellar distribution. Our results are also consistent with a similar study by the EAGLE simulation team.

  16. Toward a tripartite model of intrinsic motivation.

    Science.gov (United States)

    Carbonneau, Noémie; Vallerand, Robert J; Lafrenière, Marc-André K

    2012-10-01

    Intrinsic motivation (IM) refers to engaging in an activity for the pleasure inherent in the activity. The present article presents a tripartite model of IM consisting of IM to know (i.e., engaging in an activity to experience pleasure while learning and trying to understand something new), IM toward accomplishment (i.e., engaging in an activity for the pleasure experienced when attempting task mastery), and IM to experience stimulation (i.e., engaging in an activity for feelings of sensory pleasure). The tripartite model of IM posits that each type of IM can result from task, situational, and personality determinants and can lead to specific types of cognitive, affective, and behavioral outcomes. The purpose of this research was to test some predictions derived from this model. Across 4 studies (Study 1: N = 331; Study 2: N = 113; Study 3: N = 58; Study 4: N = 135), the 3 types of IM as well as potential determinants and consequences were assessed. Results revealed that experiencing one type of IM over the others depends in part on people's personality styles. Also, each type of IM was found to predict specific outcomes (i.e., affective states and behavioral choices). The implications of the tripartite model of IM for motivation research are discussed. © 2011 The Authors. Journal of Personality © 2011, Wiley Periodicals, Inc.

  17. Gompertz' survivorship law as an intrinsic principle of aging

    NARCIS (Netherlands)

    Sas, Arthur A.; Snieder, Harold; Korf, Jakob

    We defend the hypothesis that life-spanning population survivorship curves, as described by Gompertz' law and composed from cross-sectional data (here mortality), reflect an intrinsic aging principle active in each subject of that population. In other words Gompertz' law reflects aging of a

  18. Intrinsic gettering of nickel impuriy deep levels in silicon substrate ...

    African Journals Online (AJOL)

    The intrinsic gettering of nickel impurity in p-type silicon substrate has been investigated. The density of electrically active nickel in intentionally contaminated silicon was determined before and after oxygen precipitation by means of resistivity measurements. These data, coupled with minority carrier lifetime and infrared ...

  19. Semisupervised Support Vector Machines With Tangent Space Intrinsic Manifold Regularization.

    Science.gov (United States)

    Sun, Shiliang; Xie, Xijiong

    2016-09-01

    Semisupervised learning has been an active research topic in machine learning and data mining. One main reason is that labeling examples is expensive and time-consuming, while there are large numbers of unlabeled examples available in many practical problems. So far, Laplacian regularization has been widely used in semisupervised learning. In this paper, we propose a new regularization method called tangent space intrinsic manifold regularization. It is intrinsic to data manifold and favors linear functions on the manifold. Fundamental elements involved in the formulation of the regularization are local tangent space representations, which are estimated by local principal component analysis, and the connections that relate adjacent tangent spaces. Simultaneously, we explore its application to semisupervised classification and propose two new learning algorithms called tangent space intrinsic manifold regularized support vector machines (TiSVMs) and tangent space intrinsic manifold regularized twin SVMs (TiTSVMs). They effectively integrate the tangent space intrinsic manifold regularization consideration. The optimization of TiSVMs can be solved by a standard quadratic programming, while the optimization of TiTSVMs can be solved by a pair of standard quadratic programmings. The experimental results of semisupervised classification problems show the effectiveness of the proposed semisupervised learning algorithms.

  20. Intrinsic thermodynamics of inhibitor binding to human carbonic anhydrase IX.

    Science.gov (United States)

    Linkuvienė, Vaida; Matulienė, Jurgita; Juozapaitienė, Vaida; Michailovienė, Vilma; Jachno, Jelena; Matulis, Daumantas

    2016-04-01

    Human carbonic anhydrase 9th isoform (CA IX) is an important marker of numerous cancers and is increasingly interesting as a potential anticancer drug target. Various synthetic aromatic sulfonamide-bearing compounds are being designed as potent inhibitors of CA IX. However, sulfonamide compound binding to CA IX is linked to several reactions, the deprotonation of the sulfonamide amino group and the protonation of the CA active site Zn(II)-bound hydroxide. These linked reactions significantly affect the affinities and other thermodynamic parameters such as enthalpies and entropies of binding. The observed and intrinsic affinities of compound binding to CA IX were determined by the fluorescent thermal shift assay. The enthalpies and entropies of binding were determined by the isothermal titration calorimetry. The pKa of CA IX was determined to be 6.8 and the enthalpy of CA IX-Zn(II)-bound hydroxide protonation was -24 kJ/mol. These values enabled the analysis of intrinsic thermodynamics of a library of compounds binding to CA IX. The most strongly binding compounds exhibited the intrinsic affinity of 0.01 nM and the observed affinity of 2 nM. The intrinsic thermodynamic parameters of compound binding to CA IX helped to draw the compound structure to thermodynamics relationship. It is important to distinguish the intrinsic from observed parameters of any disease target protein interaction with its inhibitors as drug candidates when drawing detailed compound structure to thermodynamics correlations. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Incentives and intrinsic motivation in healthcare

    Directory of Open Access Journals (Sweden)

    Mikel Berdud

    2016-11-01

    Conclusions: The conclusions could act as a guide to support the optimal design of incentive policies and schemes within health organisations when healthcare professionals are intrinsically motivated.

  2. Algebraic description of intrinsic modes in nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Leviatan, A. (Los Alamos National Lab., NM (USA))

    1990-01-01

    We present a procedure for extracting normal modes in algebraic number-conserving systems of interacting bosons relevant for collective states in even-even nuclei. The Hamiltonian is resolved into intrinsic (bandhead related) and collective (in-band related) parts. Shape parameters are introduced through non-spherical boson bases. Intrinsic modes decoupled from the spurious modes are obtained from the intrinsic part of the Hamiltonian in the limit of large number of bosons. Intrinsic states are constructed and serve to evaluate electromagnetic transition rates. The method is illustrated for systems with one type of boson as well as with proton-neutron bosons. (author).

  3. Algebraic description of intrinsic modes in nuclei

    International Nuclear Information System (INIS)

    Leviatan, A.

    1990-01-01

    We present a procedure for extracting normal modes in algebraic number-conserving systems of interacting bosons relevant for collective states in even-even nuclei. The Hamiltonian is resolved into intrinsic (bandhead related) and collective (in-band related) parts. Shape parameters are introduced through non-spherical boson bases. Intrinsic modes decoupled from the spurious modes are obtained from the intrinsic part of the Hamiltonian in the limit of large number of bosons. Intrinsic states are constructed and serve to evaluate electromagnetic transition rates. The method is illustrated for systems with one type of boson as well as with proton-neutron bosons. (author)

  4. The Emerging Neuroscience of Intrinsic Motivation: A New Frontier in Self-Determination Research.

    Science.gov (United States)

    Di Domenico, Stefano I; Ryan, Richard M

    2017-01-01

    Intrinsic motivation refers to people's spontaneous tendencies to be curious and interested, to seek out challenges and to exercise and develop their skills and knowledge, even in the absence of operationally separable rewards. Over the past four decades, experimental and field research guided by self-determination theory (SDT; Ryan and Deci, 2017) has found intrinsic motivation to predict enhanced learning, performance, creativity, optimal development and psychological wellness. Only recently, however, have studies begun to examine the neurobiological substrates of intrinsic motivation. In the present article, we trace the history of intrinsic motivation research, compare and contrast intrinsic motivation to closely related topics (flow, curiosity, trait plasticity), link intrinsic motivation to key findings in the comparative affective neurosciences, and review burgeoning neuroscience research on intrinsic motivation. We review converging evidence suggesting that intrinsically motivated exploratory and mastery behaviors are phylogenetically ancient tendencies that are subserved by dopaminergic systems. Studies also suggest that intrinsic motivation is associated with patterns of activity across large-scale neural networks, namely, those that support salience detection, attentional control and self-referential cognition. We suggest novel research directions and offer recommendations for the application of neuroscience methods in the study of intrinsic motivation.

  5. Geochemical indicators of intrinsic bioremediation

    International Nuclear Information System (INIS)

    Borden, R.C.; Gomez, C.A.; Becker, M.T.

    1995-01-01

    A detailed field investigation has been completed at a gasoline-contaminated aquifer near Rocky Point, NC, to examine possible indicators of intrinsic bioremediation and identify factors that may significantly influence the rae and extent of bioremediation. The dissolved plume of benzene, toluene, ethylbenzene, and xylene (BTEX) in ground water is naturally degrading. Toluene and o-xylene are most rapidly degraded followed by m-, p-xylene, and benzene. Ethylbenzene appears to degrade very slowly under anaerobic conditions present in the center of the plume. The rate and extent of biodegradation appears to be strongly influenced by the type and quantity of electron acceptors present in the aquifer. At the upgradient edge of the plume, nitrate, ferric iron, and oxygen are used as terminal electron acceptors during hydrocarbon biodegradation. The equivalent of 40 to 50 mg/l of hydrocarbon is degraded based on the increase in dissolved CO 2 relative to background ground water. Immediately downgradient of the source area, sulfate and iron are the dominant electron acceptors. Toluene and o-xylene are rapidly removed in this region. Once the available oxygen, nitrate, and sulfate are consumed, biodegradation is limited and appears to be controlled by mixing and aerobic biodegradation at the plume fringes

  6. LEADERSHIP STYLE AND EMPLOYEES' INTRINSIC JOB ...

    African Journals Online (AJOL)

    Abstract. This study investigates the impact of leadership style on employees' intrinsic job satisfaction in the Cross River State Newspaper Corporation, Calabar,. Nigeria. The study examined the problem of dissatisfaction in the work place as far as intrinsic factors of job satisfaction are concerned. Structured questionnaire ...

  7. Intrinsic bioremediation of landfills interim report

    International Nuclear Information System (INIS)

    Brigmon, R.L.; Fliermans, C.B.

    1997-01-01

    Intrinsic bioremediation is a risk management option that relies on natural biological and physical processes to contain the spread of contamination from a source. Evidence is presented in this report that intrinsic bioremediation is occurring at the Sanitary Landfill is fundamental to support incorportion into a Corrective Action Plan (CAP)

  8. Differential scanning microcalorimetry of intrinsically disordered proteins.

    Science.gov (United States)

    Permyakov, Sergei E

    2012-01-01

    Ultrasensitive differential scanning calorimetry (DSC) is an indispensable thermophysical technique enabling to get direct information on enthalpies accompanying heating/cooling of dilute biopolymer solutions. The thermal dependence of protein heat capacity extracted from DSC data is a valuable source of information on intrinsic disorder level of a protein. Application details and limitations of DSC technique in exploration of protein intrinsic disorder are described.

  9. Intrinsic bioremediation of landfills interim report

    Energy Technology Data Exchange (ETDEWEB)

    Brigmon, R.L. [Westinghouse Savannah River Company, Aiken, SC (United States); Fliermans, C.B.

    1997-07-14

    Intrinsic bioremediation is a risk management option that relies on natural biological and physical processes to contain the spread of contamination from a source. Evidence is presented in this report that intrinsic bioremediation is occurring at the Sanitary Landfill is fundamental to support incorportion into a Corrective Action Plan (CAP).

  10. An Intrinsic Coordinate System for Fingerprint Matching

    NARCIS (Netherlands)

    Bazen, A.M.; Gerez, Sabih H.; Bigun, J.; Smeraldi, F.

    2001-01-01

    In this paper, an intrinsic coordinate system is proposed for fingerprints. First the fingerprint is partitioned in regular regions, which are regions that contain no singular points. In each regular region, the intrinsic coordinate system is defined by the directional field. When using the

  11. Accurate representation of geostrophic and hydrostatic balance in unstructured mesh finite element ocean modelling

    Science.gov (United States)

    Maddison, J. R.; Marshall, D. P.; Pain, C. C.; Piggott, M. D.

    Accurate representation of geostrophic and hydrostatic balance is an essential requirement for numerical modelling of geophysical flows. Potentially, unstructured mesh numerical methods offer significant benefits over conventional structured meshes, including the ability to conform to arbitrary bounding topography in a natural manner and the ability to apply dynamic mesh adaptivity. However, there is a need to develop robust schemes with accurate representation of physical balance on arbitrary unstructured meshes. We discuss the origin of physical balance errors in a finite element discretisation of the Navier-Stokes equations using the fractional timestep pressure projection method. By considering the Helmholtz decomposition of forcing terms in the momentum equation, it is shown that the components of the buoyancy and Coriolis accelerations that project onto the non-divergent velocity tendency are the small residuals between two terms of comparable magnitude. Hence there is a potential for significant injection of imbalance by a numerical method that does not compute these residuals accurately. This observation is used to motivate a balanced pressure decomposition method whereby an additional "balanced pressure" field, associated with buoyancy and Coriolis accelerations, is solved for at increased accuracy and used to precondition the solution for the dynamical pressure. The utility of this approach is quantified in a fully non-linear system in exact geostrophic balance. The approach is further tested via quantitative comparison of unstructured mesh simulations of the thermally driven rotating annulus against laboratory data. Using a piecewise linear discretisation for velocity and pressure (a stabilised P1P1 discretisation), it is demonstrated that the balanced pressure decomposition method is required for a physically realistic representation of the system.

  12. Carotenoid content and root color of cultivated carrot: a candidate-gene association study using an original broad unstructured population.

    Directory of Open Access Journals (Sweden)

    Matthieu Jourdan

    Full Text Available Accumulated in large amounts in carrot, carotenoids are an important product quality attribute and therefore a major breeding trait. However, the knowledge of carotenoid accumulation genetic control in this root vegetable is still limited. In order to identify the genetic variants linked to this character, we performed an association mapping study with a candidate gene approach. We developed an original unstructured population with a broad genetic basis to avoid the pitfall of false positive detection due to population stratification. We genotyped 109 SNPs located in 17 candidate genes – mostly carotenoid biosynthesis genes – on 380 individuals, and tested the association with carotenoid contents and color components. Total carotenoids and β-carotene contents were significantly associated with genes zeaxanthin epoxydase (ZEP, phytoene desaturase (PDS and carotenoid isomerase (CRTISO while α-carotene was associated with CRTISO and plastid terminal oxidase (PTOX genes. Color components were associated most significantly with ZEP. Our results suggest the involvement of the couple PDS/PTOX and ZEP in carotenoid accumulation, as the result of the metabolic and catabolic activities respectively. This study brings new insights in the understanding of the carotenoid pathway in non-photosynthetic organs.

  13. Managing Competition “Unstructured Decision Making” Benefits for Executives, Enterprise and Society

    Directory of Open Access Journals (Sweden)

    Carlos Ernesto Martín-Pérez

    2016-06-01

    Full Text Available In an increasingly uncertain and changing environment, the success of the decisions is limited and thus obtains the expected results. Hence the need to manage professional competences in executives, as those ones encourages and contributes to job performance. For this reason, we want to argue the impact of managing competition “unstructured decision making” by executives, enterprises and Cuban society. The results are expressed in the description of the process and the advantages that executives, enterprises and society could obtain in general.

  14. Numerical test of the open void method of slide line with unstructured polygon grids

    Science.gov (United States)

    Lin, Wenzhou; Lin, Zhong; Liu, Quan

    2017-07-01

    An open void method of slide line is developed based on unstructured arbitrary polygon grids. An method of distinguishing open or closed void state of node and grid, and calculation method of velocity of node in slide line is given with open or closed state. Many conditions including different kinds of grids, different velocity and multi-medium are simulated in a test of a metallic flyer impacting another flyer and then separating. A test of Detonation driving metallic flyer are is simulated, which prove the rationality and adaptability of method.

  15. Sensor-based whole-arm obstacle avoidance for unstructured environments

    International Nuclear Information System (INIS)

    Wintenberg, A.L.; Butler, P.L.; Babcock, S.M.; Ericson, M.N.; Armstrong, G.A.; Britton, C.L. Jr.; Hamel, W.R.

    1992-01-01

    Whole-arm obstacle avoidance is needed for a variety of robotic applications in the Environmental Restoration and Waste Management (ER ampersand WM) Program. Typical industrial applications of robotics involve well-defined workspaces, allowing a predetermined knowledge of collision-free paths for manipulator motion. However, many hazardous environments are unstructured or poorly defined, providing a significant potential for collisions between manipulators and the environment. In order to allow applications of robotics in such situations, a sensing system is under development which will provide protection against collisions. Specifics of this system including system architecture and projected implementation are described

  16. On the role of dimensionality and sample size for unstructured and structured covariance matrix estimation

    Science.gov (United States)

    Morgera, S. D.; Cooper, D. B.

    1976-01-01

    The experimental observation that a surprisingly small sample size vis-a-vis dimension is needed to achieve good signal-to-interference ratio (SIR) performance with an adaptive predetection filter is explained. The adaptive filter requires estimates as obtained by a recursive stochastic algorithm of the inverse of the filter input data covariance matrix. The SIR performance with sample size is compared for the situations where the covariance matrix estimates are of unstructured (generalized) form and of structured (finite Toeplitz) form; the latter case is consistent with weak stationarity of the input data stochastic process.

  17. Unsteady Euler algorithm with unstructured dynamic mesh for complex-aircraft aeroelastic analysis

    Science.gov (United States)

    Batina, John T.

    1989-01-01

    A finite-volume unstructured-grid FEM scheme with multistage Runge-Kutta time stepping is applied to the three-dimensional time-dependent Euler equations for inviscid flows on complex aircraft configurations undergoing structural deformation. The derivation of the model, the solution procedure, and the computer implementation are described, and results are presented graphically for a NASA Langley supersonic fighter aircraft model in steady and unsteady (harmonic oscillation in complete-vehicle bending mode) flow regimes. Good agreement between FEM predictions and experimental data is demonstrated.

  18. Does intrinsic motivation enhance motor cortex excitability?

    Science.gov (United States)

    Radel, Rémi; Pjevac, Dusan; Davranche, Karen; d'Arripe-Longueville, Fabienne; Colson, Serge S; Lapole, Thomas; Gruet, Mathieu

    2016-11-01

    Intrinsic motivation (IM) is often viewed as a spontaneous tendency for action. Recent behavioral and neuroimaging evidence indicate that IM, in comparison to extrinsic motivation (EM), solicits the motor system. Accordingly, we tested whether IM leads to greater excitability of the motor cortex than EM. To test this hypothesis, we used two different tasks to induce the motivational orientation using either words representing each motivational orientation or pictures previously linked to each motivational orientation through associative learning. Single-pulse transcranial magnetic stimulation over the motor cortex was applied when viewing the stimuli. Electromyographic activity was recorded on the contracted first dorsal interosseous muscle. Two indexes of corticospinal excitability (the amplitude of motor-evoked potential and the length of cortical silent period) were obtained through unbiased automatic detection and analyzed using a mixed model that provided both statistical power and a high level of control over all important individual, task, and stimuli characteristics. Across the two tasks and the two indices of corticospinal excitability, the exposure to IM-related stimuli did not lead to a greater corticospinal excitability than EM-related stimuli or than stimuli with no motivational valence (ps > .20). While these results tend to dismiss the advantage of IM at activating the motor cortex, we suggest alternative hypotheses to explain this lack of effect, which deserves further research. © 2016 Society for Psychophysiological Research.

  19. Disturbance Observer Based Control of Multirotor Helicopters Based on a Universal Model with Unstructured Uncertainties

    Directory of Open Access Journals (Sweden)

    Ye Xie

    2015-01-01

    Full Text Available To handle different perspectives of unstructured uncertainties, two robust control techniques on the basis of a universal model are studied in this paper. Rather than building a model only applicable to a specific small-scale multirotor helicopter (MHeli, the paper proposes a modeling technique to develop a universal model-framework. Particularly, it is straightforward to apply the universal model to a certain MHeli because the contribution and allocation matrix is proposed in the model-framework. Based on the model uncertainties, the load perturbation of the rotor is the primary focus due to its indispensable importance in the tracking performance. In contrast to the common methods, it is proposed to take this unstructured uncertainty in that external disturbance and designs disturbance observer (DOB. In addition, a class of lead-compensator is specifically designed as for compensating phase lag induced by DOB. Compared with H∞ loop-shaping, greater robust tracking performance on rejecting load perturbation could be achieved as a tradeoff between robust stability and tracking performance which is successfully avoided with DOB-based control strategy.

  20. A parallel code base on discontinuous Galerkin method on three dimensional unstructured meshes for MHD equations

    Science.gov (United States)

    Li, Xujing; Zheng, Weiying

    2016-10-01

    A new parallel code based on discontinuous Galerkin (DG) method for hyperbolic conservation laws on three dimensional unstructured meshes is developed recently. This code can be used for simulations of MHD equations, which are very important in magnetic confined plasma research. The main challenges in MHD simulations in fusion include the complex geometry of the configurations, such as plasma in tokamaks, the possibly discontinuous solutions and large scale computing. Our new developed code is based on three dimensional unstructured meshes, i.e. tetrahedron. This makes the code flexible to arbitrary geometries. Second order polynomials are used on each element and HWENO type limiter are applied. The accuracy tests show that our scheme reaches the desired three order accuracy and the nonlinear shock test demonstrate that our code can capture the sharp shock transitions. Moreover, One of the advantages of DG compared with the classical finite element methods is that the matrices solved are localized on each element, making it easy for parallelization. Several simulations including the kink instabilities in toroidal geometry will be present here. Chinese National Magnetic Confinement Fusion Science Program 2015GB110003.

  1. Error Correction of Measured Unstructured Road Profiles Based on Accelerometer and Gyroscope Data

    Directory of Open Access Journals (Sweden)

    Jinhua Han

    2017-01-01

    Full Text Available This paper describes a noncontact acquisition system composed of several time synchronized laser height sensors, accelerometers, gyroscope, and so forth in order to collect the road profiles of vehicle riding on the unstructured roads. A method of correcting road profiles based on the accelerometer and gyroscope data is proposed to eliminate the adverse impacts of vehicle vibration and attitudes change. Because the power spectral density (PSD of gyro attitudes concentrates in the low frequency band, a method called frequency division is presented to divide the road profiles into two parts: high frequency part and low frequency part. The vibration error of road profiles is corrected by displacement data obtained through two times integration of measured acceleration data. After building the mathematical model between gyro attitudes and road profiles, the gyro attitudes signals are separated from low frequency road profile by the method of sliding block overlap based on correlation analysis. The accuracy and limitations of the system have been analyzed, and its validity has been verified by implementing the system on wheeled equipment for road profiles’ measuring of vehicle testing ground. The paper offers an accurate and practical approach to obtaining unstructured road profiles for road simulation test.

  2. Anisotropic three-dimensional inversion of CSEM data using finite element techniques on unstructured grids

    Science.gov (United States)

    Wang, Feiyan; Petter Morten, Jan; Spitzer, Klaus

    2018-01-01

    In this paper, we present a recently developed anisotropic three-dimensional (3-D) inversion framework for interpreting controlled-source electromagnetic (CSEM) data in the frequency domain. The framework integrates a high-order finite element forward operator and a Gauss-Newton inversion algorithm. Conductivity constraints are applied using a parameter transformation. We discretize the continuous forward and inverse problems on unstructured grids for a flexible treatment of arbitrarily complex geometries. Moreover, an unstructured mesh is more desirable in comparison to a single rectilinear mesh for multi-source problems because local grid refinement will not significantly influence the mesh density outside the region of interest. The non-uniform spatial discretization facilitates parameterization of the inversion domain at a suitable scale. For a rapid simulation of multi-source EM data, we opt to use a parallel direct solver. We further accelerate the inversion process by decomposing the entire data set into subsets with respect to frequencies (and transmitters if memory requirement is affordable). The computational tasks associated with each data subset are distributed to different processes and run in parallel. We validate the scheme using a synthetic marine CSEM model with rough bathymetry, and finally, apply it to an industrial-size 3-D data set from the Troll field oil province in the North Sea acquired in 2008 to examine its robustness and practical applicability.

  3. Efficient Parallelization of a Dynamic Unstructured Application on the Tera MTA

    Science.gov (United States)

    Oliker, Leonid; Biswas, Rupak

    1999-01-01

    The success of parallel computing in solving real-life computationally-intensive problems relies on their efficient mapping and execution on large-scale multiprocessor architectures. Many important applications are both unstructured and dynamic in nature, making their efficient parallel implementation a daunting task. This paper presents the parallelization of a dynamic unstructured mesh adaptation algorithm using three popular programming paradigms on three leading supercomputers. We examine an MPI message-passing implementation on the Cray T3E and the SGI Origin2OOO, a shared-memory implementation using cache coherent nonuniform memory access (CC-NUMA) of the Origin2OOO, and a multi-threaded version on the newly-released Tera Multi-threaded Architecture (MTA). We compare several critical factors of this parallel code development, including runtime, scalability, programmability, and memory overhead. Our overall results demonstrate that multi-threaded systems offer tremendous potential for quickly and efficiently solving some of the most challenging real-life problems on parallel computers.

  4. CSA: A Credibility Search Algorithm Based on Different Query in Unstructured Peer-to-Peer Networks

    Directory of Open Access Journals (Sweden)

    Hongyan Mei

    2014-01-01

    Full Text Available Efficient searching for resources has become a challenging task with less network bandwidth consumption in unstructured peer-to-peer (P2P networks. Heuristic search mechanism is an effective method which depends on the previous searches to guide future ones. In the proposed methods, searching for high-repetition resources is more effective. However, the performances of the searches for nonrepetition or low-repetition or rare resources need to be improved. As for this problem, considering the similarity between social networks and unstructured P2P networks, we present a credibility search algorithm based on different queries according to the trust production principle in sociology and psychology. In this method, queries are divided into familiar queries and unfamiliar queries. For different queries, we adopt different ways to get the credibility of node to its each neighbor. And then queries should be forwarded by the neighbor nodes with higher credibility. Experimental results show that our method can improve query hit rate and reduce search delay with low bandwidth consumption in three different network topologies under static and dynamic network environments.

  5. Introducing a distributed unstructured mesh into gyrokinetic particle-in-cell code, XGC

    Science.gov (United States)

    Yoon, Eisung; Shephard, Mark; Seol, E. Seegyoung; Kalyanaraman, Kaushik

    2017-10-01

    XGC has shown good scalability for large leadership supercomputers. The current production version uses a copy of the entire unstructured finite element mesh on every MPI rank. Although an obvious scalability issue if the mesh sizes are to be dramatically increased, the current approach is also not optimal with respect to data locality of particles and mesh information. To address these issues we have initiated the development of a distributed mesh PIC method. This approach directly addresses the base scalability issue with respect to mesh size and, through the use of a mesh entity centric view of the particle mesh relationship, provides opportunities to address data locality needs of many core and GPU supported heterogeneous systems. The parallel mesh PIC capabilities are being built on the Parallel Unstructured Mesh Infrastructure (PUMI). The presentation will first overview the form of mesh distribution used and indicate the structures and functions used to support the mesh, the particles and their interaction. Attention will then focus on the node-level optimizations being carried out to ensure performant operation of all PIC operations on the distributed mesh. Partnership for Edge Physics Simulation (EPSI) Grant No. DE-SC0008449 and Center for Extended Magnetohydrodynamic Modeling (CEMM) Grant No. DE-SC0006618.

  6. Motion planning for autonomous vehicle based on radial basis function neural network in unstructured environment.

    Science.gov (United States)

    Chen, Jiajia; Zhao, Pan; Liang, Huawei; Mei, Tao

    2014-09-18

    The autonomous vehicle is an automated system equipped with features like environment perception, decision-making, motion planning, and control and execution technology. Navigating in an unstructured and complex environment is a huge challenge for autonomous vehicles, due to the irregular shape of road, the requirement of real-time planning, and the nonholonomic constraints of vehicle. This paper presents a motion planning method, based on the Radial Basis Function (RBF) neural network, to guide the autonomous vehicle in unstructured environments. The proposed algorithm extracts the drivable region from the perception grid map based on the global path, which is available in the road network. The sample points are randomly selected in the drivable region, and a gradient descent method is used to train the RBF network. The parameters of the motion-planning algorithm are verified through the simulation and experiment. It is observed that the proposed approach produces a flexible, smooth, and safe path that can fit any road shape. The method is implemented on autonomous vehicle and verified against many outdoor scenes; furthermore, a comparison of proposed method with the existing well-known Rapidly-exploring Random Tree (RRT) method is presented. The experimental results show that the proposed method is highly effective in planning the vehicle path and offers better motion quality.

  7. Unstructured grids and an element based conservative approach for a black-oil reservoir simulation

    Energy Technology Data Exchange (ETDEWEB)

    Nogueira, Regis Lopes; Fernandes, Bruno Ramon Batista [Federal University of Ceara, Fortaleza, CE (Brazil). Dept. of Chemical Engineering; Araujo, Andre Luiz de Souza [Federal Institution of Education, Science and Technology of Ceara - IFCE, Fortaleza (Brazil). Industry Department], e-mail: andre@ifce.edu.br; Marcondes, Francisco [Federal University of Ceara, Fortaleza, CE (Brazil). Dept. of Metallurgical Engineering and Material Science], e-mail: marcondes@ufc.br

    2010-07-01

    Unstructured meshes presented one upgrade in modeling the main important features of the reservoir such as discrete fractures, faults, and irregular boundaries. From several methodologies available, the Element based Finite Volume Method (EbFVM), in conjunction with unstructured meshes, is one methodology that deserves large attention. In this approach, the reservoir, for 2D domains, is discretized using a mixed two-dimensional mesh using quadrilateral and triangle elements. After the initial step of discretization, each element is divided into sub-elements and the mass balance for each component is developed for each sub-element. The equations for each control-volume using a cell vertex construction are formulated through the contribution of different neighboured elements. This paper presents an investigation of an element-based approach using the black-oil model based on pressure and global mass fractions. In this approach, even when all gas phase is dissolved in oil phase the global mass fraction of gas will be different from zero. Therefore, no additional numerical procedure is necessary in order to treat the gas phase appear/disappearance. In this paper the above mentioned approach is applied to multiphase flows involving oil, gas, and water. The mass balance equations in terms of global mass fraction of oil, gas and water are discretized through the EbFVM and linearized by the Newton's method. The results are presented in terms of volumetric rates of oil, gas, and water and phase saturations. (author)

  8. Methods in the analysis of mobile robots behavior in unstructured environment

    Science.gov (United States)

    Mondoc, Alina; Dolga, Valer; Gorie, Nina

    2012-11-01

    A mobile robot can be described as a mechatronic system that must execute an application in a working environment. From mechatronic concept, the authors highlight mechatronic system structure based on its secondary function. Mobile robot will move, either in a known environment - structured environment may be described in time by an appropriate mathematical model or in an unfamiliar environment - unstructured - the random aspects prevail. Starting from a point robot must reach a START STOP point in the context of functional constraints imposed on the one hand, the application that, on the other hand, the working environment. The authors focus their presentation on unstructured environment. In this case the evolution of mobile robot is based on obtaining information in the work environment, their processing and integration results in action strategy. Number of sensory elements used is subject to optimization parameter. Starting from a known structure of mobile robot, the authors analyze the possibility of developing a mathematical model variants mathematical contact wheel - ground. It analyzes the various types of soil and the possibility of obtaining a "signature" on it based on sensory information. Theoretical aspects of the problem are compared to experimental results obtained in robot evolution. The mathematical model of the robot system allowed the simulation environment and its evolution in comparison with the experimental results estimated.

  9. ComPASS : a tool for distributed parallel finite volume discretizations on general unstructured polyhedral meshes

    Directory of Open Access Journals (Sweden)

    Dalissier E.

    2013-12-01

    Full Text Available The objective of the ComPASS project is to develop a parallel multiphase Darcy flow simulator adapted to general unstructured polyhedral meshes (in a general sense with possibly non planar faces and to the parallelization of advanced finite volume discretizations with various choices of the degrees of freedom such as cell centres, vertices, or face centres. The main targeted applications are the simulation of CO2 geological storage, nuclear waste repository and reservoir simulations. The CEMRACS 2012 summer school devoted to high performance computing has been an ideal framework to start this collaborative project. This paper describes what has been achieved during the four weeks of the CEMRACS project which has been focusing on the implementation of basic features of the code such as the distributed unstructured polyhedral mesh, the synchronization of the degrees of freedom, and the connection to scientific libraries including the partitioner METIS, the visualization tool PARAVIEW, and the parallel linear solver library PETSc. The parallel efficiency of this first version of the ComPASS code has been validated on a toy parabolic problem using the Vertex Approximate Gradient finite volume spatial discretization with both cell and vertex degrees of freedom, combined with an Euler implicit time integration.

  10. Segmentation of Large Unstructured Point Clouds Using Octree-Based Region Growing and Conditional Random Fields

    Science.gov (United States)

    Bassier, M.; Bonduel, M.; Van Genechten, B.; Vergauwen, M.

    2017-11-01

    Point cloud segmentation is a crucial step in scene understanding and interpretation. The goal is to decompose the initial data into sets of workable clusters with similar properties. Additionally, it is a key aspect in the automated procedure from point cloud data to BIM. Current approaches typically only segment a single type of primitive such as planes or cylinders. Also, current algorithms suffer from oversegmenting the data and are often sensor or scene dependent. In this work, a method is presented to automatically segment large unstructured point clouds of buildings. More specifically, the segmentation is formulated as a graph optimisation problem. First, the data is oversegmented with a greedy octree-based region growing method. The growing is conditioned on the segmentation of planes as well as smooth surfaces. Next, the candidate clusters are represented by a Conditional Random Field after which the most likely configuration of candidate clusters is computed given a set of local and contextual features. The experiments prove that the used method is a fast and reliable framework for unstructured point cloud segmentation. Processing speeds up to 40,000 points per second are recorded for the region growing. Additionally, the recall and precision of the graph clustering is approximately 80%. Overall, nearly 22% of oversegmentation is reduced by clustering the data. These clusters will be classified and used as a basis for the reconstruction of BIM models.

  11. A survey of simultaneous localization and mapping on unstructured lunar complex environment

    Science.gov (United States)

    Wang, Yiqiao; Zhang, Wei; An, Pei

    2017-10-01

    Simultaneous localization and mapping (SLAM) technology is the key to realizing lunar rover's intelligent perception and autonomous navigation. It embodies the autonomous ability of mobile robot, and has attracted plenty of concerns of researchers in the past thirty years. Visual sensors are meaningful to SLAM research because they can provide a wealth of information. Visual SLAM uses merely images as external information to estimate the location of the robot and construct the environment map. Nowadays, SLAM technology still has problems when applied in large-scale, unstructured and complex environment. Based on the latest technology in the field of visual SLAM, this paper investigates and summarizes the SLAM technology using in the unstructured complex environment of lunar surface. In particular, we focus on summarizing and comparing the detection and matching of features of SIFT, SURF and ORB, in the meanwhile discussing their advantages and disadvantages. We have analyzed the three main methods: SLAM Based on Extended Kalman Filter, SLAM Based on Particle Filter and SLAM Based on Graph Optimization (EKF-SLAM, PF-SLAM and Graph-based SLAM). Finally, this article summarizes and discusses the key scientific and technical difficulties in the lunar context that Visual SLAM faces. At the same time, we have explored the frontier issues such as multi-sensor fusion SLAM and multi-robot cooperative SLAM technology. We also predict and prospect the development trend of lunar rover SLAM technology, and put forward some ideas of further research.

  12. Algebraic description of intrinsic modes in nuclei

    International Nuclear Information System (INIS)

    Leviatan, A.

    1989-01-01

    We present a procedure for extracting normal modes in algebraic number-conserving systems of interacting bosons relevant for collective states in even-even nuclei. The Hamiltonian is resolved into intrinsic (bandhead related) and collective (in-band related) parts. Shape parameters are introduced through non-spherical boson bases. Intrinsic modes decoupled from the spurious modes are obtained from the intinsic part of the Hamiltonian in the limit of large number of bosons. Intrinsic states are constructed and serve to evaluate electromagnetic transition rates. The method is illustrated for systems with one type of boson as well as with proton-neutron bosons. 28 refs., 1 fig

  13. Algebraic description of intrinsic modes in nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Leviatan, A.

    1989-01-01

    We present a procedure for extracting normal modes in algebraic number-conserving systems of interacting bosons relevant for collective states in even-even nuclei. The Hamiltonian is resolved into intrinsic (bandhead related) and collective (in-band related) parts. Shape parameters are introduced through non-spherical boson bases. Intrinsic modes decoupled from the spurious modes are obtained from the intinsic part of the Hamiltonian in the limit of large number of bosons. Intrinsic states are constructed and serve to evaluate electromagnetic transition rates. The method is illustrated for systems with one type of boson as well as with proton-neutron bosons. 28 refs., 1 fig.

  14. Folding propensity of intrinsically disordered proteins by osmotic stress

    International Nuclear Information System (INIS)

    Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.

    2016-01-01

    Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR). Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scattering (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.

  15. Dynamic Neural Fields with Intrinsic Plasticity.

    Science.gov (United States)

    Strub, Claudius; Schöner, Gregor; Wörgötter, Florentin; Sandamirskaya, Yulia

    2017-01-01

    Dynamic neural fields (DNFs) are dynamical systems models that approximate the activity of large, homogeneous, and recurrently connected neural networks based on a mean field approach. Within dynamic field theory, the DNFs have been used as building blocks in architectures to model sensorimotor embedding of cognitive processes. Typically, the parameters of a DNF in an architecture are manually tuned in order to achieve a specific dynamic behavior (e.g., decision making, selection, or working memory) for a given input pattern. This manual parameters search requires expert knowledge and time to find and verify a suited set of parameters. The DNF parametrization may be particular challenging if the input distribution is not known in advance, e.g., when processing sensory information. In this paper, we propose the autonomous adaptation of the DNF resting level and gain by a learning mechanism of intrinsic plasticity (IP). To enable this adaptation, an input and output measure for the DNF are introduced, together with a hyper parameter to define the desired output distribution. The online adaptation by IP gives the possibility to pre-define the DNF output statistics without knowledge of the input distribution and thus, also to compensate for changes in it. The capabilities and limitations of this approach are evaluated in a number of experiments.

  16. Intrinsic endometriosis of ureter: a case report

    International Nuclear Information System (INIS)

    Hong, Myung Sun; Kim, Ho Chul; Yun, Ku Sup; Choi, Chul Soon; Bae, Sang Hoon; Kim, Sung Yong; Shin, Hyung Sik

    1995-01-01

    Endometriosis is a rare cause of an ureteral obstruction. We report a case of intrinsic ureteral endometriosis resulting in severe hydroureteronephrosis. The diagnosis of ureteral endometriosis may be considered in women with flank pain and ureteric obstruction within true pelvis

  17. The Intrinsic Dynamics of Psychological Process

    NARCIS (Netherlands)

    Vallacher, Robin R.; van Geert, Paul; Nowak, Andrzej

    2015-01-01

    Psychological processes unfold on various timescales in accord with internally generated patterns. The intrinsic dynamism of psychological process is difficult to investigate using traditional methods emphasizing cause–effect relations, however, and therefore is rarely incorporated into social

  18. Deuterium NMR, induced and intrinsic cholesteric lyomesophases

    International Nuclear Information System (INIS)

    Alcantara, M.R.

    1982-01-01

    Induced and intrinsic cholesteric lyotropic mesophases were studied. Induced cholesteric lyomesophases based on potassium laurate (KL) system, with small amounts of cholesterol added, were studied by deuterium NMR and by polarizing microscopy. Order profiles obtained from deuterium NMR of KL perdenderated chains in both induced cholesteric and normal mesophases were compared. The intrinsic cholesteric lyotropic mesophases were based on the amphiphile potassium N-lauroyl serinate (KLNS) in the resolved levo form. The study of the type I intrinsic cholesteric mesophase was made by optical microscopy under polarized light and the type II intrinsic cholesteric lyomesophase was characterized by deuterium NMR. The new texture was explained by the use of the theory of disclinations developed for thermotropic liquid crystals, specially for cholesteric type. (M.J.C.) [pt

  19. Intrinsic and acquired resistance mechanisms in enterococcus

    Science.gov (United States)

    Hollenbeck, Brian L.; Rice, Louis B.

    2012-01-01

    Enterococci have the potential for resistance to virtually all clinically useful antibiotics. Their emergence as important nosocomial pathogens has coincided with increased expression of antimicrobial resistance by members of the genus. The mechanisms underlying antibiotic resistance in enterococci may be intrinsic to the species or acquired through mutation of intrinsic genes or horizontal exchange of genetic material encoding resistance determinants. This paper reviews the antibiotic resistance mechanisms in Enterococcus faecium and Enterococcus faecalis and discusses treatment options. PMID:23076243

  20. Intrinsically photosensitive retinal ganglion cell function in relation to age

    DEFF Research Database (Denmark)

    Herbst, Kristina; Sander, Birgit; Lund-Andersen, Henrik

    2012-01-01

    The activity of melanopsin containing intrinsically photosensitive ganglion retinal cells (ipRGC) can be assessed by a means of pupil responses to bright blue (appr.480 nm) light. Due to age related factors in the eye, particularly, structural changes of the lens, less light reaches retina. The aim...... of this study was to examine how age and in vivo measured lens transmission of blue light might affect pupil light responses, in particular, mediated by the ipRGC....

  1. Dynamics of intrinsic electrophysiological properties in spinal cord neurones

    DEFF Research Database (Denmark)

    Russo, R E; Hounsgaard, J

    1999-01-01

    The spinal cord is engaged in a wide variety of functions including generation of motor acts, coding of sensory information and autonomic control. The intrinsic electrophysiological properties of spinal neurones represent a fundamental building block of the spinal circuits executing these tasks. ....... Specialised, cell specific electrophysiological phenotypes gradually differentiate during development and are continuously adjusted in the adult animal by metabotropic synaptic interactions and activity-dependent plasticity to meet a broad range of functional demands....

  2. Incentives and intrinsic motivation in healthcare.

    Science.gov (United States)

    Berdud, Mikel; Cabasés, Juan M; Nieto, Jorge

    It has been established in the literature that workers within public organisations are intrinsically motivated. This paper is an empirical study of the healthcare sector using methods of qualitative analysis research, which aims to answer the following hypotheses: 1) doctors are intrinsically motivated; 2) economic incentives and control policies may undermine doctors' intrinsic motivation; and 3) well-designed incentives may encourage doctors' intrinsic motivation. We conducted semi-structured interviews à-la-Bewley with 16 doctors from Navarre's Healthcare Service (Servicio Navarro de Salud-Osasunbidea), Spain. The questions were based on current theories of intrinsic motivation and incentives to test the hypotheses. Interviewees were allowed to respond openly without time constraints. Relevant information was selected, quantified and analysed by using the qualitative concepts of saturation and codification. The results seem to confirm the hypotheses. Evidence supporting hypotheses 1 and 2 was gathered from all interviewees, as well as indications of the validity of hypothesis 3 based on interviewees' proposals of incentives. The conclusions could act as a guide to support the optimal design of incentive policies and schemes within health organisations when healthcare professionals are intrinsically motivated. Copyright © 2016 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

  3. Intrinsic disorder in the BK channel and its interactome.

    Directory of Open Access Journals (Sweden)

    Zhenling Peng

    Full Text Available The large-conductance Ca2+-activated K+ (BK channel is broadly expressed in various mammalian cells and tissues such as neurons, skeletal and smooth muscles, exocrine cells, and sensory cells of the inner ear. Previous studies suggest that BK channels are promiscuous binders involved in a multitude of protein-protein interactions. To gain a better understanding of the potential mechanisms underlying BK interactions, we analyzed the abundance, distribution, and potential mechanisms of intrinsic disorder in 27 BK channel variants from mouse cochlea, 104 previously reported BK-associated proteins (BKAPS from cytoplasmic and membrane/cytoskeletal regions, plus BK β- and γ-subunits. Disorder was evaluated using the MFDp algorithm, which is a consensus-based predictor that provides a strong and competitive predictive quality and PONDR, which can determine long intrinsically disordered regions (IDRs. Disorder-based binding sites or molecular recognition features (MoRFs were found using MoRFpred and ANCHOR. BKAP functions were categorized based on Gene Ontology (GO terms. The analyses revealed that the BK variants contain a number of IDRs. Intrinsic disorder is also common in BKAPs, of which ∼ 5% are completely disordered. However, intrinsic disorder is very differently distributed within BK and its partners. Approximately 65% of the disordered segments in BK channels are long (IDRs (>50 residues, whereas >60% of the disordered segments in BKAPs are short IDRs that range in length from 4 to 30 residues. Both α and γ subunits showed various amounts of disorder as did hub proteins of the BK interactome. Our analyses suggest that intrinsic disorder is important for the function of BK and its BKAPs. Long IDRs in BK are engaged in protein-protein and protein-ligand interactions, contain multiple post-translational modification sites, and are subjected to alternative splicing. The disordered structure of BK and its BKAPs suggests one of the underlying

  4. Tudor staphylococcal nuclease is a structure-specific ribonuclease that degrades RNA at unstructured regions during microRNA decay.

    Science.gov (United States)

    Li, Chia-Lung; Yang, Wei-Zen; Shi, Zhonghao; Yuan, Hanna S

    2018-02-13

    Tudor staphylococcal nuclease (TSN) is an evolutionarily conserved ribonuclease in eukaryotes that is composed of five staphylococcal nuclease-like domains (SN1 to SN5) and a Tudor domain. TSN degrades hyper-edited double-stranded RNA, including primary miRNA precursors containing multiple I-U and U-I pairs, and mature miRNA during miRNA decay. However, how TSN binds and degrades its RNA substrates remains unclear. Here, we show that the C. elegans TSN (cTSN) is a monomeric Ca 2+ -dependent ribonuclease, cleaving RNA chains at the 5'-side of the phosphodiester linkage to produce degraded fragments with 5'-hydroxyl and 3'-phosphate ends. cTSN degrades single-stranded RNA and double-stranded RNA containing mismatched base pairs, but is not restricted to those containing multiple I-U and U-I pairs. cTSN has at least two catalytic active sites located in the SN1 and SN3 domains, since mutations of the putative Ca 2+ -binding residues in these two domains strongly impaired its ribonuclease activity. We further show by small-angle X-ray scattering that rice osTSN has a flexible two-lobed structure with open to closed conformations, indicating that TSN may change its conformation upon RNA binding. We conclude that TSN is a structure-specific ribonuclease targeting not only single-stranded RNA, but also unstructured regions of double-stranded RNA. This study provides the molecular basis for how TSN cooperates with RNA editing to eliminate duplex RNA in cell defense, and how TSN selects and degrades RNA during microRNA decay. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  5. Transport of Intrinsic Plutonium Colloids in Saturated Porous Media

    Science.gov (United States)

    Zhou, D.; Abdel-Fattah, A.; Boukhalfa, H.; Ware, S. D.; Tarimala, S.; Keller, A. A.

    2011-12-01

    Actinide contaminants were introduced to the subsurface environment as a result of nuclear weapons development and testing, as well as for nuclear power generation and related research activities for defense and civilian applications. Even though most actinide species were believed to be fairly immobile once in the subsurface, recent studies have shown the transport of actinides kilometers away from their disposal sites. For example, the treated liquid wastes released into Mortandad Canyon at the Los Alamos National Laboratory were predicted to travel less than a few meters; however, plutonium and americium have been detected 3.4 km away from the waste outfall. A colloid-facilitated mechanism has been suggested to account for this unexpected transport of these radioactive wastes. Clays, oxides, organic matters, and actinide hydroxides have all been proposed as the possible mobile phase. Pu ions associated with natural colloids are often referred to as pseudo-Pu colloids, in contrast with the intrinsic Pu colloids that consist of Pu oxides. Significant efforts have been made to investigate the role of pseudo-Pu colloids, while few studies have evaluated the environmental behavior of the intrinsic Pu colloids. Given the fact that Pu (IV) has extremely low solubility product constant, it can be inferred that the transport of Pu in the intrinsic form is highly likely at suitable environmental conditions. This study investigates the transport of intrinsic Pu colloids in a saturated alluvium material packed in a cylindrical column (2.5-cm Dia. x 30-cm high) and compares the results to previous data on the transport of pseudo Pu colloids in the same material. A procedure to prepare a stable intrinsic Pu colloid suspension that produced consistent and reproducible electrokinetic and stability data was developed. Electrokinetic properties and aggregation stability were characterized. The Pu colloids, together with trillium as a conservative tracer, were injected into the

  6. The circadian response of intrinsically photosensitive retinal ganglion cells.

    Directory of Open Access Journals (Sweden)

    Andrew J Zele

    Full Text Available Intrinsically photosensitive retinal ganglion cells (ipRGC signal environmental light level to the central circadian clock and contribute to the pupil light reflex. It is unknown if ipRGC activity is subject to extrinsic (central or intrinsic (retinal network-mediated circadian modulation during light entrainment and phase shifting. Eleven younger persons (18-30 years with no ophthalmological, medical or sleep disorders participated. The activity of the inner (ipRGC and outer retina (cone photoreceptors was assessed hourly using the pupil light reflex during a 24 h period of constant environmental illumination (10 lux. Exogenous circadian cues of activity, sleep, posture, caffeine, ambient temperature, caloric intake and ambient illumination were controlled. Dim-light melatonin onset (DLMO was determined from salivary melatonin assay at hourly intervals, and participant melatonin onset values were set to 14 h to adjust clock time to circadian time. Here we demonstrate in humans that the ipRGC controlled post-illumination pupil response has a circadian rhythm independent of external light cues. This circadian variation precedes melatonin onset and the minimum ipRGC driven pupil response occurs post melatonin onset. Outer retinal photoreceptor contributions to the inner retinal ipRGC driven post-illumination pupil response also show circadian variation whereas direct outer retinal cone inputs to the pupil light reflex do not, indicating that intrinsically photosensitive (melanopsin retinal ganglion cells mediate this circadian variation.

  7. A multiscale restriction-smoothed basis method for high contrast porous media represented on unstructured grids

    Science.gov (United States)

    Møyner, Olav; Lie, Knut-Andreas

    2016-01-01

    A wide variety of multiscale methods have been proposed in the literature to reduce runtime and provide better scaling for the solution of Poisson-type equations modeling flow in porous media. We present a new multiscale restricted-smoothed basis (MsRSB) method that is designed to be applicable to both rectilinear grids and unstructured grids. Like many other multiscale methods, MsRSB relies on a coarse partition of the underlying fine grid and a set of local prolongation operators (multiscale basis functions) that map unknowns associated with the fine grid cells to unknowns associated with blocks in the coarse partition. These mappings are constructed by restricted smoothing: Starting from a constant, a localized iterative scheme is applied directly to the fine-scale discretization to compute prolongation operators that are consistent with the local properties of the differential operators. The resulting method has three main advantages: First of all, both the coarse and the fine grid can have general polyhedral geometry and unstructured topology. This means that partitions and good prolongation operators can easily be constructed for complex models involving high media contrasts and unstructured cell connections introduced by faults, pinch-outs, erosion, local grid refinement, etc. In particular, the coarse partition can be adapted to geological or flow-field properties represented on cells or faces to improve accuracy. Secondly, the method is accurate and robust when compared to existing multiscale methods and does not need expensive recomputation of local basis functions to account for transient behavior: Dynamic mobility changes are incorporated by continuing to iterate a few extra steps on existing basis functions. This way, the cost of updating the prolongation operators becomes proportional to the amount of change in fluid mobility and one reduces the need for expensive, tolerance-based updates. Finally, since the MsRSB method is formulated on top of a cell

  8. The effect of professional culture on intrinsic motivation among physicians in an academic medical center.

    Science.gov (United States)

    Janus, Katharina

    2014-01-01

    Today, most healthcare organizations aim to manage professionals' motivation through monetary incentives, such as pay for performance. However, addressing motivation extrinsically can involve negative effects, such as disturbed teamwork, gaming the system, and crowd-out of intrinsic motivation. To offset these side effects, it is crucial to support professionals' intrinsic motivation actively, which is largely determined by enjoyment- and obligation-based social norms that derive from professionals' culture. For this study, a professional culture questionnaire was designed and validated, the results of which uncovered three factors: relationship to work, relationship to colleagues, and relationship to organization. These factors served as independent variables for regression analyses. Second, Amabile's validated work preference inventory was used to measure intrinsic motivation as a dependent variable. The regression analysis was controlled for sex, age, and experience. The study revealed that relationship to work had the strongest (and a positive) impact on intrinsic motivation in general and on Amabile's intrinsic subscales, enjoyment and challenge. Relationship to organization had a negative impact on intrinsic motivation and both subscales, and relationship to colleagues showed a low positive significance for the intrinsic scale only. Healthcare organizations have mostly focused on targeting professionals' extrinsic motivation. However, managing dimensions of professional culture can help support professionals' intrinsic motivation without incurring the side effects of monetary incentives.

  9. Unstructured Large Eddy Simulation of the passive control of the flow in a weapon bay

    Science.gov (United States)

    Levasseur, V.; Sagaut, P.; Mallet, M.; Chalot, F.

    2008-11-01

    The control of cavity flows has been investigated by the means of Large Eddy Simulations. The computations have been carried out on unstructured meshes to assess the efficiency of two passive acoustic oscillation suppression devices: the rod-in-crossflow and the flat-top spoiler. Despite a sustained interest and many experiments, a clear explanation for observed reduction in the flow-induced structure load is still missing. This work explores different hypotheses: the modification of the mean field and its linear stability properties, a pure deflection effect of the separated shear layer, or scale coupling between the rod wake and the turbulent mixing layer over the cavity. The aim here is to enhance the experimental database and provide leads towards a better understanding of the phenomena. The selected test-case is a cavity of length/depth ratio equal to 5, at Mach and Reynolds number of M=0.85 and ReL=7.10, respectively.

  10. Adaptive unstructured simulations of diaphragm rupture and perforation opening to start hypersonic air inlets

    International Nuclear Information System (INIS)

    Timofeev, E.V.; Tahir, R.B.; Voinovich, P.A.; Moelder, S.

    2004-01-01

    The concept of 'twin' grid nodes is discussed in the context of unstructured, adaptive meshes that are suitable for highly unsteady flows. The concept is applicable to internal boundary contours (within the computational domain) where the boundary conditions may need to be changed dynamically; for instance, an impermeable solid wall segment can be redefined as a fully permeable invisible boundary segment during the course of the simulation. This can be used to simulate unsteady gas flows with internal boundaries where the flow conditions may change rapidly and drastically. As a demonstration, the idea is applied to study the starting process in hypersonic air inlets by rupturing a diaphragm or by opening wall-perforations. (author)

  11. LanguageNet: A Novel Framework for Processing Unstructured Text Information

    DEFF Research Database (Denmark)

    Qureshi, Pir Abdul Rasool; Memon, Nasrullah; Wiil, Uffe Kock

    2011-01-01

    In this paper we present LanguageNet—a novel framework for processing unstructured text information from human generated content. The state of the art information processing frameworks have some shortcomings: modeled in generalized form, trained on fixed (limited) data sets, and leaving...... the specialization necessary for information consolidation to the end users. The proposed framework is the first major attempt to address these shortcomings. LanguageNet provides extended support of graphical methods contributing added value to the capabilities of information processing. We discuss the benefits...... of the framework and compare it with the available state of the art. We also describe how the framework improves the information gathering process and contribute towards building systems with better performance in the domain of Open Source Intelligence....

  12. Multidimensional Unstructured-Grid Liquid Rocket Engine Nozzle Performance and Heat Transfer Analysis

    Science.gov (United States)

    Wang, Ten-See

    2004-01-01

    The objective of this study is to conduct a unified computational analysis for computing design parameters such as axial thrust, convective and radiative wall heat fluxes for regeneratively cooled liquid rocket engine nozzles, so as to develop a computational strategy for computing those parameters through parametric investigations. The computational methodology is based on a multidimensional, finite-volume, turbulent, chemically reacting, radiating, unstructured-grid, and pressure-based formulation, with grid refinement capabilities. Systematic parametric studies on effects of wall boundary conditions, combustion chemistry, radiation coupling, computational cell shape, and grid refinement were performed and assessed. Under the computational framework of this study, it is found that the computed axial thrust performance, flow features, and wall heat fluxes compared well with those of available data and calculations, using a strategy of structured-grid dominated mesh, finite-rate chemistry, and cooled wall boundary condition.

  13. PARALLEL SMAC ALGORITHMS TO SOLVE SHALLOW WATER EQUATION WITH UNSTRUCTURED COLLOCATED GRID SYSTEM

    Science.gov (United States)

    Yamashita, Haruka; Ushijima, Satoru

    A computational method to solve shallow water equations has been investigated with an SMAC method which is usually employed in the simulation for incompressible fluids. In particular, this numerical method is implemented in the unstructured collocated grid system with the distributed memory system to increase the parallel efficiency. The developed computational method was applied to the 1D dam-break problem and the free-surface flows in a meandering open channel. As a result of the 1D dam-break simulations, it was confirmed that this method improve the numerical stability. While, in the case of the meandering open channel, it was confirmed that the predicted water depth and depth-averaged velocity distributions are qualitatively in good agreement with the experimental results and that the reasonable parallel efficiencies are attained by parallel computations.

  14. Studies on aerodynamic interferences between the components of transport airplane using unstructured Navier-Stokes simulations

    International Nuclear Information System (INIS)

    Wang, G.; Ye, Z.

    2005-01-01

    It is well known that the aerodynamic interference flows widely exist between the components of conventional transport airplane, for example, the wing-fuselage juncture flow, wing-pylon-nacelle flow and tail-fuselage juncture flow. The main characteristic of these aerodynamic interferences is flow separation, which will increase the drag, reduce the lift and cause adverse influence on the stability and controllability of the airplane. Therefore, the modern civil transport designers should do their best to eliminate negative effects of aerodynamic interferences, which demands that the aerodynamic interferences between the aircraft components should be predicted and analyzed accurately. Today's CFD techniques provide us powerful and efficient analysis tools to achieve this objective. In this paper, computational investigations of the interferences between transport aircraft components have been carried out by using a viscous flow solver based on mixed element type unstructured meshes. (author)

  15. Parallel implementation of a dynamic unstructured chimera method in the DLR finite volume TAU-code

    International Nuclear Information System (INIS)

    Madrane, A.; Raichle, A.; Stuermer, A.

    2004-01-01

    Aerodynamic problems involving moving geometries have many applications, including store separation, high-speed train entering into a tunnel, simulation of full configurations of the helicopter and fast maneuverability. Overset grid method offers the option of calculating these procedures. The solution process uses a grid system that discretizes the problem domain by using separately generated but overlapping unstructured grids that update and exchange boundary information through interpolation. However, such computations are complicated and time consuming. Parallel computing offers a very effective way to improve the productivity in doing computational fluid dynamics (CFD). Therefore the purpose of this study is to develop an efficient parallel computation algorithm for analyzing the flowfield of complex geometries using overset grids method. The strategy adopted in the parallelization of the overset grids method including the use of data structures and communication, is described. Numerical results are presented to demonstrate the efficiency of the resulting parallel overset grids method. (author)

  16. Detailed Aerodynamic Analysis of a Shrouded Tail Rotor Using an Unstructured Mesh Flow Solver

    Science.gov (United States)

    Lee, Hee Dong; Kwon, Oh Joon

    The detailed aerodynamics of a shrouded tail rotor in hover has been numerically studied using a parallel inviscid flow solver on unstructured meshes. The numerical method is based on a cell-centered finite-volume discretization and an implicit Gauss-Seidel time integration. The calculation was made for a single blade by imposing a periodic boundary condition between adjacent rotor blades. The grid periodicity was also imposed at the periodic boundary planes to avoid numerical inaccuracy resulting from solution interpolation. The results were compared with available experimental data and those from a disk vortex theory for validation. It was found that realistic three-dimensional modeling is important for the prediction of detailed aerodynamics of shrouded rotors including the tip clearance gap flow.

  17. Parallel FE Electron-Photon Transport Analysis on 2-D Unstructured Mesh

    International Nuclear Information System (INIS)

    Drumm, C.R.; Lorenz, J.

    1999-01-01

    A novel solution method has been developed to solve the coupled electron-photon transport problem on an unstructured triangular mesh. Instead of tackling the first-order form of the linear Boltzmann equation, this approach is based on the second-order form in conjunction with the conventional multi-group discrete-ordinates approximation. The highly forward-peaked electron scattering is modeled with a multigroup Legendre expansion derived from the Goudsmit-Saunderson theory. The finite element method is used to treat the spatial dependence. The solution method is unique in that the space-direction dependence is solved simultaneously, eliminating the need for the conventional inner iterations, a method that is well suited for massively parallel computers

  18. A GPU-enabled Finite Volume solver for global magnetospheric simulations on unstructured grids

    Science.gov (United States)

    Lani, Andrea; Yalim, Mehmet Sarp; Poedts, Stefaan

    2014-10-01

    This paper describes an ideal Magnetohydrodynamics (MHD) solver for global magnetospheric simulations based on a B1 +B0 splitting approach, which has been implemented within the COOLFluiD platform and adapted to run on modern heterogeneous architectures featuring General Purpose Graphical Processing Units (GPGPUs). The code is based on a state-of-the-art Finite Volume discretization for unstructured grids and either explicit or implicit time integration, suitable for both steady and time accurate problems. Innovative object-oriented design and coding techniques mixing C++ and CUDA are discussed. Performance results of the modified code on single and multiple processors are presented and compared with those provided by the original solver.

  19. A conservative MHD scheme on unstructured Lagrangian grids for Z-pinch hydrodynamic simulations

    Science.gov (United States)

    Wu, Fuyuan; Ramis, Rafael; Li, Zhenghong

    2018-03-01

    A new algorithm to model resistive magnetohydrodynamics (MHD) in Z-pinches has been developed. Two-dimensional axisymmetric geometry with azimuthal magnetic field Bθ is considered. Discretization is carried out using unstructured meshes made up of arbitrarily connected polygons. The algorithm is fully conservative for mass, momentum, and energy. Matter energy and magnetic energy are managed separately. The diffusion of magnetic field is solved using a derivative of the Symmetric-Semi-Implicit scheme, Livne et al. (1985) [23], where unconditional stability is obtained without needing to solve large sparse systems of equations. This MHD package has been integrated into the radiation-hydrodynamics code MULTI-2D, Ramis et al. (2009) [20], that includes hydrodynamics, laser energy deposition, heat conduction, and radiation transport. This setup allows to simulate Z-pinch configurations relevant for Inertial Confinement Fusion.

  20. Cell-vertex discretization of shallow water equations on mixed unstructured meshes

    Science.gov (United States)

    Danilov, Sergey; Androsov, Alexey

    2015-04-01

    Finite-volume discretizations can be formulated on unstructured meshes composed of different polygons. A staggered cell-vertex finite-volume discretization, keeping the velocity degrees of freedom on cell centroids and scalar degrees of freedom on vertices, presents one possible choice. Its performance is analyzed on mixed meshes composed of triangles and quads. Although triangular meshes are most flexible geometrically, quads are more efficient numerically and do not support spurious inertial modes of the triangular cell-vertex discretization. Mixed meshes composed of triangles and quads combine benefits of both. In particular, triangular transitional zones can be used to join quadrilateral meshes of differing resolution, i. e., to provide smooth nesting of a fine mesh into a coarse one. Based on a set of examples involving shallow water equations it is shown that mixed meshes offer a viable approach provided some background biharmonic viscosity (or the biharmonic filter) is used to stabilize the triangular part of the mesh.

  1. A Third Order Accurate Cellwise Relaxation Implicit Discontinuous Galerkin Scheme for Unstructured Hybrid Meshes

    Directory of Open Access Journals (Sweden)

    Hiroyuki Asada

    2014-01-01

    Full Text Available A third order accurate cellwise relaxation implicit Discontinuous Galerkin (DG scheme for RANS simulations using unstructured hybrid meshes is presented. A scalar parabolic equation is first examined to clarify what is really important in construction of implicit matrix to keep its diagonal dominance for the third and fourth order cellwise relaxation implicit DG schemes. In addition, discussions are given to approximated construction of implicit matrix for reducing computational cost. Then, the third order accurate cellwise relaxation implicit DG scheme for RANS simulations is successfully developed utilizing the expertise learned in the study of solving the parabolic equation. Superior spatial accuracy of the third order accurate cellwise relaxation implicit DG scheme for RANS simulations, while retaining reasonable convergence properties, is demonstrated for typical aerospace applications.

  2. A matrix-free implicit treatment for all speed flows on unstructured grids

    International Nuclear Information System (INIS)

    Kloczko, Th.

    2006-03-01

    The aim of this research work is the development of an efficient implicit scheme for computing compressible and low-speed flows on unstructured meshes. The first part is devoted to the review and analysis of some standard block-implicit treatments for the two-dimensional Euler and Navier-Stokes equations with a view to identify the best candidate for a fair comparison with the matrix-free treatment. The second part forms the main original contribution of this research work. It describes and analyses a matrix-free treatment that can be applied to any type of flow (inviscid/viscous, low Mach/highly compressible, steady/unsteady). The third part deals with the implementation of this treatment within the CAST3M code, and the demonstration of its advantages over existing techniques for computing applications of interest for the CEA: low-Mach number steady and unsteady flows in a Tee junction for example

  3. Machine Vision for Object Detection and Profiling in an Unstructured Environment

    International Nuclear Information System (INIS)

    Kinoshita, R.A.; Walton, M.C.

    2002-01-01

    The Handling and Sorting System for 55-Gallon Drums (HANDSS-55) is a DOE project to develop an automated method for retrieving items that are not acceptable at the Waste Isolation Pilot Plant (WIPP) from 55-gallon drums of low-level waste. The HANDSS-55 is a modular system that opens drums, sorts the waste, and then repackages the remaining waste in WIPP compliant barrels. The Sorting Station module relies on a non-contact measurement system to quickly provide a 3D profile of the sorting area. It then analyses the 3D profile and a color image to determine the position and orientation of an operator selected waste item. The item is then removed from the sorting area by a robotic arm. The use of both image and profile information for object determination provides a fast, effective method of finding and retrieving selected objects in the unstructured environment of the sorting module

  4. Portable Parallel Programming for the Dynamic Load Balancing of Unstructured Grid Applications

    Science.gov (United States)

    Biswas, Rupak; Das, Sajal K.; Harvey, Daniel; Oliker, Leonid

    1999-01-01

    The ability to dynamically adapt an unstructured -rid (or mesh) is a powerful tool for solving computational problems with evolving physical features; however, an efficient parallel implementation is rather difficult, particularly from the view point of portability on various multiprocessor platforms We address this problem by developing PLUM, tin automatic anti architecture-independent framework for adaptive numerical computations in a message-passing environment. Portability is demonstrated by comparing performance on an SP2, an Origin2000, and a T3E, without any code modifications. We also present a general-purpose load balancer that utilizes symmetric broadcast networks (SBN) as the underlying communication pattern, with a goal to providing a global view of system loads across processors. Experiments on, an SP2 and an Origin2000 demonstrate the portability of our approach which achieves superb load balance at the cost of minimal extra overhead.

  5. Solution of 3D heat conduction equations using the discontinuous Galerkin method on unstructured grids

    Directory of Open Access Journals (Sweden)

    Ruslan V. Zhalnin

    2015-09-01

    Full Text Available The discontinuous Galerkin method with discontinuous basic functions which is characterized by a high order of accuracy of the obtained solution is now widely used. In this paper a new way of approximation of diffusion terms for discontinuous Galerkin method for solving diffusion-type equations is proposed. The method uses piecewise polynomials that are continuous on a macroelement surrounding the nodes in the unstructured mesh but discontinuous between the macroelements. In the proposed numerical scheme the spaced grid is used. On one grid an approximation of the unknown quantity is considered, on the other is the approximation of additional variables. Additional variables are components of the heat flux. For the numerical experiment the initial-boundary problem for three-dimensional heat conduction equation is chosen. Calculations of three-dimensional modeling problems including explosive factors show a good accuracy of offered method.

  6. A Framework for Parallel Unstructured Grid Generation for Complex Aerodynamic Simulations

    Science.gov (United States)

    Zagaris, George; Pirzadeh, Shahyar Z.; Chrisochoides, Nikos

    2009-01-01

    A framework for parallel unstructured grid generation targeting both shared memory multi-processors and distributed memory architectures is presented. The two fundamental building-blocks of the framework consist of: (1) the Advancing-Partition (AP) method used for domain decomposition and (2) the Advancing Front (AF) method used for mesh generation. Starting from the surface mesh of the computational domain, the AP method is applied recursively to generate a set of sub-domains. Next, the sub-domains are meshed in parallel using the AF method. The recursive nature of domain decomposition naturally maps to a divide-and-conquer algorithm which exhibits inherent parallelism. For the parallel implementation, the Master/Worker pattern is employed to dynamically balance the varying workloads of each task on the set of available CPUs. Performance results by this approach are presented and discussed in detail as well as future work and improvements.

  7. Rollover-free navigation for a mobile agent in an unstructured environment.

    Science.gov (United States)

    Park, Jae Byung; Lee, Jeong Hee; Lee, Beom Hee

    2006-08-01

    This paper introduces a navigation method for a teleoperated mobile agent (or robot) moving in an unstructured environment that includes unknown obstacles and uneven terrain, based on a guided-navigation algorithm (GNA) and a rollover-prevention algorithm (RPA). Although the mobile agent is primarily driven by an operator at a remote site, it reacts autonomously for avoiding collision with obstacles and for preventing rollover when it suspects/detects possible collision or rollover. The autonomous reactive motion is normally unexpected, thus there exists the inconsistency between the intended motion and the controlled motion of the agent from the operator. A force-reflection technique utilizing a force-feedback joystick is developed to manipulate this inconsistency. To verify the feasibility and effectiveness of the proposed navigation method, experiments with the Robot for Hazardous Application-Double Tracks (ROBHAZ-DT) (actual mobile agent) are successfully carried out.

  8. EMPHASIS(TM)/Nevada Unstructured FEM Implementation Version 2.1.1.

    Energy Technology Data Exchange (ETDEWEB)

    Turner, C. David; Pointon, Timothy D.; Cartwright, Keith

    2014-08-01

    EMPHASIS TM /NEVADA is the SIERRA/NEVADA toolkit implementation of portions of the EMP HASIS TM code suite. The purpose of the toolkit i m- plementation is to facilitate coupling to other physics drivers such as radi a- tion transport as well as to better manage code design, implementation, co m- plexity, and important verification and validation processes. This document describes the theory and implementation of the unstructured finite - element method solver , associated algorithms, and selected verification and valid a- tion . Acknowledgement The author would like to recognize all of the ALEGRA team members for their gracious and willing support through this initial Nevada toolkit - implementation process. Although much of the knowledge needed was gleaned from document a- tion and code context, they were always willing to consult personally on some of the less obvious issues and enhancements necessary.

  9. Riding Bare-Back on unstructured meshes for 21. century criticality calculations - 244

    International Nuclear Information System (INIS)

    Kelley, K.C.; Martz, R.L.; Crane, D.L.

    2010-01-01

    MCNP has a new capability that permits tracking of neutrons and photons on an unstructured mesh which is embedded as a mesh universe within its legacy geometry capability. The mesh geometry is created through Abaqus/CAE using its solid modeling capabilities. Transport results are calculated for mesh elements through a path length estimator while element to element tracking is performed on the mesh. The results from MCNP can be exported to Abaqus/CAE for visualization or other-physics analysis. The simple Godiva criticality benchmark problem was tested with this new mesh capability. Computer run time is proportional to the number of mesh elements used. Both first and second order polyhedrons are used. Models that used second order polyhedrons produced slightly better results without significantly increasing computer run time. Models that used first order hexahedrons had shorter runtimes than models that used first order tetrahedrons. (authors)

  10. Matrix equation decomposition and parallel solution of systems resulting from unstructured finite element problems in electromagnetics

    Energy Technology Data Exchange (ETDEWEB)

    Cwik, T. [California Institute of Technology, Pasadena, CA (United States); Katz, D.S. [Cray Research, El Segundo, CA (United States)

    1996-12-31

    Finite element modeling has proven useful for accurately simulating scattered or radiated electromagnetic fields from complex three-dimensional objects whose geometry varies on the scale of a fraction of an electrical wavelength. An unstructured finite element model of realistic objects leads to a large, sparse, system of equations that needs to be solved efficiently with regard to machine memory and execution time. Both factorization and iterative solvers can be used to produce solutions to these systems of equations. Factorization leads to high memory requirements that limit the electrical problem size of three-dimensional objects that can be modeled. An iterative solver can be used to efficiently solve the system without excessive memory use and in a minimal amount of time if the convergence rate is controlled.

  11. An Evolutionarily Conserved Mechanism for Intrinsic and Transferable Polymyxin Resistance.

    Science.gov (United States)

    Xu, Yongchang; Wei, Wenhui; Lei, Sheng; Lin, Jingxia; Srinivas, Swaminath; Feng, Youjun

    2018-04-10

    Polymyxins, a family of cationic antimicrobial cyclic peptides, act as a last line of defense against severe infections by Gram-negative pathogens with carbapenem resistance. In addition to the intrinsic resistance to polymyxin E (colistin) conferred by Neisseria eptA , the plasmid-borne mobilized colistin resistance gene mcr-1 has been disseminated globally since the first discovery in Southern China, in late 2015. However, the molecular mechanisms for both intrinsic and transferable resistance to colistin remain largely unknown. Here, we aim to address this gap in the knowledge of these proteins. Structural and functional analyses of EptA and MCR-1 and -2 have defined a conserved 12-residue cavity that is required for the entry of the lipid substrate, phosphatidylethanolamine (PE). The in vitro and in vivo data together have allowed us to visualize the similarities in catalytic activity shared by EptA and MCR-1 and -2. The expression of either EptA or MCR-1 or -2 is shown to remodel the surface of enteric bacteria (e.g., Escherichia coli , Salmonella enterica , Klebsiella pneumoniae , etc.), rendering them resistant to colistin. The parallels in the PE substrate-binding cavities among EptA, MCR-1, and MCR-2 provide a comprehensive understanding of both intrinsic and transferable colistin resistance. Domain swapping between EptA and MCR-1 and -2 reveals that the two domains (transmembrane [TM] region and p hospho e thanol a mine [PEA] transferase) are not functionally exchangeable. Taken together, the results represent a common mechanism for intrinsic and transferable PEA resistance to polymyxin, a last-resort antibiotic against multidrug-resistant pathogens. IMPORTANCE EptA and MCR-1 and -2 remodel the outer membrane, rendering bacteria resistant to colistin, a final resort against carbapenem-resistant pathogens. Structural and functional analyses of EptA and MCR-1 and -2 reveal parallel PE lipid substrate-recognizing cavities, which explains intrinsic and

  12. An Arbitrary Lagrangian-Eulerian Discretization of MHD on 3D Unstructured Grids

    Energy Technology Data Exchange (ETDEWEB)

    Rieben, R N; White, D A; Wallin, B K; Solberg, J M

    2006-06-12

    We present an arbitrary Lagrangian-Eulerian (ALE) discretization of the equations of resistive magnetohydrodynamics (MHD) on unstructured hexahedral grids. The method is formulated using an operator-split approach with three distinct phases: electromagnetic diffusion, Lagrangian motion, and Eulerian advection. The resistive magnetic dynamo equation is discretized using a compatible mixed finite element method with a 2nd order accurate implicit time differencing scheme which preserves the divergence-free nature of the magnetic field. At each discrete time step, electromagnetic force and heat terms are calculated and coupled to the hydrodynamic equations to compute the Lagrangian motion of the conducting materials. By virtue of the compatible discretization method used, the invariants of Lagrangian MHD motion are preserved in a discrete sense. When the Lagrangian motion of the mesh causes significant distortion, that distortion is corrected with a relaxation of the mesh, followed by a 2nd order monotonic remap of the electromagnetic state variables. The remap is equivalent to Eulerian advection of the magnetic flux density with a fictitious mesh relaxation velocity. The magnetic advection is performed using a novel variant of constrained transport (CT) that is valid for unstructured hexahedral grids with arbitrary mesh velocities. The advection method maintains the divergence free nature of the magnetic field and is second order accurate in regions where the solution is sufficiently smooth. For regions in which the magnetic field is discontinuous (e.g. MHD shocks) the method is limited using a novel variant of algebraic flux correction (AFC) which is local extremum diminishing (LED) and divergence preserving. Finally, we verify each stage of the discretization via a set of numerical experiments.

  13. Counting Cats: Spatially Explicit Population Estimates of Cheetah (Acinonyx jubatus) Using Unstructured Sampling Data.

    Science.gov (United States)

    Broekhuis, Femke; Gopalaswamy, Arjun M

    2016-01-01

    Many ecological theories and species conservation programmes rely on accurate estimates of population density. Accurate density estimation, especially for species facing rapid declines, requires the application of rigorous field and analytical methods. However, obtaining accurate density estimates of carnivores can be challenging as carnivores naturally exist at relatively low densities and are often elusive and wide-ranging. In this study, we employ an unstructured spatial sampling field design along with a Bayesian sex-specific spatially explicit capture-recapture (SECR) analysis, to provide the first rigorous population density estimates of cheetahs (Acinonyx jubatus) in the Maasai Mara, Kenya. We estimate adult cheetah density to be between 1.28 ± 0.315 and 1.34 ± 0.337 individuals/100km2 across four candidate models specified in our analysis. Our spatially explicit approach revealed 'hotspots' of cheetah density, highlighting that cheetah are distributed heterogeneously across the landscape. The SECR models incorporated a movement range parameter which indicated that male cheetah moved four times as much as females, possibly because female movement was restricted by their reproductive status and/or the spatial distribution of prey. We show that SECR can be used for spatially unstructured data to successfully characterise the spatial distribution of a low density species and also estimate population density when sample size is small. Our sampling and modelling framework will help determine spatial and temporal variation in cheetah densities, providing a foundation for their conservation and management. Based on our results we encourage other researchers to adopt a similar approach in estimating densities of individually recognisable species.

  14. Counting Cats: Spatially Explicit Population Estimates of Cheetah (Acinonyx jubatus Using Unstructured Sampling Data.

    Directory of Open Access Journals (Sweden)

    Femke Broekhuis

    Full Text Available Many ecological theories and species conservation programmes rely on accurate estimates of population density. Accurate density estimation, especially for species facing rapid declines, requires the application of rigorous field and analytical methods. However, obtaining accurate density estimates of carnivores can be challenging as carnivores naturally exist at relatively low densities and are often elusive and wide-ranging. In this study, we employ an unstructured spatial sampling field design along with a Bayesian sex-specific spatially explicit capture-recapture (SECR analysis, to provide the first rigorous population density estimates of cheetahs (Acinonyx jubatus in the Maasai Mara, Kenya. We estimate adult cheetah density to be between 1.28 ± 0.315 and 1.34 ± 0.337 individuals/100km2 across four candidate models specified in our analysis. Our spatially explicit approach revealed 'hotspots' of cheetah density, highlighting that cheetah are distributed heterogeneously across the landscape. The SECR models incorporated a movement range parameter which indicated that male cheetah moved four times as much as females, possibly because female movement was restricted by their reproductive status and/or the spatial distribution of prey. We show that SECR can be used for spatially unstructured data to successfully characterise the spatial distribution of a low density species and also estimate population density when sample size is small. Our sampling and modelling framework will help determine spatial and temporal variation in cheetah densities, providing a foundation for their conservation and management. Based on our results we encourage other researchers to adopt a similar approach in estimating densities of individually recognisable species.

  15. An unstructured-mesh finite-volume MPDATA for compressible atmospheric dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Kühnlein, Christian, E-mail: christian.kuehnlein@ecmwf.int; Smolarkiewicz, Piotr K., E-mail: piotr.smolarkiewicz@ecmwf.int

    2017-04-01

    An advancement of the unstructured-mesh finite-volume MPDATA (Multidimensional Positive Definite Advection Transport Algorithm) is presented that formulates the error-compensative pseudo-velocity of the scheme to rely only on face-normal advective fluxes to the dual cells, in contrast to the full vector employed in previous implementations. This is essentially achieved by expressing the temporal truncation error underlying the pseudo-velocity in a form consistent with the flux-divergence of the governing conservation law. The development is especially important for integrating fluid dynamics equations on non-rectilinear meshes whenever face-normal advective mass fluxes are employed for transport compatible with mass continuity—the latter being essential for flux-form schemes. In particular, the proposed formulation enables large-time-step semi-implicit finite-volume integration of the compressible Euler equations using MPDATA on arbitrary hybrid computational meshes. Furthermore, it facilitates multiple error-compensative iterations of the finite-volume MPDATA and improved overall accuracy. The advancement combines straightforwardly with earlier developments, such as the nonoscillatory option, the infinite-gauge variant, and moving curvilinear meshes. A comprehensive description of the scheme is provided for a hybrid horizontally-unstructured vertically-structured computational mesh for efficient global atmospheric flow modelling. The proposed finite-volume MPDATA is verified using selected 3D global atmospheric benchmark simulations, representative of hydrostatic and non-hydrostatic flow regimes. Besides the added capabilities, the scheme retains fully the efficacy of established finite-volume MPDATA formulations.

  16. Three-dimensional tsunami propagation simulations using an unstructured mesh finite element model

    Science.gov (United States)

    Oishi, Yusuke; Piggott, Matthew D.; Maeda, Takuto; Kramer, Stephan C.; Collins, Gareth S.; Tsushima, Hiroaki; Furumura, Takashi

    2013-06-01

    Large-scale tsunami propagation simulations from the fault region to the coast are conducted using a three-dimensional (3-D) parallel unstructured mesh finite element code (Fluidity-ICOM). Unlike conventional 2-D approximation models, our tsunami model solves the full 3-D incompressible Navier-Stokes (NS) equations. The model is tested against analytical solutions to simple dispersive wave propagation problems. Comparisons of our 3-D NS model results with those from linear shallow water and linear dispersive wave models demonstrate that the 3-D NS model simulates the dispersion of very short wavelength components more accurately than the 2-D models. This improved accuracy is achieved using only a small number (three to five) of vertical layers in the mesh. The numerical error in the wave velocity compared with the linear wave theory is less than 3% up to kH = 40, where k is the wave number and H is the sea depth. The same 2-D and 3-D models are also used to simulate two earthquake-generated tsunamis off the coast of Japan: the 2004 off Kii peninsula and the 2011 off Tohoku tsunamis. The linear dispersive and NS models showed good agreement in the leading waves but differed especially in their near-source, short wavelength dispersive wave components. This is consistent with the results from earlier tests, suggesting that the 3-D NS simulations are more accurate. The computational performance on a parallel computer showed good scalability up to 512 cores. By using a combination of unstructured meshes and high-performance computers, highly accurate 3-D tsunami simulations can be conducted in a practical timescale.

  17. Parallel CFD Algorithms for Aerodynamical Flow Solvers on Unstructured Meshes. Parts 1 and 2

    Science.gov (United States)

    Barth, Timothy J.; Kwak, Dochan (Technical Monitor)

    1995-01-01

    The Advisory Group for Aerospace Research and Development (AGARD) has requested my participation in the lecture series entitled Parallel Computing in Computational Fluid Dynamics to be held at the von Karman Institute in Brussels, Belgium on May 15-19, 1995. In addition, a request has been made from the US Coordinator for AGARD at the Pentagon for NASA Ames to hold a repetition of the lecture series on October 16-20, 1995. I have been asked to be a local coordinator for the Ames event. All AGARD lecture series events have attendance limited to NATO allied countries. A brief of the lecture series is provided in the attached enclosure. Specifically, I have been asked to give two lectures of approximately 75 minutes each on the subject of parallel solution techniques for the fluid flow equations on unstructured meshes. The title of my lectures is "Parallel CFD Algorithms for Aerodynamical Flow Solvers on Unstructured Meshes" (Parts I-II). The contents of these lectures will be largely review in nature and will draw upon previously published work in this area. Topics of my lectures will include: (1) Mesh partitioning algorithms. Recursive techniques based on coordinate bisection, Cuthill-McKee level structures, and spectral bisection. (2) Newton's method for large scale CFD problems. Size and complexity estimates for Newton's method, modifications for insuring global convergence. (3) Techniques for constructing the Jacobian matrix. Analytic and numerical techniques for Jacobian matrix-vector products, constructing the transposed matrix, extensions to optimization and homotopy theories. (4) Iterative solution algorithms. Practical experience with GIVIRES and BICG-STAB matrix solvers. (5) Parallel matrix preconditioning. Incomplete Lower-Upper (ILU) factorization, domain-decomposed ILU, approximate Schur complement strategies.

  18. JIGSAW-GEO (1.0): locally orthogonal staggered unstructured grid generation for general circulation modelling on the sphere

    Science.gov (United States)

    Engwirda, Darren

    2017-06-01

    An algorithm for the generation of non-uniform, locally orthogonal staggered unstructured spheroidal grids is described. This technique is designed to generate very high-quality staggered Voronoi-Delaunay meshes appropriate for general circulation modelling on the sphere, including applications to atmospheric simulation, ocean-modelling and numerical weather prediction. Using a recently developed Frontal-Delaunay refinement technique, a method for the construction of high-quality unstructured spheroidal Delaunay triangulations is introduced. A locally orthogonal polygonal grid, derived from the associated Voronoi diagram, is computed as the staggered dual. It is shown that use of the Frontal-Delaunay refinement technique allows for the generation of very high-quality unstructured triangulations, satisfying a priori bounds on element size and shape. Grid quality is further improved through the application of hill-climbing-type optimisation techniques. Overall, the algorithm is shown to produce grids with very high element quality and smooth grading characteristics, while imposing relatively low computational expense. A selection of uniform and non-uniform spheroidal grids appropriate for high-resolution, multi-scale general circulation modelling are presented. These grids are shown to satisfy the geometric constraints associated with contemporary unstructured C-grid-type finite-volume models, including the Model for Prediction Across Scales (MPAS-O). The use of user-defined mesh-spacing functions to generate smoothly graded, non-uniform grids for multi-resolution-type studies is discussed in detail.

  19. An Automated Approach to the Generation of Structured Building Information Models from Unstructured 3d Point Cloud Scans

    DEFF Research Database (Denmark)

    Tamke, Martin; Evers, Henrik Leander; Wessel, Raoul

    2016-01-01

    In this paper we present and evaluate an approach for the automatic generation of building models in IFC BIM format from unstructured Point Cloud scans, as they result from 3dlaser scans of buildings. While the actual measurement process is relatively fast, 85% of the overall time are spend on th...

  20. Thermal Protection System Cavity Heating for Simplified and Actual Geometries Using Computational Fluid Dynamics Simulations with Unstructured Grids

    Science.gov (United States)

    McCloud, Peter L.

    2010-01-01

    Thermal Protection System (TPS) Cavity Heating is predicted using Computational Fluid Dynamics (CFD) on unstructured grids for both simplified cavities and actual cavity geometries. Validation was performed using comparisons to wind tunnel experimental results and CFD predictions using structured grids. Full-scale predictions were made for simplified and actual geometry configurations on the Space Shuttle Orbiter in a mission support timeframe.

  1. A superlinearly convergent finite volume method for the incompressible Navier-Stokes equations on staggered unstructured grids

    International Nuclear Information System (INIS)

    Vidovic, D.; Segal, A.; Wesseling, P.

    2004-01-01

    A method for linear reconstruction of staggered vector fields with special treatment of the divergence is presented. An upwind-biased finite volume scheme for solving the unsteady incompressible Navier-Stokes equations on staggered unstructured triangular grids that uses this reconstruction is described. The scheme is applied to three benchmark problems and is found to be superlinearly convergent in space

  2. A numerical formulation using unstructured grids for modeling two-phase flows in porous media considering heterogeneities and capillarity effects

    International Nuclear Information System (INIS)

    Hurtado, F.S.V.; Maliska, C.R.

    2005-01-01

    This paper briefly describes a two-dimensional numerical formulation using unstructured grids, developed for simulating two-phase immiscible displacements in porous media. The Element-based Finite Volume Method (EbFVM) is used for discretizing the model differential equations. (authors)

  3. A numerical formulation using unstructured grids for modeling two-phase flows in porous media considering heterogeneities and capillarity effects

    Energy Technology Data Exchange (ETDEWEB)

    Hurtado, F.S.V.; Maliska, C.R. [Santa Catarina Federal Univ., Computational Fluid Dynamics Lab., Mechanical Engineering Dept., Florianopolis, SC (Brazil)

    2005-07-01

    This paper briefly describes a two-dimensional numerical formulation using unstructured grids, developed for simulating two-phase immiscible displacements in porous media. The Element-based Finite Volume Method (EbFVM) is used for discretizing the model differential equations. (authors)

  4. Simulating drainage and imbibition experiments in a high-porosity micromodel using an unstructured pore network model

    NARCIS (Netherlands)

    Joekar Niasar, V.; Hassanizadeh, S.M.; Pyrak-Nolte, L.J.; Berentsen, C.W.J.

    2009-01-01

    Development of pore network models based on detailed topological data of the pore space is essential for predicting multiphase flow in porous media. In this work, an unstructured pore network model has been developed to simulate a set of drainage and imbibition laboratory experiments performed on a

  5. Unstructured socialization and territorialization. A street-ethnographic take on urban youth in a medium-sized town in Denmark

    DEFF Research Database (Denmark)

    Gravesen, David Thore; Frostholm, Peter Hornbæk

    Abstract / Journal of youth studies Conference 2015 Peter Frostholm Olesen & David Thore Gravesen Unstructured socialization and territorialization. A street-ethnographic take on urban youth in a medium-sized town in Denmark. In 2013, the municipality in Horsens, a medium-sized provincial town in...... and negotiate the facilities, and to what extend the urban site plays a role in the way the adolescents create, cultivate and maintain their cultural everyday life and social relationships. Key-words: Urban youth, place, space, unstructured socialization, peer culture......Abstract / Journal of youth studies Conference 2015 Peter Frostholm Olesen & David Thore Gravesen Unstructured socialization and territorialization. A street-ethnographic take on urban youth in a medium-sized town in Denmark. In 2013, the municipality in Horsens, a medium-sized provincial town...... and sense of belonging to certain districts of the city. Through positioning battles of various kinds the groups fight for space and place for their unstructured socialization processes with their peers. Officially, the municipality donated the facility to give local children and young people an opportunity...

  6. In Search of the Neural Circuits of Intrinsic Motivation

    Science.gov (United States)

    Kaplan, Frederic; Oudeyer, Pierre-Yves

    2007-01-01

    Children seem to acquire new know-how in a continuous and open-ended manner. In this paper, we hypothesize that an intrinsic motivation to progress in learning is at the origins of the remarkable structure of children's developmental trajectories. In this view, children engage in exploratory and playful activities for their own sake, not as steps toward other extrinsic goals. The central hypothesis of this paper is that intrinsically motivating activities correspond to expected decrease in prediction error. This motivation system pushes the infant to avoid both predictable and unpredictable situations in order to focus on the ones that are expected to maximize progress in learning. Based on a computational model and a series of robotic experiments, we show how this principle can lead to organized sequences of behavior of increasing complexity characteristic of several behavioral and developmental patterns observed in humans. We then discuss the putative circuitry underlying such an intrinsic motivation system in the brain and formulate two novel hypotheses. The first one is that tonic dopamine acts as a learning progress signal. The second is that this progress signal is directly computed through a hierarchy of microcortical circuits that act both as prediction and metaprediction systems. PMID:18982131

  7. In search of the neural circuits of intrinsic motivation

    Directory of Open Access Journals (Sweden)

    Frederic Kaplan

    2007-10-01

    Full Text Available Children seem to acquire new know-how in a continuous and open-ended manner. In this paper, we hypothesize that an intrinsic motivation to progress in learning is at the origins of the remarkable structure of children's developmental trajectories. In this view, children engage in exploratory and playful activities for their own sake, not as steps toward other extrinsic goals. The central hypothesis of this paper is that intrinsically motivating activities correspond to expected decrease in prediction error. This motivation system pushes the infant to avoid both predictable and unpredictable situations in order to focus on the ones that are expected to maximize progress in learning. Based on a computational model and a series of robotic experiments, we show how this principle can lead to organized sequences of behavior of increasing complexity characteristic of several behavioral and developmental patterns observed in humans. We then discuss the putative circuitry underlying such an intrinsic motivation system in the brain and formulate two novel hypotheses. The first one is that tonic dopamine acts as a learning progress signal. The second is that this progress signal is directly computed through a hierarchy of microcortical circuits that act both as prediction and metaprediction systems.

  8. Effects of Different Ways of Introducing a Reading Task on Intrinsic Motivation and Comprehension

    Science.gov (United States)

    Bråten, Ivar; Johansen, Roy-Petter; Strømsø, Helge I.

    2017-01-01

    This study compared the effects of two brief prereading instructional practices--hands-on activities and prior knowledge activation--on sixth-graders' intrinsic motivation for reading a text and reading comprehension. Both hands-on activities and prior knowledge activation substantially improved reading comprehension relative to a control…

  9. Functions of intrinsic disorder in transmembrane proteins

    DEFF Research Database (Denmark)

    Kjaergaard, Magnus; Kragelund, Birthe B.

    2017-01-01

    mechanisms. (3) Trafficking of membrane proteins. (4) Transient membrane associations. (5) Post-translational modifications most notably phosphorylation and (6) disorder-linked isoform dependent function. We finish the review by discussing the future challenges facing the membrane protein community regarding......Intrinsic disorder is common in integral membrane proteins, particularly in the intracellular domains. Despite this observation, these domains are not always recognized as being disordered. In this review, we will discuss the biological functions of intrinsically disordered regions of membrane...... proteins, and address why the flexibility afforded by disorder is mechanistically important. Intrinsically disordered regions are present in many common classes of membrane proteins including ion channels and transporters; G-protein coupled receptors (GPCRs), receptor tyrosine kinases and cytokine...

  10. Management Control, Intrinsic Motivation and Creativity

    DEFF Research Database (Denmark)

    Godt Gregersen, Mikkel

    of the conclusion is that intrinsic motivation and management control can coexist under the conditions that all three basic needs, i.e. autonomy, competence and relatedness, are supported. This can happen when control takes point of departure in the individual employee. The second part of the conclusion......This thesis consists of a cape and three papers. The overall research question is: How can intrinsic motivation and management control coexist in a creative environment and how can coordination be possible in such a context? The cape ties together the research done in the three papers....... It is divided into six sections. The first section introduces the concepts of intrinsic motivation, creativity and management control. This is followed by a section on management control in a creative context. These two sections frame the thesis and introduce the setting in which the research has been done...

  11. Insulin aggregation tracked by its intrinsic TRES

    Science.gov (United States)

    Chung, Li Hung C.; Birch, David J. S.; Vyshemirsky, Vladislav; Ryadnov, Maxim G.; Rolinski, Olaf J.

    2017-12-01

    Time-resolved emission spectra (TRES) have been used to detect conformational changes of intrinsic tyrosines within bovine insulin at a physiological pH. The approach offers the ability to detect the initial stages of insulin aggregation at the molecular level. The data analysis has revealed the existence of at least three fluorescent species undergoing dielectric relaxation and significant spectral changes due to insulin aggregation. The results indicate the suitability of the intrinsic TRES approach for insulin studies and for monitoring its stability during storage and aggregation in insulin delivery devices.

  12. Intrinsic viscosity of a suspension of cubes

    KAUST Repository

    Mallavajula, Rajesh K.

    2013-11-06

    We report on the viscosity of a dilute suspension of cube-shaped particles. Irrespective of the particle size, size distribution, and surface chemistry, we find empirically that cubes manifest an intrinsic viscosity [η]=3.1±0.2, which is substantially higher than the well-known value for spheres, [η]=2.5. The orientation-dependent intrinsic viscosity of cubic particles is determined theoretically using a finite-element solution of the Stokes equations. For isotropically oriented cubes, these calculations show [η]=3.1, in excellent agreement with our experimental observations. © 2013 American Physical Society.

  13. Intrinsic entropy perturbations from the dark sector

    Science.gov (United States)

    Celoria, Marco; Comelli, Denis; Pilo, Luigi

    2018-03-01

    Perfect fluids are modeled by using an effective field theory approach which naturally gives a self-consistent and unambiguous description of the intrinsic non-adiabatic contribution to pressure variations. We study the impact of intrinsic entropy perturbation on the superhorizon dynamics of the curvature perturbation Script R in the dark sector. The dark sector, made of dark matter and dark energy is described as a single perfect fluid. The non-perturbative vorticity's dynamics and the Weinberg theorem violation for perfect fluids are also studied.

  14. A model of intrinsic symmetry breaking

    International Nuclear Information System (INIS)

    Ge, Li; Li, Sheng; George, Thomas F.; Sun, Xin

    2013-01-01

    Different from the symmetry breaking associated with a phase transition, which occurs when the controlling parameter is manipulated across a critical point, the symmetry breaking presented in this Letter does not need parameter manipulation. Instead, the system itself suddenly undergoes symmetry breaking at a certain time during its evolution, which is intrinsic symmetry breaking. Through a polymer model, it is revealed that the origin of the intrinsic symmetry breaking is nonlinearity, which produces instability at the instance when the evolution crosses an inflexion point, where this instability breaks the original symmetry

  15. Psychological need satisfaction, intrinsic motivation and affective response to exercise in adolescents

    Science.gov (United States)

    Schneider, Margaret L.; Kwan, Bethany M.

    2013-01-01

    Objectives To further understanding of the factors influencing adolescents’ motivations for physical activity, the relationship of variables derived from Self-Determination Theory to adolescents’ affective response to exercise was examined. Design Correlational. Method Adolescents (N = 182) self-reported psychological needs satisfaction (perceived competence, relatedness, and autonomy) and intrinsic motivation related to exercise. In two clinic visits, adolescents reported their affect before, during, and after a moderate-intensity and a hard-intensity exercise task. Results Affective response to exercise and psychological needs satisfaction independently contributed to the prediction of intrinsic motivation in hierarchical linear regression models. The association between affective response to exercise and intrinsic motivation was partially mediated by psychological needs satisfaction. Conclusions Intrinsic motivation for exercise among adolescents may be enhanced when the environment supports perceived competence, relatedness, and autonomy, and when adolescents participate in activities that they find enjoyable. PMID:24015110

  16. Psychological need satisfaction, intrinsic motivation and affective response to exercise in adolescents.

    Science.gov (United States)

    Schneider, Margaret L; Kwan, Bethany M

    2013-09-01

    To further understanding of the factors influencing adolescents' motivations for physical activity, the relationship of variables derived from Self-Determination Theory to adolescents' affective response to exercise was examined. Correlational. Adolescents ( N = 182) self-reported psychological needs satisfaction (perceived competence, relatedness, and autonomy) and intrinsic motivation related to exercise. In two clinic visits, adolescents reported their affect before, during, and after a moderate-intensity and a hard-intensity exercise task. Affective response to exercise and psychological needs satisfaction independently contributed to the prediction of intrinsic motivation in hierarchical linear regression models. The association between affective response to exercise and intrinsic motivation was partially mediated by psychological needs satisfaction. Intrinsic motivation for exercise among adolescents may be enhanced when the environment supports perceived competence, relatedness, and autonomy, and when adolescents participate in activities that they find enjoyable.

  17. Intrinsic connectivity networks within cerebellum and beyond in eating disorders.

    Science.gov (United States)

    Amianto, F; D'Agata, F; Lavagnino, L; Caroppo, P; Abbate-Daga, G; Righi, D; Scarone, S; Bergui, M; Mortara, P; Fassino, S

    2013-10-01

    Cerebellum seems to have a role both in feeding behavior and emotion regulation; therefore, it is a region that warrants further neuroimaging studies in eating disorders, severe conditions that determine a significant impairment in the physical and psychological domain. The aim of this study was to examine the cerebellum intrinsic connectivity during functional magnetic resonance imaging resting state in anorexia nervosa (AN), bulimia nervosa (BN), and healthy controls (CN). Resting state brain activity was decomposed into intrinsic connectivity networks (ICNs) using group spatial independent component analysis on the resting blood oxygenation level dependent time courses of 12 AN, 12 BN, and 10 CN. We extracted the cerebellar ICN and compared it between groups. Intrinsic connectivity within the cerebellar network showed some common alterations in eating disordered compared to healthy subjects (e.g., a greater connectivity with insulae, vermis, and paravermis and a lesser connectivity with parietal lobe); AN and BN patients were characterized by some peculiar alterations in connectivity patterns (e.g., greater connectivity with the insulae in AN compared to BN, greater connectivity with anterior cingulate cortex in BN compared to AN). Our data are consistent with the presence of different alterations in the cerebellar network in AN and BN patients that could be related to psychopathologic dimensions of eating disorders.

  18. Comparing Intrinsic Connectivity Models for the Primary Auditory Cortices

    Science.gov (United States)

    Hamid, Khairiah Abdul; Yusoff, Ahmad Nazlim; Mohamad, Mazlyfarina; Hamid, Aini Ismafairus Abd; Manan, Hanani Abd

    2010-07-01

    This fMRI study is about modeling the intrinsic connectivity between Heschl' gyrus (HG) and superior temporal gyrus (STG) in human primary auditory cortices. Ten healthy male subjects participated and required to listen to white noise stimulus during the fMRI scans. Two intrinsic connectivity models comprising bilateral HG and STG were constructed using statistical parametric mapping (SPM) and dynamic causal modeling (DCM). Group Bayes factor (GBF), positive evidence ratio (PER) and Bayesian model selection (BMS) for group studies were used in model comparison. Group results indicated significant bilateral asymmetrical activation (puncorr < 0.001) in HG and STG. Comparison results showed strong evidence of Model 2 as the preferred model (STG as the input center) with GBF value of 5.77 × 1073 The model is preferred by 6 out of 10 subjects. The results were supported by BMS results for group studies. One-sample t-test on connection values obtained from Model 2 indicates unidirectional parallel connections from STG to bilateral HG (p<0.05). Model 2 was determined to be the most probable intrinsic connectivity model between bilateral HG and STG when listening to white noise.

  19. Stochastic synchronization of neuronal populations with intrinsic and extrinsic noise.

    KAUST Repository

    Bressloff, Paul C

    2011-05-03

    We extend the theory of noise-induced phase synchronization to the case of a neural master equation describing the stochastic dynamics of an ensemble of uncoupled neuronal population oscillators with intrinsic and extrinsic noise. The master equation formulation of stochastic neurodynamics represents the state of each population by the number of currently active neurons, and the state transitions are chosen so that deterministic Wilson-Cowan rate equations are recovered in the mean-field limit. We apply phase reduction and averaging methods to a corresponding Langevin approximation of the master equation in order to determine how intrinsic noise disrupts synchronization of the population oscillators driven by a common extrinsic noise source. We illustrate our analysis by considering one of the simplest networks known to generate limit cycle oscillations at the population level, namely, a pair of mutually coupled excitatory (E) and inhibitory (I) subpopulations. We show how the combination of intrinsic independent noise and extrinsic common noise can lead to clustering of the population oscillators due to the multiplicative nature of both noise sources under the Langevin approximation. Finally, we show how a similar analysis can be carried out for another simple population model that exhibits limit cycle oscillations in the deterministic limit, namely, a recurrent excitatory network with synaptic depression; inclusion of synaptic depression into the neural master equation now generates a stochastic hybrid system.

  20. Logarithmic distributions prove that intrinsic learning is Hebbian.

    Science.gov (United States)

    Scheler, Gabriele

    2017-01-01

    In this paper, we present data for the lognormal distributions of spike rates, synaptic weights and intrinsic excitability (gain) for neurons in various brain areas, such as auditory or visual cortex, hippocampus, cerebellum, striatum, midbrain nuclei. We find a remarkable consistency of heavy-tailed, specifically lognormal, distributions for rates, weights and gains in all brain areas examined. The difference between strongly recurrent and feed-forward connectivity (cortex vs. striatum and cerebellum), neurotransmitter (GABA (striatum) or glutamate (cortex)) or the level of activation (low in cortex, high in Purkinje cells and midbrain nuclei) turns out to be irrelevant for this feature. Logarithmic scale distribution of weights and gains appears to be a general, functional property in all cases analyzed. We then created a generic neural model to investigate adaptive learning rules that create and maintain lognormal distributions. We conclusively demonstrate that not only weights, but also intrinsic gains, need to have strong Hebbian learning in order to produce and maintain the experimentally attested distributions. This provides a solution to the long-standing question about the type of plasticity exhibited by intrinsic excitability.

  1. AICHA: An atlas of intrinsic connectivity of homotopic areas.

    Science.gov (United States)

    Joliot, Marc; Jobard, Gaël; Naveau, Mikaël; Delcroix, Nicolas; Petit, Laurent; Zago, Laure; Crivello, Fabrice; Mellet, Emmanuel; Mazoyer, Bernard; Tzourio-Mazoyer, Nathalie

    2015-10-30

    Atlases of brain anatomical ROIs are widely used for functional MRI data analysis. Recently, it was proposed that an atlas of ROIs derived from a functional brain parcellation could be advantageous, in particular for understanding how different regions share information. However, functional atlases so far proposed do not account for a crucial aspect of cerebral organization, namely homotopy, i.e. that each region in one hemisphere has a homologue in the other hemisphere. We present AICHA (for Atlas of Intrinsic Connectivity of Homotopic Areas), a functional brain ROIs atlas based on resting-state fMRI data acquired in 281 individuals. AICHA ROIs cover the whole cerebrum, each having 1-homogeneity of its constituting voxels intrinsic activity, and 2-a unique homotopic contralateral counterpart with which it has maximal intrinsic connectivity. AICHA was built in 4 steps: (1) estimation of resting-state networks (RSNs) using individual resting-state fMRI independent components, (2) k-means clustering of voxel-wise group level profiles of connectivity, (3) homotopic regional grouping based on maximal inter-hemispheric functional correlation, and (4) ROI labeling. AICHA includes 192 homotopic region pairs (122 gyral, 50 sulcal, and 20 gray nuclei). As an application, we report inter-hemispheric (homotopic and heterotopic) and intra-hemispheric connectivity patterns at different sparsities. ROI functional homogeneity was higher for AICHA than for anatomical ROI atlases, but slightly lower than for another functional ROI atlas not accounting for homotopy. AICHA is ideally suited for intrinsic/effective connectivity analyses, as well as for investigating brain hemispheric specialization. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. The Intrinsic Far-infrared Continua of Type-1 Quasars

    Energy Technology Data Exchange (ETDEWEB)

    Lyu, Jianwei; Rieke, George H., E-mail: jianwei@email.arizona.edu [Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States)

    2017-06-01

    The range of currently proposed active galactic nucleus (AGN) far-infrared templates results in uncertainties in retrieving host galaxy information from infrared observations and also undermines constraints on the outer part of the AGN torus. We discuss how to test and reconcile these templates. Physically, the fraction of the intrinsic AGN IR-processed luminosity compared with that from the central engine should be consistent with the dust-covering factor. In addition, besides reproducing the composite spectral energy distributions (SEDs) of quasars, a correct AGN IR template combined with an accurate library of star-forming galaxy templates should be able to reproduce the IR properties of the host galaxies, such as the luminosity-dependent SED shapes and aromatic feature strengths. We develop tests based on these expected behaviors and find that the shape of the AGN intrinsic far-IR emission drops off rapidly starting at ∼20 μ m and can be matched by an Elvis et al.-like template with a minor modification. Despite the variations in the near- to mid-IR bands, AGNs in quasars and Seyfert galaxies have remarkably similar intrinsic far-IR SEDs at λ ∼ 20–100 μ m, suggesting a similar emission character of the outermost region of the circumnuclear torus. The variations of the intrinsic AGN IR SEDs among the type-1 quasar population can be explained by the changing relative strengths of four major dust components with similar characteristic temperatures, and there is evidence for compact AGN-heated dusty structures at sub-kiloparsec scales in the far-IR.

  3. Frustration-induced protein intrinsic disorder.

    Science.gov (United States)

    Matsushita, Katsuyoshi; Kikuchi, Macoto

    2013-03-14

    Spontaneous folding into a specific native structure is the most important property of protein to perform their biological functions within organisms. Spontaneous folding is understood on the basis of an energy landscape picture based on the minimum frustration principle. Therefore, frustration seemingly only leads to protein functional disorder. However, frustration has recently been suggested to have a function in allosteric regulation. Functional frustration has the possibility to be a key to our deeper understanding of protein function. To explore another functional frustration, we theoretically examined structural frustration, which is designed to induce intrinsic disorder of a protein and its function through the coupled folding and binding. We extended the Wako-Saitô-Muñoz-Eaton model to take into account a frustration effect. With the model, we analyzed the binding part of neuron-restrictive silencer factor and showed that designed structural frustration in it induces intrinsic disorder. Furthermore, we showed that the folding and the binding are cooperative in interacting with a target protein. The cooperativity enables an intrinsically disordered protein to exhibit a sharp switch-like folding response to binding chemical potential change. Through this switch-like response, the structural frustration may contribute to the regulation function of interprotein interaction of the intrinsically disordered protein.

  4. Simple intrinsic defects in InAs :

    Energy Technology Data Exchange (ETDEWEB)

    Schultz, Peter Andrew

    2013-03-01

    This Report presents numerical tables summarizing properties of intrinsic defects in indium arsenide, InAs, as computed by density functional theory using semi-local density functionals, intended for use as reference tables for a defect physics package in device models.

  5. INTRINSIC AND EXTRINSIC MOTIVATION IN THE SELECTION ...

    African Journals Online (AJOL)

    A psychological perspective is considered that applies intrinsic and extrinsic motivational concepts to communication phenomena. The paper also tries to develop an analytical understanding of human communication-related behavior with respect to the two types of motives. Proposals are also put forward to communication ...

  6. Intrinsic and Extrinsic Motivation among Collegiate Instrumentalists

    Science.gov (United States)

    Diaz, Frank M.

    2010-01-01

    The purpose of this study was to gather and compare information on measures of intrinsic and extrinsic motivation among instrumentalists enrolled in collegiate ensembles. A survey instrument was developed to gather information concerning demographic data and responses to questions on motivational preference. Participants were undergraduate and…

  7. A rotational integral formula for intrinsic volumes

    DEFF Research Database (Denmark)

    Jensen, Eva Bjørn Vedel; Rataj, J.

    2008-01-01

    A rotational version of the famous Crofton formula is derived. The motivation for deriving the formula comes from local stereology, a new branch of stereology based on sections through fixed reference points. The formula shows how rotational averages of intrinsic volumes measured on sections...

  8. Original Paper Detecting Nosocomial Intrinsic Infections through ...

    African Journals Online (AJOL)

    2011-04-20

    Apr 20, 2011 ... Key Words: Bacterial pathogens, Endogenous indicators, NosocomiaI infection, Surgery. Received 30 October 2010/ Accepted 30 March 2011. INTRODUCTION. Micro-organisms from intrinsic and extrinsic sources have been known to cause nosocomial infections (CDC, 1991). The human body enables.

  9. Organisational Learning and Employees' Intrinsic Motivation

    Science.gov (United States)

    Remedios, Richard; Boreham, Nick

    2004-01-01

    This study examined the effects of organisational learning initiatives on employee motivation. Four initiatives consistent with theories of organisational learning were a priori ranked in terms of concepts that underpin intrinsic-motivation theory. Eighteen employees in a UK petrochemical company were interviewed to ascertain their experiences of…

  10. Intrinsic Motivation, Organizational Justice, and Creativity

    Science.gov (United States)

    Hannam, Kalli; Narayan, Anupama

    2015-01-01

    For employees to generate creative ideas that are not only original, but also useful to their company, they must interact with their workplace environment to determine organizational needs. Therefore, it is important to consider aspects of the individual as well as their environment when studying creativity. Intrinsic motivation, a predictor of…

  11. Discovery of Intrinsic Primitives on Triangle Meshes

    KAUST Repository

    Solomon, Justin

    2011-04-01

    The discovery of meaningful parts of a shape is required for many geometry processing applications, such as parameterization, shape correspondence, and animation. It is natural to consider primitives such as spheres, cylinders and cones as the building blocks of shapes, and thus to discover parts by fitting such primitives to a given surface. This approach, however, will break down if primitive parts have undergone almost-isometric deformations, as is the case, for example, for articulated human models. We suggest that parts can be discovered instead by finding intrinsic primitives, which we define as parts that posses an approximate intrinsic symmetry. We employ the recently-developed method of computing discrete approximate Killing vector fields (AKVFs) to discover intrinsic primitives by investigating the relationship between the AKVFs of a composite object and the AKVFs of its parts. We show how to leverage this relationship with a standard clustering method to extract k intrinsic primitives and remaining asymmetric parts of a shape for a given k. We demonstrate the value of this approach for identifying the prominent symmetry generators of the parts of a given shape. Additionally, we show how our method can be modified slightly to segment an entire surface without marking asymmetric connecting regions and compare this approach to state-of-the-art methods using the Princeton Segmentation Benchmark. © 2011 The Author(s).

  12. Effects of GABA, Neural Regulation, and Intrinsic Cardiac Factors on Heart Rate Variability in Zebrafish Larvae.

    Science.gov (United States)

    Vargas, Rafael Antonio

    2017-04-01

    Heart rate (HR) is a periodic activity that is variable over time due to intrinsic cardiac factors and extrinsic neural control, largely by the autonomic nervous system. Heart rate variability (HRV) is analyzed by measuring consecutive beat-to-beat intervals. This variability can contain information about the factors regulating cardiac activity under normal and pathological conditions, but the information obtained from such analyses is not yet fully understood. In this article, HRV in zebrafish larvae was evaluated under normal conditions and under the effect of substances that modify intrinsic cardiac activity and cardiac activity modulated by the nervous system. We found that the factors affecting intrinsic activity have negative chronotropic and arrhythmogenic effects at this stage of development, whereas neural modulatory factors have a lesser impact. The results suggest that cardiac activity largely depends on the intrinsic properties of the heart tissue in the early stages of development and, to a lesser extent, in the maturing nervous system. We also report, for the first time, the influence of the neurotransmitter gamma amino butyric acid on HRV. The results demonstrate the larval zebrafish model as a useful tool in the study of intrinsic cardiac activity and its role in heart diseases.

  13. Role of the EHD2 unstructured loop in dimerization, protein binding and subcellular localization.

    Directory of Open Access Journals (Sweden)

    Kriti Bahl

    Full Text Available The C-terminal Eps 15 Homology Domain proteins (EHD1-4 play important roles in regulating endocytic trafficking. EHD2 is the only family member whose crystal structure has been solved, and it contains an unstructured loop consisting of two proline-phenylalanine (PF motifs: KPFRKLNPF. In contrast, despite EHD2 having nearly 70% amino acid identity with its paralogs, EHD1, EHD3 and EHD4, the latter proteins contain a single KPF or RPF motif, but no NPF motif. In this study, we sought to define the precise role of each PF motif in EHD2's homo-dimerization, binding with the protein partners, and subcellular localization. To test the role of the NPF motif, we generated an EHD2 NPF-to-NAF mutant to mimic the homologous sequences of EHD1 and EHD3. We demonstrated that this mutant lost both its ability to dimerize and bind to Syndapin2. However, it continued to localize primarily to the cytosolic face of the plasma membrane. On the other hand, EHD2 NPF-to-APA mutants displayed normal dimerization and Syndapin2 binding, but exhibited markedly increased nuclear localization and reduced association with the plasma membrane. We then hypothesized that the single PF motif of EHD1 (that aligns with the KPF of EHD2 might be responsible for both binding and localization functions of EHD1. Indeed, the EHD1 RPF motif was required for dimerization, interaction with MICAL-L1 and Syndapin2, as well as localization to tubular recycling endosomes. Moreover, recycling assays demonstrated that EHD1 RPF-to-APA was incapable of supporting normal receptor recycling. Overall, our data suggest that the EHD2 NPF phenylalanine residue is crucial for EHD2 localization to the plasma membrane, whereas the proline residue is essential for EHD2 dimerization and binding. These studies support the recently proposed model in which the EHD2 N-terminal region may regulate the availability of the unstructured loop for interactions with neighboring EHD2 dimers, thus promoting

  14. Electromagnetic forward modelling for realistic Earth models using unstructured tetrahedral meshes and a meshfree approach

    Science.gov (United States)

    Farquharson, C.; Long, J.; Lu, X.; Lelievre, P. G.

    2017-12-01

    Real-life geology is complex, and so, even when allowing for the diffusive, low resolution nature of geophysical electromagnetic methods, we need Earth models that can accurately represent this complexity when modelling and inverting electromagnetic data. This is particularly the case for the scales, detail and conductivity contrasts involved in mineral and hydrocarbon exploration and development, but also for the larger scale of lithospheric studies. Unstructured tetrahedral meshes provide a flexible means of discretizing a general, arbitrary Earth model. This is important when wanting to integrate a geophysical Earth model with a geological Earth model parameterized in terms of surfaces. Finite-element and finite-volume methods can be derived for computing the electric and magnetic fields in a model parameterized using an unstructured tetrahedral mesh. A number of such variants have been proposed and have proven successful. However, the efficiency and accuracy of these methods can be affected by the "quality" of the tetrahedral discretization, that is, how many of the tetrahedral cells in the mesh are long, narrow and pointy. This is particularly the case if one wants to use an iterative technique to solve the resulting linear system of equations. One approach to deal with this issue is to develop sophisticated model and mesh building and manipulation capabilities in order to ensure that any mesh built from geological information is of sufficient quality for the electromagnetic modelling. Another approach is to investigate other methods of synthesizing the electromagnetic fields. One such example is a "meshfree" approach in which the electromagnetic fields are synthesized using a mesh that is distinct from the mesh used to parameterized the Earth model. There are then two meshes, one describing the Earth model and one used for the numerical mathematics of computing the fields. This means that there are no longer any quality requirements on the model mesh, which

  15. Three-Dimensional High-Order Spectral Volume Method for Solving Maxwell's Equations on Unstructured Grids

    Science.gov (United States)

    Liu, Yen; Vinokur, Marcel; Wang, Z. J.

    2004-01-01

    A three-dimensional, high-order, conservative, and efficient discontinuous spectral volume (SV) method for the solutions of Maxwell's equations on unstructured grids is presented. The concept of discontinuous 2nd high-order loca1 representations to achieve conservation and high accuracy is utilized in a manner similar to the Discontinuous Galerkin (DG) method, but instead of using a Galerkin finite-element formulation, the SV method is based on a finite-volume approach to attain a simpler formulation. Conventional unstructured finite-volume methods require data reconstruction based on the least-squares formulation using neighboring cell data. Since each unknown employs a different stencil, one must repeat the least-squares inversion for every cell at each time step, or to store the inversion coefficients. In a high-order, three-dimensional computation, the former would involve impractically large CPU time, while for the latter the memory requirement becomes prohibitive. In the SV method, one starts with a relatively coarse grid of triangles or tetrahedra, called spectral volumes (SVs), and partition each SV into a number of structured subcells, called control volumes (CVs), that support a polynomial expansion of a desired degree of precision. The unknowns are cell averages over CVs. If all the SVs are partitioned in a geometrically similar manner, the reconstruction becomes universal as a weighted sum of unknowns, and only a few universal coefficients need to be stored for the surface integrals over CV faces. Since the solution is discontinuous across the SV boundaries, a Riemann solver is thus necessary to maintain conservation. In the paper, multi-parameter and symmetric SV partitions, up to quartic for triangle and cubic for tetrahedron, are first presented. The corresponding weight coefficients for CV face integrals in terms of CV cell averages for each partition are analytically determined. These discretization formulas are then applied to the integral form of

  16. Three-dimensional Gravity Inversion with a New Gradient Scheme on Unstructured Grids

    Science.gov (United States)

    Sun, S.; Yin, C.; Gao, X.; Liu, Y.; Zhang, B.

    2017-12-01

    Stabilized gradient-based methods have been proved to be efficient for inverse problems. Based on these methods, setting gradient close to zero can effectively minimize the objective function. Thus the gradient of objective function determines the inversion results. By analyzing the cause of poor resolution on depth in gradient-based gravity inversion methods, we find that imposing depth weighting functional in conventional gradient can improve the depth resolution to some extent. However, the improvement is affected by the regularization parameter and the effect of the regularization term becomes smaller with increasing depth (shown as Figure 1 (a)). In this paper, we propose a new gradient scheme for gravity inversion by introducing a weighted model vector. The new gradient can improve the depth resolution more efficiently, which is independent of the regularization parameter, and the effect of regularization term will not be weakened when depth increases. Besides, fuzzy c-means clustering method and smooth operator are both used as regularization terms to yield an internal consecutive inverse model with sharp boundaries (Sun and Li, 2015). We have tested our new gradient scheme with unstructured grids on synthetic data to illustrate the effectiveness of the algorithm. Gravity forward modeling with unstructured grids is based on the algorithm proposed by Okbe (1979). We use a linear conjugate gradient inversion scheme to solve the inversion problem. The numerical experiments show a great improvement in depth resolution compared with regular gradient scheme, and the inverse model is compact at all depths (shown as Figure 1 (b)). AcknowledgeThis research is supported by Key Program of National Natural Science Foundation of China (41530320), China Natural Science Foundation for Young Scientists (41404093), and Key National Research Project of China (2016YFC0303100, 2017YFC0601900). ReferencesSun J, Li Y. 2015. Multidomain petrophysically constrained inversion and

  17. Simulation of geothermal water extraction in heterogeneous reservoirs using dynamic unstructured mesh optimisation

    Science.gov (United States)

    Salinas, P.; Pavlidis, D.; Jacquemyn, C.; Lei, Q.; Xie, Z.; Pain, C.; Jackson, M.

    2017-12-01

    It is well known that the pressure gradient into a production well increases with decreasing distance to the well. To properly capture the local pressure drawdown into the well a high grid or mesh resolution is required; moreover, the location of the well must be captured accurately. In conventional simulation models, the user must interact with the model to modify grid resolution around wells of interest, and the well location is approximated on a grid defined early in the modelling process.We report a new approach for improved simulation of near wellbore flow in reservoir scale models through the use of dynamic mesh optimisation and the recently presented double control volume finite element method. Time is discretized using an adaptive, implicit approach. Heterogeneous geologic features are represented as volumes bounded by surfaces. Within these volumes, termed geologic domains, the material properties are constant. Up-, cross- or down-scaling of material properties during dynamic mesh optimization is not required, as the properties are uniform within each geologic domain. A given model typically contains numerous such geologic domains. Wells are implicitly coupled with the domain, and the fluid flows is modelled inside the wells. The method is novel for two reasons. First, a fully unstructured tetrahedral mesh is used to discretize space, and the spatial location of the well is specified via a line vector, ensuring its location even if the mesh is modified during the simulation. The well location is therefore accurately captured, the approach allows complex well trajectories and wells with many laterals to be modelled. Second, computational efficiency is increased by use of dynamic mesh optimization, in which an unstructured mesh adapts in space and time to key solution fields (preserving the geometry of the geologic domains), such as pressure, velocity or temperature, this also increases the quality of the solutions by placing higher resolution where required

  18. A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR

    Directory of Open Access Journals (Sweden)

    Natsuko Goda

    2015-07-01

    Full Text Available Intrinsically disordered proteins (IDPs that lack stable conformations and are highly flexible have attracted the attention of biologists. Therefore, the development of a systematic method to identify polypeptide regions that are unstructured in solution is important. We have designed an “indirect/reflected” detection system for evaluating the physicochemical properties of IDPs using nuclear magnetic resonance (NMR. This approach employs a “chimeric membrane protein”-based method using the thermostable membrane protein PH0471. This protein contains two domains, a transmembrane helical region and a C-terminal OB (oligonucleotide/oligosaccharide binding-fold domain (named NfeDC domain, connected by a flexible linker. NMR signals of the OB-fold domain of detergent-solubilized PH0471 are observed because of the flexibility of the linker region. In this study, the linker region was substituted with target IDPs. Fifty-three candidates were selected using the prediction tool POODLE and 35 expression vectors were constructed. Subsequently, we obtained 15N-labeled chimeric PH0471 proteins with 25 IDPs as linkers. The NMR spectra allowed us to classify IDPs into three categories: flexible, moderately flexible, and inflexible. The inflexible IDPs contain membrane-associating or aggregation-prone sequences. This is the first attempt to use an indirect/reflected NMR method to evaluate IDPs and can verify the predictions derived from our computational tools.

  19. Intrinsic plasticity complements LTP in parallel fiber input gain control in cerebellar Purkinje cells

    Science.gov (United States)

    Belmeguenai, Amor; Hosy, Eric; Bengtsson, Fredrik; Pedroarena, Christine; Piochon, Claire; Teuling, Eva; He, Qionger; Ohtsuki, Gen; De Jeu, Marcel T.G.; Elgersma, Ype; De Zeeuw, Chris I.; Jörntell, Henrik; Hansel, Christian

    2010-01-01

    Synaptic gain control and information storage in neural networks are mediated by alterations in synaptic transmission, such as in long-term potentiation (LTP). Here, we show using both in vitro and in vivo recordings from the rat cerebellum that tetanization protocols for the induction of LTP at parallel fiber (PF) to Purkinje cell synapses can also evoke increases in intrinsic excitability. This form of intrinsic plasticity shares with LTP a requirement for the activation of protein phosphatases 1, 2A, and 2B for induction. Purkinje cell intrinsic plasticity resembles CA1 hippocampal pyramidal cell intrinsic plasticity in that it requires activity of protein kinase A (PKA) and casein kinase 2 (CK2) and is mediated by a downregulation of SK-type calcium-sensitive K conductances. In addition, Purkinje cell intrinsic plasticity similarly results in enhanced spine calcium signaling. However, there are fundamental differences: first, while in the hippocampus increases in excitability result in a higher probability for LTP induction, intrinsic plasticity in Purkinje cells lowers the probability for subsequent LTP induction. Second, intrinsic plasticity raises the spontaneous spike frequency of Purkinje cells. The latter effect does not impair tonic spike firing in the target neurons of inhibitory Purkinje cell projections in the deep cerebellar nuclei (DCN), but lowers the Purkinje cell signal-to-noise ratio, thus reducing the PF readout. These observations suggest that intrinsic plasticity accompanies LTP of active PF synapses, while it reduces at weaker, non-potentiated synapses the probability for subsequent potentiation and lowers the impact on the Purkinje cell output. PMID:20943904

  20. Learning to learn - intrinsic plasticity as a metaplasticity mechanism for memory formation.

    Science.gov (United States)

    Sehgal, Megha; Song, Chenghui; Ehlers, Vanessa L; Moyer, James R

    2013-10-01

    "Use it or lose it" is a popular adage often associated with use-dependent enhancement of cognitive abilities. Much research has focused on understanding exactly how the brain changes as a function of experience. Such experience-dependent plasticity involves both structural and functional alterations that contribute to adaptive behaviors, such as learning and memory, as well as maladaptive behaviors, including anxiety disorders, phobias, and posttraumatic stress disorder. With the advancing age of our population, understanding how use-dependent plasticity changes across the lifespan may also help to promote healthy brain aging. A common misconception is that such experience-dependent plasticity (e.g., associative learning) is synonymous with synaptic plasticity. Other forms of plasticity also play a critical role in shaping adaptive changes within the nervous system, including intrinsic plasticity - a change in the intrinsic excitability of a neuron. Intrinsic plasticity can result from a change in the number, distribution or activity of various ion channels located throughout the neuron. Here, we review evidence that intrinsic plasticity is an important and evolutionarily conserved neural correlate of learning. Intrinsic plasticity acts as a metaplasticity mechanism by lowering the threshold for synaptic changes. Thus, learning-related intrinsic changes can facilitate future synaptic plasticity and learning. Such intrinsic changes can impact the allocation of a memory trace within a brain structure, and when compromised, can contribute to cognitive decline during the aging process. This unique role of intrinsic excitability can provide insight into how memories are formed and, more interestingly, how neurons that participate in a memory trace are selected. Most importantly, modulation of intrinsic excitability can allow for regulation of learning ability - this can prevent or provide treatment for cognitive decline not only in patients with clinical disorders but

  1. Development of a Two-Phase Flow Analysis Code based on a Unstructured-Mesh SIMPLE Algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jong Tae; Park, Ik Kyu; Cho, Heong Kyu; Yoon, Han Young; Kim, Kyung Doo; Jeong, Jae Jun

    2008-09-15

    For analyses of multi-phase flows in a water-cooled nuclear power plant, a three-dimensional SIMPLE-algorithm based hydrodynamic solver CUPID-S has been developed. As governing equations, it adopts a two-fluid three-field model for the two-phase flows. The three fields represent a continuous liquid, a dispersed droplets, and a vapour field. The governing equations are discretized by a finite volume method on an unstructured grid to handle the geometrical complexity of the nuclear reactors. The phasic momentum equations are coupled and solved with a sparse block Gauss-Seidel matrix solver to increase a numerical stability. The pressure correction equation derived by summing the phasic volume fraction equations is applied on the unstructured mesh in the context of a cell-centered co-located scheme. This paper presents the numerical method and the preliminary results of the calculations.

  2. Meta-analysis and other approaches for synthesizing structured and unstructured data in plant pathology.

    Science.gov (United States)

    Scherm, H; Thomas, C S; Garrett, K A; Olsen, J M

    2014-01-01

    The term data deluge is used widely to describe the rapidly accelerating growth of information in the technical literature, in scientific databases, and in informal sources such as the Internet and social media. The massive volume and increased complexity of information challenge traditional methods of data analysis but at the same time provide unprecedented opportunities to test hypotheses or uncover new relationships via mining of existing databases and literature. In this review, we discuss analytical approaches that are beginning to be applied to help synthesize the vast amount of information generated by the data deluge and thus accelerate the pace of discovery in plant pathology. We begin with a review of meta-analysis as an established approach for summarizing standardized (structured) data across the literature. We then turn to examples of synthesizing more complex, unstructured data sets through a range of data-mining approaches, including the incorporation of 'omics data in epidemiological analyses. We conclude with a discussion of methodologies for leveraging information contained in novel, open-source data sets through web crawling, text mining, and social media analytics, primarily in the context of digital disease surveillance. Rapidly evolving computational resources provide platforms for integrating large and complex data sets, motivating research that will draw on new types and scales of information to address big questions.

  3. Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review.

    Science.gov (United States)

    Kreimeyer, Kory; Foster, Matthew; Pandey, Abhishek; Arya, Nina; Halford, Gwendolyn; Jones, Sandra F; Forshee, Richard; Walderhaug, Mark; Botsis, Taxiarchis

    2017-09-01

    We followed a systematic approach based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses to identify existing clinical natural language processing (NLP) systems that generate structured information from unstructured free text. Seven literature databases were searched with a query combining the concepts of natural language processing and structured data capture. Two reviewers screened all records for relevance during two screening phases, and information about clinical NLP systems was collected from the final set of papers. A total of 7149 records (after removing duplicates) were retrieved and screened, and 86 were determined to fit the review criteria. These papers contained information about 71 different clinical NLP systems, which were then analyzed. The NLP systems address a wide variety of important clinical and research tasks. Certain tasks are well addressed by the existing systems, while others remain as open challenges that only a small number of systems attempt, such as extraction of temporal information or normalization of concepts to standard terminologies. This review has identified many NLP systems capable of processing clinical free text and generating structured output, and the information collected and evaluated here will be important for prioritizing development of new approaches for clinical NLP. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Semi-implicit anisotropic cosmic ray transport on an unstructured moving mesh

    Science.gov (United States)

    Pakmor, Rüdiger; Pfrommer, Christoph; Simpson, Christine M.; Kannan, Rahul; Springel, Volker

    2016-11-01

    In the interstellar medium of galaxies and the intracluster gas of galaxy clusters, the charged particles making up cosmic rays are moving almost exclusively along (but not across) magnetic field lines. The resulting anisotropic transport of cosmic rays in the form of diffusion or streaming not only affects the gas dynamics but also rearranges the magnetic fields themselves. The coupled dynamics of magnetic fields and cosmic rays can thus impact the formation and evolution of galaxies and the thermal evolution of galaxy clusters in critical ways. Numerically studying these effects requires solvers for anisotropic diffusion that are accurate, efficient, and robust, requirements that have proved difficult to be satisfied in practice. Here, we present an anisotropic diffusion solver on an unstructured moving mesh that is conservative, does not violate the entropy condition, allows for semi-implicit time integration with individual timesteps, and only requires solving a single linear system of equations per timestep. We apply our new scheme to a large number of test problems and show that it works as well or better than previous implementations. Finally, we demonstrate for a numerically demanding simulation of the formation of an isolated disc galaxy that our local time-stepping scheme reproduces the results obtained with global time-stepping at a fraction of the computational cost.

  5. AN EOS-BASED NUMERICAL SIMULATION OF THERMAL RECOVERY PROCESS USING UNSTRUCTURED MESHES

    Directory of Open Access Journals (Sweden)

    F. Marcondes

    2015-03-01

    Full Text Available Abstract In the past thirty years, the development of compositional reservoir simulators using an equation of state (EOS has been addressed in the literature. However, the development of compositional thermal simulators in conjunction with the EOS formulation, in particular, has not been addressed extensively. In this work, a fully implicit, thermal, compositional EOS-based simulator in conjunction with unstructured meshes has been developed. In this model, an equation of state is used for equilibrium calculations among phases. Also, the physical properties are calculated based on an EOS, hence obviating the need for using steam tables for calculation of water/steam properties. The governing equations for the model comprise fugacity equations, material balance, pore volume constraint and energy equation. The governing partial differential equations are solved using the EbFVM (Element based Finite Volume Method. Results for several case studies consisting of 2D and 3D reservoirs are presented in order to demonstrate the applicability of the method.

  6. Simulating multi-scale oceanic processes around Taiwan on unstructured grids

    Science.gov (United States)

    Yu, Hao-Cheng; Zhang, Yinglong J.; Yu, Jason C. S.; Terng, C.; Sun, Weiling; Ye, Fei; Wang, Harry V.; Wang, Zhengui; Huang, Hai

    2017-11-01

    We validate a 3D unstructured-grid (UG) model for simulating multi-scale processes as occurred in Northwestern Pacific around Taiwan using recently developed new techniques (Zhang et al., Ocean Modeling, 102, 64-81, 2016) that require no bathymetry smoothing even for this region with prevalent steep bottom slopes and many islands. The focus is on short-term forecast for several months instead of long-term variability. Compared with satellite products, the errors for the simulated Sea-surface Height (SSH) and Sea-surface Temperature (SST) are similar to a reference data-assimilated global model. In the nearshore region, comparison with 34 tide gauges located around Taiwan indicates an average RMSE of 13 cm for the tidal elevation. The average RMSE for SST at 6 coastal buoys is 1.2 °C. The mean transport and eddy kinetic energy compare reasonably with previously published values and the reference model used to provide boundary and initial conditions. The model suggests ∼2-day interruption of Kuroshio east of Taiwan during a typhoon period. The effect of tidal mixing is shown to be significant nearshore. The multi-scale model is easily extendable to target regions of interest due to its UG framework and a flexible vertical gridding system, which is shown to be superior to terrain-following coordinates.

  7. Simulating the Agulhas system in global ocean models - nesting vs. multi-resolution unstructured meshes

    Science.gov (United States)

    Biastoch, Arne; Sein, Dmitry; Durgadoo, Jonathan V.; Wang, Qiang; Danilov, Sergey

    2018-01-01

    Many questions in ocean and climate modelling require the combined use of high resolution, global coverage and multi-decadal integration length. For this combination, even modern resources limit the use of traditional structured-mesh grids. Here we compare two approaches: A high-resolution grid nested into a global model at coarser resolution (NEMO with AGRIF) and an unstructured-mesh grid (FESOM) which allows to variably enhance resolution where desired. The Agulhas system around South Africa is used as a testcase, providing an energetic interplay of a strong western boundary current and mesoscale dynamics. Its open setting into the horizontal and global overturning circulations also requires global coverage. Both model configurations simulate a reasonable large-scale circulation. Distribution and temporal variability of the wind-driven circulation are quite comparable due to the same atmospheric forcing. However, the overturning circulation differs, owing each model's ability to represent formation and spreading of deep water masses. In terms of regional, high-resolution dynamics, all elements of the Agulhas system are well represented. Owing to the strong nonlinearity in the system, Agulhas Current transports of both configurations and in comparison with observations differ in strength and temporal variability. Similar decadal trends in Agulhas Current transport and Agulhas leakage are linked to the trends in wind forcing.

  8. Agglomeration multigrid methods with implicit Runge-Kutta smoothers applied to aerodynamic simulations on unstructured grids

    Science.gov (United States)

    Langer, Stefan

    2014-11-01

    For unstructured finite volume methods an agglomeration multigrid with an implicit multistage Runge-Kutta method as a smoother is developed for solving the compressible Reynolds averaged Navier-Stokes (RANS) equations. The implicit Runge-Kutta method is interpreted as a preconditioned explicit Runge-Kutta method. The construction of the preconditioner is based on an approximate derivative. The linear systems are solved approximately with a symmetric Gauss-Seidel method. To significantly improve this solution method grid anisotropy is treated within the Gauss-Seidel iteration in such a way that the strong couplings in the linear system are resolved by tridiagonal systems constructed along these directions of strong coupling. The agglomeration strategy is adapted to this procedure by taking into account exactly these anisotropies in such a way that a directional coarsening is applied along these directions of strong coupling. Turbulence effects are included by a Spalart-Allmaras model, and the additional transport-type equation is approximately solved in a loosely coupled manner with the same method. For two-dimensional and three-dimensional numerical examples and a variety of differently generated meshes we show the wide range of applicability of the solution method. Finally, we exploit the GMRES method to determine approximate spectral information of the linearized RANS equations. This approximate spectral information is used to discuss and compare characteristics of multistage Runge-Kutta methods.

  9. Unstructured Grid Adaptation: Status, Potential Impacts, and Recommended Investments Toward CFD Vision 2030

    Science.gov (United States)

    Park, Michael A.; Krakos, Joshua A.; Michal, Todd; Loseille, Adrien; Alonso, Juan J.

    2016-01-01

    Unstructured grid adaptation is a powerful tool to control discretization error for Computational Fluid Dynamics (CFD). It has enabled key increases in the accuracy, automation, and capacity of some fluid simulation applications. Slotnick et al. provides a number of case studies in the CFD Vision 2030 Study: A Path to Revolutionary Computational Aerosciences to illustrate the current state of CFD capability and capacity. The authors forecast the potential impact of emerging High Performance Computing (HPC) environments forecast in the year 2030 and identify that mesh generation and adaptivity continue to be significant bottlenecks in the CFD work flow. These bottlenecks may persist because very little government investment has been targeted in these areas. To motivate investment, the impacts of improved grid adaptation technologies are identified. The CFD Vision 2030 Study roadmap and anticipated capabilities in complementary disciplines are quoted to provide context for the progress made in grid adaptation in the past fifteen years, current status, and a forecast for the next fifteen years with recommended investments. These investments are specific to mesh adaptation and impact other aspects of the CFD process. Finally, a strategy is identified to diffuse grid adaptation technology into production CFD work flows.

  10. Autonomous planning and control of soft untethered grippers in unstructured environments.

    Science.gov (United States)

    Ongaro, Federico; Scheggi, Stefano; Yoon, ChangKyu; den Brink, Frank van; Oh, Seung Hyun; Gracias, David H; Misra, Sarthak

    2017-01-01

    The use of small, maneuverable, untethered and reconfigurable robots could provide numerous advantages in various micromanipulation tasks. Examples include microassembly, pick-and-place of fragile micro-objects for lab-on-a-chip applications, assisted hatching for in-vitro fertilization and minimally invasive surgery. This study assesses the potential of soft untethered magnetic grippers as alternatives or complements to conventional tethered or rigid micromanipulators. We demonstrate closed-loop control of untethered grippers and automated pick-and-place of biological material on porcine tissue in an unstructured environment. We also demonstrate the ability of the soft grippers to recognize and sort non-biological micro-scale objects. The fully autonomous nature of the experiments is made possible by the integration of planning and decision-making algorithms, as well as by closed-loop temperature and electromagnetic motion control. The grippers are capable of completing pick-and-place tasks of biological material at an average velocity of 1.8 ±0.71 mm/s and a drop-off error of 0.62 ±0.22 mm. Color-sensitive sorting of three micro-scale objects is completed at a velocity of 1.21 ±0.68 mm/s and a drop-off error of 0.85 ±0.41 mm. Our findings suggest that improved autonomous untethered grippers could augment the capabilities of current soft-robotic instruments especially in advancedtasks involving manipulation.

  11. Unstructured-Mesh Terrain Analysis and Incident Solar Radiation for Continuous Hydrologic Modeling in Mountain Watersheds

    Directory of Open Access Journals (Sweden)

    Hernan A. Moreno

    2018-03-01

    Full Text Available This article presents a methodology for estimating total incoming solar radiation from Triangular Irregular Network (TIN topographic meshes. The algorithm also computes terrain slope degree and aspect (slope orientation and accounts for self shading and cast shadows, sky view fractions for diffuse radiation, remote albedo and atmospheric backscattering, by using a vectorial approach within a topocentric coordinate system establishing geometric relations between groups of TIN elements and the sun position. A normal vector to the surface of each TIN element describes its slope and aspect while spherical trigonometry allows computing a unit vector defining the position of the sun at each hour and day of the year. Sky view fraction, useful to determine diffuse and backscattered radiation, is computed for each TIN element at prescribed azimuth intervals targeting the steepest elevation gradient. A comparison between the sun zenith angle and the steepest gradient allows deciding whether or not the pivot element is shaded. Finally, remote albedo is computed from the sky view fraction complementary functions for observed albedo values of the surrounding terrain. The sensitivity of the different radiative components to seasonal changes in atmospheric transmissivitties and surrounding albedo is tested in a mountainous watershed in Wyoming. This methodology represents an improvement on the current algorithms to compute terrain and radiation values on unstructured-mesh terrain models. All terrain-related features (e.g., slope, aspect, sky view fraction can be pre-computed and stored for easy access into a subsequent, progressive-in-time, numerical simulation.

  12. A High-Order Finite Spectral Volume Method for Conservation Laws on Unstructured Grids

    Science.gov (United States)

    Wang, Z. J.; Liu, Yen; Kwak, Dochan (Technical Monitor)

    2001-01-01

    A time accurate, high-order, conservative, yet efficient method named Finite Spectral Volume (FSV) is developed for conservation laws on unstructured grids. The concept of a 'spectral volume' is introduced to achieve high-order accuracy in an efficient manner similar to spectral element and multi-domain spectral methods. In addition, each spectral volume is further sub-divided into control volumes (CVs), and cell-averaged data from these control volumes is used to reconstruct a high-order approximation in the spectral volume. Riemann solvers are used to compute the fluxes at spectral volume boundaries. Then cell-averaged state variables in the control volumes are updated independently. Furthermore, TVD (Total Variation Diminishing) and TVB (Total Variation Bounded) limiters are introduced in the FSV method to remove/reduce spurious oscillations near discontinuities. A very desirable feature of the FSV method is that the reconstruction is carried out only once, and analytically, and is the same for all cells of the same type, and that the reconstruction stencil is always non-singular, in contrast to the memory and CPU-intensive reconstruction in a high-order finite volume (FV) method. Discussions are made concerning why the FSV method is significantly more efficient than high-order finite volume and the Discontinuous Galerkin (DG) methods. Fundamental properties of the FSV method are studied and high-order accuracy is demonstrated for several model problems with and without discontinuities.

  13. Unstructured-mesh modeling of the Congo river-to-sea continuum

    Science.gov (United States)

    Bars, Yoann Le; Vallaeys, Valentin; Deleersnijder, Éric; Hanert, Emmanuel; Carrere, Loren; Channelière, Claire

    2016-04-01

    With the second largest outflow in the world and one of the widest hydrological basins, the Congo River is of a major importance both locally and globally. However, relatively few studies have been conducted on its hydrology, as compared to other great rivers such as the Amazon, Nile, Yangtze, or Mississippi. The goal of this study is therefore to help fill this gap and provide the first high-resolution simulation of the Congo river-estuary-coastal sea continuum. To this end, we are using a discontinuous-Galerkin finite element marine model that solves the two-dimensional depth-averaged shallow water equations on an unstructured mesh. To ensure a smooth transition from river to coastal sea, we have considered a model that encompasses both hydrological and coastal ocean processes. An important difficulty in setting up this model was to find data to parameterize and validate it, as it is a rather remote and understudied area. Therefore, an important effort in this study has been to establish a methodology to take advantage of all the data sources available including nautical charts that had to be digitalized. The model surface elevation has then been validated with respect to an altimetric database. Model results suggest the existence of gyres in the vicinity of the river mouth that have never been documented before. The effect of those gyres on the Congo River dynamics has been further investigated by simulating the transport of Lagrangian particles and computing the water age.

  14. Time integration algorithms for the two-dimensional Euler equations on unstructured meshes

    Science.gov (United States)

    Slack, David C.; Whitaker, D. L.; Walters, Robert W.

    1994-01-01

    Explicit and implicit time integration algorithms for the two-dimensional Euler equations on unstructured grids are presented. Both cell-centered and cell-vertex finite volume upwind schemes utilizing Roe's approximate Riemann solver are developed. For the cell-vertex scheme, a four-stage Runge-Kutta time integration, a fourstage Runge-Kutta time integration with implicit residual averaging, a point Jacobi method, a symmetric point Gauss-Seidel method and two methods utilizing preconditioned sparse matrix solvers are presented. For the cell-centered scheme, a Runge-Kutta scheme, an implicit tridiagonal relaxation scheme modeled after line Gauss-Seidel, a fully implicit lower-upper (LU) decomposition, and a hybrid scheme utilizing both Runge-Kutta and LU methods are presented. A reverse Cuthill-McKee renumbering scheme is employed for the direct solver to decrease CPU time by reducing the fill of the Jacobian matrix. A comparison of the various time integration schemes is made for both first-order and higher order accurate solutions using several mesh sizes, higher order accuracy is achieved by using multidimensional monotone linear reconstruction procedures. The results obtained for a transonic flow over a circular arc suggest that the preconditioned sparse matrix solvers perform better than the other methods as the number of elements in the mesh increases.

  15. Cell-centered high-order hyperbolic finite volume method for diffusion equation on unstructured grids

    Science.gov (United States)

    Lee, Euntaek; Ahn, Hyung Taek; Luo, Hong

    2018-02-01

    We apply a hyperbolic cell-centered finite volume method to solve a steady diffusion equation on unstructured meshes. This method, originally proposed by Nishikawa using a node-centered finite volume method, reformulates the elliptic nature of viscous fluxes into a set of augmented equations that makes the entire system hyperbolic. We introduce an efficient and accurate solution strategy for the cell-centered finite volume method. To obtain high-order accuracy for both solution and gradient variables, we use a successive order solution reconstruction: constant, linear, and quadratic (k-exact) reconstruction with an efficient reconstruction stencil, a so-called wrapping stencil. By the virtue of the cell-centered scheme, the source term evaluation was greatly simplified regardless of the solution order. For uniform schemes, we obtain the same order of accuracy, i.e., first, second, and third orders, for both the solution and its gradient variables. For hybrid schemes, recycling the gradient variable information for solution variable reconstruction makes one order of additional accuracy, i.e., second, third, and fourth orders, possible for the solution variable with less computational work than needed for uniform schemes. In general, the hyperbolic method can be an effective solution technique for diffusion problems, but instability is also observed for the discontinuous diffusion coefficient cases, which brings necessity for further investigation about the monotonicity preserving hyperbolic diffusion method.

  16. Experiences with Text Mining Large Collections of Unstructured Systems Development Artifacts at JPL

    Science.gov (United States)

    Port, Dan; Nikora, Allen; Hihn, Jairus; Huang, LiGuo

    2011-01-01

    Often repositories of systems engineering artifacts at NASA's Jet Propulsion Laboratory (JPL) are so large and poorly structured that they have outgrown our capability to effectively manually process their contents to extract useful information. Sophisticated text mining methods and tools seem a quick, low-effort approach to automating our limited manual efforts. Our experiences of exploring such methods mainly in three areas including historical risk analysis, defect identification based on requirements analysis, and over-time analysis of system anomalies at JPL, have shown that obtaining useful results requires substantial unanticipated efforts - from preprocessing the data to transforming the output for practical applications. We have not observed any quick 'wins' or realized benefit from short-term effort avoidance through automation in this area. Surprisingly we have realized a number of unexpected long-term benefits from the process of applying text mining to our repositories. This paper elaborates some of these benefits and our important lessons learned from the process of preparing and applying text mining to large unstructured system artifacts at JPL aiming to benefit future TM applications in similar problem domains and also in hope for being extended to broader areas of applications.

  17. Large-Scale Parallel Viscous Flow Computations using an Unstructured Multigrid Algorithm

    Science.gov (United States)

    Mavriplis, Dimitri J.

    1999-01-01

    The development and testing of a parallel unstructured agglomeration multigrid algorithm for steady-state aerodynamic flows is discussed. The agglomeration multigrid strategy uses a graph algorithm to construct the coarse multigrid levels from the given fine grid, similar to an algebraic multigrid approach, but operates directly on the non-linear system using the FAS (Full Approximation Scheme) approach. The scalability and convergence rate of the multigrid algorithm are examined on the SGI Origin 2000 and the Cray T3E. An argument is given which indicates that the asymptotic scalability of the multigrid algorithm should be similar to that of its underlying single grid smoothing scheme. For medium size problems involving several million grid points, near perfect scalability is obtained for the single grid algorithm, while only a slight drop-off in parallel efficiency is observed for the multigrid V- and W-cycles, using up to 128 processors on the SGI Origin 2000, and up to 512 processors on the Cray T3E. For a large problem using 25 million grid points, good scalability is observed for the multigrid algorithm using up to 1450 processors on a Cray T3E, even when the coarsest grid level contains fewer points than the total number of processors.

  18. Navigation of military and space unmanned ground vehicles in unstructured terrains

    Science.gov (United States)

    Lescoe, Paul; Lavery, David; Bedard, Roger

    1991-01-01

    Development of unmanned vehicles for local navigation in terrains unstructured by humans is reviewed. Modes of navigation include teleoperation or remote control, computer assisted remote driving (CARD), and semiautonomous navigation (SAN). A first implementation of a CARD system was successfully tested using the Robotic Technology Test Vehicle developed by Jet Propulsion Laboratory. Stereo pictures were transmitted to a remotely located human operator, who performed the sensing, perception, and planning functions of navigation. A computer provided range and angle measurements and the path plan was transmitted to the vehicle which autonomously executed the path. This implementation is to be enhanced by providing passive stereo vision and a reflex control system for autonomously stopping the vehicle if blocked by an obstacle. SAN achievements include implementation of a navigation testbed on a six wheel, three-body articulated rover vehicle, development of SAN algorithms and code, integration of SAN software onto the vehicle, and a successful feasibility demonstration that represents a step forward towards the technology required for long-range exploration of the lunar or Martian surface. The vehicle includes a passive stereo vision system with real-time area-based stereo image correlation, a terrain matcher, a path planner, and a path execution planner.

  19. A positional estimation technique for an autonomous land vehicle in an unstructured environment

    Science.gov (United States)

    Talluri, Raj; Aggarwal, J. K.

    1990-01-01

    This paper presents a solution to the positional estimation problem of an autonomous land vehicle navigating in an unstructured mountainous terrain. A Digital Elevation Map (DEM) of the area in which the robot is to navigate is assumed to be given. It is also assumed that the robot is equipped with a camera that can be panned and tilted, and a device to measure the elevation of the robot above the ground surface. No recognizable landmarks are assumed to be present in the environment in which the robot is to navigate. The solution presented makes use of the DEM information, and structures the problem as a heuristic search in the DEM for the possible robot location. The shape and position of the horizon line in the image plane and the known camera geometry of the perspective projection are used as parameters to search the DEM. Various heuristics drawn from the geometric constraints are used to prune the search space significantly. The algorithm is made robust to errors in the imaging process by accounting for the worst care errors. The approach is tested using DEM data of areas in Colorado and Texas. The method is suitable for use in outdoor mobile robots and planetary rovers.

  20. Radiation Coupling with the FUN3D Unstructured-Grid CFD Code

    Science.gov (United States)

    Wood, William A.

    2012-01-01

    The HARA radiation code is fully-coupled to the FUN3D unstructured-grid CFD code for the purpose of simulating high-energy hypersonic flows. The radiation energy source terms and surface heat transfer, under the tangent slab approximation, are included within the fluid dynamic ow solver. The Fire II flight test, at the Mach-31 1643-second trajectory point, is used as a demonstration case. Comparisons are made with an existing structured-grid capability, the LAURA/HARA coupling. The radiative surface heat transfer rates from the present approach match the benchmark values within 6%. Although radiation coupling is the focus of the present work, convective surface heat transfer rates are also reported, and are seen to vary depending upon the choice of mesh connectivity and FUN3D ux reconstruction algorithm. On a tetrahedral-element mesh the convective heating matches the benchmark at the stagnation point, but under-predicts by 15% on the Fire II shoulder. Conversely, on a mixed-element mesh the convective heating over-predicts at the stagnation point by 20%, but matches the benchmark away from the stagnation region.

  1. Modeling and simulation of xylitol production in bioreactor by Debaryomyces nepalensis NCYC 3413 using unstructured and artificial neural network models.

    Science.gov (United States)

    Pappu, J Sharon Mano; Gummadi, Sathyanarayana N

    2016-11-01

    This study examines the use of unstructured kinetic model and artificial neural networks as predictive tools for xylitol production by Debaryomyces nepalensis NCYC 3413 in bioreactor. An unstructured kinetic model was proposed in order to assess the influence of pH (4, 5 and 6), temperature (25°C, 30°C and 35°C) and volumetric oxygen transfer coefficient kLa (0.14h(-1), 0.28h(-1) and 0.56h(-1)) on growth and xylitol production. A feed-forward back-propagation artificial neural network (ANN) has been developed to investigate the effect of process condition on xylitol production. ANN configuration of 6-10-3 layers was selected and trained with 339 experimental data points from bioreactor studies. Results showed that simulation and prediction accuracy of ANN was apparently higher when compared to unstructured mechanistic model under varying operational conditions. ANN was found to be an efficient data-driven tool to predict the optimal harvest time in xylitol production. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. MULTI-GRID METHOD OF CONVERGENCE SPEEDING-UP FOR THE SOLUTION OF GAS DYNAMICS PROBLEMS ON UNSTRUCTURED MESHES

    Directory of Open Access Journals (Sweden)

    K. N. Volkov

    2014-07-01

    Full Text Available An approach for effective implementation of numerical methods and computational algorithms is developed to simulate flows of non-viscous and viscous compressible gas in the complex domains. The convergence speeding-up method of iterative process is discussed based on the usage of multi-grid technologies to the solution of large systems of finite difference equations. Euler and Navier-Stokes equations are quantized on structured and unstructured meshes with highresolution schemes in time and space. Multi-grid method is implemented on the basis of standard C/F splitting of variables and standard interpolation method. A specific approach is proposed to overcome the problems related to storing the matrix coefficients of different signs. A problem of flow around an airfoil is used to demonstrate the possibilities of computational tools developed. The results computed for non-viscous and viscous gas on structured and unstructured meshes are presented with the usage of various components of multi-grid technology. Comparison of computation speed and convergence factors on structured and unstructured meshes showed the economy of the developed approach and weak dependence of quality characteristics on the number of mesh points. The choice of optimal inner iterations number made it possible to decrease computation time for 10%. Obtained results can be applied while software creating for fluid dynamics problems in the complex configuration domains.

  3. Intrinsic Motivation in Open Source Software Development

    DEFF Research Database (Denmark)

    Bitzer, J.; W., Schrettl,; Schröder, Philipp

    2004-01-01

    This papers sheds light on the puzzling evidence that even though open source software (OSS) is a public good, it is developed for free by highly qualified, young and motivated individuals, and evolves at a rapid pace. We show that once OSS development is understood as the private provision...... of a public good, these features emerge quite naturally. We adapt a dynamic private-provision-of-public-goods model to reflects key aspects of the OSS phenomenon. In particular, instead of relying on extrinsic motives for programmers (e.g. signaling) the present model is driven by intrinsic motives of OSS...... programmers, such as user-programmers, play value or \\emph{homo ludens} payoff, and gift culture benefits. Such intrinsic motives feature extensively in the wider OSS literature and turn out to add new insights to the economic analysis....

  4. Documentation Requirements, Intrinsic Motivation, and Worker Absence

    DEFF Research Database (Denmark)

    Andersen, Lotte Bøgh; Kristensen, Nicolai; Pedersen, Lene Holm

    2015-01-01

    Command systems are widely used to monitor public service provision, but little is known about unintended effects on individual workers’ motivation and work effort. Using insights from motivation crowding theory, we estimate a SEM model that captures how Danish childcare assistants and social...... and higher sickness absence. The association is statistically significant, but very small in substantive terms. The result is nevertheless consistent with the expectation in motivation crowding theory and contributes to the literature by including a new, reliable behavioral variable—sickness absence....../healthcare assistants perceive documentation requirements. We analyze how this perception relates to intrinsic motivation measured in a survey and sickness absence as reported in administrative registers, and find that individuals who perceive documentation requirements as controlling have lower intrinsic motivation...

  5. Intrinsic point defects in aluminum antimonide

    OpenAIRE

    Åberg, Daniel; Erhart, Paul; Williamson, Andrew J.; Lordi, Vincenzo

    2010-01-01

    Calculations within density functional theory on the basis of the local density approximation are carried out to study the properties of intrinsic point defects in aluminum antimonide. Special care is taken to address finite-size effects, band gap error, and symmetry reduction in the defect structures. The correction of the band gap is based on a set of GW calculations. The most important defects are identified to be the aluminum interstitial $Al_{i,Al}^{1+}$, the antimony antisites $Sb_{Al}^...

  6. Intrinsic luminescence of alkali silicate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Arbuzov, V.I.; Grabovskis, V.Y.; Tolstoi, M.N.; Vitol, I.K.

    1986-09-01

    This study obtains additional information on L centers and their role in electron excitation and intrinsic luminescence of a whole series. (Li, Na, K, Rb, and Cs) of alkali silicate glasses. The authors compare the features of the interaction with radiation of specimens of glass and crystal of a similar chemical composition, since silicates of alkali metals can be obtained in both the glassy and crystalline states.

  7. Intrinsic work motivation and pension reform acceptance

    OpenAIRE

    Heinemann, Friedrich; Hennighausen, Tanja; Moessinger, Marc-Daniel

    2011-01-01

    Although demographic change leaves pay-as-you-go pension systems unsustainable, reforms, such as a higher pension age, are highly unpopular. This contribution looks into the role of intrinsic motivation as a driver for pension reform acceptance. Theoretical reasoning suggests that this driver should be relevant: The choice among different pension reform options (increasing pension age, increasing contributions, cutting pensions) can be analyzed within the framework of an optimal job separatio...

  8. A structural model of intrinsic motivation

    OpenAIRE

    Aguilar, Javier; González, Daniel; Aguilar, Amira

    2017-01-01

    The main purpose of this research was to develop and test a structural model of intrinsic motivation among students of the University of Sonora to the curriculum of their careers. A secondary objective was to overcome the limitations of the model developed among students of the UNAM. Eight psychometric scales developed by the authors in previous studies were used, which showed satisfactory reliability and validity values. The model tested was similar to the sample of the UNAM, except for the ...

  9. Moral Distress, Workplace Health, and Intrinsic Harm.

    Science.gov (United States)

    Weber, Elijah

    2016-05-01

    Moral distress is now being recognized as a frequent experience for many health care providers, and there's good evidence that it has a negative impact on the health care work environment. However, contemporary discussions of moral distress have several problems. First, they tend to rely on inadequate characterizations of moral distress. As a result, subsequent investigations regarding the frequency and consequences of moral distress often proceed without a clear understanding of the phenomenon being discussed, and thereby risk substantially misrepresenting the nature, frequency, and possible consequences of moral distress. These discussions also minimize the intrinsically harmful aspects of moral distress. This is a serious omission. Moral distress doesn't just have a negative impact on the health care work environment; it also directly harms the one who experiences it. In this paper, I claim that these problems can be addressed by first clarifying our understanding of moral distress, and then identifying what makes moral distress intrinsically harmful. I begin by identifying three common mistakes that characterizations of moral distress tend to make, and explaining why these mistakes are problematic. Next, I offer an account of moral distress that avoids these mistakes. Then, I defend the claim that moral distress is intrinsically harmful to the subject who experiences it. I conclude by explaining how acknowledging this aspect of moral distress should reshape our discussions about how best to deal with this phenomenon. © 2015 John Wiley & Sons Ltd.

  10. Intrinsic electron trapping in amorphous oxide

    Science.gov (United States)

    Strand, Jack; Kaviani, Moloud; Afanas’ev, Valeri V.; Lisoni, Judit G.; Shluger, Alexander L.

    2018-03-01

    We demonstrate that electron trapping at intrinsic precursor sites is endemic in non-glass-forming amorphous oxide films. The energy distributions of trapped electron states in ultra-pure prototype amorphous (a)-HfO2 insulator obtained from exhaustive photo-depopulation experiments demonstrate electron states in the energy range of 2–3 eV below the oxide conduction band. These energy distributions are compared to the results of density functional calculations of a-HfO2 models of realistic density. The experimental results can be explained by the presence of intrinsic charge trapping sites formed by under-coordinated Hf cations and elongated Hf–O bonds in a-HfO2. These charge trapping states can capture up to two electrons, forming polarons and bi-polarons. The corresponding trapping sites are different from the dangling-bond type defects responsible for trapping in glass-forming oxides, such as SiO2, in that the traps are formed without bonds being broken. Furthermore, introduction of hydrogen causes formation of somewhat energetically deeper electron traps when a proton is immobilized next to the trapped electron bi-polaron. The proposed novel mechanism of intrinsic charge trapping in a-HfO2 represents a new paradigm for charge trapping in a broad class of non-glass-forming amorphous insulators.

  11. Comparison of effect of regular unstructured physical training and athletic level training on body composition and cardio respiratory fitness in adolescents.

    Science.gov (United States)

    Subramanian, Senthil Kumar; Sharma, Vivek Kumar; A, Vinayathan

    2013-09-01

    Childhood obesity and hypertension are global problems that are on the rise in India. Improving physical activity is an accepted main line of strategy for overcoming poor body composition, hypertension and reduced cardio respiratory fitness (CRF) all of which are considered as independent risk factors for the development of future cardiovascular complications. Present study was conducted to evaluate the effect of regular unstructured physical training and athletic level training on anthropometric measures, body composition, blood pressure and cardio respiratory fitness in adolescents. This is a collaborative study between the Department of physiology, Jawaharlal Institute of Postgraduate Medical Education and Research and Residential school, Jawahar Navodhya Vidyalaya, Puducherry, India. Student volunteers in the age group of 12-17 years were classified into athletes (group 1) and physically active non-athletes (group 2). Parameters measured and calculated were weight, height, body mass index, waist and hip circumference, body fat percentage (BF%), fat free mass (FFM), Systolic (SBP) & Diastolic blood pressure (DBP), Mean arterial pressure (MAP), Rate pressure product (RPP) and Predicted VO2 max. Mean difference between the groups was analysed using unpaired Student's t-test. All statistical analysis was carried out for two-tailed significance at the 5 % level using SPSS version 19 (SPSSInc, USA). Anthropometric measures, body composition measures and blood pressure values of both the group students were within the normal limits. There was no significant difference in anthropometric and body composition parameters between the group 1 and group 2 students. DBP, MAP and RPP were significantly lower in group 1 students when compared to group 2 students. VO2 max values were more in group 1 girls as compared to group 2 girls while the values of boys were comparable between the two groups. Regular unstructured physical activity for 60 minutes daily for the duration of

  12. Adapting to life: simulating an ecosystem within an unstructured adaptive mesh ocean model

    Science.gov (United States)

    Hill, J.; Piggott, M. D.; Popova, E. E.; Ham, D. A.; Srokosz, M. A.

    2010-12-01

    Ocean oligotrophic gyres are characterised by low rates of primary production. Nevertheless their great area, covering roughly a third of the Earth's surface, and probably constituting the largest ecosystem on the planet means that they play a crucial role in global biogeochemistry. Current models give values of primary production two orders of magnitude lower than those observed, thought to be due to the non-resolution of sub-mesoscale phenomena, which play a significant role in nutrient supply in such areas. However, which aspects of sub-mesoscale processes are responsible for the observed higher productivity is an open question. Existing models are limited by two opposing requirements: to have high enough spatial resolution to resolve fully the processes involved (down to order 1km) and the need to realistically simulate the full gyre. No model can currently satisfy both of these constraints. Here, we detail Fluidity-ICOM, a non-hydrostatic, finite-element, unstructured mesh ocean model. Adaptive mesh techniques allow us to focus resolution where and when we require it. We present the first steps towards performing a full North Atlantic simulation, by showing that adaptive mesh techniques can be used in conjunction with both turbulent parametrisations and ecosystems models in psuedo-1D water columns. We show that the model can successfully reproduce the annual variation of the mixed layer depth at keys locations within the North Atlantic gyre, with adaptive meshing producing more accurate results than the fixed mesh simulations, with fewer degrees of freedom. Moreover, the model is capable of reproducing the key behaviour of the ecosystem in those locations.

  13. Construction of biological networks from unstructured information based on a semi-automated curation workflow.

    Science.gov (United States)

    Szostak, Justyna; Ansari, Sam; Madan, Sumit; Fluck, Juliane; Talikka, Marja; Iskandar, Anita; De Leon, Hector; Hofmann-Apitius, Martin; Peitsch, Manuel C; Hoeng, Julia

    2015-06-17

    Capture and representation of scientific knowledge in a structured format are essential to improve the understanding of biological mechanisms involved in complex diseases. Biological knowledge and knowledge about standardized terminologies are difficult to capture from literature in a usable form. A semi-automated knowledge extraction workflow is presented that was developed to allow users to extract causal and correlative relationships from scientific literature and to transcribe them into the computable and human readable Biological Expression Language (BEL). The workflow combines state-of-the-art linguistic tools for recognition of various entities and extraction of knowledge from literature sources. Unlike most other approaches, the workflow outputs the results to a curation interface for manual curation and converts them into BEL documents that can be compiled to form biological networks. We developed a new semi-automated knowledge extraction workflow that was designed to capture and organize scientific knowledge and reduce the required curation skills and effort for this task. The workflow was used to build a network that represents the cellular and molecular mechanisms implicated in atherosclerotic plaque destabilization in an apolipoprotein-E-deficient (ApoE(-/-)) mouse model. The network was generated using knowledge extracted from the primary literature. The resultant atherosclerotic plaque destabilization network contains 304 nodes and 743 edges supported by 33 PubMed referenced articles. A comparison between the semi-automated and conventional curation processes showed similar results, but significantly reduced curation effort for the semi-automated process. Creating structured knowledge from unstructured text is an important step for the mechanistic interpretation and reusability of knowledge. Our new semi-automated knowledge extraction workflow reduced the curation skills and effort required to capture and organize scientific knowledge. The

  14. Accurate, finite-volume methods for 3D MHD on unstructured Lagrangian meshes

    International Nuclear Information System (INIS)

    Barnes, D.C.; Rousculp, C.L.

    1998-10-01

    Previous 2D methods for magnetohydrodynamics (MHD) have contributed both to development of core code capability and to physics applications relevant to AGEX pulsed-power experiments. This strategy is being extended to 3D by development of a modular extension of an ASCI code. Extension to 3D not only increases complexity by problem size, but also introduces new physics, such as magnetic helicity transport. The authors have developed a method which incorporates all known conservation properties into the difference scheme on a Lagrangian unstructured mesh. Because the method does not depend on the mesh structure, mesh refinement is possible during a calculation to prevent the well known problem of mesh tangling. Arbitrary polyhedral cells are decomposed into tetrahedrons. The action of the magnetic vector potential, A · δl, is centered on the edges of this extended mesh. For ideal flow, this maintains ∇ · B = 0 to round-off error. Vertex forces are derived by the variation of magnetic energy with respect to vertex positions, F = -∂W B /∂r. This assures symmetry as well as magnetic flux, momentum, and energy conservation. The method is local so that parallelization by domain decomposition is natural for large meshes. In addition, a simple, ideal-gas, finite pressure term has been included. The resistive diffusion part is calculated using the support operator method, to obtain an energy conservative, symmetric method on an arbitrary mesh. Implicit time difference equations are solved by preconditioned, conjugate gradient methods. Results of convergence tests are presented. Initial results of an annular Z-pinch implosion problem illustrate the application of these methods to multi-material problems

  15. Intrinsic properties of so-called dormant probiotic bacteria, determined by flow cytometric viability assays.

    Science.gov (United States)

    Lahtinen, Sampo J; Ouwehand, Arthur C; Reinikainen, Johanna P; Korpela, Jaakko M; Sandholm, Jouko; Salminen, Seppo J

    2006-07-01

    Plate counting and four culture-independent flow cytometric assays were used to determine the viability and intrinsic properties of three probiotic strains during storage. The strains showed reduction in plate counts but were able to maintain esterase activity, intact cytoplasmic membrane, and pH gradient. The apparently uncultivable probiotic cells were active and stress resistant.

  16. Intrinsic Properties of So-Called Dormant Probiotic Bacteria, Determined by Flow Cytometric Viability Assays

    OpenAIRE

    Lahtinen, Sampo J.; Ouwehand, Arthur C.; Reinikainen, Johanna P.; Korpela, Jaakko M.; Sandholm, Jouko; Salminen, Seppo J.

    2006-01-01

    Plate counting and four culture-independent flow cytometric assays were used to determine the viability and intrinsic properties of three probiotic strains during storage. The strains showed reduction in plate counts but were able to maintain esterase activity, intact cytoplasmic membrane, and pH gradient. The apparently uncultivable probiotic cells were active and stress resistant.

  17. Influential Effects of Intrinsic-Extrinsic Incentive Factors on Management Performance in New Energy Enterprises.

    Science.gov (United States)

    Wang, Ping; Lu, Zhengnan; Sun, Jihong

    2018-02-08

    Background : New energy has become a key trend for global energy industry development. Talent plays a very critical role in the enhancement of new energy enterprise competitiveness. As a key component of talent, managers have been attracting more and more attention. The increase in job performance relies on, to a certain extent, incentive mechanism. Based on the Two-factor Theory, differences in influences and effects of different incentives on management performance have been checked in this paper from an empirical perspective. Methods : This paper selects the middle and low level managers in new energy enterprises as research samples and classifies the managers' performance into task performance, contextual performance and innovation performance. It uses manager performance questionnaires and intrinsic-extrinsic incentive factor questionnaires to investigate and study the effects and then uses Amos software to analyze the inner link between the intrinsic-extrinsic incentives and job performance. Results : Extrinsic incentives affect task performance and innovation performance positively. Intrinsic incentives impose active significant effects on task performance, contextual performance, and innovation performance. The intrinsic incentive plays a more important role than the extrinsic incentive. Conclusions : Both the intrinsic-extrinsic incentives affect manager performance positively and the intrinsic incentive plays a more important role than the extrinsic incentive. Several suggestions to management should be given based on these results.

  18. Positive consequences of intrinsically rewarding work: A model to ...

    African Journals Online (AJOL)

    This study sought to empirically test a theoretical model outlining the relationships between intrinsic rewards, intrinsic motivation, work engagement and intention to quit, in an attempt to empirically assess whether intrinsic rewards result in improved levels of motivation, engagement and retention. Using a sample of 587 ...

  19. The value of nature: Economic, intrinsic, or both?

    Science.gov (United States)

    There has been a long standing argument that ecosystems have intrinsic value and therefore there is no need to put a price tag on Mother Nature. The concept of intrinsic value reflects the perspective that nature has value in its own right, independent of human uses. Intrinsic va...

  20. Personalizing Sample Databases with Facebook Information to Increase Intrinsic Motivation

    Science.gov (United States)

    Marzo, Asier; Ardaiz, Oscar; Sanz de Acedo, María Teresa; Sanz de Acedo, María Luisa

    2017-01-01

    Motivation is fundamental for students to achieve successful and complete learning. Motivation can be extrinsic, i.e., driven by external rewards, or intrinsic, i.e., driven by internal factors. Intrinsic motivation is the most effective and must be inspired by the task at hand. Here, a novel strategy is presented to increase intrinsic motivation…

  1. Intrinsic Motivation: An Overlooked Component for Student Success

    Science.gov (United States)

    Augustyniak, Robert A.; Ables, Adrienne Z.; Guilford, Philip; Lujan, Heidi L.; Cortright, Ronald N.; DiCarlo, Stephen E.

    2016-01-01

    Intrinsic motivation to learn involves engaging in learning opportunities because they are seen as enjoyable, interesting, or relevant to meeting one's core psychological needs. As a result, intrinsic motivation is associated with high levels of effort and task performance. Students with greater levels of intrinsic motivation demonstrate strong…

  2. Elements of the Competitive Situation That Affect Intrinsic Motivation.

    Science.gov (United States)

    Reeve, Johnmarshall; Deci, Edward L.

    1996-01-01

    Explores the effects of three elements of the competitive situation (competitive set, competitive outcome, and interpersonal context) on intrinsic motivation in a sample of college students (n=100). Competitive outcome and interpersonal context affected intrinsic motivation: winning increased intrinsic motivation, while pressured interpersonal…

  3. Respiratory neuron characterization reveals intrinsic bursting properties in isolated adult turtle brainstems (Trachemys scripta).

    Science.gov (United States)

    Johnson, Stephen M; Hedrick, Michael S; Krause, Bryan M; Nilles, Jacob P; Chapman, Mark A

    2016-04-01

    It is not known whether respiratory neurons with intrinsic bursting properties exist within ectothermic vertebrate respiratory control systems. Thus, isolated adult turtle brainstems spontaneously producing respiratory motor output were used to identify and classify respiratory neurons based on their firing pattern relative to hypoglossal (XII) nerve activity. Most respiratory neurons (183/212) had peak activity during the expiratory phase, while inspiratory, post-inspiratory, and novel pre-expiratory neurons were less common. During synaptic blockade conditions, ∼10% of respiratory neurons fired bursts of action potentials, with post-inspiratory cells (6/9) having the highest percentage of intrinsic burst properties. Most intrinsically bursting respiratory neurons were clustered at the level of the vagus (X) nerve root. Synaptic inhibition blockade caused seizure-like activity throughout the turtle brainstem, which shows that the turtle respiratory control system is not transformed into a network driven by intrinsically bursting respiratory neurons. We hypothesize that intrinsically bursting respiratory neurons are evolutionarily conserved and represent a potential rhythmogenic mechanism contributing to respiration in adult turtles. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Effect of intrinsic motivation on affective responses during and after exercise: latent curve model analysis.

    Science.gov (United States)

    Shin, Myoungjin; Kim, Inwoo; Kwon, Sungho

    2014-12-01

    Understanding the relationship between affect and exercise is helpful in predicting human behavior with respect to exercise participation. The goals of the present study were to investigate individual differences in affective response during and after exercise and to identify the role of intrinsic motivation in affective changes. 30 active male college students (M age = 21.4 yr.) who regularly participated in sports activities volunteered to answer a questionnaire measuring intrinsic motivation toward running activities and performed a 20-min. straight running protocol at heavy intensity (about 70% of VO2max). Participants' affective responses were measured every 5 min. from the beginning of the run to 10 min. after completing the run. Latent curve model analysis indicated that individuals experienced different changes in affective state during exercise, moderated by intrinsic motivation. Higher intrinsic motivation was associated with more positive affect during exercise. There were no significant individual differences in the positive tendency of the participants' affective responses after exercise over time. Intrinsic motivation seems to facilitate positive feelings during exercise and encourages participation in exercise.

  5. Metacognitive mastery and intrinsic motivation in schizophrenia.

    Science.gov (United States)

    Vohs, Jenifer L; Lysaker, Paul H

    2014-01-01

    Deficits in intrinsic motivation (IM) have been linked to poorer outcome in schizophrenia, but its proximal mechanisms remain poorly understood. This study examined whether metacognitive mastery, or the capacity to use knowledge of self, others, and context to identify and cope with psychological difficulties, predicted levels of IM for 6 months among 75 participants with prolonged schizophrenia. Repeated-measures analysis of variance revealed that high metacognitive mastery predicted consistently higher levels of IM; however, intermediate and low mastery did not produce unique IM profiles. The findings suggest that metacognitive mastery may have an important role in IM over time and could be a meaningful treatment target.

  6. Symplectic Structure of Intrinsic Time Gravity

    Directory of Open Access Journals (Sweden)

    Eyo Eyo Ita

    2016-08-01

    Full Text Available The Poisson structure of intrinsic time gravity is analysed. With the starting point comprising a unimodular three-metric with traceless momentum, a trace-induced anomaly results upon quantization. This leads to a revision of the choice of momentum variable to the (mixed index traceless momentric. This latter choice unitarily implements the fundamental commutation relations, which now take on the form of an affine algebra with SU(3 Lie algebra amongst the momentric variables. The resulting relations unitarily implement tracelessness upon quantization. The associated Poisson brackets and Hamiltonian dynamics are studied.

  7. Intrinsically conductive polymer thin film piezoresistors

    DEFF Research Database (Denmark)

    Lillemose, Michael; Spieser, Martin; Christiansen, N.O.

    2008-01-01

    We report on the piezoresistive effect in the intrinsically conductive polymer, polyaniline. A process recipe for indirect patterning of thin film polyaniline has been developed. Using a specially designed chip, the polyaniline thin films have been characterised with respect to resistivity...... and strain sensitivity using two- and four-point measurement method. We have found that polyaniline has a negative gauge factor of K = -4.9, which makes it a candidate for piezoresistive read-out in polymer based MEMS-devices. (C) 2007 Elsevier B.V. All rights reserved....

  8. Intrinsic chirp of single-cycle pulses

    International Nuclear Information System (INIS)

    Lin Qiang; Zheng Jian; Dai Jianming; Ho, I-Chen; Zhang, X.-C.

    2010-01-01

    The Fourier transform-limited electromagnetic pulse has been regarded to be free of chirps for a long time. This is no longer true if the pulse duration goes down to or less than one optical cycle. We report the experimental observation of intrinsic chirps in such pulses with the sub-single-cycle terahertz (THz) waveforms obtained with a standard THz time-domain spectroscopy system. The results confirm the break down of the carrier-envelope (CE) expression for single-cycle optical pulses, and may influence the experimental measurements and theoretical modeling with single-cycle pulses.

  9. Length-dependent prediction of protein intrinsic disorder

    Directory of Open Access Journals (Sweden)

    Dunker A Keith

    2006-04-01

    Full Text Available Abstract Background Due to the functional importance of intrinsically disordered proteins or protein regions, prediction of intrinsic protein disorder from amino acid sequence has become an area of active research as witnessed in the 6th experiment on Critical Assessment of Techniques for Protein Structure Prediction (CASP6. Since the initial work by Romero et al. (Identifying disordered regions in proteins from amino acid sequences, IEEE Int. Conf. Neural Netw., 1997, our group has developed several predictors optimized for long disordered regions (>30 residues with prediction accuracy exceeding 85%. However, these predictors are less successful on short disordered regions (≤30 residues. A probable cause is a length-dependent amino acid compositions and sequence properties of disordered regions. Results We proposed two new predictor models, VSL2-M1 and VSL2-M2, to address this length-dependency problem in prediction of intrinsic protein disorder. These two predictors are similar to the original VSL1 predictor used in the CASP6 experiment. In both models, two specialized predictors were first built and optimized for short (≤30 residues and long disordered regions (>30 residues, respectively. A meta predictor was then trained to integrate the specialized predictors into the final predictor model. As the 10-fold cross-validation results showed, the VSL2 predictors achieved well-balanced prediction accuracies of 81% on both short and long disordered regions. Comparisons over the VSL2 training dataset via 10-fold cross-validation and a blind-test set of unrelated recent PDB chains indicated that VSL2 predictors were significantly more accurate than several existing predictors of intrinsic protein disorder. Conclusion The VSL2 predictors are applicable to disordered regions of any length and can accurately identify the short disordered regions that are often misclassified by our previous disorder predictors. The success of the VSL2 predictors

  10. Activations of Both Extrinsic and Intrinsic Pathways in HCT 116 Human Colorectal Cancer Cells Contribute to Apoptosis through p53-Mediated ATM/Fas Signaling by Emilia sonchifolia Extract, a Folklore Medicinal Plant

    Directory of Open Access Journals (Sweden)

    Yu-Hsuan Lan

    2012-01-01

    Full Text Available Emilia sonchifolia (L. DC (Compositae, an herbaceous plant found in Taiwan and India, is used as folk medicine. The clinical applications include inflammation, rheumatism, cough, cuts fever, dysentery, analgesic, and antibacteria. The activities of Emilia sonchifolia extract (ESE on colorectal cancer cell death have not been fully investigated. The purpose of this study explored the induction of apoptosis and its molecular mechanisms in ESE-treated HCT 116 human colorectal cancer cells in vitro. The methanolic ESE was characterized, and γ-humulene was formed as the major constituent (63.86%. ESE induced cell growth inhibition in a concentration- and time-dependent response by MTT assay. Apoptotic cells (DNA fragmentation, an apoptotic catachrestic were found after ESE treatment by TUNEL assay and DNA gel electrophoresis. Alternatively, ESE stimulated the activities of caspase-3, -8, and -9 and their specific caspase inhibitors protected against ESE-induced cytotoxicity. ESE promoted the mitochondria-dependent and death-receptor-associated protein levels. Also, ESE increased ROS production and upregulated the levels of ATM, p53, and Fas in HCT 116 cells. Strikingly, p53 siRNA reversed ESE-reduced viability involved in p53-mediated ATM/Fas signaling in HCT 116 cells. In summary, our result is the first report suggesting that ESE may be potentially efficacious in the treatment of colorectal cancer.

  11. Intrinsic regulation of enteroendocrine fate by Numb.

    Science.gov (United States)

    Sallé, Jérémy; Gervais, Louis; Boumard, Benjamin; Stefanutti, Marine; Siudeja, Katarzyna; Bardin, Allison J

    2017-07-03

    How terminal cell fates are specified in dynamically renewing adult tissues is not well understood. Here we explore terminal cell fate establishment during homeostasis using the enteroendocrine cells (EEs) of the adult Drosophila midgut as a paradigm. Our data argue against the existence of local feedback signals, and we identify Numb as an intrinsic regulator of EE fate. Our data further indicate that Numb, with alpha-adaptin, acts upstream or in parallel of known regulators of EE fate to limit Notch signaling, thereby facilitating EE fate acquisition. We find that Numb is regulated in part through its asymmetric and symmetric distribution during stem cell divisions; however, its de novo synthesis is also required during the differentiation of the EE cell. Thus, this work identifies Numb as a crucial factor for cell fate choice in the adult Drosophila intestine. Furthermore, our findings demonstrate that cell-intrinsic control mechanisms of terminal cell fate acquisition can result in a balanced tissue-wide production of terminally differentiated cell types. © 2017 The Authors.

  12. Intrinsic position uncertainty impairs overt search performance.

    Science.gov (United States)

    Semizer, Yelda; Michel, Melchi M

    2017-08-01

    Uncertainty regarding the position of the search target is a fundamental component of visual search. However, due to perceptual limitations of the human visual system, this uncertainty can arise from intrinsic, as well as extrinsic, sources. The current study sought to characterize the role of intrinsic position uncertainty (IPU) in overt visual search and to determine whether it significantly limits human search performance. After completing a preliminary detection experiment to characterize sensitivity as a function of visual field position, observers completed a search task that required localizing a Gabor target within a field of synthetic luminance noise. The search experiment included two clutter conditions designed to modulate the effect of IPU across search displays of varying set size. In the Cluttered condition, the display was tiled uniformly with feature clutter to maximize the effects of IPU. In the Uncluttered condition, the clutter at irrelevant locations was removed to attenuate the effects of IPU. Finally, we derived an IPU-constrained ideal searcher model, limited by the IPU measured in human observers. Ideal searchers were simulated based on the detection sensitivity and fixation sequences measured for individual human observers. The IPU-constrained ideal searcher predicted performance trends similar to those exhibited by the human observers. In the Uncluttered condition, performance decreased steeply as a function of increasing set size. However, in the Cluttered condition, the effect of IPU dominated and performance was approximately constant as a function of set size. Our findings suggest that IPU substantially limits overt search performance, especially in crowded displays.

  13. Intrinsically disordered proteins drive membrane curvature.

    Science.gov (United States)

    Busch, David J; Houser, Justin R; Hayden, Carl C; Sherman, Michael B; Lafer, Eileen M; Stachowiak, Jeanne C

    2015-07-24

    Assembly of highly curved membrane structures is essential to cellular physiology. The prevailing view has been that proteins with curvature-promoting structural motifs, such as wedge-like amphipathic helices and crescent-shaped BAR domains, are required for bending membranes. Here we report that intrinsically disordered domains of the endocytic adaptor proteins, Epsin1 and AP180 are highly potent drivers of membrane curvature. This result is unexpected since intrinsically disordered domains lack a well-defined three-dimensional structure. However, in vitro measurements of membrane curvature and protein diffusivity demonstrate that the large hydrodynamic radii of these domains generate steric pressure that drives membrane bending. When disordered adaptor domains are expressed as transmembrane cargo in mammalian cells, they are excluded from clathrin-coated pits. We propose that a balance of steric pressure on the two surfaces of the membrane drives this exclusion. These results provide quantitative evidence for the influence of steric pressure on the content and assembly of curved cellular membrane structures.

  14. Doubly truncated FosB isoform (Delta2DeltaFosB) induces osteosclerosis in transgenic mice and modulates expression and phosphorylation of Smads in osteoblasts independent of intrinsic AP-1 activity

    DEFF Research Database (Denmark)

    Sabatakos, George; Rowe, Glenn C; Kveiborg, Marie

    2008-01-01

    INTRODUCTION: Activator protein (AP)-1 family members play important roles in the development and maintenance of the adult skeleton. Transgenic mice that overexpress the naturally occurring DeltaFosB splice variant of FosB develop severe osteosclerosis. Translation of Deltafosb mRNA produces both...... that overexpress only Delta2DeltaFosB using the enolase 2 (ENO2) promoter-driven bitransgenic Tet-Off system. RESULTS: Despite Delta2DeltaFosB's failure to induce transcription of an AP-1 reporter gene, the transgenic mice exhibited both the bone and the fat phenotypes seen in the ENO2-DeltaFosB mice. Both Delta......6 expression. CONCLUSIONS: DeltaFosB's AP-1 transactivating function is not needed to induce increased bone formation, and Delta2DeltaFosB may act, at least in part, by increasing Smad1 expression, phosphorylation, and translocation to the nucleus....

  15. Intrinsically secure fast reactors with dense cores

    International Nuclear Information System (INIS)

    Slessarev, Igor

    2007-01-01

    Secure safety, resistance to weapons material proliferation and problems of long-lived wastes remain the most important 'painful points' of nuclear power. Many innovative reactor concepts have been developed aimed at a radical enhancement of safety. The promising potential of innovative nuclear reactors allows for shifting accents in current reactor safety 'strategy' to reveal this worth. Such strategy is elaborated focusing on the priority for intrinsically secure safety features as well as on sure protection being provided by the first barrier of defence. Concerning the potential of fast reactors (i.e. sodium cooled, lead-cooled, etc.), there are no doubts that they are able to possess many favourable intrinsically secure safety features and to lay the proper foundation for a new reactor generation. However, some of their neutronic characteristics have to be radically improved. Among intrinsically secure safety properties, the following core parameters are significantly important: reactivity margin values, reactivity feed-back and coolant void effects. Ways of designing intrinsically secure safety features in fast reactors (titled hereafter as Intrinsically Secure Fast Reactors - ISFR) can be found in the frame of current reactor technologies by radical enhancement of core neutron economy and by optimization of core compositions. Simultaneously, respecting resistance to proliferation, by using non-enriched fuel feed as well as a core breeding gain close to zero, are considered as the important features (long-lived waste problems will be considered in a separate paper). This implies using the following reactor design options as well as closed fuel cycles with natural U as the reactor feed: ·Ultra-plate 'dense cores' of the ordinary (monolithic) type with negative total coolant void effects. ·Modular type cores. Multiple dense modules can be embedded in the common reflector for achieving the desired NPP total power. The modules can be used also independently (as

  16. The Neuroscience of Growth Mindset and Intrinsic Motivation.

    Science.gov (United States)

    Ng, Betsy

    2018-01-26

    Our actions can be triggered by intentions, incentives or intrinsic values. Recent neuroscientific research has yielded some results about the growth mindset and intrinsic motivation. With the advances in neuroscience and motivational studies, there is a global need to utilize this information to inform educational practice and research. Yet, little is known about the neuroscientific interplay between growth mindset and intrinsic motivation. This paper attempts to draw on the theories of growth mindset and intrinsic motivation, together with contemporary ideas in neuroscience, outline the potential for neuroscientific research in education. It aims to shed light on the relationship between growth mindset and intrinsic motivation in terms of supporting a growth mindset to facilitate intrinsic motivation through neural responses. Recent empirical research from the educational neuroscience perspective that provides insights into the interplay between growth mindset and intrinsic motivation will also be discussed.

  17. Extension of centered hydrodynamical schemes to unstructured deforming conical meshes : the case of circles

    Directory of Open Access Journals (Sweden)

    Bernard-Champmartin Aude

    2013-01-01

    Full Text Available In a prior work [CEMRACS10], a curvilinear bi-dimensional finite volume extension of Lagrangian centered schemes GLACE [GLACE] on unstructured cells, whose edges are parameterized by rational quadratic Bézier curves was proposed and we showed numerical results for this scheme. Now, we extend the EUCCLHYD scheme [EUCCLHYD] to these cells. To simulate flows with evolving large deformations, we write a formalism allowing the time evolution of the conic parameter. As an example, this allows an edge changing from an ellipse segment to a hyperbolic one. In this framework, we consider the case of a mesh whose edges are circle segments with non fixed centers. We show that this formalism extends also the previous work [GLACE CIRCLE] (which is equivalent to [CEMRACS10] when conic edges are all circles. This is a necessary first step toward general conical deformation. Dans un travail précédent [CEMRACS10], une extension volume fini bi-dimensionnelle curviligne du schéma Lagrangien centré GLACE [GLACE] sur des cellules non structurées dont les bords sont paramétrés par des courbes de Bézier quadratiques rationnelles a été proposée. Maintenant, nous proposons une extension du schéma EUCCLHYD [EUCCLHYD] à ce type de cellules et pour lequel nous montrons quelques résultats numériques. Pour pouvoir suivre un écoulement subissant de grandes variations de forme, nous écrivons un formalisme qui permet l’évolution en temps du paramètre de chaque conique. Ainsi, un bord de maille peut d’un segment d’ellipse devenir en cours de calcul un segment d’hyperbole. Dans ce cadre, nous considérons le cas particulier d’un maillage dont les bords de cellules sont des arcs de cercle avec des centres non fixes. Nous montrons que ce formalisme constitue également une extension directe d’un travail précédent [GLACE CIRCLE] (qui équivaut à [CEMRACS10] dans le cas où les bords coniques sont tous des cercles. Ce résultat constitue une

  18. CVD-MPFA full pressure support, coupled unstructured discrete fracture-matrix Darcy-flux approximations

    Science.gov (United States)

    Ahmed, Raheel; Edwards, Michael G.; Lamine, Sadok; Huisman, Bastiaan A. H.; Pal, Mayur

    2017-11-01

    Two novel control-volume methods are presented for flow in fractured media, and involve coupling the control-volume distributed multi-point flux approximation (CVD-MPFA) constructed with full pressure support (FPS), to two types of discrete fracture-matrix approximation for simulation on unstructured grids; (i) involving hybrid grids and (ii) a lower dimensional fracture model. Flow is governed by Darcy's law together with mass conservation both in the matrix and the fractures, where large discontinuities in permeability tensors can occur. Finite-volume FPS schemes are more robust than the earlier CVD-MPFA triangular pressure support (TPS) schemes for problems involving highly anisotropic homogeneous and heterogeneous full-tensor permeability fields. We use a cell-centred hybrid-grid method, where fractures are modelled by lower-dimensional interfaces between matrix cells in the physical mesh but expanded to equi-dimensional cells in the computational domain. We present a simple procedure to form a consistent hybrid-grid locally for a dual-cell. We also propose a novel hybrid-grid for intersecting fractures, for the FPS method, which reduces the condition number of the global linear system and leads to larger time steps for tracer transport. The transport equation for tracer flow is coupled with the pressure equation and provides flow parameter assessment of the fracture models. Transport results obtained via TPS and FPS hybrid-grid formulations are compared with the corresponding results of fine-scale explicit equi-dimensional formulations. The results show that the hybrid-grid FPS method applies to general full-tensor fields and provides improved robust approximations compared to the hybrid-grid TPS method for fractured domains, for both weakly anisotropic permeability fields and very strong anisotropic full-tensor permeability fields where the TPS scheme exhibits spurious oscillations. The hybrid-grid FPS formulation is extended to compressible flow and the

  19. A novel consistent and well-balanced algorithm for simulations of multiphase flows on unstructured grids

    Science.gov (United States)

    Patel, Jitendra Kumar; Natarajan, Ganesh

    2017-12-01

    consistent transport and balanced force treatment results in a numerically stable solution procedure and physically consistent results. The algorithm proposed in this study qualifies as a robust approach to simulate multiphase flows with high density ratios on unstructured meshes and may be realised in existing flow solvers with relative ease.

  20. Modeling oil spills transportation in seas based on unstructured grid, finite-volume, wave-ocean model

    Science.gov (United States)

    Wang, Jinhua; Shen, Yongming

    A three-dimensional integrated model is developed for simulating transport and fate of oil spills in seas. The model contains two main modules, flow and transport-fate modules. The flow module uses an unstructured finite-volume wave-ocean coupling model. Using unstructured meshes provides great flexibility for modeling the flow in complex geometries of tidal creeks, barriers and islands, with refined grid resolution in regions of interest and not elsewhere. In the transport-fate module the oil dispersion is solved using a particle-tracking method. Horizontal diffusion is simulated using random walk techniques in a Monte Carlo framework, whereas the vertical diffusion process is solved on the basis of the Langeven equation. The model simulates the most significant processes that affect the motion of oil particles, such as advection, surface spreading, evaporation, dissolution, emulsification and turbulent diffusion as well as the interaction of the oil particles with the shoreline, sedimentation and the temporal variations of oil viscosity, density and surface-tension. Detailed comparisons of simulations with analytical solutions and numerical simulations made with the popular structured finite difference model ROMS (the Regional Ocean Modeling System) for two idealized cases: wind-induced long-surface gravity waves in a circular lake and freshwater discharge onto the continental shelf with curved coastlines, are presented. With a better fit to the curvature of the coastline using unstructured nonoverlapping triangle grid cells, the developed model system provides improved numerical accuracy in simulating the oil spill trajectory. Also keep in mind that attention must be paid to choose the horizontal and vertical resolution in simulating the oil trajectory in the coastal ocean.